Mount Abu (Rajasthan): Processed food, an overly sanitised environment and an urban lifestyle can reduce beneficial bacteria in your gut, which primes the body against India’s epidemic of lifestyle diseases, according to Vineet Ahuja, gastroenterology professor at the All India Institute of Medical Sciences, and co-author of new paper that finds rural India with the healthiest guts.

Rural Indians living in low altitudes have healthier guts than urban Indians living in their vicinity and rural Indians living at high altitudes, according to the study by Indian and British scientists, published in the journal Nature Scientific Reports.

A healthy gut boosts the immune system, performs a host of essential body functions--such as synthesise enzymes and vitamins, repress the virulence of disease-causing bacteria and reduce the toxicity of foreign chemical substances in the body--and up to 90% of the diverse bacteria it hosts are protective.

The scientists studied three groups of healthy individuals, from rural and urban Ballabhgarh in Haryana and rural Leh, which was chosen as a study site because it is an “insular region”, away from the influence of urbanisation that has impacted diets, lifestyles and disease profiles in the rest of the country.

“We wanted to test who would come first among equals,” Ahuja, 52, told IndiaSpend.

Overall, the guts of these groups were dominated by good bacteria called firmicutes (62%) and bacteroidetes (24%), with smaller quantities of bad bacteria called actinobacteria (5.2%) and proteobacteria (4.2%). However, the researchers found significant differences in the gut microbiomes of these groups, which they attributed to topographical location and diet.

“Topography encompasses both geography as well as ethnicity,” explained Ahuja, an avid high-altitude trekker.

Rural dwellers with the healthiest guts lived adjacent to the urban population with the least healthy guts, suggesting that physical environment, diet and lifestyle play a significant role in maintaining a healthy gut microbiome.

This finding is significant because research over the last decade has led to a greater understanding of the role of gut flora in causing disease. “We now know that gut flora can affect every part of the body, not just the intestine, but may be contributing to pathogenesis or development of chronic diseases such as diabetes, coronary artery disease and even neurological disorders,” said Ahuja.

Diabetes is India’s fastest growing disease according to the 2016 Global Burden of Disease Report, as IndiaSpend reported in September 2017. India currently represents 49% of the world’s diabetes burden, with an estimated 72 million cases in 2017.

Heart disease is the leading cause of death in India, killing 1.7 million Indians in 2016, according to the same source.

“We hope that this understanding will encourage healthier dietary and lifestyle choices,” said Ahuja. “Ancient wisdom suggested that all diseases start in the stomach. We never fully accepted that, however the gut microbiome studies are certainly suggestive of the idea that most diseases have a link with a change in microbes calling the gut their habitat.”

Ahuja’s interview to us:

Your study notes the transition from infectious to non-infectious diseases. What role do gut bacteria play in this change in disease epidemiology?

Typically, the onset of a non-communicable disease can be traced to a genetic predisposition, an aberrant immune response and the physical environment, which includes diet and lifestyles. The quality of your gut microbiome depends on the food you eat and the physical environment you live in. Processed food is not conducive to the proliferation of good bacteria in the gut nor is living in a highly sanitised environment. Gut bacteria plays a key role in maintaining a healthy immune system. Our finding that rural dwellers of Ballabhgarh living adjacent to their urban counterparts have significantly healthier guts suggests the impact of physical environment as well as dietary habits is huge. In India, the increasing adoption of a Western diet and the change in lifestyle associated with urbanisation is a major factor for changes in the gut microbiome and the subsequent rise of non-communicable diseases.

How does food impact gut flora? What do your study findings tell us about an ideal diet? Is any kind of diet better from the perspective of maintaining a healthy gut microbiome?

Different sorts of food encourage the growth of different strain of microbes. To cite an example from our study: Individuals in Leh abstain from eating dairy and, correspondingly, we found their gut microbiome lacked pseudomonas, a bad bacteria associated with dairy products.

We found some association between the individual’s choice of cooking oil and gut flora. Roseburia, a kind of protective bacteria, had the highest abundance in individuals consuming sunflower oil. To link this with my explanation that a certain kind of food encourages the growth of certain bacteria, species belonging to roseburia have been shown to have the ability to breakdown poly-unsaturated fatty acids (PUFA), especially linoleic acids, in our gut microbiome. We found collinsella to be specifically abundant in the gut microbiome of individuals consuming ghee. Interestingly, collinsella has been previously linked with high serum cholesterol and with symptomatic atherosclerosis. In our study, sunflower oil was the predominant cooking medium choice of the Leh population, while the Ballabhgarh individuals preferred mustard oil, soya bean oil and ghee (clarified butter).

We did not find any adverse effect of a non-vegetarian diet on gut flora. In fact, we found a higher abundance of the protective prevotella bacteria in individuals with a non-vegetarian diet. This was interesting, as prevotella have traditionally been shown to be associated with individuals having a fibre-rich vegetarian diet.

