Podcasts about 16S rRNA

Check out the Tone LUX Red Light Collection: Get 20% OFF with the code VANESSA In this episode of The Optimal Protein Podcast, we explore a groundbreaking study published in Scientific Reports that reveals a fascinating connection between the gut microbiome and visceral fat, commonly known as belly fat. We dive deep into how specific gut bacteria influence fat storage, why microbiome diversity is key, and what dietary strategies you can implement to reduce visceral fat while staying keto or low-carb compliant. Tune in to learn how dietary diversity, fiber, and probiotics can transform your gut health and metabolic fitness. Jump to the start of the study breakdown: 15:57 Get 20% off the New 2nd Generation Tone Device HERE  with the code VANESSA Key Topics Discussed: 1. What Is Visceral Fat? • Definition of visceral fat and how it differs from subcutaneous fat. • The health risks associated with excess visceral fat, including insulin resistance, inflammation, and cardiovascular disease. 2. Study Breakdown: • Overview of the 2019 study in Scientific Reports. • How microbiome diversity was measured using 16S rRNA gene sequencing. • The role of specific bacterial strains like Akkermansia muciniphila and Faecalibacterium prausnitzii in reducing visceral fat. • The correlation between fiber intake, plant diversity, and lower visceral fat levels. Resources Mentioned: • The Study: Gut microbiome composition and its potential association with visceral fat deposition • Microsetta Initiative: Research on microbiome diversity and plant-based diets. Get 20% off the New 2nd Generation Tone Device HERE  with the code VANESSA Follow @ketogenicgirl for updates on the latest studies and strategies to optimize protein intake and metabolic health.  Follow @optimalproteinpodcast on Instagram to see visuals and posts mentioned on this podcast. Link to join the facebook group for the podcast: https://www.facebook.com/groups/2017506024952802/   The content provided in this podcast is for informational purposes only and should not be construed as medical advice. Consult with a healthcare professional before making significant changes to your diet or exercise regimen.  

Send us a textWelcome to Alternative Dog Moms - a podcast about what's happening in the fresh food community and the pet industry. Kimberly Gauthier is the blogger behind Keep the Tail Wagging, and Erin Scott hosts the Believe in Dog podcast.CHAPTERS:Kimberly & Erin are back and talking about  fundraisers for Save-A-Mutt and B-More Dog (0:54)Erin attended the NOVA Pet Summit featuring Susan Thixton, Animal Biome, Dr. Karen Becker & Rodney Habib (4:16)Dr. Rob Silver has a book coming out, Kimberly learned to speak mushroom and Shout-Outs (19:13)Have you heard of Essential Fatty Acid C15?  And why Erin's nerding out on this (22:07)Dr. Josie Beug's warning to pet parents (26:31)Article warning veterinarians about the dangers of falling for marketing claims by pharmaceutical companies (34:29)Kimberly's interactions on TikTok with anti-raw feeders (35:11)What Erin learned on a spay/neuter webinar hosted by an animal welfare organization (42:43)Raw Feeding Derangement Syndrome is real (44:11)LINKS DISCUSSED:Dr. Rob Silver's book "There's a Mushroom for That" (https://www.wellpetdispensary.com/books/theres-a-mushroom-for-that/)Dave Asprey podcast episode "The Fat You Didn't Know You Needed" (https://pod.link/451295014/episode/ff9ffe4a6bd520c71c272fb38b3c6398)Billy's video with Dr. Katie Woodley talking about C15 (https://www.youtube.com/live/makD4oeQMw8?si=COh7Ot2hoGZyXrVb)Dr. Josie Beug's warning to pet parents (https://www.facebook.com/josie.beug.dvm/posts/pfbid0UrRhaPGtuo6X52Y9Mm5fBVd1TmqioEyJYzois3CWvA5RFX1m2Caj7kL3UoKtz4SYl)Article warning veterinarians about the dangers of falling for marketing claims by pharmaceutical companies (https://www.veterinarypracticenews.com/beyond-promotional-claims/)Article: Silicone tags as an effective method of monitoring environmental contaminant exposures in a geographically diverse sample of dogs from the Dog Aging Project (https://www.frontiersin.org/journals/veterinary-science/articles/10.3389/fvets.2024.1394061/full)Article: Species-level characterization of the core microbiome in healthy dogs using full-length 16S rRNA gene sequencing (https://www.frontiersin.org/journals/veterinary-science/articles/10.3389/fvets.2024.1405470/full)Gold Bead Implants (https://holisticveterinaryhealing.com/pet-gold-bead-implants-germantown-md/)OUR BLOG/PODCASTS...Kimberly: Keep the Tail Wagging, KeepTheTailWagging.comErin Scott: Thanks for listening to our podcast. You can learn more about Erin Scott's first podcast at BelieveInDogPodcast.com. And you can learn more about raw feeding, raising dogs naturally, and Kimberly's dogs at KeepTheTailWagging.com. And don't forget to subscribe to The Alternative Dog Moms.

donaciones por PayPal a yolupor@hotmai.com Grupos de Telegram https://t.me/sanofuerteyfeliz https://t.me/ComparticiondeFluidosHumanos REDES SOCIALES Y PODCAST https://linktr.ee/sanofuertefeliz.com Libro Camino a la Extinción: Microbioma y Disbiosis - autor Sergio Vallejo https://amzn.eu/d/gHHUrqo Un banco internacional de heces para salvar a la humanidad de la extinción masiva https://www.larazon.es/salud/bienestar/banco-internacional-heces-salvar-humanidad_2023042664491be42a35640001e4eb8f.html https://es.wired.com/articulos/microbiota-vault-evitaria-extincion-masiva-del-humano https://pubmed.ncbi.nlm.nih.gov/31852769/ Estudio que asignó al azar a 165 pacientes con síndrome del intestino irritable a placebo, 30 g de FMT o 60 g de FMT en una proporción de 1:1:1. El material para FMT se obtuvo de un donante sano y bien caracterizado, se congeló y se administró a través de un gastroscopio. El resultado primario fue una reducción de los síntomas del SII a los 3 meses después del FMT. El resultado secundario fue una reducción en el índice de disbiosis y un cambio en el perfil bacteriano intestinal, analizado por secuenciación del gen 16S rRNA, 1 mes después de FMT. Resultados: Se produjeron respuestas en el 23,6 %, 76,9 % y 89,1 % de los pacientes que recibieron placebo, 30 g de FMT y 60 g de FMT, respectivamente. Estos estuvieron acompañados de mejoras significativas en la fatiga y la calidad de vida en los pacientes que recibieron FMT. Los perfiles bacterianos intestinales también cambiaron significativamente en los grupos que recibieron FMT. Los eventos adversos de FMT fueron síntomas gastrointestinales autolimitados leves. https://www.sciencedirect.com/science/article/abs/pii/S0016508520349374 En la semana 12, el 56 % de los pacientes que recibieron heces de donantes informaron una mejoría en ambos criterios de valoración primarios en comparación con el 26 % de los pacientes que recibieron placebo. Los pacientes que recibieron heces de donantes tuvieron mejoras significativas en el nivel de malestar. Las muestras fecales de los que respondieron tenían una mayor diversidad de microbiomas antes de la administración del material del donante que las muestras fecales de los que no respondieron y una composición inicial distinta . Después de un solo FMT, el 21 % de los pacientes que recibieron heces de donantes informaron efectos que duraron más de 1 año en comparación con el 5 % de los pacientes que recibieron heces de placebo. Un segundo FMT redujo los síntomas en el 67 % de los pacientes con una respuesta inicial a las heces del donante, pero no en los pacientes sin respuesta previa. Conclusiones En un ensayo aleatorizado de pacientes con SII refractario al tratamiento con hinchazón predominante, el FMT alivió los síntomas en comparación con el placebo (trasplante autólogo), aunque los efectos disminuyeron durante 1 año. Un segundo FMT restableció la respuesta de los pacientes con una respuesta previa. La respuesta se asoció con la composición de los microbiomas fecales antes del FMT; https://www.sciencedirect.com/science/article/pii/S0016508522006254 Se desconoce la eficacia a largo plazo y los posibles eventos adversos del trasplante de microbiota fecal para el síndrome del intestino irritable. Este estudio realizó un seguimiento de 3 años de los pacientes en nuestro ensayo clínico anterior para aclarar estos aspectos. Métodos Este estudio incluyó a 125 pacientes: 38 en un grupo de placebo, 42 que recibieron 30 g de heces de donante y 45 que recibieron 60 g de heces de donante. Las heces se administraron al duodeno. Los pacientes proporcionaron una muestra fecal y completaron 5 cuestionarios al inicio y a los 2 y 3 años después de FMT. Las bacterias fecales y el índice de disbiosis se analizaron utilizando la reacción en cadena de la polimerasa del gen del ARN ribosomal 16S , amplificación de ADN/hibridación de sonda que cubre las regiones V3 a V9. Resultados Las tasas de respuesta fueron del 26,3 %, 69,1 % y 77,8 % en los grupos de placebo, 30 g y 60 g, respectivamente, a los 2 años después del FMT, y del 27,0 %, 64,9 % y 71,8 %, respectivamente, a los 3 años después de FMT. Las tasas de respuesta fueron significativamente más altas en los grupos de 30 gy 60 g que en el grupo de placebo. Los pacientes en los grupos de 30 g y 60 g tenían significativamente menos síntomas de SII y fatiga, y una mejor calidad de vida tanto a los 2 como a los 3 años después del FMT. El índice de disbiosis disminuyó solo en los grupos de tratamiento activo a los 2 y 3 años después de FMT. Las señales fluorescentes de 10 bacterias tenían correlaciones significativas con los síntomas del SII y la fatiga después del FMT en los grupos de 30 g y 60 g. No se registraron eventos adversos a largo plazo.

We are back talking about systematics, and SeqCode; a nomenclatural code for prokaryotes described from sequence data. Marike Palmer is a Postdoctoral researcher in the School of Life Sciences at the University of Nevada Las Vegas and Miguel Rodriguez is an Assistant Professor of Bioinformatics at the University of Innsbruck in the departments of Microbiology and the Digital Science Center (DiSC). Link to paper: https://www.nature.com/articles/s41564-022-01214-9 History paper: https://www.sciencedirect.com/science/article/pii/S0723202022000121 They discussed the SeqCode, a nomenclature code for Prokaryotes described from sequence data. The SeqCode was created to provide a specific nomenclature code for previously uncultivated organisms. Palmer explained that the impetus for the SeqCode was the need to accommodate previously uncultivated organisms under a specific nomenclature code. She emphasized that the SeqCode was written to allow any peer-reviewed publication, but noted that the authors have designed three paths of validation in the SeqCode. They hope that anyone proposing a name will work with the curriculum team to ensure the best quality descriptions, names, etymology, and solidification. Rodriguez discussed the SeqCode's governance, which is already in place, and they have made them public so that anyone interested can join the SeqCode community. The governance structure comprises an executive board, committees, and working groups. The position's co-opted members hold some of the committees of these committees, while some are chosen by ballot. The hosts sought to clarify the relationship between the Isme Society, which is backing the SeqCode, and the wider field in general. Rodriguez explained that ISME is simply providing support as an umbrella organization for the SeqCode. Palmer and Rodriguez clarified that the SeqCode is not a competing code but rather a parallel one that aims to accommodate previously uncultivated organisms. The SeqCode was created to provide a specific nomenclature code for previously uncultivated organisms. Palmer noted that most scientists culture prokaryotes not for naming but to advance their knowledge of these organisms through physiology experiments. They emphasized that the new system is the result of a long collaborative effort that involved many different viewpoints and philosophies. The episode also discussed the practical requirements for naming under the new system, which include standards for the completeness and contamination levels required in the genome sequence data. Palmer noted that while the 16S rRNA gene sequence was not required for naming, it was recommended for improved accuracy in cross-talk between different taxonomies. The conversation highlighted the importance and challenges of naming microorganisms and the ongoing efforts to create a system that is inclusive of all microorganisms, both cultivated and uncultivated. Rodriguez and Palmer also discussed the SeqCode, a nature code for naming prokaryotes described from sequence data. They agreed that high-quality genomes should be the main control types to ensure the system builds up rather than breaks down. They noted the challenge of obtaining full genomes of some organisms, such as obligate intracellular parasites but suggested obtaining housekeeping genes as a potential solution. They further explained the technical issue of estimating completeness or contamination for many taxa, but Palmer confirmed that registering a name on the SeqCode registry requires adding such estimates. It emphasized the importance of collaboration within the scientific community and the need to create a system that is inclusive of all microorganisms. It also highlighted the challenges inherent in the process of naming microorganisms but demonstrated that it is an ongoing process, and that scientists are working to create a system that is accurate, practical, and beneficial for all.

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.12.22.521569v1?rss=1 Authors: Sharma, N., Sharma, M., Thakkar, D., Kumar, H., Smetanova, S., Buresova, L., Andrla, P., Khairnar, A. Abstract: Background: The contribution of gastrointestinal (GI) inflammation and local exposure to neurotoxins in the gut offers the most in-depth explanation of Parkinson's disease (PD) etiopathogenesis through abnormal accumulation and spreading of alpha-synuclein (-syn) aggregates from the gut to the brain. Objectives: This study was designed to investigate whether dextran sodium sulfate (DSS)-mediated colitis may have lasting effects on dopaminergic pathways in the brain and whether or not colitis exacerbated susceptibility to later exposure to the neurotoxin rotenone. Methods: To induce chronic colitis, 10 months old C57BL/6 mice were pre-exposed to 3 cycles of 7 days of 1% (w/v) DSS administration in drinking water followed by 14 days of regular drinking water. After colitis-induction, animals received a low dose of intragastric rotenone for the next 8 weeks, followed by testing for Parkinsonian behavior and GI phenotypes of inflammation. At the end of the 8th week after colitis, colon, brain stem, and midbrain tissue were isolated and analyzed for -syn, inflammatory markers, and dopaminergic neuronal loss. Gut microbial composition was assessed by 16S rRNA sequencing analysis. Results: We found that local rotenone exposure for 8 weeks did not affect colitis severity and colonic tight junction (TJ) protein expression (ZO-1, Occludin, and Claudin-1). On the other hand, we found that while eight weeks of chronic rotenone administration led to an increase in inflammatory markers, the presence of pre-existing colitis resulted in a considerable change in gut microbiota composition and a decrease in TJ's protein expression. In addition, the administration of rotenone in mice post-colitis caused gastrointestinal function impairment and poor behavioral performances. Itworsened rotenone-induced -syn pathology in the colon, which extended upward and resulted in severe dopaminergic neuron loss and significant astroglia activation in the dorsal motor nucleus of the vagus (DMV), locus coeruleus, substantia nigra as well as in striatum. Interestingly, in the case of rotenone alone, we found that -syn induced ChAT+ neuronal death is restricted to the DMV. These findings indicate that long-term rotenone exposure in conjunction with early inflammatory intestinal milieu exacerbates the progression of -syn pathology and aggravates neurodegeneration in the intragastric mouse PD model. Conclusions: This work provides detailed insight into the involvement of GI inflammation triggered after a neurotoxic insult in the colon and explores their potential to impact central dopaminergic degeneration in PD. This way, we can identify potential therapeutic targets that stop the enteric inflammatory processes involved in progressing PD. Copy rights belong to original authors. Visit the link for more info Podcast created by Paper Player, LLC

As we enter into the holiday season, many of us look forward to celebrating long-standing traditions with family and friends, which is no different from us here on the podcast! While not necessarily as long-standing as some of the other classic holiday traditions, after 2.5 years on air, we on this podcast have established our own end-of-year tradition, which is to take a look back at some of our favorite papers or more intriguing manuscripts published in the Journal of Clinical Microbiology over the past year. And so as you'll see, thanks to the different areas of expertise and general interest among our panel today, we've selected quite a variety of papers to discuss, ranging from evaluation of new blood culture systems to use of metagenomics for infective endocarditis and to the potential application of interferon gamma release assays for detection of Histoplasma infections. And so, suffice it to say, there will be something of interest for everyone listening. But, for those watching today, you are clearly getting an extra special treat as you get to see us do this episode wearing our best holiday gear and accessories.  Guest: Dr. Trish Simner. Links: Nasal Swab Performance by Collection Timing, Procedure, and Method of Transport for Patients with SARS-CoV-2. DOI: https://doi.org/10.1128/JCM.00569-21 Multicenter Postimplementation Assessment of the Positive Predictive Value of SARS-CoV-2 Antigen-Based Point-of-Care Tests Used for Screening of Asymptomatic Continuing Care Staff. DOI: https://doi.org/10.1128/JCM.01411-21 Laboratory Safety: Handling Burkholderia pseudomallei Isolates without a Biosafety Cabinet. DOI: https://doi.org/10.1128/JCM.00424-21 The clinical utility of 2 high-throughput 16S rRNA gene sequencing workflows for taxonomic assignment of unidentifiable bacterial pathogens in MALDI-TOF MS. DOI: https://doi.org/10.1128/JCM.01769-21 Performance of Fully Automated Antimicrobial Disk Diffusion Susceptibility Testing Using Copan WASP Colibri Coupled to the Radian In-Line Carousel and Expert System. DOI: 10.1128/JCM.00777-21 Benefits Derived from Full Laboratory Automation in Microbiology: A Tale of Four Laboratories. DOI https://doi.org/10.1128/JCM.01969-20 Reflex Detection of Ciprofloxacin Resistance in Neisseria gonorrhoeae by Use of the SpeeDx ResistancePlus GC Assay. DOI: https://doi.org/10.1128/JCM.00089-21 Comparative Performance of Latest-Generation and FDA-Cleared Serology Tests for the Diagnosis of Chagas Disease. DOI: https://doi.org/10.1128/JCM.00158-21 Diagnosing Pulmonary Tuberculosis by Using Sequence-Specific Purification of Urine Cell-Free DNA. DOI: https://doi.org/10.1128/JCM.00074-21 Indeterminate QuantiFERON Gold Plus Results Reveal Deficient Interferon Gamma Responses in Severely Ill COVID-19 Patients. DOI: https://doi.org/10.1128/JCM.00811-21 Visit journals.asm.org/journal/jcm to read articles and/or submit a manuscript. Follow JCM on Twitter via @JClinMicro

