Podcasts about actinobacteria

When you're dealing with chronic illness from mold or other environmental toxins, having the right support can make all the difference. In this episode, I'm joined by Lauren—aka The Biotoxin Lady—who knows this firsthand.She's sharing her personal journey with mold-related illness and how it led her to become a health coach, helping others navigate these complex issues.We'll dive into:The crucial role health coaches play in recoveryHow mold, bacteria (like Actinobacteria), and endotoxins impact healthThe connection between medical practitioners, remediation, and real healingIf you're trying to piece together the puzzle of your health, this episode is for you!Want to learn more from Lauren? IG: @thebiotoxinlady.cirsEpisode Breakdown:00:00 Intro – Why this conversation matters01:13 Lauren's personal battle with mold illness03:17 What biotoxins really do to the body07:20 How health coaches help people get their lives back11:37 Why your environment matters just as much as treatment18:58 Understanding bacteria & endotoxins (and why they're a big deal)22:33 Actinobacteria in your home & body—what to know26:31 Final thoughts & practical next stepsIG: @MoldFindersNot sure the best way to get started?Follow these simple steps to hit the ground running…Step 1: Subscribe To Our Podcast!Step 2: Want a Test More Advanced Than ERMI? www.TheDustTest.com⁠Step 3: Already Have An ERMI? Find Out What It Actually Means. ⁠⁠www.ErmiCode.com⁠Step 4: Text Me (yes, it's really me!) The Mold Phone: 949-528-8704Step 5: Book A FREE Consultation www.yesweinspect.com/call

Why You Should Listen:  In this episode, you will learn about the role of Actinobacteria and Endotoxins in CIRS. About My Guest: My guest for this episode is Dr. Ritchie Shoemaker.  Ritchie Shoemaker, MD is a recognized leader in patient care, research, and an education pioneer in the field of biotoxin related illness.  While illness acquired following exposure to the interior environment of water-damaged buildings (WDB) comprises the bulk of Dr. Shoemaker's daily practice, other illnesses caused by exposure to biologically-produced toxins are quite similar in their “final common pathway.”  What this means is that while the illness might begin acutely with exposure to fungi, spirochetes, apicomplexans, dinoflagellates and cyanobacteria, for example, in its chronic form, each of these illnesses has similar symptoms, lab findings, and Visual Contrast Sensitivity (VCS) findings.  Taken together the inflammatory illness from each of these diverse sources is known as  Chronic Inflammatory Response Syndrome. Key Takeaways: Is CIRS generally caused by a single trigger or multiple triggers? What HLA-DR types may be susceptible to Actinobacteria or endotoxins? How does one determine when MARCoNS are making polycyclic ethers? What is the latest on biotoxin illness testing through HumanBiomics? Is it the Actinobacteria or a toxin produced by the bacteria that leads to illness? Is it best to start by testing the environment or by testing the person? Are some Actinobacteria a healthy part of our microbiome? What criteria are used to evaluate Actinobacteria testing? Is the solution to Actinobacteria a traditional remediation? How do people acquire skin Actinobacteria? How are skin Actinobacteria reduced over time? Are Actinobacteria in the sinuses a factor? How are Actinobacteria in the oral cavity addressed? How do endotoxins enter the body? Can endotoxin production be from endogenous bacteria? What is the best way to establish CIRS causation? What is the role of beta glucans in CIRS? Connect With My Guest:  SurvivingMold.com Related Resources: Actinobacteria Presentation Endotoxin Presentation Interview Date: January 22, 2025 Transcript: To review a transcript of this show, visit https://BetterHealthGuy.com/Episode211. Additional Information: To learn more, visit https://BetterHealthGuy.com. Disclaimer:  The content of this show is for informational purposes only and is not intended to diagnose, treat, or cure any illness or medical condition. Nothing in today's discussion is meant to serve as medical advice or as information to facilitate self-treatment. As always, please discuss any potential health-related decisions with your own personal medical authority. 

