The Science, Microbes & Health Podcast

International Scientific Association for Probiotics and Prebiotics (ISAPP)
  • 4.7 (3)
  • Life Sciences
  • Updated Biweekly

This podcast covers emerging topics and challenges in the science of probiotics, prebiotics, synbiotics, postbiotics and fermented foods. This is the podcast of The International Scientific Association for Probiotics and Prebiotic (ISAPP), a nonprofit scientific organization dedicated to advancing the science of these fields.

  1. Sep 24

    Highlights of the HealthFerm initiative, with Prof. Christophe Courtin

    This episode features Prof. Christophe Courtin from KU Leuven (Belgium), speaking about the European HealthFerm initiative. HealthFerm began in September 2022 and brought together multiple institutions and companies to advance the project with a grant of 30 million Euros. The main aim of the project was to improve public acceptance of plant-based foods through fermentation. A citizen science component of the project involved gathering fermented food samples from all over Europe, both home fermenters and small bakeries, to analyze the microorganisms. The researchers received over 650 sourdough starter samples and around 200 other fermented foods samples; from these, they identified some new species that still need to be named. Another part of the project involved a clinical trial on how the body responds if short-chain fatty acids are released in the small intestine versus in the colon. They found that small intestinal release increased GLP-1 levels more than PYY; the opposite happened with colonic release. Another study in the project compared oat to fermented oat, and found that the fermentation changed the fiber (degree of polymerization), and also led to positive health effects. Prof. Courtin says the potential for future research in this area is to find out how to add nutritional benefits through fermentation (for example, vitamin B12 in plant-based foods), as well as how to change the fiber profile in a food to yield specific health benefits. Episode abbreviations and links: Study on properties of a plant-based gurt: Process-induced changes in starch, dietary fiber, and protein in a fermented plant-based dairy alternative (yo)gurt. Paper exploring oat fermentation: Enzyme activity and constituent extractability of kilned and non-kilned oats at pH values relevant for acidic food fermentations. Study on gut microbiota signatures of type 2 diabetes risk: Gut microbiome composition and functional potential associate with incident type 2 diabetes in 4,685 adults from a Swedish prospective cohort About Prof. Christophe Courtin: Prof. Christophe Courtin is a full professor at the Laboratory of Food Chemistry and Biochemistry at KU Leuven, Belgium. His research focuses on cereal constituents, the enzymes that degrade them and microorganisms in cereal processing. The emphasis is on a basic understanding of the structure and properties of these constituents as well as on their technological and health functionality in cereal-based processes and products. Expertise and an extensive network in this area have been built up through over 40 supervised PhDs, projects and national and international collaborations. He coordinates HealthFerm, a 23 partner Horizon Europe project. He is author of 380 peer-reviewed papers (WoS h-index: 74) and inventor on 12 patent families. Recent awards are the Harald Perten Prize (ICC, 2021) and the Belfort Lecture Award (Whistler Centre for Carbohydrate Research, Purdue University, 2023).

  2. Sep 4

    Epidemiological insights on the gut microbiota in colorectal cancer,  with Dr. Mingyang Song ScD