There is something beautiful about intelligence; it reveals how much we can become when we put ourselves to the task of searching and asking the right question.I am always fascinated by knowledge because our becoming, being, and living all rise and fall on the back of what we know. All of these begin with our intellect, the sum of our cognitive facilities, and the capacity for reasoning. This is where light comes to our mind, we develop, and our external world becomes a recipient of our realities.On this episode of the Word Café Podcast, I am honored to have someone who has embraced her intelligence as a gift and built a future.  Her name is Dr Nwamaka AkpodieteDr. Nwamaka Akpodiete is a post-doctoral research associate in vector biology with Target malaria, based at Keele University, United Kingdom. She conducts molecular ecological studies to understand the population dynamics and ecology of the African malaria mosquito Anopheles gambiae. Additionally, she provides support and training in molecular ecology, ecological statistics, and scientific writing at African partner institutions. Nwamaka has a 12-year of work experience in Higher Education involving teaching, mentoring, laboratory and field research, project supervision, and related administrative roles.   Nwamaka has a broad-based undergraduate and postgraduate education and research training in biology, biochemistry, molecular biology techniques, next-generation sequencing, entomology, zoology, and environmental sciences. Her BSc (Animal and Environmental Biology) research project was on the ecological dynamics of soil microarthropods about hydrocarbon pollution. She identified some bioindicators of soil pollution and microarthropod species indicative of soil recovery. This interest in environmental health led to an MSc in Environmental Quality Management. Nwamaka's MSc project was on the dipteran larvae in polluted water bodies in Port Harcourt, Rivers State, Nigeria. The project linked disease vectors such as Anopheles gambiae s.l. and Culex quinquefasciatus to indiscriminate waste disposal in Port Harcourt City, Nigeria. She also holds an MSc in Entomology and Pest Management from the University of Port Harcourt.  Her research interest in public and environmental health culminated in a Ph.D. in Entomology at Keele University, United Kingdom. Her Ph.D. research was focused on the evolutionary larval divergence in Anopheles gambiae s.l. About rice field domestication in Africa and improvement of An. gambiae s.l. Mass-rearing protocols for release. She also evaluated the use of zeolite in mosquito rearing and the characterization of microbial communities in the insectary via 16S rRNA gene sequencing. The study revealed ecological consequences of environmental manipulation, which has resulted in the speciation event in the malaria vector An. coluzzii, resulting in the year-round transmission of malaria and increased urban malaria. The findings from her Ph.D. research are relevant for malaria vector control, irrigated agricultural and urbanization policy reevaluation, and improvement of sterile insect techniques and gene drive protocols.  Nwamaka is actively involved in malaria campaigns@Zeromalaria to eradicate malaria in Africa.Support the show

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.09.27.509283v1?rss=1 Authors: Fongang, B., Satizabal, C. L., Kautz, T. F., Ngouongo, Y. W., SherraeMuhammad, J. A., Vasquez, E., Mathews, J., Goss, M., Saklad, A. R., Himali, J., Beiser, A., Cavazos, J. E., Mahaney, M. C., Maestre, G., DeCarli, C., Shipp, E. L., Vasan, R. S., Seshadri, S. Abstract: A bidirectional communication exists between the brain and the gut, in which the gut microbiota influences cognitive function and vice-versa. Gut dysbiosis has been linked to several diseases, including Alzheimer's disease and related dementias (ADRD). However, the relationship between gut dysbiosis and markers of cerebral small vessel disease (cSVD), a major contributor to ADRD, is unknown. In this cross-sectional study, we examined the connection between the gut microbiome, cognitive, and neuroimaging markers of cSVD in the Framingham Heart Study (FHS). Markers of cSVD included white matter hyperintensities (WMH), peak width of skeletonized mean diffusivity (PSMD), and executive function (EF), estimated as the difference between the trail-making tests B and A. We included 972 FHS participants with MRI scans, neurocognitive measures, and stool samples and quantified the gut microbiota composition using 16S rRNA sequencing. We used multivariable association and differential abundance analyses adjusting for age, sex, BMI, and education level to estimate the association between gut microbiota and WMH, PSMD, and EF measures. Our results suggest an increased abundance of Pseudobutyrivibrio and Ruminococcus genera was associated with lower WMH and PSMD (p-values less than 0.001), as well as better executive function (p-values less than 0.01). In addition, in both differential and multivariable analyses, we found that the gram-negative bacterium Barnesiella intestinihominis was strongly associated with markers indicating a higher cSVD burden. Finally, functional analyses using PICRUSt implicated various KEGG pathways, including microbial quorum sensing, AMP/GMP-activated protein kinase, phenylpyruvate, and {beta}-hydroxybutyrate production previously associated with cognitive performance and dementia. Our study provides important insights into the association between the gut microbiome and cSVD, but further studies are needed to replicate the findings. Copy rights belong to original authors. Visit the link for more info Podcast created by PaperPlayer

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2022.09.11.507297v1?rss=1 Authors: Tran, T. D. B., Nguyen, H., Sodergren, E., Center for Systems Neurogenetics of Addiction,, Dickson, P. E., Wright, S., Philip, V. M., Weinstock, G. M., Chesler, E. A., Zhou, Y., Bubier, J. A. Abstract: The gut microbiome is thought to play a critical role in the onset and development of psychiatric disorders, including depression and substance use disorder (SUD). To test the hypothesis that the microbiome affects addiction predisposing behaviors and cocaine intravenous self-administration (IVSA) and to identify specific microbes involved in the relationship, we performed 16S rRNA gene sequencing on feces from 228 diversity outbred mice. Twelve open field measures, two light-dark assay measures, one hole board and novelty place preference measure significantly differed between mice that acquired cocaine IVSA (ACQ) and those that failed to acquire IVSA (FACQ). We found that ACQ mice are more active and exploratory and display decreased fear than FACQ mice. The microbial abundances that differentiated ACQ from FACQ mice were an increased abundance of Barnesiella, Ruminococcus, and Robinsoniella and decreased Clostridium IV in ACQ mice. There was a sex-specific correlation between ACQ and microbial abundance, a reduced Lactobacillus abundance in ACQ male mice, and a decreased Blautia abundance in female ACQ mice. The abundance of Robinsoniella was correlated, and Clostridium IV inversely correlated with the number of doses of cocaine self-administered during acquisition. Functional analysis of the microbiome composition of a subset of mice suggested that gut-brain modules encoding glutamate metabolism genes are associated with the propensity to self-administer cocaine. These findings establish associations between the microbiome composition and glutamate metabolic potential and the ability to acquire cocaine IVSA thus indicating the potential translational impact of targeting the gut microbiome or microbial metabolites for treatment of SUD. Copy rights belong to original authors. Visit the link for more info Podcast created by PaperPlayer

Listen to a blog summary of a recent research paper published by Oncotarget, entitled, "Immunotherapy Response Predicted by Machine Learning & Gut Microbiomes." __________________________________________ Immunotherapy has become a powerful breakthrough in cancer treatment, however, 50% of patients do not respond to immunotherapy. What internal or external features inhibit or confer patient or tumor response to immune system-harnessing therapeutics? These patient/tumor features that impact responsiveness to immunotherapy have yet to be fully elucidated. “Increasing evidence has emerged that gut microbial communities help shape the host immune system [9–11].” Full blog - https://www.oncotarget.org/2022/09/01/immunotherapy-response-predicted-by-machine-learning-gut-microbiomes/ DOI - https://doi.org/10.18632/oncotarget.28252 Correspondence to - Heidi H. Kong - konghe@mail.nih.gov Sign up for free Altmetric alerts about this article - https://oncotarget.altmetric.com/details/email_updates?id=10.18632/oncotarget.28252 Keywords - gut microbiome; immunotherapy; 16S rRNA; machine learning; metagenomics About Oncotarget Oncotarget is a primarily oncology-focused, peer-reviewed, open access journal. Papers are published continuously within yearly volumes in their final and complete form, and then quickly released to Pubmed. To learn more about Oncotarget, please visit www.oncotarget.com and connect with us: SoundCloud - @oncotarget Facebook - www.facebook.com/Oncotarget/ Twitter - twitter.com/oncotarget Instagram - www.instagram.com/oncotargetjrnl/ YouTube - www.youtube.com/OncotargetYouTube LinkedIn - www.linkedin.com/company/oncotarget Pinterest - www.pinterest.com/oncotarget/ Reddit - www.reddit.com/user/Oncotarget/ Media Contact MEDIA@IMPACTJOURNALS.COM 18009220957

Listen to the press release about a new research paper published in Volume 13 of Oncotarget, “Predicting cancer immunotherapy response from gut microbiomes using machine learning models.” ___________________________________ A new research paper was published in Oncotarget on July 19, 2022, entitled, “Predicting cancer immunotherapy response from gut microbiomes using machine learning models.” “In the last decade, the use of cancer immunotherapy targeting immune checkpoint inhibitors (ICIs) to boost T cell mediated cancer cell clearance has significantly improved cancer patient survival [1].” Cancer immunotherapy has significantly improved patient survival. Yet, half of patients do not respond to immunotherapy. Gut microbiomes have been linked to clinical responsiveness of melanoma patients on immunotherapies; however, different taxa have been associated with response status with implicated taxa inconsistent between studies. In this new study, by Hai Liang, Jay-Hyun Jo, Zhiwei Zhang, Margaret A. MacGibeny, Jungmin Han, Diana M. Proctor, Monica E. Taylor, You Che, Paul Juneau, Andrea B. Apolo, John A. McCulloch, Diwakar Davar, Hassane M. Zarour, Amiran K. Dzutsev, Isaac Brownell, Giorgio Trinchieri, James L. Gulley, and Heidi H. Kong from the National Institutes of Health Library, National Cancer Institute, National Human Genome Research Institute, West Virginia University, Zimmerman Associates Inc., and the University of Pittsburgh, researchers used a tumor-agnostic approach to find common gut microbiome features of response among immunotherapy patients with different advanced stage cancers. Full press release - https://www.oncotarget.com/news/pr/oncotarget-predicting-cancer-immunotherapy-response-from-gut-microbiomes-using-machine-learning-models/ DOI - https://doi.org/10.18632/oncotarget.28252 Correspondence to - Heidi H. Kong - konghe@mail.nih.gov Sign up for free Altmetric alerts about this article - https://oncotarget.altmetric.com/details/email_updates?id=10.18632%2Foncotarget.28252 Keywords - gut microbiome, immunotherapy, 16S rRNA, machine learning, metagenomics About Oncotarget Oncotarget is a peer-reviewed, open access biomedical journal covering research on all aspects of oncology. To learn more about Oncotarget, please visit https://www.oncotarget.com and connect with us: SoundCloud - https://soundcloud.com/oncotarget Facebook - https://www.facebook.com/Oncotarget/ Twitter - https://twitter.com/oncotarget Instagram - https://www.instagram.com/oncotargetjrnl/ YouTube - https://www.youtube.com/OncotargetYouTube LinkedIn - https://www.linkedin.com/company/oncotarget Pinterest - https://www.pinterest.com/oncotarget/ Reddit - https://www.reddit.com/user/Oncotarget/ Oncotarget is published by Impact Journals, LLC: https://www.ImpactJournals.com Media Contact MEDIA@IMPACTJOURNALS.COM 18009220957

Original Transplants Episode 64: Supply Chain Resilience Original Transplants Podcast Episode 64: Supply Chain Resilience finds Satoyama Homestead stewards Will and Sarah planning for the year ahead in 2022 in the bee yard, chicken coop, and edible landscape. Will is researching spring bee package suppliers following the demise of his beehives, with one colony absconding and the other dead-out. In better news, the four pullets he raised from chicks during the summer are fully integrated into the flock and have begun egg-laying. Sarah is slowly prepping the vegetable garden beds for the off-season and plans to identify some of the weeds to see if any are useful and should be saved during clean-up. The homesteaders are enjoying the previous season's harvest, including glazing a roast ham with kiwiberry preserves and using dehydrated vegetables on veggie pizza. Will explains harvesting vermicompost and leachate from the worm farm, and the homesteaders plan new storage methods to prevent clumping in key homemade soup ingredients borax and washing soda. Sarah looks forward to enjoying bird watching with Lucy and her birdseed bell from Santa, and is browsing seed catalogs to plan next year's vegetable garden. The homesteaders review new science about the discovery of microplastics in infants at ten times the rate in adults, and discuss agricultural news about how to evaluate your supply chain vulnerabilities and make your supply chain more resilient. Notes Infants have more microplastics in their feces than adults, study finds - American Chemical Society https://www.acs.org/content/acs/en/pressroom/newsreleases/2021/september/infants-have-more-microplastics-in-their-feces-than-adults-study-finds.html Microplastics revealed in the placentas of unborn babies - The Guardian https://www.theguardian.com/environment/2020/dec/22/microplastics-revealed-in-placentas-unborn-babies Vermicomposting for beginners - Rodale Institute https://rodaleinstitute.org/science/articles/vermicomposting-for-beginners/ Bacterial diversity in a finished compost and vermicompost: differences revealed by cultivation-independent analyses of PCR-amplified 16S rRNA genes - Applied Microbiology and Biotechnology via Academia.edu https://www.academia.edu/20157205/Bacterial_diversity_in_a_finished_compost_and_vermicompost_differences_revealed_by_cultivation_independent_analyses_of_PCR_amplified_16S_rRNA_genes Assessing the impact of composting and vermicomposting on bacterial community size and structure, and microbial functional diversity of an olive-mill waste - Bioresource Technology https://doi.org/10.1016/j.biortech.2008.08.014 What to do about hard clumpy borax and washing soda - The Make Your Own Zone https://www.themakeyourownzone.com/clumpy-hard-borax-washing-soda/ How vulnerable is your personal supply chain? - Charles Hugh Smith, Of Two Minds Blog https://www.oftwominds.com/blogdec21/personal-supply-chain12-21.html