The subjects from Leh were also observed to have the least abundance of bad bacteria called proteobacteria, and a significantly high abundance of good bacteria such as faecalibacterium and lachnospiraceae that perform anti-inflammatory functions.

As a general rule, processed food is not conducive to the proliferation of good bacteria in the gut. Urbanisation and a Western diet have been incriminated for the rise in autoimmune disorders and inflammatory disorders in Indian cities. A vegetarian diet is believed to introduce the friendly-bacteria firmicutes.

Having said that, I must add ours was a small study with a sample size of 84. We need bigger studies to understand the association between diet and gut flora.

That gram-positive bacteria (firmicutes) are the most abundant in the Indian gut is a major finding of this study, according to co-corresponding author Dr Bhabatosh Das of the Translational Health Science and Technology Institute, Faridabad, a collaborating institute. In the Western gut, the most abundant bacteria are bacteroidetes.

Why does a change in gut microbiome predispose humans to diseases? What sort of diseases can gut microbiome cause?

Medical research in the last decade has expanded our understanding of the composition of the human body. We now know that the body is a superorganism, for every one human cell we are composed of nine bacterial cells which live in the gut. This new thinking is changing how we look at the association between gut microbiome and disease. The gut microbiome used to be thought capable of causing diseases of the gut or intestine but now we know that it may be related to the pathogenesis of diseases seemingly unrelated to the gut such as multiple sclerosis (a neurological disease) or diabetes (a disorder of the endocrine system).

Of course the sort of disease that gut bacteria causes will depend on whether the dysbiosis, meaning microbial imbalance, is acute or chronic. An abrupt change in gut bacteria can potentiate an acute disease such as diarrhoea. However, chronic dysbiosis can predispose a person to non-communicable diseases such as malnourishment, inflammatory bowel disease, fatty liver, obesity, metabolic and neuronal diseases, colorectal cancer, coronary heart disease, rheumatoid arthritis and autoimmune and psychiatric disorders.

You found the highest microbial diversity in the rural community residing in sea-level Ballabhgarh. Why is microbial diversity essential? You also found the intra-cohort variation within the gut microbiome was the lowest in the Leh population. What does this tell us?

Gut bacteria don’t just help digest food. They synthesise enzymes, vitamins, neurotransmitters and other metabolites such as folic acid and short chain fatty acids, which our body is not encoded to produce, but which are vital for health and boost immunity. Microbiomes metabolise bile salts, repress the virulence of intestinal pathogens (disease-causing bacteria) and reduce the toxicity of foreign chemical substances in the body. And they do a lot more. The thing is: different families of gut bacteria perform different functions. So the ideal condition is to have highly diverse gut bacteria and a rich gene pool so that no essential function performed by microbiomes is left out.

The high homogeneity in the gut microbiome of our sample in Leh shows that fewer people have migrated to that place. Members of one family (or a highly insular community) tend to have similar gut environments. Migration introduces new gut microbiomes to a community. Incidentally, Leh was chosen as a study site for this very reason. It has been insulated from autoimmune disorders as well as inflammatory immune disorders which are affecting more people in India’s major cities.

Faecal microbiota transplant is a relatively new treatment for inflammatory bowel disease, whereby the whole gut environment is introduced in the gut of a diseased patient to help him or her regain a healthy gut flora. As such, it is different from administering probiotics, or only good bacteria. The transplant process involves mixing faecal matter from a donor with a saline solution, straining it, and placing it in the patient by colonoscopy, endoscopy, sigmoidoscopy or enema. In Western countries, faecal microbiota transplant has emerged as the standard of care for patients with recurrent clostridium difficile infection and is emerging as a novel therapy for these patients. What might be the impact of your findings on the way this transplant procedure is performed in India?

Infection with clostridium difficile bacteria is still relatively uncommon in India but looking at the speed at which lifestyles are changing, its incidence is bound to rise. Incidentally, Inflammatory Bowel Disease is fairly common in India and the country probably has amongst the highest disease burden in the world if we judge by absolute number of patients. We started offering faecal microbiota transplant in 2013 and at present, perform it on about one in 10 inflammatory bowel disease patients who do not respond to conventional therapies. Despite the unaesthetic appeal of faecal microbiome transplantation, surprisingly, our patients have been fairly accepting of it. When we started out, we used to harvest gut microbiome from the patient’s spouse or a close relative. Gradually we discovered that their gut microbiome was usually too similar to that of the patient, and hence impeded the success of the treatment. So we switched to using an unrelated, screened, anonymous donor. Our study findings tell us who would make the best donors for this treatment--healthy adults from rural India.

(Bahri is a freelance writer and editor based in Mount Abu, Rajasthan.)

We welcome feedback. Please write to We reserve the right to edit responses for language and grammar.