The Science, Microbes & Health Podcast

• How ecological dynamics affect pathogens in the gut, with Prof. Kevin Foster PhD

  This episode features Prof. Kevin Foster PhD from University of Oxford (UK), speaking about his lab’s ecological approach to the gut microbiome and efforts to understand and predict dynamics of different species in the microbiome. They also focus on how these ecological dynamics map onto health outcomes, and how they inform interventions. In a 2023 paper, they explored the concept of colonization resistance in the gut, and why certain bacteria or combinations of bacteria are particularly good at preventing pathogens from thriving. Both diversity and composition are important for determining the extent to which a community resists a pathogen. But a microbiome may equally resist a probiotic that’s introduced because the probiotic microorganism doesn’t have access to a unique nutrient. How bacteria interact with each other can help determine resiliency or stability of the microbiome overall. While it’s true that hundreds of species of bacteria exist in the gut, the scale at which the microbes interact locally is much more limited (on the scale of tens of species). Episode abbreviations and links: 2023 paper examining colonization resistance against 2 pathogens: Microbiome diversity protects against pathogens by nutrient blocking.  About Prof. Kevin Foster PhD: Professor Kevin Foster FRS is the Chair of Microbiology at the Dunn School of Pathology, University of Oxford. Prior to this, he was Professor of Evolutionary Biology in the departments of Biology and Biochemistry at Oxford. Before Oxford, he had a lab at Harvard as a Bauer Fellow in the FAS Center for Systems Biology. He did his undergrad at Cambridge in Natural Sciences and his Ph.D. at the University of Sheffield in evolutionary biology. Professor Foster’s research integrates the traditional fields of ecology and evolution with the latest methods in computation, microbiology, molecular genetics, and the study of the mammalian microbiome. The lab focuses on how bacteria compete and succeed in their communities and seeks to use this to manipulate gut communities for better health.

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• Applying the tools of ecology to manage microbiomes in people with cancer, with Dr. Joao Xavier PhD

  This episode features Dr. Joao Xavier PhD, a systems biologist from Memorial Sloan Kettering Cancer Center, speaking about the application of ecological principles and tools to individuals being treated for cancer. His lab combines multi-omics profiling with ecological models to generate insights on how microbes interact with each other, for application to clinical risk prediction and microbiota-focused interventions. He has studied individuals receiving bone marrow transplantation, who take antibiotics to prepare for treatment; the antibiotics cause significant gut microbiota shifts and the risk of bloodstream infections increases, so his lab is looking at whether the gut microbiota could mitigate this risk. Currently microbiome monitoring is not being used clinically in patients receiving cancer treatments, but a path exists for gaining the evidence needed to make this feasible and useful. Potentially, microbiome monitoring could allow physicians to move from reactive treatment with antibiotics to proactive intervention that prevents serious infections. Or the clinician could simulate potential treatment scenarios and figure out which one is the most beneficial. Probiotics could be administered to shape the microbiome – but rather than adding microorganisms that may simply be missing, these probiotics would be developed by thinking about the microbiome outcome and how to pressure the ecosystem in a certain direction. Episode abbreviations and links: Review in Nature Reviews Clinical Oncology, arguing for the relevance of microbiota management guided by ecological principles in cancer care: making the case for Ecological management of the microbiota in patients with cancer Mouse study investigating what may drive an increase in oral bacteria within the fecal microbiota and how it may link to patient outcomes: Oral bacteria relative abundance in faeces increases due to gut microbiota depletion and is linked with patient outcomes About Dr. Joao Xavier PhD: Joao B. Xavier, PhD, is a faculty member in the Program for Computational and Systems Biology at Memorial Sloan Kettering Cancer Center in New York. His lab combines experiments, computational modeling, and clinical data to study how the human microbiota influences cancer treatment outcomes. Dr. Xavier’s work has uncovered links between gut bacteria, immune recovery, and infection risk in patients undergoing intensive therapies such as allogeneic hematopoietic stem cell transplantation. He recently authored a Nature Reviews Clinical Oncology article (2025) proposing “ecological management” of the microbiota in oncology. This approach applies principles of ecosystem management to preserve beneficial microbes, minimize treatment-related damage, and guide precision interventions. He was awarded the 2026 ASM Microbiome Data Prize by the American Society for Microbiology in recognition of these contributions. His group collaborates broadly across clinical and basic sciences to develop microbiota-informed strategies that could improve responses to chemotherapy, immunotherapy, and infection control.