Time to talk about the most widespread infection in the world, Helicobacter pylori. Following the accidental abandonment of incubated plates, H. Pylori colonies were discovered, launching a larger investigation into the microbiology of the human stomach. More research is needed on this disease-causing gram-negative bacterium, but our hosts provide the basics of its characteristics, transmission routes, and prevention in this episode.   More about Helicobacter pylori: Persistence strategies of the bacterial pathogen Helicobacter pylori Gastroenteritis and Transmission of Helicobacter pylori Infection in Households Nobel prize is awarded to doctors who discovered H pylori Pathogen Safety Data Sheets Trends in Hospitalizations for Peptic Ulcer Disease H pylori finds its home  Stay tuned for more episodes, posting on the first Thursday of each month. Subscribe to our show wherever you get your podcasts and find more info at weebeastiespodcast.com   The Wee Beasties podcast is a production of Nephros, Inc., a company committed to improving the human relationship with water through leading, accessible technology. ***   SHOW TRANSCRIPT: Christian: I am back with Dr. Kimothy Smith. Kimothy, welcome back!  Kimothy: Thanks, Christian.  Christian: All right…how are we doing today Kimothy? How's life?  Kimothy: I'm feeling a lot of stress, and I've got a pain in my stomach. I think I'm getting an ulcer.  Christian: Today's the right day to have this conversation, I think. We're talking about pathogens on this podcast, so I hear?  Kimothy: Cool! Let's go.  Christian: I was watching that documentary, Human Nature, last night. Have you seen it yet? It's about genomics, personalized medicine using CRISPR cas9 and the scope of genetic and molecular engineering to cure disease, but also do wild projects like bringing back a wooly mammoth. Cool stuff. Worth a watch if you have some time.  Kimothy: I'll check it out, but I tend to be a bit old school. And, I don't mean to go too deep on the old school stuff here, but, have you seen Jurassic Park? Do you really want to bring back a wooly mammoth?  Christian: What is that line from Jeff Golblum in Jurassic Park? “Your scientists were so preoccupied with whether or not they could, they didn't stop to think if they should?”  Kimothy: Yeah, definitely.  Christian: Well, what's our next waterborne pathogen?  Kimothy: Apropos to my ulcer generation, it is Helicobacter pylori.  Christian: H. pylori, I'm not super familiar with this one, but if memory serves this is spiral-shaped bacteria that makes a home in your stomach and can cause ulcers and even stomach cancer in some cases, right?  Kimothy: Yeah, you're on the right track, Christian. According to a 2013 report1 in Nature, H. pylori is the most widespread infection in the world, infecting at least half of the global population. The World Health Organization (WHO) recognized H. pylori as a group 1 carcinogen in 1994, but the backstory on this little bug isn't that straight forward.  H. pylori was discovered more recently, in comparison to the other microorganisms we've discussed – it was discovered in 1983 – and, interestingly enough, it was first found as a colony in the human stomach in a really unexpected stroke of luck after two doctors were trying to demonstrate a connection between the severity of gastric distress experienced by their patients and the number of bacteria present. In part, this discovery prompted scientists to begin a larger investigation into the microbiology of the human stomach using 16S rRNA analysis – and now we know that the stomach and the rest of the human gut has an extraordinarily diverse microbiome of bacteria which is critical to our immune response and other autonomic faculties. And I must tell you, Christian, as a side note, I've heard an urban legend that your microbiome can determine if you have a sweet tooth or not. Have you heard that?  Christian: I have not, but I've got a horrible sweet tooth. I'm always wanting sweets. So, I'm sort of wondering if we should run a 16S rRNA analysis of my gut biopsy.  Kimothy: Keep your microbiome to yourself, please.  Christian: Yeah, so this was part of what catalyzed the gut microbiome frenzy in the 90's. But wait, what was the stroke of luck? And, if good bacteria is so critical to our gut and immune response how is H. pylori, a pathogenic bacterium, able to stay alive in there?  Kimothy: Yeah, Christian, I'm glad you asked. So, the stroke of luck was in the successful culture. The two Australian doctors credited with the discovery just mistakenly left a plate in the incubator a lot longer than they had intended, and they just happen to get H. pylori colonies on it.  Those that have worked with H. pylori before will know just how persnickety the bacteria is – it is exceedingly difficult to grow outside of its habitat.  Christian: And why is that?  Kimothy: Well, let me get into the weeds a bit here. So, like many of the other pathogens we've discussed, H. pylori is a gram-negative bacterium, which means it has that extra LPS (lipopolysaccharide) barrier on its outer membrane. So, for starters, its more protected simply by its composition as a gram-negative bacterium. However, H. pylori has a really cool mechanism that allows it to transform its shape when it's under stress – examples of stress may include a change in pH or salinity, or an increase in the gases present – like nitrogen, carbon dioxide, and oxygen.    Christian: Uh huh…so what does it change its shape to?  Kimothy: Well, as I was saying a moment ago, H. pylori is hard to grow on a plate outside its ideal habitat.  It turns out that even in its ideal habitat, the stomach, the bacterium only thrives in these really specific conditions of pH and gas and any deviation from those conditions will cause the cells to become dormant and actually change shape. So check this out: H. pylori is spiral or helix-shaped (that's where the name comes from, Helico-bacter) and form follows function here, so it needs to burrow into the epithelium in the stomach lining in order to survive, so it uses its spiral shape and several flagella to literally corkscrew itself into our stomach to take residence. But, if the cell becomes stressed because a change in any of those conditions – pH, salt, gas, or temperature – it will slow down its metabolic machinery and change from its spiral shape and into a coccoid form.  It's still unclear if this transformation under stress is a selected adaptation or something else.  Several studies point to H. pylori's transformation as an evolutionary adaptation to cope with stress and others show no relationship.  There need to be more experiments to tease this out, but it is clear that a VBNC state is common with H. pylori, which again makes this a very, very difficult organism to culture from biopsies.  Christian: OK, we did get pretty deep there, let me just recap real quick: H. pylori is a gram-negative pathogen that is spiral (helix-shaped) with several flagella, which make it very motile; it is really selective about its environment (which is the stomach) and it doesn't grow well at all outside of that environment, in fact it usually enters a VBNC state if it becomes stressed in any way and when it's stress it changes shape into a coccoid form – this is a smaller spherical shape, right? I think the etymology of coccoid is actual berry in Greek, right? So, it transforms from a rod-spiral to a berry-shape? Lastly, and most importantly H. pylori results in the host ultimately getting stomach ulcers and even cancer, right?  OK, but we've been talking a lot about this pathogen living in stomachs, H. pylori is also in bulk water, though.   Kimothy: Yes, so the route of infection for H. pylori is still a bit mysterious and not always well-characterized to researchers. Contaminated water sources are certainly a means of infection, but so is fecal-oral and mucous-oral routes. This can result from living in close quarters with a large community and just not have access to proper disinfectants on touchable surfaces.  Once one person in a close-quarters household acquires H. pylori the R0 in that sample size will increase over time according to a Stanford Medical School manuscript in 2006.  R0 is just a term we use to describe the rate of infection to other individuals.    Christian: So the good news, if there is good news, is that educating people on transmission routes and increasing access to disinfectants can likely really disrupt or lower the R0.  Kimothy: That's right, Christian.  I'd like to come back to bulk water and liquid biopsies though if I may for a moment. Because H. pylori is so challenging to culture one of the best and most reliable ways to detect and study H. pylori is by using molecular diagnostic tools such as NGS using 16S rRNA and qPCR. We've talked about pathogens that cause pneumonia and acute respiratory infections, we've talked about pathogens that infect the blood, and now we have a pathogen that infects your gut with little to no indication of infection in most patients.  And although worldwide infection rates are going down, largely because of what you mentioned – access to clean water and surface disinfectants, the best way we can track and surveil this bug is by using these new diagnostic tools. Culturing for this bug is just too time consuming, unreliable, and not specific enough. It's analog in a digital world.  Christian: All right, well H. pylori…the peptic ulcer disease-causing gram-negative bacterium.  One more thing before we go – I know you're not a medical doctor, but how is H. pylori usually treated? Just a super dose of antibiotics?   Kimothy: Yeah, bacterium is very susceptible to antibiotic regimens, so it can usually be eradicated with a high-powered antibiotic.    Christian: Well, cool deal. We'll put some links in the show notes to some of these manuscripts we've mentioned in case you're interested. Kimothy, as always, thanks so much for the chat today.  Kimothy: You bet, Christian.

Pomegranate peel has protective effects against enteropathogenic bacteria US Department of Agriculture, August 31, 2021 A recent study by the U.S. Department of Agriculture revealed that pomegranate peel extract contains bioactive compounds that have potential antibacterial activity. The study's findings were published in the journal Nutrition Research. Pomegranate fruit peel is considered an agricultural waste product. However, it is a rich source of polyphenols like punicalins, punicalagins and ellagic acids. Earlier studies have shown that products derived from pomegranates have health benefits, including antibacterial activity, in vitro. There is limited evidence, however, of their antibacterial activity in vivo. For this study, researchers sought to determine the antibacterial properties of pomegranate peel extract in vivo. In particular, they focused on the punicalin, punicalagin and ellagic acid present in the peel extract. The researchers infected C3H/He mice with the bacterial pathogen Citrobacter rodentium, a bacterium that mimics the enteropathogenic bacterium, Escherichia coli. Prior to infection, the mice were orally treated with water or pomegranate peel extract. Twelve days after infection, the researchers examined C. rodentium colonization of the colon and spleen, as well as changes in tissue and gene expression. Fecal excretions were also analyzed for C. rodentium. The results revealed that the pomegranate peel extract reduced weight loss and mortality induced by C. rodentium infection. The extract also reduced C. rodentium colonization of the spleen. Additionally, pomegranate peel extract decreased the extent of damage in the colon caused by C. rodentium infection. In sum, pomegranate fruit peel extract contains bioactive compounds that can help reduce the severity of C. rodentium infection in vivo.   Vitamin D may protect against young-onset colorectal cancer Dana-Farber Cancer Institute and Harvard  School of Public Health, September 1, 2021 Consuming higher amounts of Vitamin D - mainly from dietary sources - may help protect against developing young-onset colorectal cancer or precancerous colon polyps, according to the first study to show such an association. The study, recently published online in the journal Gastroenterology, by scientists from Dana-Farber Cancer Institute, the Harvard T.H. Chan School of Public Health, and other institutions, could potentially lead to recommendations for higher vitamin D intake as an inexpensive complement to screening tests as a colorectal cancer prevention strategy for adults younger than age 50. While the overall incidence of colorectal cancer has been declining, cases have been increasing in younger adults - a worrisome trend that has yet to be explained. The authors of the study, including senior co-authors Kimmie Ng, MD, MPH, of Dana-Farber, and Edward Giovannucci, MD, DSc., of the T.H. Chan School, noted that vitamin D intake from food sources such as fish, mushrooms, eggs, and milk has decreased in the past several decades. There is growing evidence of an association between vitamin D and risk of colorectal cancer mortality. However, prior to the current study, no research has examined whether total vitamin D intake is associated with the risk of young-onset colorectal cancer. “Vitamin D has known activity against colorectal cancer in laboratory studies. Because vitamin D deficiency has been steadily increasing over the past few years, we wondered whether this could be contributing to the rising rates of colorectal cancer in young individuals,” said Ng, director of the Young-Onset Colorectal Cancer Center at Dana-Farber. “We found that total vitamin D intake of 300 IU per day or more - roughly equivalent to three 8-oz. glasses of milk - was associated with an approximately 50% lower risk of developing young-onset colorectal cancer.” The results of the study were obtained by calculating the total vitamin D intake - both from dietary sources and supplements - of 94,205 women participating in the Nurses' Health Study II (NHS II). This study is a prospective cohort study of nurses aged 25 to 42 years that began in 1989. The women are followed every two years by questionnaires on demographics, diet and lifestyle factors, and medical and other health-related information. The researchers focused on a primary endpoint - young-onset colorectal cancer, diagnosed before 50 years of age. They also asked on a follow-up questionnaire whether they had had a colonoscopy or sigmoidoscopy where colorectal polyps (which may be precursors to colorectal cancer) were found. During the period from 1991 to 2015 the researchers documented 111 cases of young-onset colorectal cancer and 3,317 colorectal polyps. Analysis showed that higher total vitamin D intake was associated with a significantly reduced risk of early-onset colorectal cancer. The same link was found between higher vitamin D intake and risk of colon polyps detected before age 50. The association was stronger for dietary vitamin D - principally from dairy products - than from vitamin D supplements. The study authors said that finding could be due to chance or to unknown factors that are not yet understood. Interestingly, the researchers didn't find a significant association between total vitamin D intake and risk of colorectal cancer diagnosed after age 50. The findings were not able to explain this inconsistency, and the scientists said further research in a larger sample is necessary to determine if the protective effect of vitamin D is actually stronger in young-onset colorectal cancer. In any case, the investigators concluded that higher total vitamin D intake is associated with decreased risks of young-onset colorectal cancer and precursors (polyps). “Our results further support that vitamin D may be important in younger adults for health and possibly colorectal cancer prevention,” said Ng. “It is critical to understand the risk factors that are associated with young-onset colorectal cancer so that we can make informed recommendations about diet and lifestyle, as well as identify high risk individuals to target for earlier screening.”     Choosing personal exercise goals, then tackling them immediately is key to sustaining change University of Pennsylvania, September 1, 2021 When people set their own exercise goals – and then pursue them immediately – it's more likely to result in lasting positive changes, according to a new study at the Perelman School of Medicine at the University of Pennsylvania. The results of this research are especially important because they were found among an underserved population that is at particularly high risk of having or developing heart conditions. The study was published in JAMA Cardiology. “Most behavior change programs involve goal-setting, but the best way to design that process is unknown,” said lead author Mitesh Patel, MD, MBA, an associate professor of Medicine at Penn and vice president for Clinical Transformation at Ascension. “Our clinical trial demonstrated that physical activity increased the most when patients chose their goals rather than being assigned them, and when the goals started immediately rather than starting lower and gradually increasing over time. These findings are particularly important because the patients were from lower-income neighborhoods and may face a number of challenges in achieving health goals.” This study consisted of 500 patients from low-income neighborhoods, mainly in West Philadelphia but also elsewhere in and outside of the city. Participants either had a cardiovascular disease or were assessed to have a near-10 percent risk of developing one within a decade. These high-risk patients stood to greatly gain from increased physical activity. Patel's previous work at the Penn Medicine Nudge Unit often focused on the use of gamification, a concept used to create behavioral change by turning it into a game. The work usually tested whether playing a game attached to physical activity goals could make significant increases against not playing a game, or between different versions of a game. As with past studies, every participant was given a wearable step tracker that recorded their daily step counts through Penn's Way to Health platform. But what set this study apart from many of its predecessors was that the main outcomes of the research were less about participation in the games themselves and more about how goals were established, as well as when participants were encouraged to pursue them. Once every participant got their wearable step counter, they were given a week or two to get used to it. This time period also functioned as a baseline-setting period for everyone's pre-intervention daily step count. After that, participants were randomly assigned to the control group, which didn't have step goals or games attached, or one of the gaming groups with goals. Those in the gamified group also went through two other sets of random assignments. One determined whether they'd have input on their step goal, or whether they'd just be assigned a standard one. The second decided whether each participant would immediately start working toward their goals (for the entire 16-week intervention), or whether they'd ramp up to it, with minor increases in goals, until the full goals kicked in at week nine. After analyzing the results, the researchers saw that the only group of participants who achieved significant increases in activity were those who chose their own goals and started immediately. They had the highest average increase in their steps compared to the group with no goals, roughly 1,384 steps per day. And, in addition to raw step counts, the study also measured periods of sustained, high activity, amounting to an average increase of 4.1 minutes daily. Comparatively, those who were assigned their goals or had full goals delayed for half the intervention only increased their daily steps above the control group's average by between 500 and 600 steps. “Individuals who select their own goals are more likely to be intrinsically motivated to follow through on them,” said Kevin Volpp, MD, PhD, director of the Center for Health Incentives and Behavioral Economics. “They feel like the goal is theirs and this likely enables greater engagement.” The study didn't end when the researchers turned the games off. Participants kept their activity trackers, and in the eight weeks following the intervention, the group that chose their goals and started immediately kept up their progress. In fact, they achieved almost the exact same average in steps – just three less than during the active games. “It is exciting to see that the group that increased their activity levels by the most steps maintained those levels during follow-up,” Patel said. “This indicates that gamification with self-chosen and immediate goals helped these patients form a new habit.” Many programs, whether offered through work or by health insurance companies, offer incentives for boosts in physical activity. But these goals are often fairly static and assigned based on round numbers. Patel, Volpp, and colleagues believe this research suggests that adjusting goal setting in these programs can have a significant impact. And if these adjustments lead to gains among people with lower incomes, whom cardiovascular disease kill at 76 percent higher rates, that could be particularly important.           “Goal-setting is a fundamental element of almost every physical activity program, whether through a smartphone app or in a workplace wellness program,” Volpp said. “Our findings reveal a simple approach that could be used to improve the impact of these programs and the health of their patients.”   Comparing seniors who relocate long-distance shows that where you live affects your longevity Massachusetts Institute of Technology, September 1, 2021 Would you like to live longer? It turns out that where you live, not just how you live, can make a big difference. That's the finding of an innovative study co-authored by an MIT economist, which examines senior citizens across the U.S. and concludes that some locations enhance longevity more than others, potentially for multiple reasons. The results show that when a 65-year-old moves from a metro area in the 10th percentile, in terms of how much those areas enhance longevity, to a metro area the 90th percentile, it increases that person's life expectancy by 1.1 years. That is a notable boost, given that mean life expectancy for 65-year-olds in the U.S. is 83.3 years. "There's a substantively important causal effect of where you live as an elderly adult on mortality and life expectancy across the United States," says Amy Finkelstein, a professor in MIT's Department of Economics and co-author of a newly published paper detailing the findings. Researchers have long observed significant regional variation in life expectancy in the U.S., and often attributed it to "health capital"—tendencies toward obesity, smoking, and related behavioral factors in the regional populations. But by analyzing the impact of moving, the current study can isolate and quantify the effect that the location itself has on residents. As such, the research delivers important new information about large-scale drivers of U.S. health outcomes—and raises the question of what it is about different places that affects the elderly's life expectancy. One clear possibility is the nature of available medical care. Other possible drivers of longevity include climate, pollution, crime, traffic safety, and more. "We wanted to separate out the role of people's prior experiences and behaviors—or health capital—from the role of place or environment," Finkelstein says. The paper, "Place-Based Drivers of Mortality: Evidence of Migration," is published in the August issue of the American Economic Review. The co-authors are Finkelstein, the John and Jennie S. MacDonald Professor of Economics at MIT, and Matthew Gentzkow and Heidi Williams, who are both professors of economics at Stanford University. To conduct the study, Finkelstein, Gentzkow, and Williams analyzed Medicare records from 1999 to 2014, focusing on U.S. residents between the ages of 65 and 99. Ultimately the research team studied 6.3 million Medicare beneficiaries. About 2 million of those moved from one U.S. "commuting zone" to another, and the rest were a random 10 percent sample of people who had not moved over the 15-year study period. (The U.S. Census Bureau defines about 700 commuting zones nationally.) A central element of the study involves seeing how different people who were originally from the same locations fared when moving to different destinations. In effect, says Finkelstein, "The idea is to take two elderly people from a given origin, say, Boston. One moves to low-mortality Minneapolis, one moves to high-mortality Houston. We then compare thow long each lives after they move." Different people have different health profiles before they move, of course. But Medicare records include detailed claims data, so the researchers applied records of 27 different illnesses and conditions—ranging from lung cancer and diabetes to depression—to a standard mortality risk model, to categorize the overall health of seniors when they move. Using these "very, very rich pre-move measures of their health," Finkelstein notes, the researchers tried to account for pre-existing health levels of seniors from the same location who moved to different places. Still, even assessing people by 27 measures does not completely describe their health, so Finkelstein, Gentzkow, and Williams also estimated what fraction of people's health conditions they had not observed—essentially by calibrating the observed health of seniors against health capital levels in places they were moving from. They then consider how observed health varies across individuals from the same location moving to different destinations and, assuming that differences in unobserved health—such as physical mobility—vary in the same way as observed differences in health, they adjust their estimates accordingly. All told, the study found that many urban areas on the East and West Coasts—including New York City, San Francisco, and Miami—have positive effects on longevity for seniors moving there. Some Midwestern metro areas, including Chicago, also score well. By contrast, a large swath of the deep South has negative effects on longevity for seniors moving there, including much of Alabama, Arkansas, Louisiana, and northern Florida. Much of the Southwest, including parts of Texas, Oklahoma, New Mexico, and Arizona, fares similarly poorly. The scholars also estimate that health capital accounts for about 70 percent of the difference in longevity across areas of the U.S., and that location effects account for about 15 percent of the variation. "Yes, health capital is important, but yes, place effects also matter," Finkelstein says. Other leading experts in health economics say they are impressed by the study. Jonathan Skinner, the James O. Freeman Presidential Professor of Economics, Emeritus, at Dartmouth College, says the scholars "have provided a critical insight" into the question of place effects "by considering older people who move from one place to another, thus allowing the researchers to cleanly identify the pure effect of the new location on individual health—an effect that is often different from the health of long-term residents. This is an important study that will surely be cited and will influence health policy in coming years." The Charlotte Effect: What makes a difference? Indeed, the significance of place effects on life expectancy is also evident in another pattern the study found. Some locations—such as Charlotte, North Carolina—have a positive effect on longevity but still have low overall life expectancy, while other places—such as Santa Fe New Mexico—have high overall life expectancy, but a below-average effect on the longevity of seniors who move there. Again, the life expectancy of an area's population is not the same thing as that location's effect on longevity. In places where, say, smoking is highly prevalent, population-wide longevity might be subpar, but other factors might make it a place where people of average health will live longer. The question is why. "Our [hard] evidence is about the role of place," Finkelstein says, while noting that the next logical step in this vein of research is to look for the specific factors at work. "We know something about Charlotte, North Carolina, makes a difference, but we don't yet know what." With that in mind, Finkelstein, Gentzkow, and Williams, along with other colleagues, are working on a pair of new studies about health care practices to see what impact place-based differences may have; one study focuses on doctors, and the other looks at the prescription opioid epidemic. In the background of this research is a high-profile academic and policy discussion about the impact of health care utilization. One perspective, associated with the Dartmouth Atlas of Health Care project, suggests that the large regional differences in health care use it has documented have little impact on mortality. But the current study, by quantifying the variable impact of place, suggest there may be, in turn, a bigger differential impact in health care utilization yet to be identified. For her part, Finkelstein says she would welcome further studies digging into health care use or any other factor that might explain why different places have different effects on life expectancy; the key is uncovering more hard evidence, wherever it leads. "Differences in health care across places are large and potentially important," Finkelstein says. "But there are also differences in pollution, weather, [and] other aspects. … What we need to do now is get inside the black box of 'the place' and figure out what it is about them that matters for longevity."   Gut bacteria influence brain development Researchers discover biomarkers that indicate early brain injury in extreme premature infants University of Vienna (Austria), September 3, 2021 The early development of the gut, the brain and the immune system are closely interrelated. Researchers refer to this as the gut-immune-brain axis. Bacteria in the gut cooperate with the immune system, which in turn monitors gut microbes and develops appropriate responses to them. In addition, the gut is in contact with the brain via the vagus nerve as well as via the immune system. "We investigated the role this axis plays in the brain development of extreme preterm infants," says the first author of the study, David Seki. "The microorganisms of the gut microbiome - which is a vital collection of hundreds of species of bacteria, fungi, viruses and other microbes - are in equilibrium in healthy people. However, especially in premature babies, whose immune system and microbiome have not been able to develop fully, shifts are quite likely to occur. These shifts may result in negative effects on the brain," explains the microbiologist and immunologist. Patterns in the microbiome provide clues to brain damage "In fact, we have been able to identify certain patterns in the microbiome and immune response that are clearly linked to the progression and severity of brain injury," adds David Berry, microbiologist and head of the research group at the Centre for Microbiology and Environmental Systems Science (CMESS) at the University of Vienna as well as Operational Director of the Joint Microbiome Facility of the Medical University of Vienna and University of Vienna. "Crucially, such patterns often show up prior to changes in the brain. This suggests a critical time window during which brain damage of extremely premature infants may be prevented from worsening or even avoided." Comprehensive study of the development of extremely premature infants Starting points for the development of appropriate therapies are provided by the biomarkers that the interdisciplinary team was able to identify. "Our data show that excessive growth of the bacterium Klebsiella and the associated elevated γδ-T-cell levels can apparently exacerbate brain damage," explains Lukas Wisgrill, Neonatologist from the Division of Neonatology, Pediatric Intensive Care Medicine and Neuropediatrics at the Department of Pediatric and Adolescent Medicine at the Medical University of Vienna. "We were able to track down these patterns because, for a very specific group of newborns, for the first time we explored in detail how the gut microbiome, the immune system and the brain develop and how they interact in this process," he adds. The study monitored a total of 60 premature infants, born before 28 weeks gestation and weighing less than 1 kilogram, for several weeks or even months. Using state-of-the-art methods - the team examined the microbiome using 16S rRNA gene sequencing, among other methods - the researchers analysed blood and stool samples, brain wave recordings (e.g. aEEG) and MRI images of the infants' brains. Research continues with two studies The study, which is an inter-university clusterproject under the joint leadership by Angelika Berger (Medical University of Vienna) and David Berry (University of Vienna), is the starting point for a research project that will investigate the microbiome and its significance for the neurological development of prematurely born children even more thoroughly. In addition, the researchers will continue to follow the children of the initial study. "How the children's motoric and cognitive skills develop only becomes apparent over several years," explains Angelika Berger. "We aim to understand how this very early development of the gut-immune-brain axis plays out in the long term. " The most important cooperation partners for the project are already on board: "The children's parents have supported us in the study with great interest and openness," says David Seki. "Ultimately, this is the only reason we were able to gain these important insights. We are very grateful for that."     Amino acid supplements may boost vascular endothelial function in older adults: Study University of Alabama, August 28, 2021 A combination of HMB (a metabolite of leucine), glutamine and arginine may improve vascular function and blood flow in older people, says a new study. Scientists from the University of Alabama report that a supplement containing HMB (beta-hydroxy-beta-methylbutyrate), glutamine and arginine (Juven by Abbott Nutrition) increased flow-mediated dilation (FMD - a measure of blood flow and vascular health) by 27%, whereas no changes were observed in the placebo group. However, the researchers did not observe any changes to markers of inflammation, including high-sensitivity C-reactive protein (hsCRP) and tumor necrosis factor-alpha (TNF-alpha) “Our results indicate that 6 months of dietary supplementation with HMB, glutamine and arginine had a positive impact on vascular endothelial function in older adults,” wrote the researchers, led by Dr Amy Ellis in the European Journal of Clinical Nutrition . “These results are clinically relevant because reduced endothelial-dependent vasodilation is a known risk factor for cardiovascular diseases. “Further investigation is warranted to elucidate mechanisms and confirm benefits of foods rich in these amino acids on cardiovascular outcomes.” The study supported financially by the National Center for Complementary and Alternative Medicine. Study details Dr Ellis and her co-workers recrtuited 31 community-dwelling men and women aged between 65 and 87 to participate in their randomized, placebo-controlled trial. The participants were randomly assigned to one of two groups: The first group received the active supplements providing 3 g HMB, 14 g glutamine and 14 g arginine per day; while the second group received a placebo. After six months of intervention, the researchers found that FMD increased in the HMB + glutamine + arginine group, but no such increases were observed in the placebo group. While no changes in CRP or TNF-alpha levels were observed in the active supplement group, a trend towards an increase in CRP levels was observed in the placebo group, but this did not reach statistical significance, they noted. “Although no previous studies have examined this combination of amino acids on vascular function, we hypothesized that the active ingredients of the supplement would act synergistically to improve endothelial function by reducing oxidative stress and inflammation,” wrote the researchers. “However, although we observed a trend for increasing hsCRP among the placebo group (P=0.059), no significant changes in hsCRP or TNF-alpha were observed for either group. “Possibly, the effects of the supplement on reducing oxidative stress and inflammation were subclinical, or the high variability in these biomarkers, particularly hsCRP, among our small sample could have precluded visible differences.” The researchers also noted that an alternate mechanism may also be responsible, adding that arginine is a precursor of the potent vasodilator nitric oxide “Although investigation of this mechanism was beyond the scope of this study, it is feasible that the arginine in the supplement improved endothelial-dependent vasodilation by providing additional substrate for nitric oxide synthesis,” they added.     Moderate coffee drinking associated with lower risk of mortality during 11-year median follow-up Semmelweis University (Bulgaria), September 1 2021.  Research presented at ESC (European Society of Cardiology) Congress 2021 revealed a lower risk of dying from any cause during an 11-year median period among light to moderate coffee drinkers in comparison with men and women who had no intake. The study included 468,629 UK Biobank participants of an average age of 56.2 years who had no indications of heart disease upon enrollment. Coffee intake was classified as none, light to moderate at 0.5 to 3 cups per day or high at over 3 cups per day. A subgroup of participants underwent magnetic resonance imaging (MRI) of the heart to assess cardiac structure and function.  Light to moderate coffee intake during the follow-up period was associated with a 12% decrease in the risk of dying from any cause, a 17% lower risk of cardiovascular mortality and a 21% reduction in the incidence of stroke in comparison with the risks associated with not drinking coffee.  “The imaging analysis indicated that, compared with participants who did not drink coffee regularly, daily consumers had healthier sized and better functioning hearts,” reported study author Judit Simon, of Semmelweis University in Budapest. “This was consistent with reversing the detrimental effects of aging on the heart.” “To our knowledge, this is the largest study to systematically assess the cardiovascular effects of regular coffee consumption in a population without diagnosed heart disease,” she announced. “Our results suggest that regular coffee consumption is safe, as even high daily intake was not associated with adverse cardiovascular outcomes and all-cause mortality after a follow-up of 10 to 15 years. Moreover, 0.5 to 3 cups of coffee per day was independently associated with lower risks of stroke, death from cardiovascular disease, and death from any cause.”

