Gut microbiome expert Dr Noel Mueller explains how early-life microbes impact health, the hidden power of fermented foods, and why Indian diets could unlock new research breakthroughs.
Published May 02, 2025 | 7:00 AM ⚊ Updated May 04, 2025 | 1:31 PM
Dr Noel Mueller, Associate Professor at the University of Colorado.
Synopsis: A diverse plant-based diet, including colourful fruits and vegetables, limiting ultra-processed foods, increasing fluid intake and physical activity, getting adequate sleep, reducing stress and limiting exposure to toxins in water, food, and hygiene products are key for a healthy gut.
In an exclusive conversation with South First, Dr Noel Mueller, Associate Professor at the University of Colorado and a leading researcher in gut microbiome science, speaks about how the gut’s health shapes everything from immunity to infant development.
He was in Bengaluru to deliver a talk on “The Human Microbiome: Fundamentals, Methodologic Challenges, and Examples,” organised by the PHFI Centre for Developmental and Lifecourse Research and the Centre for Cellular and Molecular Platforms (C-CAMP).
He spoke on why India’s dietary diversity presents a unique opportunity for future research. Excerpts from the interview
Q: Your research focuses on the gut microbiome, now the buzzword. What does it mean?
A: The microbiome refers to the microorganisms living in and on our bodies. Specifically, the gut microbiome includes bacteria, archaea, fungi, and sometimes viruses in the gastrointestinal tract — especially the large intestine. These microbes are influenced by what you eat, how well you sleep, your physical activity, and other exposures, and they’re linked to health outcomes like obesity, type 2 diabetes, cardiovascular disease, and several infections. When we talk about the microbiome, we talk about microorganisms living in and on our bodies. That’s the human microbiome specifically with relation to the gut microbiome
Q: You have researched on mother’s gut health during pregnancy and child health. Can you explain the correlation?
A: The microbiome during pregnancy — the gut and vaginal microbiome — are related not only to maternal outcomes… like gestational diabetes, preeclampsia, and preterm birth, but are also linked to the infant’s health.
At the very beginning of life itself the baby is exposed to its first microbes which help educate the immune system — teaching the foetus what is a friendly bacteria and what is a potentially pathogenic one. It also helps train the metabolic system and regulate the mucosal barriers. Those initial microbes can have a long-lasting effect.
One example is Bifidobacterium infantis, a species that breaks down human milk oligosaccharides… These are found abundantly in human milk and can’t be used by infants for energy unless they have specific microbes to break them down… So, having the right microbes is key.
Q: There’s some research linking gut health and autism. Has anything concrete been established?
A: Autism is a complex disorder. It is not my specific area of research. One exposure related to autism is maternal infection during pregnancy — typically a viral infection. Also, the microbes that are shared could play a role. It’s tricky to study autism and the microbiome, because autism is associated with dietary preferences. Children with autism tend to have a less diverse diet, which affects the microbiome. So it’s a chicken-or-egg question: Does the diet shape the microbiome or did the microbiome differences precede autism? But it’s being increasingly recognised as a potential factor and needs more study.
Q: Have you looked at regional food patterns, especially in South India, and their link to rising type 2 diabetes and obesity?
A: Yes, we’ve looked at diet and the microbiome in our studies. One study, relevant to India, used the Plant-Based Dietary Index. We separated it into healthy and unhealthy plant-based indices and looked at their relation to the microbiome.
People with a healthy plant-based diet had more microbial diversity, while those with an unhealthy plant-based diet had lower diversity. This was published in the American Journal of Clinical Nutrition — based on US diets, though. Doing this in an Indian context would be very interesting.
I’ve enjoyed the foods here and they gave me ideas for future research. Also, a recent study showed fermented foods had a stronger effect on microbiome diversity and reducing inflammation than even a high-fibre diet. South Indian diets with idli and dosa — which I had this morning — could be playing a positive role.
Q: You worked with the MAASTHI team with India in 2021 on birth method outcomes. What did you find?
A: In the US we had found babies delivered through C-sections had a higher risk of obesity. We wanted to see if this was also true in India. In the MAASTHI cohort, we found that infants born by elective C-section had a higher risk of overweight and obesity, compared to vaginally delivered infants.
Interestingly, elective C-section babies also had a higher risk of shorter growth, suggesting a link to restricted linear growth or stunting. In India, there’s the dual burden of over- and under-nutrition and whether microbiome disruption via delivery mode plays a role in this remains to be seen.
Q: Can gut microbiomes help personalise diets or medications in the future?
A: Yeah, great question. We call this precision nutrition — the idea that a diet for one person may not work the same for another. Research suggests that your microbiome can predict how you respond to food. Aaron Seagal’s team showed this in 2015.
Your microbial signature might react differently to the same foods as your neighbour’s would. It’s a growing area, and we need more data from populations outside the US and Europe — like India — since microbiomes differ by region. So, context-specific results matter.
Q: With so many gut-health products in the market, what challenges do you see in translating research to consumers?
A: It depends. From a researcher’s point of view, the challenge is communicating findings so the public knows what to trust. If you’re taking a probiotic, look into the specific strains and species and check whether the brand has published clinical research proving health benefits. Some earlier probiotics were based on ease of growing certain strains — not necessarily evidence. Now we’re seeing next-gen probiotics, often anaerobic bacteria, backed by evidence. These are harder to grow but could have more potential for improving health. Keep an eye out for these products.
Q: How does your research connect with long-term Indian studies like MAASTHI and CDLR?
A: We’re now looking at exposures beyond diet — like air pollution — and its association with the microbiome. Air pollution affects epithelial surfaces of the gut. We’re also studying water — comparing well water and city water — and found strong links to microbiome composition. Extending these findings to Indian cohorts like MAASTHI is exciting. I’m also interested in urbanisation — comparing tribal and urban populations to understand how urban lifestyle affects the microbiome.
Q: Have you explored the effects of lifestyle or climate change on gut health?
A: I haven’t specifically looked at the sedentary lifestyle and the microbiome though sedentary lifestyle is linked to poor metabolic health. With climate change — high heat could affect microbial growth. I haven’t studied this directly. It’s a great question, though.
Q: What do you think will be the biggest gut health breakthrough in the next 10 years?
A: We now have 15+ years of sequencing data. The next phase is translating that into meaningful health outcomes. I see three areas: First, therapeutic manipulation — like probiotics, targeted nutrition, or even fecal or vaginal microbiome transplants. Second, screening and diagnosis — using microbiome data to predict future disease risk. Third, precision medicine — predicting how individuals will respond to drugs or diets using their microbiome.
Q: How do you feel about the new Centre for Developmental and Life Course Research at PHFI?
A: I’m very excited. I’m happy to be here for the launch, to collaborate and contribute. I hope to come back and see how it impacts population health in India. It’s an exciting time.
Q: How can someone know if they have a healthy gut? What are 5 indicators or habits?
A: Tough question. It’s hard to put microbiomes into ‘good’ or ‘bad’ buckets. But monitor your body — regular bowel movements, lack of malaise, etc. Beyond that, be proactive: eat a diverse plant-based diet, include colourful fruits and vegetables, limit ultra-processed foods, increase fluid intake and physical activity, get adequate sleep, reduce stress and limit exposure to toxins in water, food, and hygiene products.
(Edited by Majnu Babu).