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• Insights from evolutionary ecology on microbiome assembly and modulation,  with Prof. Jens Walter PhD

  This episode features Prof. Jens Walter PhD, a microbial ecologist from University College Cork / APC Microbiome Ireland, explaining how he applies ecological and evolutionary frameworks for the purposes of understanding and modulating microbiomes. Although there appears to be a high amount of stochasticity (or randomness) in microbiomes, stochastic and deterministic elements work together to determine outcomes. Priority effects (based on arrival order of a bacterium or other microorganism) are important, with communities likely taking shape through a combination of priority effects and adaptation to the niche. The potential to modulate the microbiome is high in early life, as there are many ecological possibilities. For established microbiomes (for example, in adults), Prof. Walter’s group has found that diet (for example, the “NiMe” diet they developed) is a possible way to modulate the microbial community, although the effect on the overall ecosystem is small. Nevertheless, dietary modulation may have positive and important effects on host health. Episode abbreviations and links: Paper showing how fiber precisely modulates the gut microbiome: Precision Microbiome Modulation with Discrete Dietary Fiber Structures Directs Short-Chain Fatty Acid Production About Prof. Jens Walter PhD: Jens Walter serves as the Professor of Ecology, Food, and the Microbiome at University College Cork and the APC Microbiome Ireland. His expertise lies at the interface of evolutionary ecology of the gut microbiome and human nutrition. His research focuses on the evolutionary and ecological processes that have shaped host-microbiome symbiosis and the translation of basic microbiome science into therapeutic and nutritional strategies. Dr. Walter and his collaborators have pioneered the application of ecological theory to elucidate ecological and nutritional factors that shape gut microbiomes and have achieved targeted modulations of microbiomes via dietary strategies and live microbes. Prof. Walter has published >140 peer-reviewed publications (google scholar H-index 69, >23,000 citations) and is a ‘highly cited researcher’ according to the Web of Science group.

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• Insights from evolutionary ecology on microbiome assembly and modulation,  with Prof. Jens Walter PhD

  This episode features Prof. Jens Walter PhD, a microbial ecologist from University College Cork / APC Microbiome Ireland, explaining how he applies ecological and evolutionary frameworks for the purposes of understanding and modulating microbiomes. Although there appears to be a high amount of stochasticity (or randomness) in microbiomes, stochastic and deterministic elements work together to determine outcomes. Priority effects (based on arrival order of a bacterium or other microorganism) are important, with communities likely taking shape through a combination of priority effects and adaptation to the niche. The potential to modulate the microbiome is high in early life, as there are many ecological possibilities. For established microbiomes (for example, in adults), Prof. Walter’s group has found that diet (for example, the “NiMe” diet they developed) is a possible way to modulate the microbial community, although the effect on the overall ecosystem is small. Nevertheless, dietary modulation may have positive and important effects on host health. Episode abbreviations and links: Paper showing how fiber precisely modulates the gut microbiome: Precision Microbiome Modulation with Discrete Dietary Fiber Structures Directs Short-Chain Fatty Acid Production About Prof. Jens Walter PhD: Jens Walter serves as the Professor of Ecology, Food, and the Microbiome at University College Cork and the APC Microbiome Ireland. His expertise lies at the interface of evolutionary ecology of the gut microbiome and human nutrition. His research focuses on the evolutionary and ecological processes that have shaped host-microbiome symbiosis and the translation of basic microbiome science into therapeutic and nutritional strategies. Dr. Walter and his collaborators have pioneered the application of ecological theory to elucidate ecological and nutritional factors that shape gut microbiomes and have achieved targeted modulations of microbiomes via dietary strategies and live microbes. Prof. Walter has published >140 peer-reviewed publications (google scholar H-index 69, >23,000 citations) and is a ‘highly cited researcher’ according to the Web of Science group.

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• Eco-evolutionary processes and antimicrobial resistance in the urobiome, with Dr. Marjon de Vos PhD

  This episode features Dr. Marjon de Vos PhD from the University of Groningen (the Netherlands) speaking about microbial ecology and evolution, and in particular how these affect antimicrobial resistance. She studies the urobiome as well as the factors that contribute to urinary tract infections and successful treatment of these infections with antibiotics. Her lab combines molecular biology techniques with phenotypic and growth measurements, as well as computational modeling. She has found evidence of microbial interactions mediating evolutionary potential of microorganisms – for example, in vitro experiments showed that in the presence of Enterococcus, E. coli speeds up its rate of developing antimicrobial resistance. Thus, interactions within the bacterial ecosystem may affect pathogens’ sensitivity to antimicrobials. Prebiotics are a potential intervention: if bacteria that make a pathogen more susceptible to antimicrobials are already present in the urobiome, their numbers could be enhanced. Probiotics are another possibility. From a One Health perspective, such approaches are important to explore because they support antimicrobial stewardship and help maintain control of antimicrobials in the environment overall. Episode abbreviations and links: Preprint describing pathogens’ differing rates and evolutionary trajectories towards antibiotic resistance based on other microbes present: Microbial interactions affect the tempo and mode of antibiotic resistance evolution Paper describing ecological interactions between different bacterial species in urinary tract infections: Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections Research showing how 5 different bacteria affect the conjugation efficiency of E. coli: Community context influences the conjugation efficiency of Escherichia coli  About Dr. Marjon de Vos PhD: We investigate ecological and evolutionary processes in microbial communities, with a focus on infectious contexts. Our goal is to unravel the genotype–phenotype–fitness relationships within (evolving) communities and to identify the ecological factors that drive microbial evolution. To achieve this, we combine molecular biology techniques with phenotypic and growth measurements, as well as computational modeling. Our research places special emphasis on the urobiome and urinary tract infections in postmenopausal women, as well as on sepsis. By uncovering the fundamental ecological and evolutionary dynamics of microbial communities in infectious diseases, we aim to contribute to the development of strategies that alleviate infections and help curb the emergence and spread of antibiotic resistance.

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