Podcasts about microbial genomics

In January 2024, Aline Metris and Lindsay Hall hosted an academic-industry workshop at the Microbiology Society offices to discuss the potential long-term implications of microbiome perturbations. Since then, they've published a comprehensive summary of the findings from the workshop in Microbial Genomics. We invited them back to the Microbiology Society offices to chat with Clare about their experiences hosting the workshop and share their insights from the paper. If you'd like to read the review in Microbial Genomics you can do so by following this link. Stay tuned to the Microbiology Society socials to be the first to hear about Lindsay and Aline's further work and our other projects on the microbiome. You can also read a full auto generated transcript of the podcast on our website here. 

2024 was a very active year on research in antimicrobial resistance, highlighted by an impactful and high level political declaration to combat antimicrobial resistance by the United Nations. In this episode, trainees from NIH-funded training program (T32) on antimicrobial resistance will help me discuss the most relevant research on the field in the year 2024. Welcome to editors in conversation! Topics discussed: The best papers of 2024 in gram-positive, gram-negative, mycobacterial and parasite resistance Guests: Nathalie Chen: University of Pittsburgh, Pittsburgh, PA Alex Kang: Houston Methodist Research Institute, Houston, TX Nathan Rabbe: University of Pittsburgh, Pittsburgh, PA Taylor Blackburn: Emory University, Atlanta, GA Jacon McPherson: University of Houston, Houston, TX. Harrison Lee, MD: Associate Chief of Epidemiology and Microbial Genomics, Professor of Medicine and Epidemiology, Director, Center for Genomic Epidemiology, Director, T32 AMR, U of Pittsburgh William Shafer, PhD: Professor, Department of Microbiology and Immunology, Emory University School of Medicine, Co-Director, Emory Antibiotic Resistance Center. Director T32 AMR, Emory University This episode is brought to you by the Antimicrobial Agents and Chemotherapy Journal.  Visit asm.org/aac to browse issues and/or submit a manuscript. If you plan to publish in AAC, ASM Members get up to 50% off publishing fees. Visit asm.org/joinasm to sign up.

For this episode of Microbe Talk Clare was joined by the wonderful Gwyn Dahlquist-Axe and Francesca Standeven, archaeological scientists who study AMR and ancient human oral microbiomes. They're on the podcast to discuss their review into diet, disease and antibiotic resistance from ancient human oral microbiomes published in Microbial Genomics.You can read their review 'Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes' here. If you'd like to keep up with Francesca and Gwyn's research their Twitter (X) handles are @GDahlquistAxe and @fstandeven193 You can also read a full transcript of the podcast on our website.Music by Denys Kyshchuk from Pixabay

Nicholas Christakis, Sterling Professor of Social & Natural Science Departments of Sociolgy statistics and Data Science, Ecology and Evolutionary Biology, Biomedical Engineering and Medicine at Yale University, USA, and Nikos Kyprides, Head, Microbial Genomics & Metagenomics Super Program, Joint Genome Institute, Lawrence Berkeley National Labolatory, Department of Energy at Berkeley, USA, discuss about "Understanding human social networks by deciphering microbial interactions with AI tools".

In this podcast, we chat with Dr Brian Forde about HAIviz. HAIviz an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data. HAIviz displays and links the outbreak timeline, building map, phylogenetic tree, patient bed movements, and transmission network on a single interactive dashboard. You can view and use the tool for free at Permana, B., Harris, P. N., Roberts, L. W., Cuddihy, T., Paterson, D. L., Beatson, S. A., & Forde, B. M. (2024). HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data. Microbial Genomics, 10(2), 001200.    

In this podcast, we chat with Dr Brian Forde about HAIviz. HAIviz an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data. HAIviz displays and links the outbreak timeline, building map, phylogenetic tree, patient bed movements, and transmission network on a single interactive dashboard. You can view and use the tool for free at Permana, B., Harris, P. N., Roberts, L. W., Cuddihy, T., Paterson, D. L., Beatson, S. A., & Forde, B. M. (2024). HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data. Microbial Genomics, 10(2), 001200.    