Lion’s mane mushroom helps reduce depression and anxiety Tohoku University (Japan), March 21, 2021 Several studies have shown the potential of lion’s mane mushroom to help address several health problems including those that are related to brain function. Lion’s mane mushroom (Hericium erinaceus), also known as hedgehog mushroom, is a mushroom native to North America, Asia and Europe. Its fruiting bodies are said to contain polysaccharides that are beneficial to the human body. This mushroom has a long history of medical uses, especially in Traditional Chinese Medicine (TCM) where it was used to help support brain health. In recent years, its value in supporting cognitive health has been supported by a number of studies. The mushroom helps Reduce depression and anxiety In a study published in the journal Biomedical Research, the mushroom was tested on female participants in order to tests its effects on mental health. After taking lion’s mane mushroom cookies for four weeks, the participants reported reduced depression and anxiety. According to the researchers, this was due to two chemical constituents isolated from lion’s mane’s fruiting body called hericenones and erinacines. These two chemicals stimulate nerve growth factor (NGF) biosynthesis. NGF takes part in a number of activities in the body that are essential in maintaining and organizing neurons. By stimulating NGF biosynthesis, lion’s mane is able to help improve mental health. Meanwhile, in a study on mice, researchers from Tohoku University  in Japan discovered that lion’s mane mushroom may be used to prevent cognitive dysfunction. The Japanese researchers administered 10 micrograms of amyloid-beta peptide to the mice on days seven and 14 in their 23-day experimental period. Also, the mice subjects were fed with food containing lion’s mane mushroom over the course of the experimental period. To measure the results of their study, the team used Y-maze and the novel object recognition tests on the subjects. They discovered that the mushroom prevented the negative effects of amyloid-beta peptide on the spatial short-term and visual recognition memory of the mice. The study suggests that the mushroom might reverse even the effects of amyloid-beta peptide – a protein believed to cause Alzheimer’s disease. Lion’s mane for cognitive impairment Moreover, in another study conducted by Japanese scientists, lion’s mane mushroom showed potential in improving symptoms of mild cognitive impairment. This is the stage between aging-related cognitive decline and the development of dementia. Its symptoms include problems with memory, language, thinking or judgment. The team took 30 patients with mild cognitive impairment and gave them 250mg tablets with 96 percent lion’s mane extract to be taken in four pieces for three times a day for 16 weeks. During weeks eight, 12 and 16, the patients underwent observation wherein they showed improvement in their cognitive function as displayed by the increase of their scores on the cognitive function scale. Moreover, the researchers conducted laboratory tests on the patients and saw that the intake of lion’s mane did not result in any side effect. In addition, the patients’ scores in the cognitive function scale decreased by the time their intake of lion’s mane mushroom tablets stopped.       Quercetin-3-o-glucuronide alleviates cognitive deficit in mouse model of Alzheimer disease Hua-zhong University of Science & Technology (China), March 22, 2021   According to news reporting from Wuhan, People’s Republic of China, research stated, “Scope Alzheimer’s disease (AD) is characterized by amyloid-beta (A beta) related imbalance, Tau-hyperphosphorylation, and neuroinflammation, in which A beta and neuroinflammation can induce brain insulin resistance (IR). Gut microbiome disorder is correlated with inflammation in AD.” The news correspondents obtained a quote from the research from the Huazhong University of Science and Technology, “As of yet, there are no effective treatments clinically. Thus, it is focused on the potential benefit of quercetin-3-O-glucuronide (Q3G), a pharmacologically active flavonol glucuronide, on AD treatment by regulating brain IR and the gut microbiome. AD mice model built through intracerebroventricular injection of A beta(1-42) and AD cell model developed through the SH-SY5Y cell line and A beta(1-42) are used to explore the protective effects of Q3G on AD. Neurobehavioral test, brain insulin signaling pathway, and high-throughput pyrosequencing of 16S rRNA are assessed. Data show that Q3G attenuates neuroinflammation and brain IR in A beta(1-42)-injected mice and relieves apoptosis in A beta(1-42)-treated SH-SY5Y cells by interrupting the downstream insulin signaling. Q3G ameliorates A beta accumulation and Tau phosphorylation, restores CREB and BDNF levels in the hippocampus , and reverses A beta(1-42)-induced cognitive impairment. Besides, Q3G restores A beta(1-42)-induced reduction of short-chain fatty acids (SCFAs) and gut microbiota dysbiosis.” According to the news reporters, the research concluded: “Q3G can alleviate brain IR through directly acting on the brain or modulating the gut-brain axis, ultimately to relieve A beta(1-42)-induced cognitive dysfunction.” This research has been peer-reviewed.     Research shows possible link between number of fast-food outlets and heart attacks Hunter Medical Research Institute & University of Newcastle (UK), March 17, 2021  Researchers from the Hunter Medical Research Institute (HMRI), the University of Newcastle and Hunter New England Health (HNE Health) have found that for each new fast-food outlet the number of heart attacks per 100,000 people went up by four. Published in the latest edition of the Internal Medicine Journal the study aimed to determine whether the number of fast-foodoutlets in an area could be considered an environmental risk factor for Myocardial Infarction (heart attack). The team led by Dr. Tarunpreet Saluja from the University of Newcastle, compared all cases of Myocardial Infarction within the Hunter-New England Health District with the Fast-Food Outlet Density (FFD) of each Local Government Area within the district.  "Heart attack is one of the leading causes of death worldwide" said Dr. Saluja, "However, recent data suggests that an increasing number of heart attacks cannot be explained by known risk factors." "There is a well-established link between fast food consumption and cardiovascular diseases such as heart attack. This highlights the need to explore the role of food availability in the probability of having a heart attack." The team found that FFD was positively correlated with an increase of myocardial infarction, even after accounting for other factors such as age, obesity, hyperlipidaemia (high cholesterol), hypertension (high blood pressure), smoking status, diabetes, and socioeconomic status.  Study co-author and cardiologist at John Hunter Hospital, Professor Andrew Boyle said that while it has been known for some time that consuming fast food was bad for the heart no one had determined whether the number of stores was itself a predicting factor.  "Until now there has been very little data on the link between fast-food outlet density and heart attacks, so these results should provide an important consideration for future public‐health policy and community development," said Professor Boyle.  Study co-author and Associate Director of HMRI's Data Science Group, Dr. Christopher Oldmeadow, said that developing a new metric to calculate fast-food outlet density was key to the study and there was scope to expand the data to look at more outlets in the future.  "For this study, we focused on the 10 most popular fast-food outlets in Australia and used census data to determine the density per 100,000 people in each local government area," Dr. Oldmeadow said. "This worked for the majority of the LGAs, but there is scope to investigate the relationship between smaller, locally operated fast‐food outlets and heart attacks."   Vitamin B6 may help calm cytokine storms in COVID-19 University of Hiroshima (Japan), March 14, 2021 Vitamin B6 may help calm cytokine storms and unclog blood clots linked to novel coronavirus (COVID-19) lethality, according to a new study published in the journal Frontiers in Nutrition. In the paper, researchers from Hiroshima University pointed out growing evidence showing that vitamin B6 exerts a protective effect against chronic illnesses such as cardiovascular diseases and diabetes by suppressing inflammation, inflammasomes, oxidative stress, and carbonyl stress. Coronaviruses and influenza are among the viruses that can cause lethal lung injuries and death from acute respiratory distress syndrome worldwide. Viral infections evoke a “cytokine storm,” leading to lung capillary endothelial cell inflammation, neutrophil infiltration, and increased oxidative stress, the researchers said. The researchers said thrombosis or blood clotting and cytokine storm or hyper-inflammation might be closely linked to the graveness of COVID-19. Cytokine storms happen when the immune system dangerously goes into overdrive and starts attacking even the healthy cells. Meanwhile, blood clots linked to COVID-19 can block capillaries, damaging vital organs like the heart, lungs, liver, and kidneys, according to the study. Vitamin B6 is a known anti-thrombosis and anti-inflammation nutrient. Deficiency in this vitamin is also associated with lower immune function and higher susceptibility to viral infections. Studies have so far explored the benefits of vitamins D and C and minerals like zinc and magnesium in fortifying immune response against COVID-19. Research on vitamin B6 has been limited, the researchers said. The researchers said they hope the paper will show vitamin B6's potential in lowering the odds of patients becoming seriously ill with the coronavirus, and prompt further research. "It is of great interest to examine if vitamin B6 exerts protection against novel types of virus infection and pneumonia which will be encountered in the future,” said Thanutchaporn Kumrungsee, PhD, lead author of the paper, in a statement. “At present, there is few information regarding the protective role of nutrients against pneumonia and lung diseases.” Vitamin B6 has a close relationship with the immune system, she said. Its levels always drop in people under chronic inflammation such as obesity, diabetes, and heart diseases. “We can see from the news that obese and diabetic people are at high risk for COVID-19, said Kumrungsee. “Thus, our attempt in this paper is to shed light on the possible involvement of vitamin B6 in decreasing the severity of COVID-19.     Green space or light at night: How we can improve health University of Adelaide (Australia), March 18, 2021 There is a growing body of evidence that exposure to green space is good for our health but a new study from the University of Adelaide has found that this may equally be due to how much light we are exposed to at night. Spending time in green space can improve depressive symptoms, obesity, and sleep problems, and reduce the risk of breast and prostate cancer. Conversely, exposure to light at night, particularly urban light pollution, increases the risk of breast and prostate cancer, and can worsen depression, obesity and sleep problems.  Researchers identified a negative correlation between green space diversity and outdoor artificial light at night for Australian major cities—in other words, the greener your environment, the less the light pollution, and vice versa.  This makes intuitive sense, because the more developed an area is, the fewer trees there will be and the more lights there will be.  Published in Environmental Research, the study questions whether the health benefits of green space exposure may in part be a result of avoiding light at night.  "There seems to be a pattern here—yet, amazingly, no one has put these two things together—until now,"' said lead author Dr. Jessica Stanhope from the University of Adelaide's School of Allied Health Science and Practice.  "It is possible that these factors have been confounding each other in epidemiological studies of the associations between residential green spaces and improved health, and urban outdoor artificial light at night exposure and poor health.  "We have shown that green space is inversely associated with outdoor artificial light at night, making it unclear whether health outcomes result from the green space, the light at night, or possibly in an interaction of the two."  Researchers recommend that epidemiological studies focus on resolving this problem as a priority, so that recommendations can be made for interventions that would improve the public health. For example, to improve population health, is it more important to plant green space in urban areas to give people in cities better green space exposure, or is it better to invest that effort in reducing urban light pollution, or both?  "Some great studies have been done on the association between green space and health, which is a rapidly growing research area; and there are also very neat epidemiological studies of the adverse health effects of exposure to light at night," said Dr. Stanhope.  "It is now really important that future studies include both factors so that we can better understand their association—only then can we make better public health recommendations about planning health-giving sustainable urban landscapes."   Supplements may protect those with low vitamin D levels from severe COVID-19 Albert Einstein College of Medicine, March 20, 2021 Patients with low vitamin D levels who are hospitalized for COVID-19 may have a lower risk of dying or requiring mechanical ventilation if they receive vitamin D supplementation of at least 1,000 units weekly, according to a study presented virtually at ENDO 2021, the Endocrine Society's annual meeting. "Given how common vitamin D deficiency is in the world and the United States, we believe that this research is highly relevant right now," said co-author Sweta Chekuri, M.D., of Montefiore Health System and Albert Einstein College of Medicine in the Bronx, New York.  Research has shown that vitamin D supplementation can prevent inflammation in other respiratory diseases, but there have been limited studies examining the role of vitamin D supplementation in COVID-19. The purpose of the study was to determine whether being supplemented with vitamin D before being admitted to the hospital with COVID-19 resulted in less severe COVID-19 disease in patients with a low vitamin D level. The researchers studied 124 adult patients with low vitamin D that was measured up to 90 days before their admission for COVID-19. They compared the patients who were supplemented with at least 1,000 units of vitamin D weekly to those who had not received vitamin D supplements in terms of whether they were mechanically ventilated or died during admission. They found that patients who were supplemented were less likely to be mechanically ventilated or to die following admission, though the finding wasn't statistically significant (37.5 percent of patients who were not supplemented vs. 33.3 percent of those who were) They also found that more than half of those who should have been supplemented were not.  "Though we weren't able to show a definitive link to severe COVID-19, it is clear that patients with low vitamin D should receive supplementation not only for bone health, but also for stronger protection against severe COVID-19," said co-author Corinne Levitus, D.O., of Montefiore Health System and Albert Einstein College of Medicine. "We hope this research will encourage clinicians to discuss adding this supplement with their patients who have low vitamin D, as this may reduce the odds of people developing severe COVID-19." A study published in the Endocrine Society's Journal of Clinical Endocrinology & Metabolism last fall found over 80 percent of 200 COVID-19 patients in a hospital in Spain had vitamin D deficiency.     Study finds changes in gut microbiome connected to Alzheimer-like behavior Oregon Health & Science University, March 19, 2021 New research in mice published in the journal Scientific Reports strengthens the growing scientific consensus regarding the role of the gut microbiome in neurodegenerative disorders including Alzheimer’s disease. The study, led by researchers at Oregon Health & Science University, found a correlation between the composition of the gut microbiome and the behavioral and cognitive performance of mice carrying genes associated with Alzheimer’s. The mice carried the human amyloid precursor protein gene with dominant Alzheimer’s mutations generated by scientists in Japan. The study further suggests a relationship between microbes in the digestive tract and the expression of genes that trigger Alzheimer-like symptoms in mice. “You know the expression, ‘You are what you eat?’” said senior author Jacob Raber, Ph.D., professor of behavioral neuroscience in the OHSU School of Medicine. “This may be part of that. While all mice were fed the same diet, the gut microbiome is affected in a genotype-dependent fashion and this in turn might affect your brain.” The findings are the first to demonstrate a direct connection between the gut microbiome and cognitive and behavioral changes in an Alzheimer’s disease animal model, and they are consistent with a recently published observational study in people newly diagnosed with Alzheimer’s. In fact, a U.S. clinical trial for the treatment of mild to moderate Alzheimer’s disease is currently underway involving a compound that targets microbes in the gut. The research published breaks new ground. In addition to the cognitive and behavioral changes that were measured, the study is the first to demonstrate a relationship between changes in the gut microbiome and epigenetic changes in neural tissue in the hippocampus, an area of the brain affected in Alzheimer’s. This type of research is not possible in people. The microbiome is a complex assemblage of microorganisms such as bacteria that play a critical role in a wide range of functions in the body. In this case, researchers wanted to see if the gut microbiome affected cognitive and behavioral measures in specially bred mice at 6 months of age. So they compared wild-type mice with those genetically engineered to carry the human amyloid precursor protein gene with dominant Alzheimer’s mutations. They found changes in the gut microbiome - measured in fecal pellets - corresponded with epigenetic regulation of the apolipoprotein E and Tomm40 genes, both associated with Alzheimer’s. They found a clear correlation, but they still can’t say whether one causes the other. “Microbes may elicit an impact on behavioral and cognitive measures relevant to Alzheimer’s disease via epigenetic changes in the hippocampus,” Raber said. “Or, alternatively, it might be that the epigenetic changes in the hippocampus affect changes in the gut microbiome.” The next phase of research will determine whether it’s possible to reduce Alzheimer’s-like symptoms in genetically predisposed mice by altering their diet. “The exciting part of this is that you can manipulate the gut microbiome,” Raber said. “We can use probiotics and see what the effect is.”