    This episode features Dr. Mingyang Song ScD from Harvard University (USA), speaking about epidemiological evidence connecting the gut microbiota to colorectal cancer (CRC) and whether the evidence supports the gut microbiota as a ‘driver’ or a ‘passenger. Dr. Song explains how he and colleagues studied the gut microbiome in a subset of people from the Nurses’ Health Study. It’s known that adenoma removal reduces CRC risk, but doesn’t eliminate it. Does the gut microbiome contribute to this remaining risk? The researchers found that many years after adenoma removal, individuals had a different gut microbiota compared with healthy controls, indicating that the microbiome profile is not fully restored by adenoma removal. People with past adenoma removal had a gut microbiota that overlapped with that of current CRC patients, with the caveat that lots of heterogeneity was observed. Diet and lifestyle also correlate with both CRC development and gut microbiome composition, with some of the main factors reducing CRC risk being dietary fiber, fruits, vegetables, whole grains, and calcium. These and other healthy lifestyle factors were associated with fewer of the gut microbial members typically seen in CRC. Next, prospective studies are needed to determine whether gut microbiota changes truly precede CRC and independently contribute to risk. This line of research could also lead to a more tailored approach to CRC screening, with risk factors being taken into account. Episode abbreviations and links: Study on a subset of participants in the Nurses’ Health Study, showing those who previously experienced adenoma removal had gut microbial similarities to CRC: Long-lasting gut microbiome and fecal metabolome alterations after colorectal adenoma removal and their relationship to colorectal cancer About Dr. Mingyang Song ScD: Mingyang Song, MBBS, ScD is Associate Professor of Clinical Epidemiology and Nutrition and Faculty Director of Graduate Studies in the Department of Epidemiology at the Harvard T.H. Chan School of Public Health, and Associate Professor of Medicine at Harvard Medical School. His research focuses on two complementary areas: (1) integrating large-scale prospective cohort studies with biomarker-driven clinical trials to develop nutrition- and microbiome-based approaches for cancer prevention and treatment; and (2) combining electronic health records with molecular and spatial profiling to enable precision risk prediction and personalized colonoscopy screening and surveillance. Dr. Song has received numerous honors, including the NextGen Star Award from the American Association for Cancer Research (AACR) and the Young Investigator Award from the American Gastroenterological Association (AGA). He currently serves as the Vice Chair of the Obesity, Metabolism and Nutrition (OMN) Section at AGA, Statistics Associate Editor of Gut, Associate Editor of the Journal of the National Cancer Institute (JNCI), and Editor of the European Journal of Epidemiology.

  3. Aug 20

    Molecular mechanisms of colorectal cancer development, with Prof. Alberto Martin PhD

    This episode features Prof. Alberto Martin from University of Toronto (Canada), speaking about the molecular mechanisms by which certain bacteria – namely, pks+ E. coli – influence colorectal cancer development. pks+ E. coli secretes a toxin that causes DNA damage; likely its purpose is to keep other microorganisms in check, but it appears to have the effect of promoting colorectal cancer. A low-fiber diet starves mucolytic bacteria, reducing the mucus layer in the gut and allowing pks+ E. coli to come into contact with the colonic epithelial cells, where they secrete the toxin that causes DNA damage. Gut inflammation also factors in, because these bacteria thrive in an inflammatory environment. Interestingly, in looking at the geographic distribution of this microorganism in people around the world, its presence correlates with colorectal cancer rates. Prof. Martin’s lab has clinical trials planned to explore this connection, and other groups are looking at therapies to reduce this microorganism in the gut. Episode abbreviations and links: Paper on diet and pks+ E. coli interactions in colorectal cancer development: Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer Paper showing a large proportion of bacterial isolates from IBD patients had DNA-damaging agents: Commensal microbiota from patients with inflammatory bowel disease produce genotoxic metabolites Paper showing correlation of pks+ E. coli in the population and rates of cancer around the world: Geographical variation in the incidence of colorectal cancer and urinary tract cancer is associated with population exposure to colibactin-producing Escherichia coli Paper showing a distinct mutational signature in human cancer genomes, possibly arising from exposure to genotoxic pks+ E. coli: Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli About Prof. Alberto Martin PhD: Dr. Martin is a Professor and Sanofi Pasteur Chair in Human Immunology in the Department of Immunology at the University of Toronto. He completed his B.Sc. degree at McGill University, and his PhD degree in the Department of Immunology at the University of Toronto. He then pursued post-doctoral training at Albert Einstein College of Medicine in New York, U.S.A., with Dr. Matthew Scharff, focusing on characterizing the molecular mechanisms of antibody responses, specifically somatic hypermutation and class switch recombination, which are two processes that are central to the efficient neutralization of pathogens and toxins. In 2003, he was recruited as a faculty member to the Department of Immunology at the University of Toronto. Dr. Martin’s research program is devoted to understanding the role of genes, their interaction with the environment, and their impact on immunity and pathological conditions, including cancer. His main interest is on antibody production, on how high-affinity antibodies are generated, and how antibodies of different classes are produced. Both of these processes are necessary for an efficient antibody response. Dr. Martin is also investigating the role of the gut microbiota in the etiology of colon cancer and has characterizing the role of diet in modulating the cancer causing effects of specific pathobionts. His lab is also investigating the role of a new gene and how it promotes inflammatory bowel disease (IBD). This work highlights the metabolic effects of the skeletal muscle in supporting a metabolically taxing inflammatory process such as IBD.