For more information, visit https://thecirsgroup.com Let this be your guide to the first annual CIRS Summit! CIRS, or Chronic Inflammatory Response Syndrome, is a complex illness, so there is a ton to learn about it as you receive your diagnosis and navigate the Shoemaker protocol to heal. Jacie and Barbara joined the steering committee to plan and produce this FREE event, the first of its kind that is geared towards patients. We break down the talks and point out our favorites, so we hope this helps you decide which talks to catch during the next replay, or whether it might be worth purchasing the upgraded ticket for access to replay at your convenience. All proceeds go towards important CIRS Research. To watch the CIRS Summit, visit https://the-ultimate-cirs-summit.heysummit.com/ For more information, support, and resources in your own CIRS healing journey, visit TheCIRSGroup.com TIME STAMPS: 0:00 Intro, disclaimer, and where you can watch The CIRS Summit 5:30 Introduction to Chronic Inflammatory Response Syndrome by Jacie Gregory 6:10 Staying Healthy Post-Protocol: Managing Re-Exposures: Dr. Christian Navarro-Torres, Jenny Johnson PT, FMCHC, NBC-HWC, Jacie Gregory & Barbara Williams 7:18 Building-Related Biotoxins: Mold, Bacteria and More by Larry Schwartz 7:30 Envirobiomics: Because Health Matters: Dust Testing and Blood Panel for CIRS by Gianni Rosinni 7:55 An Inconvenient Truth: Tick Borne Infections in CIRS Patients by Dr. Margaret DiTulio DNP, APRN 8:28 The Science Behind Brain Injury and Repair by Dr. Ritchie Shoemaker 9:10 Surviving Hypersensitivity in CIRS by Dr. Christian Navarro-Torres 9:54 Mindfully Navigating CIRS Recovery with Meditation by Melanie Joy Pensak M.S. CCC-SLP, CMT-P 10:28 The Devil is in the Differential: Diagnosing Chronic Illness by Dr. Margaret DiTulio DNP, APRN 10:35 Air Oasis: Love the Air you Breathe by Jon Bennert 10:40 Processing Grief: An Essential Step to Healing by Melanie Joy Pensak M.S. CCC-SLP, CMT-P, Dr. Lauren Sparks, Brenda Stewart LPC, LMHC, CTH & Mindy Mastruserio MS, NCC, LPC, CCTP-II 11:26 Understanding Red Hot Hands and Feet: Erythromelalgia in CIRS by Dr. Lauren Sparks 11:33 Common Remediation Mistakes and How to Avoid Them by Bill Weber 12:02 Leaky Buildings, Leaky Gut by Dr. Kellyn Milani NMD 12:07 CIRS: A Trauma-Based Illness by Dr. Andrew Heyman 12:10 Unlocking the Power of Genie to Inform your Recovery from CIRS by Louise Carder 12:50 The Importance of the HLA: Genetic Susceptibility to CIRS by Dr. Scott McMahon 13:11 The Importance of Family Support by Kendrah Betz & Matthew Betz 13:22 CIRS & Hormones by Dr. Anjali Noble 13:57 Eradicating MARCoNS by Dr. Joseph Mustom 14:08 Fixing Your Cells and Brain with Plasmalogens by Dr. Dayan Goodenowe 14:49 The Use of Peptides Beyond VIP by Dr. Christian Navarro-Torres 15:08 CIRS, Dysautonomia and Upper Cervical Care by Dr. Andrea Jordheim 16:10 Navigating Disordered Eating and CIRS by Brenda Stewart LPC, LMHC, CTH 16:30 Microbiology DX: Ordering and Understanding Marcons testing by Dr. Joseph Musto 17:16 PD Labs: Patient Driven Healthcare Solutions by Ray Solano 17:30 A Unique Way To Treat CIRS & Lyme by Dr. Laura Varga 17:40 Long Covid & CIRS by Jacie Gregory 18:09 Breathwork for the Moldy Brain by Morgan Glodowski 18:29 Deciphering the Alphabet Soup: CIRS Lab Tests and Reference Ranges by Dr. Ming Dooley 19:04 A Medically Important Professional Home Inspection for a CIRS Person by John Banta 20:06 Dietary Considerations for CIRS by Julia Davies 20:37 Setting Yourself Up for Success on the Shoemaker Protocol by Dr. Eric Dorninger 21:05 Navigating Project Pitfalls and Unlocking New Methods And Solutions by Brandon Apple 22:25 Healing from CIRS Outside the US by Louise Carder, Dr. Jodie Dashore, Mark Volmer & Kate Barry PhD 23:42 The Pain That No One Discusses: Suicidal Thoughts in CIRS by Mindy Mastruserio MS, NCC, LPC, CCTP-II 24:54 Minimizing the Financial Burden of CIRS Care by Alan Gruning DO 25:11 Coagulation & CIRS by Dr. James Ryan 25:35 Testing and Treating Bacterial Endotoxins in our Environment by Michael Schrantz, CIEC 26:39 Chasing the Ghosts of Water Damages Past by Greg Weatherman 27:11 Navigating Workplace Accommodations by Jane Prescot 27:40 How to Remediate and Maintain a Healthy Car by Mike Susi 29:00 Autoimmune illnesses and CIRS by Dr Miles Nichols 29:42 Assessing Your Own Home for Water Damage by Kendra Seymour 30:06 The Impact of Medical Trauma for CIRS Patients by Dr. Lauren Sparks 30:24 The Role of Clotting Disorders, Biofilm, and Actinobacteria in CIRS by Dr. Jacki Meinhardt 30:39 MoldCo: Online, Affordable Mold Illness Care and Treatments by Ariana Thacker 30:55 Putting it All Together: Patient Takeaways from The CIRS Summit by Jenny Johnson PT, FMCHC, NBC-HWC HELPFUL LINKS: Sign up for The CIRS Summit! https://the-ultimate-cirs-summit.heysummit.com/ CIRSx talks (free!): https://www.cirsx.com/conference-archives/ CIRSx courses: https://institute.cirsx.com/ The CIRS Group: Support Community: https://thecirsgroup.com Instagram: https://www.instagram.com/thecirsgroup/ Find Jacie for carnivore, lifestyle and limbic resources: Instagram: https://www.instagram.com/ladycarnivory YouTube: https://www.youtube.com/@LadyCarnivory Blog: https://www.ladycarnivory.com/ Pre-order Jacie's book! https://a.co/d/8ZKCqz0 Find Barbara for business/finance tips and coaching: Website: https://www.actlikebarbara.com/ Instagram: https://www.instagram.com/actlikebarbara/ YouTube: https://www.youtube.com/@actlikebarbara Jacie is a Shoemaker certified Proficiency Partner, NASM certified nutrition coach, author, and carnivore recipe developer determined to share the life changing information of carnivore and CIRS to anyone who will listen. Barbara is a business and fitness coach, CIRS and ADHD advocate, speaker, and a big fan of health and freedom. Together, they co-founded The CIRS Group, an online support community to help people that are struggling with their CIRS diagnosis and treatment.