The podcast discusses an article co-authored by Andrew Page, examining the use of GPT-4 for research publication. The conversation focuses on the authorship of articles generated by GPT-4 and the implications for academic publishing. Authorship and Ethics: Andrew discusses the question of authorship when AI-generated content is involved in research articles. He explores the ethical implications and potential biases associated with AI-assisted writing, such as the omission of minority figures and novel discoveries. He emphasizes the importance of transparency when using AI and its potential to democratize research, as long as ethical guidelines are maintained. AI & Scientific Journals: The podcast delves into the current landscape of AI in academic publishing. It addresses the commercial use of AI in crafting manuscripts for research articles and the necessity of distinguishing between manual and AI-generated contributions. The possible misalignment of GPT-4's commercial objectives with academic goals is highlighted. Risks and Benefits: Andrew outlines the risks of using AI in publishing, such as unintentional plagiarism, biases, and outdated methods. He provides an example of bioinformatics software recommending deprecated methods, illustrating the need for caution. The conversation also touches upon the AI's potential to introduce bias unintentionally, citing past incidents where AI models quickly adopted extremist views. Andrew's co-authors, Niamh Tumelty and Sam Sheppard, bring different perspectives on ethics and the impact of AI on publishing. Niamh, associated with the London School of Economics, emphasizes ethical considerations, while Sam, editor-in-chief of Microbial Genomics, underscores the need to adapt to the reality of AI contributions in journal submissions. In conclusion, the podcast underscores the importance of recognizing and navigating the ethical challenges posed by AI in academic publishing. It suggests that the technology may evolve faster than policies can adapt, necessitating an ongoing conversation among researchers, publishers, and AI developers. Links: https://microbiologysociety.org/blog/microbe-talk-ai-a-useful-tool-or-dangerous-unstoppable-force.html https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001049

Niamh and Andrew are interviewed by Clare Baker from the Microbiology Society about their editorial on AI in Microbial Genomics research. Editorial on AI: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001049 Article for podcast: https://microbiologysociety.org/blog/microbe-talk-ai-a-useful-tool-or-dangerous-unstoppable-force.html

For this episode of Microbe Talk, Clare is tackling the topic of AI in Microbial Genomics research. So what better time than now, to give AI a chance to generate the description?*The below description was generated by Chat GPT*In this captivating episode of Microbe Talk, your host Clare delves into the cutting-edge realm of microbial genomics and its fascinating intersection with artificial intelligence. Joining her in this stimulating discussion are two remarkable experts, Niamh Tumelty and Andrew Page, who are at the forefront of AI-driven advancements in microbial research.Whether you're an AI aficionado, a genomics guru, or simply curious about the future of scientific discovery, this episode promises to spark your imagination and provide unparalleled insights. Join us on this journey into the realm where technology and biology intertwine, and witness the dawn of a new era in microbial research.Tune in to Microbe Talk and embark on an intellectual adventure that bridges the gap between AI and microbial genomics.Further informationMusic: Space Chillout by penguinmusic from PixabayNiamh and Andrew's guest editorial, published in Microbial Genomics can be found on the Microbiology Society Journals website here.Niamh and Andrew's podcasts:https://soundcloud.com/microbinfiehttps://soundcloud.com/research-pagesNiamh and Andrew's Twitter accounts:⁠twitter.com/niamhtumelty ⁠⁠twitter.com/andrewjpage ⁠You can read the full transcript here.