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.29.361360v1?rss=1 Authors: Dang, T., Kishino, H. Abstract: A central focus of microbiome studies is the characterization of differences in the microbiome composition across groups of samples. A major challenge is the high dimensionality of microbiome datasets, which significantly reduces the power of current approaches for identifying true differences and increases the chance of false discoveries. We have developed a new framework to address these issues by combining (i) identifying a few significant features by a massively parallel forward variable selection procedure, (ii) mapping the selected species on a phylogenetic tree, and (iii) predicting functional profiles by functional gene enrichment analysis from metagenomic 16S rRNA data. We demonstrated the performance of the proposed approach by analyzing two published datasets from large-scale case-control studies: (i) 16S rRNA gene amplicon data for Clostridioides difficile infection (CDI) and (ii) shotgun metagenomics data for human colorectal cancer (CRC). The proposed approach improved the accuracy from 81% to 99.01% for CDI and from 75.14% to 90.17% for CRC. We identified a core set of 96 species that were significantly enriched in CDI and a core set of 75 species that were enriched in CRC. Moreover, although the quality of the data differed for the functional profiles predicted from the 16S rRNA dataset and functional metagenome profiling, our approach performed well for both databases and detected main functions that can be used to diagnose and study further the growth stage of diseases. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.27.358408v1?rss=1 Authors: Hoffman, C., Siddiqui, N. Y., Fields, I., Gregory, W. T., SImon, H., Mooney, M. A., Wolfe, A. J., Karstens, L. Abstract: The human bladder contains bacteria in the absence of infection. Interest in studying these bacteria and their association with bladder conditions is increasing, but the chosen experimental method can limit the resolution of the taxonomy that can be assigned to the bacteria found in the bladder. 16S rRNA gene sequencing is commonly used to identify bacteria, but is typically restricted to genus-level identification. Our primary aim was to determine if accurate species-level identification of bladder bacteria is possible using 16S rRNA gene sequencing. We evaluated the ability of different classification schemes, each consisting of combinations of a 16S rRNA gene variable region, a reference database, and a taxonomic classification algorithm to correctly classify bladder bacteria. We show that species-level identification is possible, and that the reference database chosen is the most important component, followed by the 16S variable region sequenced. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.12.336271v1?rss=1 Authors: Zhao, Z., Woloszynek, S., Agbavor, F., Mell, J., Sokhansanj, B. A., Rosen, G. Abstract: Recurrent neural networks (RNNs) with memory (e.g. LSTMs) and attention mechanisms are widely used in natural language processing because they can capture short and long term sequential information for diverse tasks. We propose an integrated deep learning model for microbial DNA sequence data, which exploits convolutional networks, recurrent neural networks, and attention mechanisms to perform sample-associated attribute prediction---phenotype prediction---and extract interesting features, such as informative taxa and predictive k-mer context. In this paper, we develop this novel deep learning approach and evaluate its application to amplicon sequences. We focus on typically short DNA reads of 16s ribosomal RNA (rRNA) marker genes, which identify the heterogeneity of a microbial community sample. Our deep learning approach enables sample-level attribute and taxonomic prediction, with the aim of aiding biological research and supporting medical diagnosis. We demonstrate that our implementation of a novel attention-based deep network architecture, Read2Pheno, achieves read-level phenotypic prediction and, in turn, that aggregating read-level information can robustly predict microbial community properties, host phenotype, and taxonomic classification, with performance comparable to conventional approaches. Most importantly, as a further result of the training process, the network architecture will encode sequences (reads) into dense, meaningful representations: learned embedded vectors output on the intermediate layer of the network model, which can provide biological insight when visualized. Finally, we demonstrate that a model with an attention layer can automatically identify informative regions in sequences/reads which are particularly informative for classification tasks. An implementation of the attention-based deep learning network is available at https://github.com/EESI/sequence_attention. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.09.08.288811v1?rss=1 Authors: Pimentel, Z. T., Dufault-Thompson, K., Russo, K. T., Scro, A. K., Smolowitz, R., Gomez-Chiarri, M., Zhang, Y. Abstract: Marine invertebrate microbiomes play important roles in various host and ecological processes. However, a mechanistic understanding of host-microbe interactions is so far only available for a handful of model organisms. Here, an integrated taxonomic and functional analysis of the microbiome of the eastern oyster, Crassostrea virginica, was performed using 16S rRNA gene amplicon profiling, shotgun metagenomics, and genome-scale metabolic reconstruction. A relatively low number of amplicon sequence variants (ASVs) were observed in oyster tissues compared to water samples, while high variability was observed across individual oysters and among different tissue types. Targeted metagenomic sequencing of the gut microbiota led to further characterization of a dominant bacterial taxon, the class Mollicutes, which was captured by the reconstruction of a metagenome-assembled genome (MAG). Genome-scale metabolic reconstruction of the oyster Mollicutes MAG revealed a reduced set of metabolic functions and a high reliance on the uptake of host-derived nutrients. A chitin degradation and an arginine deiminase pathway were unique to the MAG as compared to other closely related Mycoplasma genomes, indicating a distinct mechanism of carbon and energy acquisition by the oyster-associated Mollicutes. A systematic reanalysis of public eastern oyster-derived microbiome data revealed the Mollicutes as a ubiquitous taxon among adult oysters despite their general absence in larvae and biodeposit samples, suggesting potential horizontal transmission via an unknown mechanism. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.07.21.213116v1?rss=1 Authors: Geary, C. G., Wilk, V. C., Barton, K. L., Jefferson, P. O., Binder, T., Bhutani, V., Baker, C., Fernando-Peiris, A. J., Mousley, A. L., Rozental, S. F. A., Thompson, H. M., Touchon, J. C., Esteban, D. J., Bergstrom, H. C. Abstract: Gut microbiota influence numerous aspects of host biology, including brain structure and function. Growing evidence implicates gut microbiota in aversive conditioning and anxiety-related behaviors, but research has focused almost exclusively on males. To investigate sex-specific effects of gut dysbiosis on aversive learning and memory, adult female and male C57BL/6N mice were orally administered a moderate dose of non-absorbable antimicrobial medications (ATMs; neomycin, bacitracin, pimaricin) or a control over 10 days. Changes in gut microbiome composition were analyzed by 16S rRNA sequencing. Open field behavior, cued aversive learning, context recall, and cued recall were assessed. Following behavioral testing, the morphology of basolateral amygdala (BLA) principal neuron dendrites and spines was characterized. Results revealed that ATMs induced distinct but overlapping patterns of gut dysbiosis across sex, with stronger effects in females. There were also sex-specific effects on behavior and neuroanatomy. Treated males but not females exhibited altered locomotor and anxiety-like behavior in the novel open field test. Treated females but not males showed impairments in aversive memory acquisition and cued recall. Context recall remained intact in both sexes, as did dendritic structure of BLA principal neurons. However, ATMs exerted sex-specific effects on spine density. A second experiment was conducted to isolate gut perturbation to cued recall. Results revealed no effect of ATMs on recall of a previously consolidated fear memory, suggesting that gut dysbiosis preferentially impacts aversive learning. These data shed new light on how gut microbiota interact with sex to influence aversive conditioning, anxiety-like behavior, and BLA dendritic spine architecture. Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.06.16.153809v1?rss=1 Authors: Noble, E. E., Davis, E. A., Tsan, L., Chen, Y.-W., Olson, C., Schade, R., Liu, C., Suarez, A. N., Jones, R. B., Goran, M. I., de La Serre, C., Yang, X., Hsiao, E. Y., Kanoski, S. Abstract: The mammalian gastrointestinal tract contains a diverse ecosystem of microbial species collectively making up the gut microbiota. Emerging evidence highlights a critical relationship between gut microbiota and neurocognitive development. Consumption of unhealthy yet palatable dietary factors associated with obesity and metabolic dysfunction (e.g., saturated fat, added sugar) alters the gut microbiota and negatively impacts neurocognitive function, particularly when consumed during early life developmental periods. Here we explore whether excessive early life consumption of added sugars negatively impacts neurocognitive development via the gut microbiome. Using a rodent model of habitual sugar-sweetened beverage (SSB) consumption during the adolescent stage of development, we first show that excessive early life sugar intake impairs hippocampal-dependent memory function when tested during adulthood while preserving other neurocognitive domains. 16S rRNA gene sequencing of the fecal and cecal microbiota reveals that early life SSB consumption alters the relative abundance of various bacterial taxa. In particular, SSB elevates fecal operational taxonomic units within the genus Parabacteroides, which negatively correlate with memory task performance. Additional results reveal that transferred enrichment of Parabacteroides species P. distasonis and P. johnsonii in adolescent rats impairs memory function during adulthood. Hippocampus transcriptome analyses identify gene expression alterations in neurotransmitter synaptic signaling, intracellular kinase signaling, metabolic function, neurodegenerative disease, and dopaminergic synaptic signaling-associated pathways as potential mechanisms linking bacterial alterations with memory impairment. Collectively these results identify a role for microbiota dysbiosis in mediating the negative effects of early life unhealthy dietary factors on neurocognitive outcomes. Copy rights belong to original authors. Visit the link for more info