  4. Aug 7

    Gut microbiome signatures of colorectal cancer, with Dr. Georg Zeller PhD

    This episode features Dr. Georg Zeller PhD from Leiden University Medical Center (the Netherlands), speaking about gut microbiome signatures of colorectal cancer across global populations. An early study Dr. Zeller completed in Peer Bork’s lab suggested that the gut microbiomes of people with colorectal cancer are distinct from controls. This signature, as well as work on the tumor microbiome, all pointed toward Fusobacterium as particularly important. Subsequent studies exploring this idea show wide variation in geography and methods. Accounting for these factors, meta-analyses have confirmed several gut microbiome characteristics that are enriched in colorectal cancer across the global population. Dr. Zeller was interested to see that bile acid metabolism is consistently enriched in the cancer metagenome. The taxonomic profile, however, appears better than the functional profile in distinguishing colorectal cancer from control samples. He emphasizes the importance of linking his insights from bioinformatic efforts to the mechanistic work being done. Initially he was hopeful that a gut microbiome diagnostic could be developed, but currently the highest achievable AUC for the classification models is around 0.85 or 0.9, which may not be adequate for enhancing current clinical tools. The possibility remains for a gut microbiome test to complement existing diagnostics. The most promising area may be targeted gut microbiome modulation for prevention of colorectal cancer, perhaps through diet. His group is also exploring the gut microbiome for early diagnosis of pancreatic cancer, possibly by combining fecal markers with other diagnostic tools. Episode links: Early study in French participants suggesting a gut microbiome signature in colorectal cancer: Potential of fecal microbiota for early-stage detection of colorectal cancer Recent meta-analysis from Zeller’s group; Meta-analysis reveals microbiome signatures for colorectal cancer that are universal across age groups and sequencing methods Tools for a combination of 16S rRNA & shotgun sequencing data and meta-analysis approaches: Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox Paper on the gut microbiota in pancreatic cancer: A faecal microbiota signature with high specificity for pancreatic cancer About Dr. Georg Zeller PhD: Georg Zeller studied Bioinformatics (major in Computer Science) at the Universities of Tübingen (DE) and Uppsala (SE). In 2010 he obtained a PhD from the University of Tübingen (DE) for work performed at the Max Planck Institutes there. Afterwards he joined Peer Bork’s group at EMBL Heidelberg (DE) as a postdoctoral researcher. From 2015 to 2024 he was an independent Team Leader establishing his microbiome research group at EMBL. In 2023 he was appointed as Associated Professor (promoted to full professor in 2025) in the newly formed Leiden University Center for Infectious Diseases (LUCID) at the Leiden University Medical Center (LUMC, NL) to head the Microbiome Systems Biology group. His research is aimed at gaining a better understanding of how the microbiome contributes to human health, disease progression and treatment success, and how it is shaped by host factors such as nutrition and pharmaceutical drugs. To address these questions, his group develops computational, statistical and experimental methods for clinical microbiome studies. His long-term goal is to harness fundamental knowledge on the human microbiome and its interactions with the host for the rational design of microbiome-targeted interventions for prevention and (co-)treatment of disease.

  5. Jul 25

    Biofilms and specific bacteria in colorectal cancer development, with Prof. Cynthia L. Sears, MD

