Scientifically Speaking: More about gut microbes which are linked to good health

On average, people with a healthy weight carried several more favorably ranked species than people struggling with obesity

Scroll through social media and you will be told that your gut is broken and that a capsule can fix it. Probiotics promise balance. Prebiotics promise strength. Influencers promise immunity, clarity, and longevity. The pitch rests on a simple idea that science already knows what a healthy gut microbiome looks like.

This is why India needs its own microbiome map, and we may be getting one soon. (Freepik | Representative file photo)

It does not. At least, not in the way you have been led to believe.

For years, microbiome research leaned on small, scattered studies. A few dozen people here, a few snapshots there. Patterns were teased out, amplified, and sold back as certainty. The gut became a marketing ploy long before it became a mapped system.

That has begun to change. A new study published in Nature has now looked at gut DNA from over 34,000 people in the United States and the United Kingdom. And instead of simple (inaccurate) statements, the researchers have embraced complexity. They evaluated 661 species of gut bacteria based on how consistently they were associated with favorable health markers, including blood sugar, cholesterol, inflammation, and body fat, among many others and created a ranking system.

The result is the ZOE Microbiome Health Ranking 2025. Bacteria near the top of this league table cluster in people with healthier metabolic profiles. Those near the bottom tend to appear in people heading towards trouble.

So what’s the big deal? The first surprise is how little we actually know about the gut microbiome. Of the fifty species most strongly tied to better health, nearly half do not even have names. We only know them as reconstructed genetic signatures. So it seems that many microbes most closely tied to human health are biological dark matter, waiting to be properly studied.

The second surprise is that even good and bad bacteria are closely related. There’s often no way to predict what effect a kind of bacteria will have from its family and type. Instead of broad brushstrokes, each family of bacteria has to be studied at the more precise level of bacterial species. It’s a beautiful reminder that even as there’s a push for applications in science and medicine, basic discoveries are what drive them even today.

Yet, a pattern emerges. For example, on average, people with a healthy weight carried several more favorably ranked species than people struggling with obesity. That might not sound like a lot, but that difference is meaningful.

Many microbiome studies tell you the link and go no further. Not this paper. The researchers turned to clinical intervention to find out what actually works. In two separate trials, they tested different approaches: personalized dietary advice in one, and a prebiotic fiber blend compared with a standard probiotic supplement in another.

Fiber-degrading specialists such as Bifidobacterium adolescentis expanded with prebiotic supplementation. Roseburia hominis, a producer of the anti-inflammatory compound butyrate, increased only when diets were meaningfully improved. The names are not as important to remember as the themes that emerge.

Probiotic supplements taken on their own had little lasting effect on the gut microbiome. On the other hand, diet reshaped the gut ecosystem. Ditch the supplements, to cultivate your gut microbiome you need to engineer your diet.

Overall, the Nature paper is an elegant piece of work in a field filled with incomplete studies that overextend their conclusions. But even this one is incomplete in a way that matters for Indians, and the researchers acknowledge that, to their credit.

Every data point in this ranking comes from Western populations. The microbiome it feeds has been shaped by dietary patterns very different from ours.

Indians eat a lot of carbohydrates, diverse pulses and millets, vegetables, and spices. Some of us are vegetarian. Many of us savor spicy food. These forces in our diets select for different microbial survivors.

This is why India needs its own microbiome map, and we may be getting one soon. Earlier this year, I visited the CSIR-Institute of Genomics and Integrative Biology in New Delhi and learned about Phenome India, a new study pairing deep gut sequencing with detailed clinical data from 10,000 Indians. It’s a large project that mirrors the ZOE effort, but for our biology, our diets, and our risk factors.

That work cannot come soon enough. We need to identify our own microbial dark matter and understand which features of the gut protect us, and which leave us vulnerable.

The microbiome has a history of hype outrunning evidence, and guts are stubborn ecosystems that resist simple fixes. Yet the microbes sharing your meal tonight are shaped by your food habits, local environment, and evolution. Understanding how they link to health is long overdue.

Anirban Mahapatra is a scientist and author, most recently of the popular science book, When The Drugs Don’t Work: The Hidden Pandemic That Could End Medicine. The views expressed are personal.