Lung cancer (LC) is one of the most serious malignant tumors, which has the fastest growing morbidity and mortality worldwide. A role of the lung microbiota in LC pathogenesis has been analyzed, but a comparable role of the gut microbiota has not yet been investigated. In this study, the gut microbiota of 30 LC patients and 30 healthy controls were examined via next-generation sequencing of 16S rRNA and analyzed for diversity and biomarkers. We found that there was no decrease in significant microbial diversity (alpha diversity) in LC patients compared to controls (P observed = 0.1422), while the composition (beta diversity) differed significantly between patients and controls (phylum [stress = 0.153], class [stress = 0.16], order [stress = 0.146], family [stress = 0.153]). Controls had a higher abundance of the bacterial phylum Actinobacteria and genus Bifidobacterium, while patients with LC showed elevated levels of Enterococcus. These bacteria were found as possible biomarkers for LC. A decline of normal function of the gut microbiome in LC patients was also observed. These results provide the basic guidance for a systematic, multilayered assessment of the role of the gut microbiome in LC, which has a promising potential for early prevention and targeted intervention. Zhuang H, Cheng L, Wang Y, et al. Dysbiosis of the Gut Microbiome in Lung Cancer. Front Cell Infect Microbiol. 2019;9:112. Published 2019 Apr 18. doi:10.3389/fcimb.2019.00112. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Sections of the Abstract, Introduction, Materials and Methods,and Discussion are presented in the Podcast. Access the full-text article here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6489541/

Jennifer Martiny describes the incredible microbial biodiversity of natural ecosystems such as soils and waterways. She explains how to add a bit of control in experiments with so many variables, and why categorizing microbial types is important for quantifying patterns. Host: Julie Wolf Subscribe (free) on iPhone, Android, RSS, or by email. You can also listen on your mobile device with the ASM Podcast app. Julie's biggest takeaways: Studying microbial community functions in their natural environment are harder to understand, but help us to parse the complexity of the natural world, in part because these experiments also include local flora and fauna that are often omitted in the controlled lab environment. Microbial cages - an actual physical barrier that contains a soil-based community - can help to disentangle the effects of the microbial community from those of the surrounding environment by adding a level of control by limiting interaction of microbes inside the nylon mesh cage with those outside of it. Are microbial functions redundant? It depends on what function you look at - respiration is a very common function, so it’s less likely to be affected by a change in microbiome composition. Other functions, such as degrading particular compounds, may have a stronger relationship between the microbes present and those functions. Microbes are hugely diverse! Jennifer’s comparison of all the diversity of the birds on Earth to a single bacterial taxon is mind-blowing! Microbial categorization may be hard, but the ability to group similar organisms is necessary to formulate hypotheses and conduct experiments. It’s important to remember the groupings are manmade and sometimes have to be reconstructed!   Featured Quotes (in order of appearance) “One of the hardest things we study is not on the microbiology side but is on the ecosystem side, measuring those biochemical functions in the environment.” (10:05) “It’s not as if we are ever going to be able to study every particular organism out there and build a model with thousands of equations; instead what we really need to do is go after trade-offs and overall relationships that may hold across large groups, and in that way have some simple rules under different conditions like drought or temperature.” (16:45) "Modern birds evolved about 100, 125 million years ago. Two sequences that share the 16S gene, if it’s roughly 97% identical, probably diverged 150 million years ago. That means we are lumping in all the diversity within the bacteria group within one taxon, calling it a species, which is the equivalent of lumping all birds together!" (18:47) “It’s a bit overwhelming to imagine that for each 16S rRNA taxon, you could have as much functional, morphological, and behavioral diversity as what we see in all of birds!” (19:39) “In biology, we’re always using an operational definition but we don’t want to get too hung up on the definition and miss all the interesting patterns going on!” (20:49) “If you can start to quantify patterns, then you can start to ask ecological and even evolutionary questions about why we see those patterns.” (33:04)   Links for this episode Jennifer Martiny Lab Home Page University of California Irvine Microbiome Initiative HOM Tidbit: TWIM 50: These things aren’t even bacteria! Carl Woese Obituary (New York Times) Carl Woese 1996 Feature (New York Times) Send your stories about our guests and/or your comments to jwolf@asmusa.org.

The following work is shedding light on the phylogenetic classification on the family of the Chlorobiacea, the members of which are showing signs of preadaptation to symbiosis. Symbioses consisting of purely prokaryotic associations between phylogenetically distinct bacterial species have been widely documented. Only few are available as a laboratory culture to elucidate the molecular basis of their interaction. One of these few model organisms is the phototrophic consortium “Chlorochromatium aggregatum”. It consists of 12-20 green sulfur bacteria epibionts surrounding a central, Betaproteobacterium in a highly ordered fashion. The phototrophic partner bacterium, belonging to the green sulfur bacteria, is available in pure culture and its physiology has been studied in detail. In this work, novel insights into the physiology of the central bacterium that was previously uncharacterized are provided. The family of the Chlorobiaceae represents a phylogenetically coherent and isolated group within the domain Bacteria. Green sulfur bacteria are obligate photolithoautotrophs that require highly reducing conditions for growth and can utilize only a very limited number of carbon substrates. These bacteria thus inhabit a very narrow ecologic niche. For the phylogenetic studies on green sulfur bacteria, 323 16S rRNA gene sequences, including cultured species as well as environmental sequences were analysed. By rarefaction analysis and statistical projection, it was shown that the data represent nearly the whole spectrum of green sulfur bacterial species that can be found in the sampled habitats. Sequences of cultured species, however, did not even cover half of the biodiversity. In the 16S rDNA gene tree, different clusters were found that in most cases correlated with physiological adaptations of the included species. By combining all sampling sites of green sulfur bacteria in a world map, large, unsampled areas were revealed and it could be shown that in some regions, a non-random distribution of GSB occurred. The wide dispersal of green sulfur bacterial species can be seen in sequences that were found ubiquitously all over the world. To imitate the phylogenetical relationships of whole genome analyses, a concatenated tree was constructed including 32 species and 3 different genetic regions, the bchG gene, the sigA gene and the fmoA gene. Comparison with the 16S rRNA gene tree showed more genetic differences between species, and led to a higher resolution and a more dependable phylogeny. A distance matrix comparison showed that the fmoA gene sequence has the highest correlation to the 16S rDNA of the sequences investigated. Additionally, a dissimilarity matrix revealed that the fmoA gene sequence provides the highest phylogenetic resolution among the sequences investigated. Therefore, we showed that the fmoA gene sequence is the most suitable among the sequences investigated to support the 16S rDNA phylogeny of green sulfur bacteria. To overcome the limitation of immobility, some green sulfur bacteria have entered into a symbiosis with motile Betaproteobacteria in a type of multicelllular association termed phototrophic consortia. Recent genomic, transcriptomic, and proteomic studies of "C. aggregatum" and its epibiont provided insights into the molecular basis and the origin of the stable association between the two very distantly related bacteria. However, to date the possibility of a metabolic coupling between the bacterial partners has not been investigated. The symbiotic exchange of metabolites between the two species was therefore investigated by tracking the flux of isotope-labeled CO2 through the two partner organisms using NanoSIMS analysis and magnetic capture, revealing a fast and simultaneous incorporation of labeled carbon into both organisms. The transferred metabolites were identified by isotopologue profiling for which the partner cells were separated by cesium chloride density gradient centrifugation, a method which identified amino acids as one group of substrates to be transferred between the two partners. The addition of external carbon substrates inhibited the transfer between the two partners, suggesting that transporters are the means by which substrates are exchanged. Genome sequencing revealed the central bacterium to be an aerobic or microaerophilic chemoheterotrophic bacterium. The existence of 32 PAS domains which are responsible for sensing various signals indicate that the central bacterium is responsible for the chemo- and phototactic responses of the consortium. The central bacterium possesses all traits of an autonomous organism. However, transcriptome analysis revealed the central bacterium to be inactive in the dark although external carbon sources were present. Thereby, a yet unexplained dependence on the epibiont is revealed which indicates a complex metabolic coupling between the two symbiotic partner organisms.

Prokaryotes consist of the domains of Bacteria and Archaea and exist since approximately 3.8 billion years. Prokaryotes, despite the small size of the individual cells, are regarded to represent the 'unseen majority' among the living world as they occur numerously in all types of habitats and contribute greatly to the biogeochemical cycle. They diversified strongly throughout their long evolutionary history. Prokaryotes have usually a short generation time and relatively small amount of genetic information as compared to eukaryotes, and large census population sizes. This renders them suitable test organisms for studying their evolutionary processes. The discipline of population genetics analyses the evolutionary change of the genotypic and phenotypic variants at the level of species. Most of the recent bacterial population genetic studies have focussed on pathogens. Little is known of the population structure of freshwater bacteria. Natural freshwater lakes harbor a considerably lower diversity of bacteria, this facilitating the study of the genetic variability of bacteria. Sphingomonadaceae represent typical constituents of freshwater bacterioplankton communities and therefore served as a target group for a high-resolution multilocus sequence analysis (MLSA) of nine housekeeping genes (atpD, dnaK, fusA, tufA, gap, groEL, gyrB, recA, rpoB) and a parallel phenotypic characterization. Among 95 strains recovered from two trophically different freshwater lakes (Starnberger See and Walchensee), only 19 different 16S rRNA gene sequences were found. Yet, each strain represented a unique MLSA haplotype and the population displayed extraordinary high levels of nucleotide diversity. A split decomposition analysis revealed eight genetically distinct subpopulations, three of which comprised a single phylotype G1A with 52 strains. The population recombination rate ρ was comparable to that of other bacteria but two to eight-fold lower than the population mutation rates θS. Consequently, the impact of recombination on the population structure of freshwater Sphingomonadaceae is markedly lower than in most other free-living aquatic bacteria investigated to date. This was supported by a linkage disequilibrium analysis on the allele distribution. Together with the large effective population size (estimate, ~6•108), our data suggest that the incipient sexual isolation of subpopulations is caused by natural selection rather than genetic drift or demographic effects. Since neutrality tests did not provide evidence for an effect of selective forces on the housekeeping genes and no consistent physiological differences were detected between the G1A subpopulations, alternative phenotypic traits are supposed to provide a selective advantage for individual subpopulations of Sphingomonadaceae. This conclusion is supported by discrete seasonal abundance patterns that were detected based on pyrosequencing of internal transcribed spacer sequences in the natural samples. MLSA is a widely applied genotyping tool in studies of the evolution and population structure of microbial organism and also represents a novel standard in microbial molecular systematics. Population genetic analysis of Sphingomonadaceae by MLSA revealed a distinct population substructure among individual 16S rRNA phylotypes, providing insights into the diversity within bacterial species. A 'species' is the main taxonomic unit in the systematics of prokaryotes, but the subject of the species concept of prokaryotes has always been controversial. Until now there is no prokaryotic species concept that is accepted by all scientists. But for practical reasons, bacterial strains are affiliated to different species on the basis of DNA-DNA reassociation and diagnostic phenotypes. As DNA-DNA hybridization is difficult to be compared between laboratories and time consuming, MLSA becomes a valuable alternative to it. The population genetic structure revealed by MLSA is strongly associated with the results from DNA-DNA relatedness values. When sufficient numbers of suitable loci are selected, the concatenated sequence similarity values can in principle be used for species delineation. To assess the population and subpopulation structure revealed by MLSA also from a taxonomic perspective, four Sphingomonadaceae strains belonging to four different subpopulations were chosen for new species description. Based on morphological, physiological and biochemical characterization, strain 247 from group G3B was affiliated to a species formerly named 'Caulobacter leidyi' and which was now reclassified as 'Sphingomonas leidyi'. Strain 382 from group G1A2 was proposed as type strain of a novel species 'Sphingomonas limneticum'. Strain 301 from group G2D was proposed as type strain of a novel species 'Sphingobium oligotrophica', and a strain 469 was proposed as type strain of a novel species 'Sphingobium boeckii', and the closely related species formerly names 'Sphingomonas suberifaciens' was reclassified as 'Sphingobium suberifaciens'.

Background: Ehrlichia species are the etiological agents of emerging and life-threatening tick-borne human zoonoses that inflict serious and fatal infections in companion animals and livestock. The aim of this paper was to phylogeneticaly characterise a new species of Ehrlichia isolated from Rhipicephalus (Boophilus) microplus from Minas Gerais, Brazil. Methods: The agent was isolated from the hemolymph of Rhipicephalus (B.) microplus engorged females that had been collected from naturally infested cattle in a farm in the state of Minas Gerais, Brazil. This agent was then established and cultured in IDE8 tick cells. The molecular and phylogenetic analysis was based on 16S rRNA, groEL, dsb, gltA and gp36 genes. We used the maximum likelihood method to construct the phylogenetic trees. Results: The phylogenetic trees based on 16S rRNA, groEL, dsb and gltA showed that the Ehrlichia spp isolated in this study falls in a clade separated from any previously reported Ehrlichia spp. The molecular analysis of the ortholog of gp36, the major immunoreactive glycoproteins in E. canis and ortholog of the E. chaffeensis gp47, showed a unique tandem repeat of 9 amino acids (VPAASGDAQ) when compared with those reported for E. canis, E. chaffeensis and the related mucin-like protein in E. ruminantium. Conclusions: Based on the molecular and phylogenetic analysis of the 16S rRNA, groEL, dsb and gltA genes we concluded that this tick-derived microorganism isolated in Brazil is a new species, named E. mineirensis (UFMG-EV), with predicted novel antigenic properties in the gp36 ortholog glycoprotein. Further studies on this new Ehrlichia spp should address questions about its transmissibility by ticks and its pathogenicity for mammalian hosts.

Sun, 1 Jan 2012 12:00:00 +0100 http://www.plosntds.org/article/info%3Adoi%2F10.1371%2Fjournal.pntd.0001756 https://epub.ub.uni-muenchen.de/15746/1/oa_15755.pdf Bretzel, Gisela; Adjei, Ohene; Loescher, Thomas; Battke, Florian; Herbinger, Karl-Heinz; Huber, Kristina Lydia; Jansson, Moritz; Sarfo, Fred Stephen; Awua-Boateng, Nana-Yaa; Amoako, Yaw Ampem; Phillips, Richard Odame; Symank, Dominik; Beissner, Marcus

Background: The aims of this study were to evaluate the host-tick-pathogen interface of Babesia spp. and Anaplasma phagocytophilum in restored areas in both questing and host-attached Ixodes ricinus and Dermacentor reticulatus and their small mammalian hosts. Methods: Questing ticks were collected from 5 sites within the city of Leipzig, Germany, in 2009. Small mammals were trapped at 3 of the 5 sites during 2010 and 2011. DNA extracts of questing and host-attached I. ricinus and D. reticulatus and of several tissue types of small mammals (the majority bank voles and yellow-necked mice), were investigated by PCR followed by sequencing for the occurrence of DNA of Babesia spp. and by real-time PCR for A. phagocytophilum. A selected number of samples positive for A. phagocytophilum were further investigated for variants of the partial 16S rRNA gene. Co-infection with Rickettsia spp. in the questing ticks was additionally investigated. Results: 4.1% of questing I. ricinus ticks, but no D. reticulatus, were positive for Babesia sp. and 8.7% of I. ricinus for A. phagocytophilum. Sequencing revealed B. microti, B. capreoli and Babesia spp. EU1 in Leipzig and sequence analysis of the partial 16S RNA gene of A. phagocytophilum revealed variants either rarely reported in human cases or associated with cervid hosts. The statistical analysis revealed significantly less ticks infected with A. phagocytophilum in a city park in Leipzig as compared to the other sampling sites. A. phagocytophilum-DNA was detected in 2 bank voles, DNA of B. microti in 1 striped field-mouse and of Babesia sp. EU1 in the skin tissue of a mole. Co-infections were detected. Conclusion: Our results show the involvement of small mammals in the natural endemic cycles of tick-borne pathogens. A more thorough understanding of the interactions of ticks, pathogens and hosts is the essential basis for effective preventive control measures.