    This episode features Prof. Cynthia L. Sears, MD from the Johns Hopkins University School of Medicine and the Bloomberg School of Public Health (USA), speaking about both biofilms and specific gut microorganisms that may contribute to colorectal cancer development. Initially, Prof. Sears became interested in enterotoxigenic Bacteroides fragilis in connection with colon cancer. Further investigation found complex biofilms with multiple bacteria fixed to the surface of the tumor. The biofilms were shown to be oncogenic, and they reassembled very quickly after antibiotic treatment. Interestingly, the biofilms were found to have C. difficile. A subset of the biofilms have a dominant amount of Fusobacterium, and the latest work shows that these bacteria are associated with advancing cancer, stage 2 or beyond. These bacteria and/or biofilms don’t necessarily trigger the onset of mutations that lead to colon cancer, but they accelerate tumor growth. Over time, the gut microbiota may be perturbed in various ways (including by antibiotics), allowing the organisms to create a niche for themselves that ultimately harms the colonic epithelial cells. Prof. Sears is optimistic about prevention strategies for colorectal cancer, such as a tool that helps predict risk in younger populations. Targeted prebiotics, too, show promise for encouraging the growth of beneficial bacteria that prevent the oncogenic species from finding a niche. Episode abbreviations and links: 2014 review by Sears and Garrett on the role of microbes in colon cancer: Microbes, Microbiota, and Colon Cancer One of the landmark 2012 papers linking Fusobacterium nucleatum to colorectal cancer: Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma Examination of biofilms on colon cancer polyps: Epidemiology of bacterial biofilms on polyps and normal tissues in a screening colonoscopy cohort Association of Fusobacterium with advancing (stage 2) colorectal cancer: Tumor-Associated Fusobacterium nucleatum and Aggressive Architectural Features in Stage II Colorectal Cancer Paper showing genotoxic microbes increasing colon tumor burden: Combining genotoxic gut bacterial strains increases tumor burden and accelerates onset in a germ-free mouse model of colon carcinogenesis About Prof. Cynthia L. Sears, MD: Cynthia L. Sears, M.D. is Professor of Medicine, Oncology and Molecular Microbiology and Immunology at the Johns Hopkins University School of Medicine and the Bloomberg School of Public Health. Through her work as an infectious diseases specialist, she studies how bacteria and the microbiome impact gut diseases, particularly human colon cancer. She has long been an active member of the Infectious Diseases Society of America (IDSA), serving as President of IDSA in 2019, is an AAAS Fellow and is currently Editor-in-Chief of The Journal of Infectious Diseases, the flagship journal of the IDSA.

  6. Jul 7

    The early life gut microbiota in the developmental origins of health & disease, with Dr. Anne Salonen PhD

    This episode features Dr. Anne Salonen PhD from University of Helsinki (Finland) speaking about her studies on the gut microbiota in early life and how it relates to health and disease. She noted that while mode of delivery (C-section or vaginal birth) is the largest factor affecting microbiota composition for the first weeks and months of life, the immunological and functional microbiota consequences of this are still unknown. However, there appear to be ‘windows of opportunity’ in which microorganisms can influence the development of the immune system, which have lasting consequences for health. Dr. Salonen describes her Finnish HELMi birth cohort, a longitudinal, prospective general population birth cohort, set up to identify factors that modify the gut microbiota and how they relate to child health and wellbeing. Children from 1055 families were sampled frequently in the first 2 years of life and followed as they grew older. The findings confirmed that early-life microbiota composition was a risk factor (among others) for certain diseases as the children developed. Prof. Salonen also described her study on inoculating the infant gut with maternal gut microbiota via milk feeding after C-section birth. They found, in an initial small study, that the gut microbiota of the infants became similar to vaginally born infants. She sees this type of inoculation as a research tool, and says the field will progress toward standardized, reproducible interventions in this area. Episode abbreviations and links: Nature Communications paper showing gut microbiota wellbeing index: Gut microbiota wellbeing index predicts overall health in a cohort of 1000 infants Paper on HELMi birth cohort showing factors affecting gut microbiota in early life: Sources of gut microbiota variation in a large longitudinal Finnish infant cohort Study of maternal fecal microbiota transplantation in infants born by C-section: Maternal Fecal Microbiota Transplantation in Cesarean-Born Infants Rapidly Restores Normal Gut Microbial Development: A Proof-of-Concept Study. Microbes inside (Salonen lab website) About Dr. Anne Salonen: Dr. Anne Salonen is a principal investigator and director of the Human Microbiome Research Program at the Medical Faculty, University of Helsinki. Her research is focused on the intestinal microbiota in health and disease, especially in early life and in relation to diet. Dr. Salonen is a PI of the Finnish Health and Early Life Microbiota (HELMI) birth cohort and involved in maternal fecal microbiota transplantation studies in C-section infants. She is the coordinator of the European Innovation Council Pathfinder project on gut microbiota in precision nutrition (fibrematch.eu). Dr. Salonen’s research also entails female reproductive tract microbiota in relation to reproductive outcomes and Human Papilloma Virus (HPV) infection. Research methodology in Salonen laboratory ranges from NGS and other omics technologies to culture-based microbiology of anaerobes, including application and development of bioinformatic tools for microbiome research. More on our research at https://www.helsinki.fi/en/researchgroups/microbes-inside.