This month, inspired by a paper published in Microbial Genomics, Clare takes a deep dive into the method of wastewater monitoring. She speaks to Professor Steve Patterson and Dr Anne Leonard about how wastewater monitoring is a useful tool which helps us understand not only the spread of diseases like COVID-19, but also antimicrobial resistance.You can read Professor Patterson's paper, published in Microbial Genomics here. https://microb.io/3or9CsS Music: pixabay Chill Abstract (Intention) Coma-Media

In this episode, sponsored by Zymo Research, we explore the microbiome and how long-read sequencing techniques are changing our approach to the field and the exciting discoveries that they have led to. To do this we speak to Kris Locken, Molecular Biologist in the Research & Development department of Zymo Research (CA, USA), and Jeremy Wilkinson, Global Marketing Specialist for Microbial Genomics at PacBio (CA, USA). Find out how microbes compare to nuts and what this means for the challenges of metagenomic sample preparation, how long reads can stack up vs short reads for metagenome assembly and much more, all in this latest episode of Talking Techniques Contents:Intro: 00:00-01:55 What is metagenomics and why is it important for microbial studies? 01:55-03:55 How has long-read sequencing impacted metagenomics? 03:55-06:05 Long-read vs short-read sequencing workflows: 06:05-07:15 Addressing barriers to long-read sequencing: 07:15-08:45 Sample preparation for long-read sequencing: 08:45-12:20 Development of long-read sequencing to improve accuracy and capabilities: 12:20-14:40 Best practice for assembly and analysis: 14:40-17:40 Exciting examples of the benefits of long-read sequencing: 17:40-20:00 What would you wish for to improve the ability long-read sequencing in microbiomics: 20:00-21:40

In this episode, sponsored by Zymo Research, we explore the microbiome and how long-read sequencing techniques are changing our approach to the field and the exciting discoveries that they have led to. To do this we speak to Kris Locken, Molecular Biologist in the Research & Development department of Zymo Research (CA, USA), and Jeremy Wilkinson, Global Marketing Specialist for Microbial Genomics at PacBio (CA, USA).Find out how microbes compare to nuts and what this means for the challenges of metagenomic sample preparation, how long reads can stack up vs short reads for metagenome assembly and much more, all in this latest episode of Talking TechniquesContents:Intro: 00:00-01:55What is metagenomics and why is it important for microbial studies? 01:55-03:55How has long-read sequencing impacted metagenomics? 03:55-06:05Long-read vs short-read sequencing workflows: 06:05-07:15Addressing barriers to long-read sequencing: 07:15-08:45Sample preparation for long-read sequencing: 08:45-12:20Development of long-read sequencing to improve accuracy and capabilities: 12:20-14:40Best practice for assembly and analysis: 14:40-17:40Exciting examples of the benefits of long-read sequencing: 17:40-20:00What would you wish for to improve the ability long-read sequencing in microbiomics: 20:00-21:40 Hosted on Acast. See acast.com/privacy for more information.

It's great to find a helpful learning resource. Here, I chat to the author of the book "Bacterial Genetics and Genomics", Prof Lori Snyder about the book, who it will be useful for and why this resource is different from others. About our Guest: Prof. Lori A. S. Snyder is a Professor in the School of Life Sciences, Pharmacy, and Chemistry at Kingston University, where she is involved in educating undergraduate and graduate students, as well as leading an active and collaborative research group. Prof. Snyder is also active in science outreach activities, including traveling lab visits, offering work experience to teenagers, and participating in public engagement events. Her research focuses on two main areas: combating antibiotic resistant infections and bacterial genetics and genomics. Her novel antimicrobials to stop infant blindness from multi-drug resistant bacterial infections have been featured in Wired (www.wired.co.uk/article/fight-against-super-gonorrhoea) and on the Sparks children's charity YouTube channel (https://www.youtube.com/watch?v=rQUl5-kC1OQ). Her use of bacterial genome sequence data to uncover new information about pathogens was featured in an interview on the Thermo Fisher Scientific YouTube channel about use of their sequencing system (https://www.youtube.com/watch?v=Z_ttuJ6l1hI&t=95s) and in 2013 her contributions were recognized by the Society for Applied Microbiology with the W H Pierce Prize (https://sfam.org.uk/resource/wh-pierce-2013-lori-snyder.html). Prof. Snyder was twice elected to the Prokaryotic Division committee of the Microbiology Society and services on the Editorial Board of its journal Microbial Genomics, as well as contributing by reviewing many research publications and grant applications.Find Prof Lori Snyder at: Twitter: @DrLoriSnyderSenior Editor: @CrumlyChuckPublisher: @CRCPressBook: https://www.routledge.com/Bacterial-Genetics-and Genomics/Snyder/p/book/9780815345695Book – missing content https://s3-eu-west-1.amazonaws.com/s3-euw1-ap-pe-ws4-cws-documents.ri-prod/9780815345695/9780815345695_missing_content.pdfBook - support materials https://routledgetextbooks.com/textbooks/9780815345695/Find Microbe Mail at: Visit the Microbe Mail website to sign up for updates E-mail: mail.microbe@gmail.comTwitter: @microbemail Instagram: Microbe_Mail