Why You Should Listen:  In this episode, you will learn about the use of GENIE testing in Chronic Inflammatory Response Syndrome. About My Guest: My guest for this episode is Dr. Ritchie Shoemaker.  Ritchie Shoemaker, MD is a recognized leader in patient care, research, and an education pioneer in the field of biotoxin related illness.  While illness acquired following exposure to the interior environment of water-damaged buildings (WDB) comprises the bulk of Dr. Shoemaker's daily practice, other illnesses caused by exposure to biologically-produced toxins are quite similar in their “final common pathway.”  What this means is that while the illness might begin acutely with exposure to fungi, spirochetes, apicomplexans, dinoflagellates and cyanobacteria, for example, in its chronic form, each of these illnesses has similar symptoms, lab findings, and Visual Contrast Sensitivity (VCS) findings.  Taken together the inflammatory illness from each of these diverse sources is known as  Chronic Inflammatory Response Syndrome. Key Takeaways: What is GENIE? Is HLA-DR still relevant? What are the common triggers of CIRS?  Actinobacteria?  Endotoxins?  Mold and mycotoxins? What is hypometabolism? How does CIRS impact insulin and blood sugar? What is apoptosis? What is the role of coagulation in CIRS? Are upregulated cytokines seen in CIRS? Can GENIE identify those that may have Lyme? What are defensins? What is Ikaros? What is the role of MAP kinases in CIRS? What do Toll receptors tell us? How are B and T cells involved in CIRS? How many CIRS markers are needed in GENIE to suggest CIRS? What is the PTSD gene? How often is histamine involved? What are the cytoskeleton and microtubules?  What can be determined around the function of Treg cells? What are the recent additions to GENIE in the realm of Parkinson's disease? What has GENIE told us about MARCoNS? Connect With My Guest:  http://SurvivingMold.com Interview Date: September 11, 2024 Transcript: To review a transcript of this show, visit https://BetterHealthGuy.com/Episode205. Additional Information: To learn more, visit https://BetterHealthGuy.com. Disclaimer:  The content of this show is for informational purposes only and is not intended to diagnose, treat, or cure any illness or medical condition. Nothing in today's discussion is meant to serve as medical advice or as information to facilitate self-treatment. As always, please discuss any potential health-related decisions with your own personal medical authority. 

Why You Should Listen:  In this episode, you will learn about the role of mold dogs as a tool used in mold inspection of an indoor environment. About My Guest: My guest for this episode is Bill Whitstine.  Bill Whitstine, CMT owns and operates the Florida Canine Academy, which trains bomb, drug, money, weapons, termite, mold, and accelerant detection canine teams.  Several years ago, Bill identified the growing problem of mold in homes and businesses and worked with researchers to further investigate the possibility that dogs could be trained to detect molds.  Bill founded Mold Dog, a subsidiary of the Florida Canine Academy, to train and certify mold-detecting dogs.  Bill has been a leader in the field of canine training since 1989 when he was the first person to attend the Maine State Police Canine Academy in Accelerant Detection.  Bill is the author of the only published book on accelerant detection canines and was the founding president of the Canine Accelerant Detection Association as well as the International Termite Detector Dog Association, which are both international organizations.  Bill has been featured on numerous shows, including several segments on the Animal Planet and The Discovery Channel. Key Takeaways: How are the dogs protected from any potential harm? What safeguards are put in place to keep the dogs healthy? How are dogs identified to become part of the training program? What is the training program for a mold dog? How many different types of mold can the dogs detect? Are the dogs able to identify Actinobacteria or endotoxins? What is the experience of a mold dog inspection? Can the dogs sense mold in an attic or crawlspace? Do appliances need to be moved to optimize the inspection? How often are dehumidifiers a source of mold exposure? Could there be false negatives or false positives? What should be done in the home in advance of the dog's visit to prepare for the inspection? How many issues does a mold dog alert on in an average inspection? Connect With My Guest:  http://Mold-Dog.com Interview Date: March 18, 2024 Transcript: To review a transcript of this show, visit https://BetterHealthGuy.com/Episode199. Additional Information: To learn more, visit https://BetterHealthGuy.com. Disclaimer:  The content of this show is for informational purposes only and is not intended to diagnose, treat, or cure any illness or medical condition. Nothing in today's discussion is meant to serve as medical advice or as information to facilitate self-treatment. As always, please discuss any potential health-related decisions with your own personal medical authority. 