  7. Jun 18

    Factors affecting infant gut microbiota development, with Prof. Christopher Stewart PhD

    This episode features Prof. Christopher Stewart PhD from Newcastle University (UK), speaking about the factors affecting gut microbiota development in both non-preterm and preterm infants. Prof. Stewart started in the field of environmental microbial ecology and then came to work in human microbiome research. He was involved in the landmark TEDDY study, which aimed to find gut microbial markers of type 1 diabetes (T1D). Although no microbial triggers of T1D were identified, the study found a number of factors that impact gut microbiome development: for example, sex, geographical location, and living with furry animals. Still, most of the variation seen in the infant gut microbiota remains unaccounted for. He noted that infants are exposed to both vaginal and gastrointestinal microorganisms during vaginal birth. In C-section-born infants, seeding of the maternal vaginal and gut microbiota may be promising, but current methods are imprecise and safety has not been established. Furthermore, diet takes over as a primary driver of gut microbiota a few weeks after birth. Prof. Stewart talked about human milk oligosaccharides (HMOs), well known to be utilized by bifidobacteria in the infant gut. His lab recently published the surprising finding that Clostridium species can also utilize HMOs – and while at first this was thought to be detrimental for the infant, further investigation showed that the HMO-utilizing Clostridium may lack the genes for producing specific toxins and end up being protective for the infant gut. Together, the microbial community in the gut may use the full suite of HMO substrates reaching the infant gut. Preterm infants are a population that needs more attention. Antibiotics affect their gut microbiomes – often in a negative way, but for the overall benefit of the baby. His lab is currently funded to study how probiotics affect the preterm infant gut microbiota, and to find strategies for more personalized approaches to administering probiotics in this population. Episode abbreviations and links: TEDDY study, revealing factors affecting gut microbiota development between 3 and 46 months of age: Temporal development of the gut microbiome in early childhood from the TEDDY study Study on how Clostridium species utilize HMOs: Clostridia from preterm infants metabolize human milk oligosaccharides to suppress pathobionts and modulate intestinal function in organoids Study on how NEC risk is linked with HMOs: Human milk oligosaccharide DSLNT and gut microbiome in preterm infants predicts necrotising enterocolitis  Publication on how probiotics impact the gut microbiota in preterm infants: Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants Some similar results have come from the CHILD Cohort Study, described here Find Prof. Stewart on LinkedIn, and learn more about his research on this website About Prof. Christopher Stewart: Professor Christopher Stewart is an internationally recognised leader in human microbiome research. He earned his PhD in Microbial Ecology from Northumbria University (UK), followed by postdoctoral training at Baylor College of Medicine (Houston, Texas), before establishing his research group at Newcastle University in 2018. His pioneering work focuses on microbial-host interactions in the gut, particularly in infants born extremely premature (32 weeks gestation). His lab integrates multi-omic analyses of clinical samples with experimental microbiology and organoid co-culture systems to uncover mechanisms of microbial influence on early-life development. More recently, he has expanded his research to support a UK-wide initiative investigating microbiome-based predictors of therapeutic response in adult inflammatory bowel disease. Professor Stewart has published over 140 peer-reviewed articles in leading journals, contributing to the discovery of novel biomarkers and targeted microbiome-based interventions. He has received numerous prestigious awards, including the Blavatnik Award for Life Sciences Laureate, the Lister Institute Research Prize, the Microbiology Society Fleming Prize, the NOSTER & Science Microbiome Finalist Prize, the Applied Microbiology International WH Pierce Prize, and the Neonatal Society Rising Star Award.  His research has broad implications for understanding diet–microbe–host interactions and improving health across the life course, miology, maternal and child health, and microbiome science, with a particular emphasis on the effects of vaginal microbiota transfer (VMT) on the microbiota composition and health outcomes of cesarean-delivered infants.