We chat to the author of SNP-sites, bioinformatics software for extracting SNPs from a multi-FASTA alignment. Sounds simple but behind all of our software are quirky details that never make it into the final paper. Software: https://github.com/sanger-pathogens/snp-sites Paper: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000056 "SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments", Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris, Microbial Genomics 2(4), (2016)

On this month’s Microbe Talk, Matt talks to Dr Arwyn Edwards; an Arctic microbiologist based at Aberystwyth University. Dr Edwards recently published a paper in Microbial Genomics entitled ‘Microbial genomics amidst the Arctic crisis’. Dr Edwards and Matt discuss the paper, the challenges of working in the Arctic and how Arctic microbial research is changing To read the article visit: www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000375

Ever wonder what it is like to study the genomics of microbes likes bacteria and viruses? Dr. Sabah Kadri talks with Dr. Egon Ozer about the field of microbial genomics, the relatively fast evolution of microbes and the study from Dr. Ozer's group studying the genomic sequences of SARS-CoV-2, the virus in the COVID-19 pandemic. Tune in as we learn about this field, its challenges and methodologies. Link to paper discussed: https://www.medrxiv.org/content/10.1101/2020.05.19.20107144v1 Contact us with questions, feedback and requests to collaborate on future episodes at computationallyyours@gmail.com. Follow us on Twitter: @compbiopodcast ; Dr. Sabah Kadri: @sabahkadri ; Arshi Arora: @arorarshi Intro/Outro music: Riatsu (Shadaab Kadri) Follow us on YouTube here. Follow us on Instagram here. --- Send in a voice message: https://anchor.fm/computationally-yours/message

Dr Philip Smith, Digital and Education Editor of Gut and Consultant Gastroenterologist at the Royal Liverpool Hospital interviews Professor Paul O'Toole; who is Professor of Microbial Genomics, Head of School of Microbiology and Principal Investigator in APC Microbiome Ireland, an SFI funded centre at University College Cork, Ireland, on "Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across 5 European countries" published in paper copy in Gut in July 2020 https://gut.bmj.com/content/69/7/1218

Dr. Klassen shares his research with fungus-growing ant symbiosis to understand how microbial interaction evolves. He explains how relevant genetics is in his research as well as other research he has done involving gene fragmentation, phylogenetic analysis and drafting genome sequences. We discuss how genome sequencing works and how the technology has advanced in the last 10 years. The device we refer to in the episode is seen below! He explains what students can expect in his spring 2015 Microbial Genomics course (MCB 3895-004). Dr. Klassen is an Assistant Professor at UCONN. He received his PhD in Microbiology and Biotechnology, University of Alberta and his Postdoctoral Study in the Department of Bacteriology, University of Wisconsin-Madison. He has his own lab in UCONN Storrs campus, Klassen Laboratory. Learn more on jonathanklassenlab.com and follow their activities on Twitter @KlassenLab.