The aim of this doctoral thesis was to investigate the factors relevant in plant interaction of two plant growth promoting rhizobacteria (PGPR). For this, the strain Acidovorax sp. N35 isolated from surface sterilized wheat roots and the two strains F4 and F7 of Rhizobium radiobacter, a bacterium associated with the plant growth promoting fungus Piriformospora indica, were chosen. First of all, the isolate N35 was characterized using phylogenetic and taxonomic methods. The 16S rRNA gene sequence analysis showed that strain N35 has the closest sequence similarities (98.2, 98.5 and 99.0 %) to the environmental Acidovorax species A. delafieldii, A. facilis and A. defluvii. The DNA-DNA hybridization values clearly separated the isolate from these three species. Additionally, phenotypic properties, such as substrate metabolization profiles as determined by a Biolog GN2 assay and cell wall fatty acid profiles concerning the fatty acids C16:0, C16:1ω7cis/trans, C17:0cyclo and C18:0cyclo and C19:0cyclo, facilitated the differentiation of the newly isolated strain N35 from its closest relatives. Thus, the strain N35 was classified as representative of a new species within the genus Acidovorax, and the name Acidovorax radicis sp. nov. is suggested. “Cand. A. radicis” N35 undergoes an irreversible phenotypic variation, resulting in different colony shapes on agar plate. In soil system, both phenotypes showed a plant growth promoting effect both on barley roots and shoots. The wild type N35 (rough colony type) had a better plant growth promoting effect on barley in comparison with phenotype variant N35v (smooth colony type). Wild type and phenotype variant cells of “cand. A. radicis” N35 were labeled with GFP and/or YFP and their separate and co-colonization behavior was investigated in a monoxenic system and a soil system using a CLSM for detection. Both types of N35 could endophytically colonize barley roots after 12 weeks inoculation in the soil system. Competitive root colonization behavior was observed after co-inoculation with differentially labeled wild type N35 and phenotype variant N35v bacteria, where the wild type showed dominant colonization of barley roots compared to the phenotype variant. Moreover, the variant N35v lost its motility due to missing flagella and swarming ability. The differences of both types at genetic level were investigated using whole genome sequence data obtained from 454 pyrosequencing (Roche) using the GS FLX Titanium chemistry. As only difference in the genome sequence, a 16 nucleotides deletion was identified in the mutL gene, which encodes for the mismatch repair protein MutL. In phenotype N35v, the frame shift caused by this deletion leads to the formation of a stop codon in the coding gene, resulting in a truncated MutL protein with a missing functional MutL C-terminal domain. This mutation occurred in exactly the same way in all investigated phenotype variants. These results suggest that MutL might be directly or indirectly responsible for the phenotypic variation in “cand. A. radicis” N35. Quorum sensing signaling molecules produced by “cand. A. radicis” N35 were identified using biosensors as well as Fourier transform ion cyclotron resonance - mass spectrometry (FT-ICR-MS) and ultra performance liquid chromatography (UPLC). Both types of “cand. A. radicis” N35 possess the same AraI/AraR quorum sensing system, which belongs to the LuxI/LuxR type. The two N35 phenotypes produced nearly the same amount of 3-OH-C10-HSL in the exponential growth phase. A co-inoculation experiment of AHL producing wild type N35 and a constructed AHL negative mutant N35 ΔaraI showed that wild type N35 had a dominant colonization behavior compared to the AHL negative mutant on barley roots in a monoxenic system. These data indicate that quorum sensing is involved in regulation of root colonization by “cand. A. radicis” N35. The second examined PGPR, R. radiobacter, which occurs naturally as endofungal bacterium in the plant growth promoting fungus P. indica, was demonstrated to colonize the surface of barley roots with fluorescence in situ hybridization (FISH) in a monoxenic system. The interaction of P. indica harboring R. radiobacter with other rhizobacteria was investigated using plate confrontation assays. Antibiotics and lipopeptides produced and excreted by the plant growth enhancing rhizobacterium Bacillus amyloliquefaciens FZB42 and the biocontrol rhizobacterium Pseudomonas fluorescens SS101 were shown to be responsible for the observed inhibition of P. indica by these bacteria. R. radiobacter F4 and F7 were able to synthesize a variety of oxo- and hydroxyl-C8- to C12-HSL compounds. In addition, both strains also produced coumaroyl-HSL when coumaric acid was supplied in the medium. The lactonase expressing transformants F4 NM13 and F7 NM13, which are the AHL negative phenotypes, abolished the lipase and siderophore activity. Considering this, quorum sensing influences the production of metabolites including lipase and siderophores in R. radiobacter F4 and F7. Further work should be directed to the question whether quorum sensing also plays a role in the interaction of the bacterium with fungus and/or plant.

Background: Equine Granulocytic Anaplasmosis (EGA) is caused by Anaplasma phagocytophilum, a tick-transmitted, obligate intracellular bacterium. In Europe, it is transmitted by Ixodes ricinus. A large number of genetic variants of A. phagocytophilum circulate in nature and have been found in ticks and different animals. Attempts have been made to assign certain genetic variants to certain host species or pathologies, but have not been successful so far. The purpose of this study was to investigate the causing agent A. phagocytophilum of 14 cases of EGA in naturally infected horses with molecular methods on the basis of 4 partial genes (16S rRNA, groEL, msp2, and msp4). Results: All DNA extracts of EDTA-blood samples of the horses gave bands of the correct nucleotide size in all four genotyping PCRs. Sequence analysis revealed 4 different variants in the partial 16S rRNA, groEL gene and msp2 genes, and 3 in the msp4 gene. One 16S rRNA gene variant involved in 11 of the 14 cases was identical to the "prototype" variant causing disease in humans in the amplified part [GenBank: U02521]. Phylogenetic analysis revealed as expected for the groEL gene that sequences from horses clustered separately from roe deer. Sequences of the partial msp2 gene from this study formed a separate cluster from ruminant variants in Europe and from all US variants. Conclusions: The results show that more than one variant of A. phagocytophilum seems to be involved in EGA in Germany. The comparative genetic analysis of the variants involved points towards different natural cycles in the epidemiology of A. phagocytophilum, possibly involving different reservoir hosts or host adaptation, rather than a strict species separation.

Abstract In this study, two topics causing major public concern related to transgenic plants were investigated: The possibility of a horizontal gene transfer from plant to bacteria and the impact of transgenic plants after herbicide treatment on root associated bacteria. The transgenic plant chosen for this study was Roundup Ready® (RR) soybean, which is tolerant to the herbicide glyphosate and is the most commonly used genetically modified crop worldwide. Glyphosate, the active ingredient of Roundup Ready®, inhibits the EPSPS enzyme (5-enolpyruvylshikimate-3-phosphate synthase). EPSPS is an enzyme involved in the shikimic acid pathway leading to the aromatic amino acid biosynthesis and its inhibition leads to growth reduction of plants and microorganisms. RR crops are glyphosate tolerant due to the introduction of the CP4-EPSPS gene coding for a glyphosate insensitive EPSPS enzyme. The transgenic construct is under expression of a CaMV 35S promoter a nos transcriptional termination element from Agrobacterium tumefaciens. Horizontal gene transfer experiments with the EPSPS gene of the RR soybean were performed under controlled laboratory conditions and were targeted to the nitrogen fixing symbiont of soybean Bradyrhizobium japonicum. This bacterium comprises the requirements of a possible receptor for the glyphosate resistance trait, as it is sensitive to the herbicide and thus the acquirement of glyphosate resistance would signify a positive adaptation to glyphosate accumulated in the roots after herbicide application. Two key conditions for gene transfer from the CP4-EPSPS gene from the RR soybean to B. japonicum were evaluated in this study: The required specific conditions for B. japonicum to undergo natural transformation and the expression of the CP4-EPSPS gene in B. japonicum. For that purpose, the CP4-EPSPS gene was cloned into a B. japonicum chromosomal integration vector and was transferred by biparental mating into the B. japonicum genome. Subsequently, the expression of the CP4-EPSPS gene in B. japonicum was tested under increasing glyphosate selection pressure. Results of these experiments indicated that B. japonicum is not naturally transformable under any conditions known from the more than 40 so far reported naturally transformable bacteria. Furthermore, the CP4-EPSPS genetic construct, as contained in RR soybean, has been shown in this study to be not active in B. japonicum. Consequently, if there would be a gene transfer of the plant CP4-EPSPS to B. japonicum, this genetic construct does not confer glyphosate resistance to B. japonicum and does not constitute any adaptive advantage to the bacterium under glyphosate selection pressure. As the genetic trait of glyphosate resistance has been found in several bacteria, it would be more probable that the common mating exchange between bacterial groups could disperse the glyphosate resistance within an environment. Moreover, in the specific case of B. japonicum, a high spontaneous mutation rate for glyphosate resistance was observed, suggesting that B. japonicum can also adapt to the glyphosate selection pressure by mutation under natural conditions. The impact of transgenic plants with their respective herbicide treatments on root associated bacteria was investigated in a greenhouse experiment. The composition and diversity of bacterial communities of RR soybean rhizospheres were analyzed and compared between glyphosate-treated and untreated plants. Samples from five harvests with two glyphosate applications were analysed by 16S rRNA gene T-RFLP analysis complemented with the evaluation of three clone libraries. Multivariate statistical analysis of the data was used to visualize changes in the microbial populations in response to glyphosate applications and in order to find groups of organisms responsible for the observed community shifts. A comparison of the rhizosphere communities revealed that a Burkholderia related group was significantly inhibited by glyphosate application, while the abundance of a group of Gemmatimonadetes related sequences increased significantly after the herbicide treatment. The significant increment of Gemmatimonadetes abundance after glyphosate application could indicate that these organisms are able to metabolize the herbicide. Shannon diversity indices were calculated based on the T-RFLP results with the aim to compare bacterial diversity in the rhizosphere of glyphosate-treated and non treated RR soybeans. Interestingly, the bacterial community associated to RR soybean roots after glyphosate application not only demonstrated effective resilience after the disturbance but in addition the bacterial diversity also increased in comparison to the untreated control samples. It is possible, that in an environment with organisms which are able to metabolize glyphosate, the key for enhancing diversity could be the succession of metabolites, which can be further utilized by a diverse range of bacteria.

In recent years, Anaplasma phagocytophilum and Rickettsia spp. have been detected in Ixodes ricinus in Germany and a focal distribution has been suggested for A. phagocytophilum. In the present study the prevalence of A. phagocytophilum and spotted fever group (SFG) rickettsiae was investigated in I. ricinus. DNA-extracts were taken from 2,862 unfed I. ricinus ticks (adults and nymphs) from eight sites in Munich, sampled over a five-month period. Single samples from three comparative sites outside of Munich were also included. A real-time PCR targeting the msp2 gene of A. phagocytophilum was used for screening and a nested PCR targeting the 16S rRNA gene for sequencing of 30% of positives. Screening for Rickettsia spp. was performed with a PCR targeting the citrate synthase gene (gltA), followed by PCRs detecting the ompA gene for all gltA positives, and the ompB and 16S rRNA genes for clarifying results of some samples. The overall prevalence was 2.90% (95% CI 2.27 to 3.48%) for A. phagocytophilum and 5.28% (95% CI 4.31 to 6.17%) for SFG rickettsiae. Only 0.31% of the ticks investigated were coinfected. Statistical analysis revealed that prevalence of A. phagocytophilum in ticks from city parks in Munich was significantly higher than in ticks from natural forest, whereas the prevalence of Rickettsia spp. was the opposite. For both, the prevalence in adults was significantly higher than in nymphs. Although wide ranges of prevalence were observed monthly, the variations were not significant along the observational period. Sequence analysis of 16S rRNA PCR products (n=31) revealed 100% homology to Ehrlichia sp. “Frankonia 2”, only one differed in one nucleotide position. All differed in one nucleotide position from the HGA agent detected in human patients. All rickettsial PCR products were also sequenced. All gltA sequences of R. helvetica (n=138) were 100% identical to each other and differed in one nucleotide position from the prototype sequence. Two different R. monacensis strains (n=13) were detected, which differed in up to 4 nucleotide positions in gltA, ompA and ompB. Further rickettsial strains (n=3) most probably belonging to rickettsial endosymbionts were also found. These results show, by molecular methods, a wide distribution of A. phagocytophilum and SFG rickettsiae in I. ricinus ticks in Southern Germany. SFG rickettsiae which are thought to be involved in human disease (R. helvetica and R. monacensis) had a significantly higher prevalence in natural forest areas. Prevalence of A. phagocytophilum was significantly higher in city parks; the genetic strain has not yet been associated with human infection.

The seasonal culturability (February, April, August) of bacterial cells from a microbial community of an alpine calcareous soil was assessed employing the MicroDrop technique using different laboratory media with humic acid analogs (HA), a mixture of polymers (POL), artificial root exudates (RO), nutrient broth, or soil extract as carbon and energy sources. Thereby, the summer August sample showed the highest culturability value in media supplemented with soil extract (13.5%). Since only 81 wells of a total number of 1008 individual growth tests were overgrown with the February soil sample, the cultivation success was the lowest for the winter environment (0.16%). The major aim of the present study, however, was to assess the cultivation success for cells even exposed to extreme environmental conditions by using defined media. Therefore, subsequent analysis focused on the cultures obtained from the February sample and in media supplemented with RO. It was shown that the monomeric organic carbon of RO proved to be superior to POL and HA for the optimization of the cultivation success (i.e., 71 of the total number of 81 cultures). The quantitative PCR approach confirmed the high coverage of the present analysis since the target groups (Firmicutes, Actinobacteria, Bacteroidetes, Alphaproteobacteria, Betaproteobacteria, Acidobacteria) constituted 73.6% of all eubacteria in the sample whereas the major part was composed of Alphaproteobacteria (49.2%) and Acidobacteria (20.1%). A total of 251 bacteria were analyzed representing 53 distinct phylotypes of which 73% are previously unknown. The majority of the cultured fraction was closely related to the Alphaproteobacteria with the largest number of different phylotypes and the highest evenness value. Although this phylum dominated the cultivated fraction, its cultivation success was hundredfold lower than its abundance in the natural community (0.4% of total cell numbers). Also the Bacteroidetes were most frequently cultured but were dominated by one phylotype (Sphingoterrabacterium pocheensis). The relative culturability of the Bacteroidetes was the highest of all groups and reached 25% of the numbers detected by real-time PCR. The lowest culturability was assessed for the Acidobacteria with only one single cultivated phylotype using media with POL supplemented with signal compounds. However, this phylotype represents a novel, previously unknown acidobacterium, strain Jbg-1. The phylum Acidobacteria mostly consists of environmental 16S rRNA gene sequences and so far comprises only the four validly described species Holophaga foetida, Geothrix fermentans, Acidobacterium capsulatum and Terriglobus roseus. In the present thesis two different novel strains of acidobacteria were isolated. Strain Jbg-1 and the second strain Wbg-1, which was recovered from a coculture with a methanotrophic bacterium established from calcareous forest soil. Both strains represent members of subdivision 1 of the phylum Acidobacteria and are closely related to each other (98.0 % 16S rRNA gene sequence similarity). At a sequence similarity of 93.8-94.7%, strains Jbg-1 and Wbg-1 are only distantly related to the closest described relative, Terriglobus roseus, and accordingly are described as members of the novel genus Edaphobacter gen. nov. Based on the DNA-DNA-similarity between strains Jbg-1 and Wbg-1 of 11.5-13.6% and their chemotaxonomic and phenotypic characteristics, the two strains are assigned to two separate species, Edaphobacter modestus sp. nov. with strain Jbg-1T (= ATCC BAA-1329T = DSM 18101T) as the type strain, and E. aggregans sp. nov. with strain Wbg-1T (= ATCC BAA-1497T = DSM 19364T) as the type strain. The two novel species are adapted to low carbon concentrations and to neutral to slightly acidic conditions. It was shown that strain Jbg-1 was also well adapted to long-term survival and to higher carbon concentrations after subcultivation. Unexpectedly, a high percentage of interspecific interaction was obtained for the cultivation approach of the February alpine soil (75% cocultures), which represented the major reason for the low cultivation success. Only 16 out of 71 cultures with RO consisted of single cultivated strains. Due to the frequent occurrence of different bacteria in the same cultures, the actual cultivation success was 4.9 fold higher than the value calculated from the abundance of positive cultures. For subsequent analysis, the effect of different treatments during the cultivation approach on the number and composition of bacteria cultured was investigated. In order to differentiate between free-living and attached cells, bacteria were detached from soil particles and used to set up parallel incubations. The detachment from soil particles prior to inoculation had no effect on the total cultivation success and on co-cultivation. Furthermore, signal compounds (cyclic AMP and N-butyryl homoserine lactone), however, increased the cultivation success and co-culturability. Addition of signal compounds yielded different types of activated bacteria and enhanced the total number of phylotypes per co-culture towards 4, 5, 6, and 7 different bacteria. The major part of the single cultivated strains represented a single phylotype, which was related to Sphingoterrabacterium pocheensis. In contrast, most co-cultures contained members of the Alpha- and Betaproteobacteria whereas relatives of Phyllobacterium brassicacearum, Rhodospirillum rubrum, Inqulinus ginsengisoli, Delftia tsuruhatensis, and Rhodocyclus tenuis were the most abundant ones. In conclusion, it is supposed that cell-to-cell interaction routinely occurs between different species of microorganisms, although the way, how these aerobic microorganisms beneficially interact remained to be shown. The elucidation of such interactions seems to be the most successful approach to enhance the culturability of interesting soil bacteria to promote their growth in pure or defined co-cultures.