In this episode of TWiM, the hidden biochemical diversity in soil-dwelling Actinobacteria that could lead to a second Golden Era of antibiotic discovery, and structures of glideosome components reveals the mechanism of gliding in apicomplexan parasites. Become a patron of TWiM. Links for this episode: Cryptic or silent? (mBio) The Streptomyces chromosome (Ann Rev Gen) Engineering Nature’s Medicines (pdf) Apicomplexan glideosome (Comm Biol) Music used on TWiM is composed and performed by Ronald Jenkees and used with permission. Send your microbiology questions and comments to twim@microbe.tv

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.30.362764v1?rss=1 Authors: Dasgupta, R., Pradhan, A. K., Ghosh, S. Abstract: Mycobacterium are a genus of Actinobacteria known to be responsible for several deadly diseases in both humans and animals, including tuberculosis. Luciferase is the primary protein in Mycobacteria that plays a role in bioluminescence. It also plays a role in some bacteria of being a source of energy transference, such as in the case of lumazine proteins. Although studies have been conducted in different luciferase in bacteria, there has been hardly any structural studies on luciferase expressed in Mycobacterium sp. EPa45. Therefore, in this paper we have studied luciferase expressed in Mycobacterium sp. EPa45 by insilico analysis of its structure from its protein sequence. We report the observed differences within luciferase reported from other strains of mycobacterium and pathogenic and non-pathogenic forms of bacteria in terms of their (i) physiochemical characteristics, (ii) protein structure, (iii) multiple sequence alignment and (iv) phylogenetic relationships. We report for the first time the relation of this specific strain of Luciferase in mycobacterium and bacterium at large. Highlights: 1. Mycobacterium sp. EPa45 shows similar characteristics to pathogenic mycobacterium 2. Analysis of Luciferase sequence and protein qualities provides insight to pathogenicity 3. The deadly nature of infectious mycobacterium, especially with luciferase sequences similar to Mycobacterium sp. EPa45, is analyzed Copy rights belong to original authors. Visit the link for more info

Link to bioRxiv paper: http://biorxiv.org/cgi/content/short/2020.10.11.335034v1?rss=1 Authors: Mehta, D., Ramesh, A. Abstract: Computational approaches are often used to predict regulatory RNAs in bacteria, but their success is limited to RNAs that are highly conserved across phyla, in sequence and structure. The ANTAR regulatory system consists of a family of RNAs (the ANTAR-target RNAs) that selectively recruit ANTAR proteins. This protein-RNA complex together regulates genes at the level of translation or transcriptional elongation. Despite the widespread distribution of ANTAR proteins in bacteria, their targets RNAs haven't been identified in certain bacterial phyla such as actinobacteria. Here, by using a computational search model that is tuned to actinobacterial genomes, we comprehensively identify ANTAR-target RNAs in actinobacteria. These RNA motifs lie in select transcripts, often overlapping with the ribosome binding site or start codon, to regulate translation. Transcripts harboring ANTAR-target RNAs majorly encode proteins involved in the transport and metabolism of cellular metabolites like sugars, amino acids and ions; or encode transcription factors that in turn regulate diverse genes. In this report, we substantially diversify and expand the family of ANTAR RNAs across bacteria. Copy rights belong to original authors. Visit the link for more info