Last month, the Society held its Annual Conference, which was held in Birmingham this year. It was a great event: over a thousand delegates attended, presenting hundreds of talks and posters. We spoke to some of the attendees about their work for this month’s podcast. Firstly, we chatted with Dr Jennifer Gardy from the BC Centre for Disease Control in Canada, who told us about her role in the Society’s new journal Microbial Genomics and about the field of genomics in general. Next up was Professor David Minnikin from the University of Birmingham, who is researching the origins of tuberculosis, which appears to have begun as an infection of ancient animals in the Pleistocene era. Dr Nick Loman, also from the University of Birmingham, who told us about his work using a seriously tiny DNA sequencing machine. Finally, Karl Dunne from, you guessed it, the University of Birmingham, talked about his PhD research, which has seen him sequence the first sample of E. coli bacteria, isolated by Theodor Escherich. Image credit: Bob Hall on Flickr under CC BY-SA 2.0

Dr. Gautam Dantas is an Assistant Professor in the Department of Pathology & Immunology, the Department of Biomedical Engineering, and the Center for Genome Sciences & Systems Biology, at Washington University School of Medicine. at Washington University in St. Louis School of Medicine. He received his PhD from the University of Washington and afterwards completed a research fellowship in Genetics at Harvard Medical School before joining the faculty at Washington University. Gautam is here with us today to tell us about his journey through life and science.

Melvyn Bragg and his guests discuss the origins of infectious disease. Infectious disease has been with us for millennia. There are reports of ancient outbreaks of plague in the Bible, and in numerous historical sources from China, the Middle East and Europe. Other infections, including smallpox, tuberculosis and measles, have also been known for centuries. But some diseases made their first appearances only recently: HIV emerged around a century ago, while the Ebola virus was first recorded in the 1970s.But where do the agents of disease come from, and what determines where and when new viruses and bacteria appear? Modern techniques allow scientists to trace the histories of infective agents through their genomes; the story of disease provides a fascinating microcosm of the machinery of evolution.With:Steve JonesProfessor of Genetics at University College LondonSir Roy AndersonProfessor of Infectious Disease Epidemiology at Imperial College LondonMark PallenProfessor of Microbial Genomics at the University of Birmingham.Producer: Thomas Morris.

Melvyn Bragg and his guests discuss the origins of infectious disease. Infectious disease has been with us for millennia. There are reports of ancient outbreaks of plague in the Bible, and in numerous historical sources from China, the Middle East and Europe. Other infections, including smallpox, tuberculosis and measles, have also been known for centuries. But some diseases made their first appearances only recently: HIV emerged around a century ago, while the Ebola virus was first recorded in the 1970s.But where do the agents of disease come from, and what determines where and when new viruses and bacteria appear? Modern techniques allow scientists to trace the histories of infective agents through their genomes; the story of disease provides a fascinating microcosm of the machinery of evolution.With:Steve JonesProfessor of Genetics at University College LondonSir Roy AndersonProfessor of Infectious Disease Epidemiology at Imperial College LondonMark PallenProfessor of Microbial Genomics at the University of Birmingham.Producer: Thomas Morris.