Soils harbor highly diverse bacterial communities. It is still poorly understood whether functional redundancy or a multitude of ecological niche modify the abundance and community composition of bacteria in soil. Understanding why soil microorganisms are so diverse and which factors control their community composition is of importance because they are essential for maintaining ecosystem processes and functions. Alterations of biotic or abiotic factors as results of natural or anthropogenic disturbances are known to influence soil bacterial diversity. However, the relation of those factors on microbial diversity is not well understood. This work examined effects of several environmental factors, specifically the presence of higher plant species, water content, land use, and soil properties, on bacterial diversity by employing two different soil sources. The reproducibility of bacterial community composition in manipulated soil was analyzed by use of group-specific phylogenetic PCR-DGGE fingerprinting. Soils were taken from lysimeters that had been planted with four different types of plant communities and the water content was adjusted. The composition of Alphaproteobacteria, Betaproteobacteria, Bacteroidetes, Chloroflexi, Plancto-mycetes, and Verrucomicrobia populations were clearly different from soils without plants compared to that of populations in planted soils. In contrast, the composition of Acidobacteria, Actinobacteria, Archaea, and Firmicutes populations did not influenced by the environmental factors tested. No clear influence of plant diversity and water content could be observed. The reproducibility of bacterial composition associated with the absence or presence of plants was true, even for the low-abundance phylotypes as shown by phylotype beta10 representing up to 0.18% of all bacterial cells in planted soils compared to 0.017% in those unplanted. A high throughput cultivation approach was performed by employing the MicroDrop and the soil slurry dilution techniques. Soil-solution-equivalent medium (pH 7.0) supplemented with artificial root exudates, yeast extract, and inducers was utilized. From 217 cultures obtained, isolate byr23-80 showing the same sequence with phylotype beta10 was recovered and studied in detail as this phylotype displayed a distinct response towards the presence of higher plant species and its sequence affiliated with uncultured bacteria, so far. The strain exhibited high physiological flexibility and was capable of utilizing major constituents of root exudates. A polyphasic taxonomic analysis and DNA-DNA hybridization data supported an assignment of strain byr23-80 as a novel species to the genus Massilia within the family Oxalobacteraceae of the subphylum Betaproteobacteria, for which the name Massilia brevitalea is proposed. Effects of land use and soil properties on the bacterial diversity and activity were determined by employing natural soil from the Kavango region, Namibia. Soil properties in fact controlled the soil respiration rates rather than land use as pristine dark loam soil had remarkably higher respiration rate than pristine sand soil. Exoenzyme activities greatly varied among sites, but did not show a clear correlation to one of the two factors. The quantitative PCR identified Acidobacteria and Actinobacteria as the most abundant phyla about of 30 and 20% of all Bacteria, respectively. Alphaproteobacteria, Bacteroidetes, and Planctomycetes accounted for below 10%, whereas Betaproteobacteria, Chloroflexi, and Firmicutes represented less than 1%. Clone library of 16S rRNA genes from pristine dark loam soil revealed a high bacterial diversity with an estimated number of about 5600 phylotypes. The PCR-DGGE fingerprinting of Acidobacteria and Actinobacteria did only show minor differences in composition of the bacterial communities among sampling sites. This study suggests that the bacterial species compositions in soil are determined to a significant extent by abiotic and biotic factors, rather than by mere chance, thereby reflecting a multitude of distinct ecological niches.

The epibiont of the phototrophic consortium “Chlorochromatium aggregatum” was isolated in pure culture. This was the first time that a symbiotic green sulfur bacterium was isolated in pure culture indicating, that the symbiosis is not an obligate one with respect to the green sulfur bacterium. The phylogenetic affiliation revealed that the epibiont belongs to the genus Chlorobium, accordingly the isolate was named Chlorobium chlorochromatii strain CaD. The cells were gram-negative, nonmotile, rod-shaped, and contained chlorosomes. Strain CaD is obligately anaerobic and photolithoautotrophic, using sulfide as electron donor. Physiologically Chlorobium chlorochromatii exhibited no conspicuous differences to free-living green sulfur bacteria. The limited number of substrates photoassimilated was the same like in other green sulfur bacteria. The pH optimum was slightly shifted to the alkaline in contrast to free-living green sulfur bacteria, which probably represents an adaptation to the symbiotic association with the central bacterium. Photosynthetic pigments were bacteriochlorophylls a and c, and γ-carotene and OH-g-carotene glucoside laurate as dominant carotenoids. The unusual carotenoid composition for green sulfur bacteria indicates a different carotenoid biosynthesis in Chl. chlorochromatii in comparison to other green sulfur bacteria. The G+C content of genomic DNA of strain CaD is 46.7 mol %. On the basis of 16S rRNA sequence comparison, the strain is distantly related to Chlorobium species within the green sulfur bacteria phylum (≤ 94.6 % sequence homology). The pure culture of Chl. chlorochromatii enabled further studies on the molecular basis of the bacterial symbiosis of “C. aggregatum”. Suppression subtractive hybridization (SSH) against 16 free-living green sulfur bacteria revealed three different sequences unique to Chl. chlorochromatii. Dot blot analysis confirmed that these sequences are only present in Chl. chlorochromatii and did not occur in the free-living relatives. Based on the sequence information, the corresponding open reading frames in the genome sequence of Chl. chlorochromatii could be identified. Whereas the large ORF Cag0616 showed rather low similarity to a hemaglutinin, ORF Cag1920 codes for a putative calcium-binding hemolysin-type protein. The gene product of ORF Cag1919 is a putative RTX-like protein. Reverse transcriptase PCR of RNA isolated from free-living and symbiotic Chl. chlorochromatii demonstrated that all three ORFs are transcribed constitutively. The C-terminal amino acid sequence of Cag1919 comprises six repetitions of the consensus motif GGXGXD and is predicted to form a Ca2+ binding beta roll structure. The RTX-type protein is most likely involved in cell-cell-adhesion within the phototrophic consortium. 45Ca autoradiography exhibited calcium-binding proteins inthe membrane fraction of Chl. chlorochromatii in the free-living as well as the symbiotic state. On the other hand, Ca2+ binding proteins were absent in the cytoplasm of Chl. chlorochromatii and in both fractions of Chlorobaculum tepidum. The proteins detected by autoradiography were considerably smaller in size than predicted from the size of ORF Cag1919. The amino acid sequence of the RTX-type C-terminus coded by Cag1919 is similar to those of a considerable number of RTX-modules in various proteobacterial proteins, suggesting that this putative symbiosis gene has been acquired via horizontal gene transfer from a proteobacterium. An improved cultivation method to selectively grow intact consortia in a monolayer biofilm was the precondition for understanding the complex interaction between epibionts and the central bacterium on the morphological basis. Therefore detailed ultrastructural investigations combining high resolution analytical SEM, TEM, 3D reconstruction and image analysis were performed to provide a structural model for phototrophic consortia. The coherence of the consortia is most likely achieved by long carbohydrate chains of lipopolysaccharides which interconnect mainly the epibionts and to some extent the central bacterium. Numerous periplasmic tubules, formed from the outer membrane of the central bacterium are in direct contact to the epibionts, resulting in a common periplasmic space which is interpreted to be important for exchange of substances. In the epibionts the attachment site to the central bacterium is characterized by absence of chlorosomes and a single contact layer (epibiont contact layer, ECL) with a thickness of 17 nm attached to the inner side of the cytoplasmic membrane of each epibiont. The ECL is also observed in pure cultures of the epibiont, however, only in about 10-20% of the cells. A striking feature of the central bacterium is the occurrence of hexagonally packed flat crystals (central bacterium crystal, CBC) which are variable in size (up to 1 μm long) and in number (statistically, 1.5 per cell), and are formed by bilayers of subunits with a spacing of 9 nm. Deducing from serial sections, the CBC is interpreted to derive from accumulation of subunits on the inner side of the cytoplasmic membrane (or membranous invaginations), first forming a monolayer (central bacterium membrane layer; CML) and subsequently forming a bilayer of 35 nm, which can be freely orientated within the cytoplasm (CBC). Comparing structural details with published data, the CBC resembles a chemosensor.

This study focuses on one brown-colored representative of the green sulfur bacteria, Chlorobium sp. BS-1, that survives by means of anoxygenic photosynthesis even at very low light intensities. This unusual representative of the green sulfur bacteria lives in the chemocline of the Black Sea, which is located at 80 to 120 m depth, offering only 0.0005 % (winter) to 0.002 % (summer) of surface irradiance (0.00075 to 0.0022 µmol Quanta m-2 s-1). The Black Sea represents the world’s biggest anoxic water body, and it is permanently stratified. An overview of the habitat Black Sea and the research on phyotosynthetic bacteria in the Black Sea chemocline gives the article Anoxygenic phototrophic bacteria in the Black Sea chemocline (pages 53 ff.) In the second article, Physiology and phylogeny of green sulfur bacteria forming a monospecific phototrophic assemblage at 100 m depth in the Black Sea (pages 75 ff.), it is shown that Chl. sp. BS-1 represents a novel phylotype in the marine cluster of green sulfur bacteria and is the only detectable phylotype of green sulfur bacteria in the Black Sea chemocline. It was shown that Chl. sp. BS-1 is the first organism known to date which fixes 14CO2 under laboratory conditions even at light intensities as low as 0.015 µmol Quanta m-2 s-1 which is much lower than the light intensity in any typical habitat of green sulfur bacteria. Therefore it is the best adapted species to extremely low light intensities documented. The major adaptive mechanism to extremely low light intensities might be a significant change in the secondary homologs of the main photosynthetic pigment, bacteriochlorophyll e (BChl e). The dominance of farnesyl esters and the presence of four unusual geranyl ester homologs of BChl e were revealed by HPLC analysis in cells shifted from 3 to 0.1 µmol Quanta m-2 s-1. Together with in situ light measurements and in situ BChl e concentrations, the growth experiments allowed for the calculation of doubling times and significance of the photosynthetic activity for the carbon and sulfur cycle in the Black Sea chemocline. With doubling times of a minimum of 3.1 years (for summer light intensity) and the contribution of only 0.002 - 0.01 % to total sulfide oxidation in the chemocline Chl. sp. BS-1 represents the slowest growing population of green sulfur bacteria known to date and does not contribute significantly to the carbon or sulfur cycle. The article Subfossil DNA sequences of green sulfur bacteria as indicators for past water column anoxia in the Black Sea (page 119 ff.) gives insight into the history of the strain Chl. sp. BS-1 and the green sulfur bacteria in the Black Sea during the last few thousand years. The Black Sea today is considered as closest contemporary analogue to past sulfidic oceans and its biogeography over several thousand years is well documented in its stratified sedimentary record. Since the 16S rRNA gene sequence of Chl. sp. BS-1 might be a useful indicator for past photic zone anoxia, the presence of its fingerprints in past periods of the Black Sea was investigated. 16S rRNA gene sequences of green sulfur bacteria from samples of Black Sea sediments up to 7 m below seafloor were amplified and sequenced. Nine green sulfur bacterial 16S rRNA gene sequences were identified. Surprisingly, not only green sulfur bacterial fingerprints were found but also closely related species clustering at the basis of the green sulfur bacterial subtree, together with not yet cultured species detected all over the world. The new cluster was called “deep-branching green sulfur bacteria” though it was not possible to enrich live organisms with medium for photosynthetic green sulfur bacteria. The chemocline strain Chl. sp. BS-1, found in Units III, II and I (>9000 years b.p. until today), and two other sequences, found in sediments of Unit IIb (between 8200 yr. b.p. and 5000 yr.b.p) only, were the only two sequences clustering with the marine green sulfur bacteria. The other green sulfur bacterial sequences clustered with freshwater or low-salt adapted species, indicating an allochthonous introduction of these sequences to the Black Sea sediments. A long-distance transport of green sulfur bacteria even through oxygenated water is possible since the group has protective mechanisms agains oxygen intoxication. In the article An obligately photosynthetic bacterial anaerobe from a deep-sea hydrothermal vent (pages 105 ff.) a strain is presented which was enriched from beneath a deep sea hydrothermal vent, Chlorobium bathyomarinum GSB1. It was shown to resist more than 16 days of oxygenated medium. Since this strain was isolated only from the vicinity of a vent and was shown to depend on photosynthesis, it might survive photosynthetically by exclusively using geothermal radiation. It might be the first green sulfur bacterium which is adapted to light intensities even lower than in the Black Sea chemocline. A lot of newly obtained sequences during this study evoked the necessity of a phylogenetic analysis. The article Biodiversity and Phylogeny of the family Chlorobiaceae based on comparison of multiple genetic regions (pages 145 ff.) discusses the phylogenetic system of the green sulfur bacteria, which is to date not satisfactory with respect to resolution of the group. A new system is presented which is based on green sulfur bacterial sequences of isolated strains and environmental sequences from the NCBI database (www.ncbi.nlm.nih.gov). The 16S rRNA gene phylogenetic tree revealed the need for a revised phylogenetic system of green sulfur bacteria and showed a close correlation of ecology, i.e. the habitat of the respective species, and phylogeny. Consequently, functional genes might reflect the adaptation to different habitats better than 16S rRNA gene sequences. Three different markers were used for an alternative phylogenetic analysis: ITS (16S-23S rRNA intergenic spacer region), bchG, and sigma factor A, respectively. Only sigma factor A showed a significantly higher resolution of the phylogenetic system of green sulfur bacteria and should be considered as more powerful tool than the16S rRNA gene to classify green sulfur bacteria.

>>Novel bacteriochlorophyll e structures and species-specific variability of pigment composition in green sulfur bacteria>Characterization and in situ carbon metabolism of phototrophic consortia>The significance of organic carbon compounds for in situ metabolism and chemotaxis of phototrophic consortia

The aim of this PhD thesis was to examine the endophytic colonization behavior of Azospirillum brasilense and Herbaspirillum sp. N3 on wheat roots. The application of the FISH method using species specific phylogenetic oligonucleotide probes and GFP tagging facilitated the detection of a differential colonization behavior by the A. brasilense strains Sp7 and Sp245 on three different wheat varieties (Triticum aestivum). For this purpose a confocal laser scanning microscope (CLSM) was used, which enabled three-dimesional analysis of bacterial colonization of the root. Especially GFP tagged strains were well suited for this application, as there was no pretreatment or sectioning of the root sample necessary. Strain Sp7 was only located on the root surface of all wheat cultivars, whereas strain Sp245 was also found inter- and intracellulary in the outer root cortex layers. There was no recognizable connection between the growth stimulating effect of the inoculum (PGPR-effect) and the localization of the bacteria. The most pronounced PGPR-effect could be observed with the Brazilian wheat cultivar, which seemed to gain greatest benefit of its partnership with A. brasilense due to a certain adaptation to the inoculum. As the production of the auxin IAA (indole-3-acetic acid) plays a major role in stimulating plant growth, the expression of the key gene ipdC (indole-3-pyruvate decarboxylase) was examined. For this, several methods were tested to generate a fusion of the ipdC promoter with a gfp or rfp reporter gene. Constructing a translational promoter fusion with the gfp variant mut3 on plasmid level made expression analyses possible. With this method the promoter region of strain Sp7 located directly upstream of the ipdC start codon was found to differ only in a few bases from strain Sp245. But further upstream a region of about 150 bases was identified in strain Sp245, which was missing in strain Sp7. For Sp245 two different fusions were constructed, which contained the Sp245 promoter region homologous to strain Sp7 and the whole promoter region of Sp245, respectively. With these constructs the importance of the promoter region only present in strain Sp245 for control and intensity of ipdC expression in A. brasilense Sp245 could be demonstrated. Additionally an induction of the corresponding ipdC promoter fusions of Sp7 and Sp245 was achieved when adding phenylalanine or tyrosine. Total promoter activity was higher in strain Sp7 than in strain Sp245, and ipdC expression appeared to be subject to a stricter control in strain Sp245. These results were confirmed, when the strains containing the promoter fusions were used as reporters for ipdC expression on wheat roots. A demonstration of the induction of the ipdC promoter by root exudates in situ was possible. Finally, isolate N3 from surface sterilized wheat roots was characterized in detail. According to the 16S rDNA sequence data the isolate was phylogenetically allocated to the genus Herbaspirillum. But a subsequent DNS-DNS hybridization ruled out, that the strain belonged to any of the known Herbaspirillum species. Thus, the isolate, which might represent a new species, was named Herbaspirillum sp. N3. A specific, 16S rRNA targeted probe was constructed, which facilitated the examination of wheat roots colonization by this bacteria using FISH. Additionally the strain was GFP tagged to enable the detection in uncut root material. By this, an unequivocal demonstration of the endophytic colonization by Herbaspirillum sp. N3 mainly within the intercellular spaces was possible.

The clinical appearance of infection due to Nocardia spp. varies widely. The law sensitivity of direct microscopy and the slow growth of the organism challenge the laboratory diagnosis. We present the case of a skin abscess in an immunocompetent man caused by Nocardia brasiliensis. Diagnosis was made by cultivation and 16S rRNA sequencing. Using indirect immunofluorescence and Western blot, a strong antibody response to the N. brasiliensis isolate could be demonstrated. Serological tests might therefore be useful for the diagnosis and management of nocardial infections, copyright (R) 2000 S. Karger AG, Basel.