Welcome back to episode 405 of the Whole View. (0:27) Today Stacy and Sarah are talking about a super interesting topic submitted a listener. Which, if you didn't know this already, we love it when you email us. Sarah shared some behind the scenes information on where listener questions come from. There are Stacy's requests, listener questions, and the really challenging listener questions. The question in discussion in this episode is one of those really hard ones that has been in the queue for a long time. Sarah was able to pull together the information for this show because she actually did a lot of research on this topic for her gut microbiome book. And of course, Sarah did extra research to address the many facets of this challenging question. Stacy is excited about this science rich show.   Listener Question Is the EWG's dirty dozen list based on strong science? (3:37) My husband listened to two episodes of the Skeptoid podcast on organic vs. conventional farming. Mr. Dunning said that we are being duped into paying extra for organic produce. It is sprayed with larger amounts of pesticides than those used in conventional farming and the organic pesticides have been shown to cause disease. My husband believes Mr. Dunning because he provides references and appears to be liberal and non-biased in other podcasts.   I have been purchasing organic produce according to the Environmental Working Group's dirty dozen list. It says on the Activist Facts website that "There’s really only one thing you need to know about the Environmental Working Group when it comes to its studies of toxins: 79 percent of members of the Society of Toxicology (scientists who know a little something about toxins) who rated the group say that the Environmental Working Group overstates the health risk of chemicals. I am walking around with holes in my shirts, and I haven't gotten the air conditioning fixed in my car, so that I can afford organic food. Am I wasting my money? I feel like I cannot trust anyone but you.   Preface Stacy wanted to refer listeners to listen back to previous episodes for information on how both Stacy and Sarah have evolved the way they purchase and prioritize their own foods within their budget. (5:06) Neither Stacy nor Sarah buys everything organically. Nothing that Stacy and Sarah are going to discuss in this episode is intended to be a judgment on you or your family or what you did in the past or what you are doing now. This is all education so that you can be empowered to make the choices that are best for your family at the correct time for you. Where Stacy's family is today, ten years later, is a lot different than where they were ten years ago. The goal of this episode is to help you so that you can walk away and ask questions. There is a larger philosophy that each family needs to adapt to what works best for them. No one is perfect. If you are starting in your journey, you don't need to forego the necessities to have organic food. There is a way to prioritize your budget in a way that is consistent with what your family believes in. Healthy living choices are so personal.   Foundational Choices & Next Level Choices Sarah wanted to emphasize that there are foundational health principles. Nutrient density diet, eating a lot of fruits and vegetables, getting enough sleep, managing stress, and living an active lifestyle. Then Sarah thinks of the next level steps like adding some biohacks, supplements, purchasing grass-fed beef, and organic fruits and vegetables. We need to first make sure that we are focusing on the foundational principles and adding in the next level choice if and when it makes sense. Eating organic is beyond the basic principles, but is overall a better choice. The EWG's overall approach is in many ways more rigorous than the American regulatory agencies. The EWG tends to align with the European Union, Health Canada, and these other regions of the world where the criterion for approving a chemical or pesticide is firmer. In America, the thought process is that chemicals are assumed fine unless proven bad. In Europe, a chemical is not ok until proven safe.   Conventional Evaluation of Pesticide Safety The FDA's safety assessment for chemicals in foods have a variety of criteria. (13:11) They look at acute chronic and subchronic toxicity, carcinogenicity, genotoxicity, reproductive and developmental toxicity, neurotoxicity, and immunotoxicity. Pesticides also go through additional impact evaluation on the environment and ecology. The vast majority of the studies evaluating the effects of pesticides show problems to human health only with occupational exposure, rather than the much lower exposure the majority of us would have simply by eating produce from crops treated with these chemicals. However, there are some challenges with this. We can see high exposure in rodents causing all kinds of problems. The assumption is that acute exposure is not the same as low dose chronic exposure.   Where the Standards Differ One of the challenges that we have in evaluating pesticides is that our exposure is already so vast. There are no humans that don't already have multiple points of exposure to pesticides. There are studies that are linking the chronic low dose exposure to pesticide residues that have correlated pesticide exposure in the food supply with a number of health issues. In the United States, there are 72 pesticides that are routinely used that are completely banned or are in the process of being completely phased out in Europe. Of the pesticides used in USA agriculture in 2016, 322 million pounds were of pesticides banned in the EU. Twenty-six million pounds were of pesticides banned in Brazil and 40 million pounds were of pesticides banned in China. Pesticides banned in the EU account for more than a quarter of all agricultural pesticide use in the USA. It is important to understand that the European Union is looking at the same science as the EPA. And they are making a different judgment based on the strength of the data. We have a challenge that our metric is, 'is it toxic' and 'does it cause cancer'. WHO Guidelines for Safety of Chemicals in Food are much more thorough, and add to the above. They include general system toxicity, allergy and hypersensitivity, and GI Tract Considerations (includes microbiome).   Pesticides and the Microbiome (Sarah’s Biggest Concern) Microbial diversity is generally considered to be the most important measurable criteria for a healthy microbiome. (24:31) The more different species you have, they tend to keep each other in balance. The bacteria basically control the growth of each other. We are also looking for the growth of these really important probiotic strains. In addition, we are looking for completely absent levels of pathogens. We are also looking at the balance between the two main phylum of bacteria in the gut. It is important to understand that rodent studies are actually really good studies for understanding the gut microbiome. We would want to eventually be able to do a similar study in humans. But what Sarah wants to emphasize is that these rodent studies are a really good model for understanding what is happening in humans. Let’s go through some of the most commonly-used pesticides in agriculture for food crops. Permethrin is a broad-spectrum chemical often used as an insecticide for cotton, corn, alfalfa, and wheat crops—unfortunately, it’s also lethal to bees. It’s also used to treat lice, ticks, and scabies.  