Puerto Rico is widely known as the "La Isla del Encanto," which translated means "The Island of Enchantment." And while its beaches, tropical rain forest, and biolumescent bays are wonders of nature, the island is not without its problems. From energy needs to economics, Puerto Rico shares many issues facing the rest of the world. In this MicrobeWorld Video episode we talk with Nadathur S. Govind, Ph.D., Professor, Marine Sciences Department at the University of Puerto Rico, Mayaguez, and William Rosado, Marine Sciences Department at the University of Puerto Rico, Mayaguez, about the sustainable biofuel program they are launching in southwestern Puerto Rico. According to Govind, the island's successful sugarcane industry died in the 1990's. In fact, local rum manufacturers now import their molasses from as far away as Malaysia. As a result, approximately 70 percent of the population in southwestern Puerto Rico is on welfare. Govind believes he can rebuild the local economy by harnessing bacterial enzymes extracted from the guts of termites and shipworms (mollusks) found in the mangroves off the coast to break down the lignocellulose in sugarcane and hibiscus. The idea is that if he can bring agricultural production back to his community, he can use the crop waste to produce ethanol to supplement Puerto Rico's demand for fuel. And since the byproduct of ethanol is carbon dioxide, he also plans to use algae to capture the gas and produce biodiesel. The waste that he has left over can then be returned to the soil as fertilizer or given to livestock as feed, completing the cycle. For more information about Govind's program please read the article, "Combining Agriculture with Microbial Genomics to Make Fuels," found in the American Society for Microbiology's Microbe magazine.

Puerto Rico is widely known as the "La Isla del Encanto," which translated means "The Island of Enchantment." And while its beaches, tropical rain forest, and biolumescent bays are wonders of nature, the island is not without its problems. From energy needs to economics, Puerto Rico shares many issues facing the rest of the world. In this MicrobeWorld Video episode we talk with Nadathur S. Govind, Ph.D., Professor, Marine Sciences Department at the University of Puerto Rico, Mayaguez, and William Rosado, Marine Sciences Department at the University of Puerto Rico, Mayaguez, about the sustainable biofuel program they are launching in southwestern Puerto Rico. According to Govind, the island's successful sugarcane industry died in the 1990's. In fact, local rum manufacturers now import their molasses from as far away as Malaysia. As a result, approximately 70 percent of the population in southwestern Puerto Rico is on welfare. Govind believes he can rebuild the local economy by harnessing bacterial enzymes extracted from the guts of termites and shipworms (mollusks) found in the mangroves off the coast to break down the lignocellulose in sugarcane and hibiscus. The idea is that if he can bring agricultural production back to his community, he can use the crop waste to produce ethanol to supplement Puerto Rico's demand for fuel. And since the byproduct of ethanol is carbon dioxide, he also plans to use algae to capture the gas and produce biodiesel. The waste that he has left over can then be returned to the soil as fertilizer or given to livestock as feed, completing the cycle. For more information about Govind's program please read the article, "Combining Agriculture with Microbial Genomics to Make Fuels," found in the American Society for Microbiology's Microbe magazine.

Puerto Rico is widely known as the "La Isla del Encanto," which translated means "The Island of Enchantment." And while its beaches, tropical rain forest, and biolumescent bays are wonders of nature, the island is not without its problems. From energy needs to economics, Puerto Rico shares many issues facing the rest of the world. In this MicrobeWorld Video episode we talk with Nadathur S. Govind, Ph.D., Professor, Marine Sciences Department at the University of Puerto Rico, Mayaguez, and William Rosado, Marine Sciences Department at the University of Puerto Rico, Mayaguez, about the sustainable biofuel program they are launching in southwestern Puerto Rico. According to Govind, the island's successful sugarcane industry died in the 1990's. In fact, local rum manufacturers now import their molasses from as far away as Malaysia. As a result, approximately 70 percent of the population in southwestern Puerto Rico is on welfare. Govind believes he can rebuild the local economy by harnessing bacterial enzymes extracted from the guts of termites and shipworms (mollusks) found in the mangroves off the coast to break down the lignocellulose in sugarcane and hibiscus. The idea is that if he can bring agricultural production back to his community, he can use the crop waste to produce ethanol to supplement Puerto Rico's demand for fuel. And since the byproduct of ethanol is carbon dioxide, he also plans to use algae to capture the gas and produce biodiesel. The waste that he has left over can then be returned to the soil as fertilizer or given to livestock as feed, completing the cycle. For more information about Govind's program please read the article, "Combining Agriculture with Microbial Genomics to Make Fuels," found in the American Society for Microbiology's Microbe magazine.