  8. May 26

    A mechanism linking the newborn skin microbiota to neurodevelopment, with Prof. Rihua Xie and Dr. Yuhang Zhang

    This episode features Prof. Rihua Xie from Guangdong Medical University (China) and Dr. Yuhang Zhang from Peking University First Hospital (China), speaking about vaginal microbiota transfer (VMT) and how it may affect neurodevelopment in newborn infants born by Cesarean section. Compared with vaginally delivered infants, C-section delivered infants have altered microbial exposures. VMT has been proposed as a way to ‘restore’ the microbiota of these infants to more closely resemble that of vaginally-born infants. A recent study by Prof. Xie and Dr. Zhang showed that the order and timing of early microbial colonization of the infant is important. They found that VMT could establish a vaginal-like skin microbiota in infants born by C-section, with two particular bacterial species that were higher after VMT. These two species led to the production of metabolites that combined on the newborn’s skin to synthesize an important lipid, which was positively correlated with neurodevelopment scores at three and six months. Subsequent mouse model work showed how this lipid could reach the brain. In the future, safety and standardization of VMT will be important priorities in this research area. Prof. Xie and Dr. Zhang emphasized that their work needs to be replicated in larger cohorts, with the eventual goal of engineering bacteria to create a probiotic intervention that delivers neurodevelopmental benefits to C-section born infants. Episode abbreviations and links: The research by Prof. Xie and Dr. Zhang demonstrating how a VMT intervention alters the skin microbiota of newborns, with a mechanistic link to neurodevelopment: Vaginal microbiota transfer ameliorates cesarean-associated neurodevelopmental deficits in mice via N-bc2S1P synthesis on neonatal skin About Prof. Rihua Xie: Dr. Ri-hua Xie (RN, PhD, FAAN) is Professor, Principal Investigator, and Chief Nurse at the School of Nursing, Southern Medical University, and the Affiliated Foshan Women and Children Hospital, Guangdong Medical University, China. Dr. Xie is widely recognized for her expertise in maternal and infant health as a clinician, researcher, and supervisor. She has published more than 90 peer-reviewed papers and 11 nursing textbooks and has received 12 competitive research grants from institutions in China and Canada. In addition to her academic work, Dr. Xie is actively engaged in community and public health service, including breastfeeding promotion and frontline support during the COVID-19 pandemic. Her research focuses on perinatal epidemiology, maternal and child health, and microbiome science, with a particular emphasis on the effects of vaginal microbiota transfer (VMT) on the microbiota composition and health outcomes of cesarean-delivered infants. About Dr. Yuhang Zhang: Yuhang Zhang, PhD in Pharmacology, is an Associate Professor and Principal Investigator at Peking University First Hospital. He received his MD-PhD from Capital Medical University and was a visiting scholar at McGill University, Canada. Dr. Zhang’s research focuses on gut microbiome, probiotics, and microbial metabolism in metabolic diseases, who has published over 20 peer‑reviewed papers as first or corresponding author in journals including Gastroenterology, Journal of Hepatology, and Nature Communications, cited >1,000 times. He has led 9 grants, including the National Natural Science Foundation of China, who was selected for the Beijing Association for Science and Technology Young Talent Program (2022) and the China Association for Science and Technology Young Talent Program (2025). The research of Dr. Zhang focuses on the integrated systems pharmacology, multiomics and microbiome‑host interactions to develop precision medicine.

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This podcast covers emerging topics and challenges in the science of probiotics, prebiotics, synbiotics, postbiotics and fermented foods. This is the podcast of The International Scientific Association for Probiotics and Prebiotic (ISAPP), a nonprofit scientific organization dedicated to advancing the science of these fields.

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