For more on this, visit this link here. PEM has higher antibacterial activity against some beneficial bacteria, (including Lactobacillus paracasei and Bifidobacterium). Than against pathogens (such as Staphylococcus aureus and Escherichia coli, which only respond to higher concentrations of PEM). Carbendazim (CBZ) is a broad-spectrum benzimidazole fungicide, widely used in agriculture. In mice, 28 days of exposure to CBZ resulted in gut dysbiosis. It suppresses the growth of some of the most important probiotic families while increasing the growth of some problematic families of bacteria. And it decreases bacterial diversity. To learn more about this pesticide, see here. Epoxiconazole (EPO) is a broad-spectrum fungicide often used on grain crops, and that works by inhibiting the metabolism of fungal cells. It reduces the production of conidia—the asexual spores of a fungus that facilitate reproduction. In rats, EPO for 90 days decreased the relative abundance of Firmicutes and increased the abundance of Bacteroidetes and Proteobacteria, while also selectively enriching Lachnospiraceae and Enterobacteriaceae. To learn more about this pesticide, see here.   More Commonly Used Pesticides Imazalil (IMZ) is a systemic fungicide used to combat fungi on vegetables and fruit (especially citrus), as well as tubers during storage. (30:39) In mice, IMZ exposure (at doses of 100 mg per kg of body weight daily for up to 14 days) reduced the cecal relative abundance of Bacteroidetes, Firmicutes, and Actinobacteria, while also reducing microbiota richness and diversity. The IMZ-treated mice also exhibited colonic inflammation. In another study of mice, low-dose, environmentally relevant exposure to IMZ (0.1, 0.5, or 2.5 mg per kg of body weight daily) for 15 weeks resulted in gut microbiota changes. These changes included reduced mucus secretion, decreased the expression of genes related to cystic fibrosis transmembrane conductance regulator (CTFR) in the ileum and colon, and generally disturbed intestinal barrier function. Stacy shared her perspective on how she looks at this information. Think through the way how these pesticides are more heavily used on grains. Chlorphyrifos (CPF) is an extremely common organophosphate pesticide used to kill insects and worms, by interfering with acetylcholine signaling and disrupting their nerve processes. It’s commonly used on fruit and vegetable crops, as well as vineyards. This is one that was going to be banned in the USA, but Scott Pruitt reversed the planned ban. You can learn more about this here. Sarah shared on this study, this study, this study, and this study. This information should stimulate a reevaluation of the use of these chemicals in the food supply. Diazinon is an organophosphate insecticide used on a variety of crops—including fruit trees, rice, sugarcane, nuts, potatoes, and corn. You can learn more about this pesticide here. It causes different changes in male rodents versus female rodents. The researchers speculated that these differences—with male mice experiencing the most severe changes—were due to sex-dependent gut microbiota profiles present before treatment. You can read more about this study here.   Two More Commonly Used Pesticides Propamocarb (PMEP) is a systemic fungicide used to control root, leaf, and soil diseases caused by oomycetes (water molds) by interfering with fatty acid and phospholipid biosynthesis and therefore changing the membrane in fungi. (41:41) It can accumulate in fruit at high levels, thus reaching humans.  You can find more information on this pesticide here. In mice, 28 days of exposure to PMEP (at levels of 300 mg/L in drinking water) induced gut dysbiosis and changes in 20 fecal metabolites, including SCFAs, succinate, bile acids, and TMA. You can read more about this study here. Glyphosate is a broad-spectrum herbicide that can kill both grasses and leafy weeds. It works by inhibiting an enzyme (5-enolpyruvylshikimic acid-3-phosphate synthase, or EPSP synthase), which is used by bacteria, archaea, fungi, algae, some protozoans and plants to synthesize folates (vitamin B9), ubiquinone, menaquinones (vitamin K2), phenolic compounds, and the aromatic amino acids tyrosine, tryptophan, and phenylalanine. The pathway this affects doesn’t exist in animals, which is part of why glyphosate has historically been considered to have low toxicity in animals.  Now that we understand that we have at least as many bacterial cells living within our body as we do human cells and that those bacteria are essential to our health, the relevance of glyphosate exposure comes into focus. Many bacterially-derived compounds that benefit human health are produced via the shikimate pathway. One rat study evaluated the impact on the microbiome of two weeks of glyphosate consumption, and showed a dose-dependent increase in fecal pH attributable to a reduction in acetic acid production, implying the metabolomic impact of glyphosate exposure.   More on Glyphosate It's not that glyphosate is necessarily directly impacting our cells, but it is dramatically impacting the gut microbiome at levels that we are already being exposed to in the food supply. (48:50) In studies in poultry, cattle, and pigs, glyphosate exposure increases the ratio of pathogenic bacteria to probiotic microbes, reducing Bifidobacteria, Lactobacillus, and Enterococcus while increasing Salmonella and Clostridium. In a long-term rat study, the impact on the gut microbiome was evaluated following nearly two years of glyphosate exposure via drinking water at three different doses. Glyphosate caused a large increase in the Bacteroidetes family S24-7 (associated with obesity and inflammation) and a decrease in Lactobacillus species in females (more modest changes in males). It also altered the Firmicutes to Bacteroidetes ratio to one more closely associated with chronic disease. The authors concluded “our data suggests that the exposure to an environmental concentration of [Roundup] residues could have a role in the current epidemic of gut dysbiosis”. This occurs even at levels well below the US ADI of 1.75 mg/kg body weight /day.  