The Science, Microbes & Health Podcast

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.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

This episode features Dr. Marie-Claire Arrieta PhD from the University of Calgary (Canada), speaking about development of the early life gut microbiome, both in preterm and non-preterm infants. Across the field, it has been established that the early days and months of an infant’s life are very determinant of immune system development as well as chronic disease later in life. In this period, environmental cues are important, with some of these cues coming from the gut microbiome – both bacteria and fungi. Preterm infants show a very different gut microbiome than non-preterm infants. Ample evidence shows probiotics given to preterm infants can bring clinical benefits such as a reduced risk of necrotizing enterocolitis, but this is separate from investigations into the infants’ gut microbiomes. Dr. Arrieta’s work has shown that probiotics can guide the gut ecosystem of preterm infants toward approximating the non-preterm gut microbiome. One gap in the research is to know more about the effects of specific strains; their work found that although bifidobacteria were more effective at colonizing in the gut, lactobacilli drove some aspects of microbiota maturation. Dr. Arrieta speculates that the case for probiotic use for preterm infants will become stronger as trials increasingly focus on health outcomes not just during the neonatal intensive care unit stay, but also later in life. The CHILD Cohort Study has found that overall in healthy infants, different patterns of gut microbiome and immune development can lead to the appearance of diseases later in life. The latest insight is that disease is linked not to specific microbes or metabolites, but to the pace of gut microbiome development. Misalignment of gut microbiome development (too early or too late) with stages of immune development is associated with later emergence of allergic disease. Several factors such as C-section birth and antibiotics may contribute to this misalignment, but breastfeeding seems to mitigate it. Dr. Arrieta has an ongoing longitudinal study on the early life microbiota and disease associations in preterm and non-preterm infants that is likely to reveal more details.

Dr. Marie-Claire Arrieta is a Professor and Research Excellence Chair at the Cumming School of Medicine, University of Calgary. Her research examines interactions between the early-life gut microbiome and infant development. Her program integrates clinical and experimental approaches to uncover mechanisms of host–microbiome communication. Her work, published in leading journals, has accumulated over 12,000 citations. She has presented her research internationally through more than 120 invited talks to scientific, medical and public audiences. A dedicated mentor, she has supervised over 45 undergraduate, medical, PhD, and postdoctoral trainees. Her contributions have been recognized with the CIHR-SickKids New Investigator Award, the Killam Emerging Research Leader Award, and election to the College of New Scholars of the Royal Society of Canada. Dr. Arrieta is co-author of the best-selling public book, Let Them Eat Dirt, and is involved in several science communication initiatives.

This episode features Prof. Hariom Yadav PhD, from the University of South Florida (USA), speaking about the skin microbiome and potential interventions for anti-aging and wound healing. Prof. Yadav noted that humans have a stable (core) microbiome on the surface of skin cells, plus a transient microbiome that depends on recent exposures. The skin microbiome constantly changes through the lifespan, and in aging, many skin conditions are correlated with the microbiome. Animal studies show a causal component of the microbiome in some of these conditions. However, because of the large skin microbiome differences from person to person and in narrow age groups, technologies or products may have to be designed in a personalized way. Prof. Yadav’s lab conducted experiments with lactobacilli and found strain-dependent effects of probiotics on anti-aging, and for some strains these effects persisted when the inactivated bacteria (postbiotics) were used. The postbiotics have commercial advantages over probiotics in this area of health. Prof. Yadav described an application in wound healing, building on the idea that microbial stimulation promotes natural skin cell growth and more fibroblasts. A standard treatment for wound healing is effective but may lead to scarring; the postbiotic treatment leaves less scarring. The efficacy of the postbiotic occurs because inactivated bacteria still give growth-promoting signals to the skin cells. Applying metabolites directly may not be as effective because bacterial cells or extracts work on host cells, which changes the skin environment and further supports positive skin microbiome changes.

Episode abbreviations and links:

About Prof. Hariom Yadav PhD:

Dr. Hariom Yadav is a Professor at the University of South Florida and Director of the USF Center for Microbiome Research, and co-founder of Postbiotics Inc (www.postbioticsinc.com) and MusB Research (www.musbhealth.com). With over 25 years of experience, he specializes in microbiome science, biotics, nutrition, longevity, and natural products for optimal wellness. He has authored 200+ peer-reviewed publications, holds/filed 7 patents, mentored over 80 scientists, and has successfully translated multiple innovations into commercially viable products.

Dr. Yadav works closely with industry partners to accelerate product development—from discovery and mechanistic validation to clinical trials and regulatory readiness. He leads global collaborative efforts, including the MELLOW (Multi-continental Evidence of Longevity and Lifestyle for Optimal Wellness) consortium, a unique platform for scalable, multi-region clinical validation. His integrated approach enables companies to build scientifically robust, market-ready products with strong differentiation and credibility. He is committed to moving science from bench to market, delivering measurable health impact and commercial success.