There is no strong dose-response. Sarah wants to emphasize that our glyphosate exposure in food is quite high. It is definitely above the cusp for an impact on our gut microbiome composition. The FDA has a report where they have been mandated to measure glyphosate residue in the food supply. In their 2016 report they measured measurable levels of glyphosate residues in 63% of corn food crops and in 67% of soybean food crops. However, they did not say how much residue was there. The 2018 report goes to a dead link now. A Swiss study of foods purchased at a grocery store showed that legumes had the highest concentrations of glyphosate residues, up to 2.95 mg/kg. United Kingdom government testing of glyphosate residues in wholegrain bread showed levels up to 0.9 mg/kg. A study of foods purchased in Philadelphia, USA metropolitan area showed 59 percent of honey samples contained glyphosate residues, and 36 percent of soy sauce contained glyphosate residues. Third-party testing of popular breakfast cereals, crackers, and cookies by the Detox Project and Food Democracy Now! showed alarming levels of glyphosate residues in all products. Roundup Ready GMOs have the highest level of glyphosate residues. Studies prove that our current levels of exposure are sufficient for measurable amounts of glyphosate to get into our bodies.  One study showed that 44% of city dwellers in 18 countries in Europe had detectable glyphosate residues in their urine, despite Europe’s more aggressive campaign against GMO foods. A pilot study in the United States of America evaluating 131 urine samples from across the country detected glyphosate residues in the urine of 86.7% of them. The highest observed detection frequency in the Midwest was at 93.3% and the lowest in the South at 69.2%.   How to Look at this Science The EWG is looking at this much more broad group of criteria and they are taking a very similar standpoint to the European Union. (58:09) A small effect is still an effect and we need to be concerned about it. When Sarah does a deep dive look to look at the impact on the gut microbiome this is where Sarah sees the biggest area of concern. Sarah thinks it is especially important because it is not currently part of the criteria by the FDA and the EPA for whether or not these chemicals are going to be approved for use. This is the thing that Sarah really thinks needs to change. The good news is that a healthy gut microbiome and high fiber consumption can actually protect us from absorbing a lot of these pesticides.  There have been studies that showed that lactobacilli can help reduce how much pesticide on our food gets into our bodies.  There are also studies that show that higher fiber consumption can at least partially reverse the gut dysbiosis. As we get back to the heart of this question, there are studies that show that the answer is no. High vegetable consumption is still really important because it does support a healthy gut microbiome, to begin with. And a healthy gut microbiome is going to protect us in a lot of ways. For example, they can protect us against heavy metals. Even if we can't afford organic to not let that dissuade us from eating that high vegetable consumption because of this. Sarah sees this as an exciting two-way street. Even though pesticide residues are impacting the composition of our guts, the composition of our gut is influenced by more than just that. It is influenced by how many fruits and vegetables we eat, mushrooms, nuts and seeds, variety, how much fish, how quality the olive oil is that we are consuming, etc. All of these things help to determine the composition of our gut microbiome. Doing all of these foundational things becomes more important when we are not necessarily in a position to be able to seek out and afford the highest food quality. It is still really important to eat a vegetable-rich diet. That's why Sarah wants to classify all of this science as the next level. The foundational principle is still eating a lot of fruits and vegetables, even if our only access to that is conventional. Beyond that, yes the Dirty Dozen and Clean Fifteen lists from the EWG are a wonderful tool. Not that Sarah agrees with everything the EWG has said, Sarah thinks that these are spot on in the sense of trying to minimize our exposure to pesticide residues.   How to Limit Pesticide Exposure Stacy feels that the podcast referenced and the information they are sharing aren't so far apart. (1:02:10) Sarah and Stacy discussed a point shared in the documentary Food Inc. that really hit this information home. We do the best that we can with what we can, and become educated on what other things we can do to support healthy living. Nothing is ever perfect. Prioritize the foods you purchase and do the best you can. It is not good to stress about these things. The dirty dozen list includes strawberries, spinach, kale, nectarines, apples, grapes, peaches, cherries, pears, tomatoes, celery and potatoes The clean fifteen list includes avocados, sweet corn, pineapple, onions, papaya, sweet peas (frozen), eggplants, asparagus, cauliflower, cantaloupes, broccoli, mushrooms, cabbage, honeydew melon, and kiwifruit. If you are going to get something off the dirty dozen conventional, look at ways that you can wash that food very well or ways you can peel the food to remove the majority of the pesticide residue. USDA certification is very expensive, so a lot of small family farms are growing organically, but don't have the certification. Talk to farmers and find out how they are growing their food. Stacy can't handle the sight of bugs in her fresh vegetables. Eating fruits and vegetables is a good thing. Perfection is not the goal. Neither Stacy nor Stacy eats 100% organic, they both do the best that they can. Sarah has found that the prices at her local farmer's market are best. Develop relationships with your local farmers, and shop at the end of the market. Stacy subscribes to Hungry Harvest, which has a waiting list right now. Sarah prescribes to MisFit Market, there is also one called Imperfect Produce. One of the things that Sarah loves about her subscription is the surprise element of it, which forces her to get creative with her meal planning. At Stacy's house they meal plan when their box arrives, based on what they received. Stacy shared more information on their meal planning process as a family, and how focused they have become to make sure they are not wasting food. Building relationships with your local farmers is a point that Stacy echoed from Sarah. Buying things in season or frozen can also be a helpful way to save money. Stacy's organic box is at least 30% off had they purchased those items at a grocery store regularly. The thing that Stacy most loves about Hungry Harvest is that they give back to the community.   Closing Thoughts Stacy thanked Sarah for all the research she did for this show! (1:23:13) If you have any follow up questions on all of this, you are welcome to email Stacy and Sarah using the contact forms on their blogs. You can comment on social media posts as well. Stacy and Sarah are always happy to hear from you! If you have been loving this show, please help spread the word to others by sharing a link to an episode you enjoyed with a family or friend, or leave a review. Stacy and Sarah so greatly appreciate your support! Thank you again for tuning in! Next week is another science-heavy show that builds off of this week's episode. We will be back again next week! (1:25:57)

Found within the a range of ecological niches, bifidobacteria represents a genus within the phylum Actinobacteria, which is one of the major phyla in the healthy intestinal tract of humans. Bifidobacteria are among the first microbes to colonise the gut and are being purported as beneficial for human health. Several research studies have reported that lower abundance of bifidobacteria in the gut precedes disease development, including gut disorders, allergy, obesity and mental disorders. Charlotte Bastiaanse, associate editor at Vitafoods Insights, talks to Dr Chyn Boon Wong, research associate at Morinaga Milk Industry Co., about Human Residential Bifidobacteria (HRB) and its role in driving wellbeing. We delve into the concept of achieving human health from the inside out and explore the commercially available HRB probiotic strains.

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/

This episode: Light increases the growth even of some bacteria that don't harvest its energy! Download Episode (9.0 MB, 9.75 minutes) Show notes: Microbe of the episode: Methylococcus thermophilus News item Takeaways Light from the sun is one of the fundamental sources of energy for life on this planet. Plants and other phototrophs—photosynthetic organisms that get their energy mainly from light—form the foundation of the food web, and organisms that feed on them or that feed on organisms that feed on them are all dependent on the ability to capture the sun's rays. There are other ways to benefit directly from the sun's energy, besides photosynthesis—some microbes have enzymes that use light energy to repair damage to DNA (the same damage that is caused by ultraviolet light), and we use sunlight to synthesize vitamin D. In this study, however, microbes are discovered to grow faster in the presence of light despite not being phototrophs or producing any light-harvesting proteins. The scientists discover some possible light-sensing proteins, though, that could regulate these microbes' behavior, allowing them to synchronize their growth cycles to phototroph partners in aquatic environments. Journal Paper: Maresca JA, Keffer JL, Hempel P, Polson SW, Shevchenko O, Bhavsar J, Powell D, Miller KJ, Singh A, Hahn MW. Light modulates the physiology of non-phototrophic Actinobacteria. J Bacteriol JB.00740-18. Other interesting stories: Finding and capturing electrosynthetic microbes directly from hot springs Lignin-eating microbe could be good source for renewable aromatic compounds Wood-eating beetle has gut for breaking down wood in microbial production line fashion   Email questions or comments to bacteriofiles at gmail dot com. Thanks for listening! Subscribe: Apple Podcasts, RSS, Google Play. Support the show at Patreon, or check out the show at Twitter or Facebook

The TWiMbionts explore the role of bacteria in the genesis of moonmilk, and how ancient host proteins can be used to engineer resistance to virus infection. Hosts:  Vincent Racaniello, Michele Swanson and Elio Schaechter. Subscribe to TWiM (free) on iPhone, Android, RSS, or by email. You can also listen on your mobile device with the Microbeworld app. Become a patron of TWiM. Links for this episode Role of Streptomyces in moonmilk (bioRxiv) TWiM 51: Cave science with Hazel Barton Moonmilk (Wikipedia) Ancient proteins for virus resistance (Cell Rep) Image credit Letters read on TWiM 157  Send your microbiology questions and comments (email or recorded audio) to twim@microbe.tv  

Bacteria necessitate multiple signal transduction systems to sense the ever-changing environments and mediate the cellular response accordingly. The major bacterial signal transduction systems are one-component system (1CS), two-component system (2CS) and extracytoplasmic function (ECF) σ factor. Compared to 1CSs and 2CSs, ECF σ factors have only been identified much later and therefore the knowledge about their molecular mechanisms and physiological roles is less profound. This thesis mainly focuses on the study of ECF σ factors from the bacterial phyla, Planctomycetes and Actinobacteria.

Bacteria necessitate multiple signal transduction systems to sense the ever-changing environments and mediate the cellular response accordingly. The major bacterial signal transduction systems are one-component system (1CS), two-component system (2CS) and extracytoplasmic function (ECF) σ factor. Compared to 1CSs and 2CSs, ECF σ factors have only been identified much later and therefore the knowledge about their molecular mechanisms and physiological roles is less profound. This thesis mainly focuses on the study of ECF σ factors from the bacterial phyla, Planctomycetes and Actinobacteria.

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.