All-important microbiomes

We are living with trillions of microorganisms — bacteria, viruses, fungi and other life forms living in and on us — which are collectively known as a microbiome. The ecological health of the vast numbers of microbiomes strongly controls many facets of human health ranging from chronic inflammation to weight gain. Various organs have distinct microbial inhabitants, but the group that has attracted the most attention in biomedical research is the one in the gut. The intestinal microbiome is a delicate ecosystem made up of billions and billions of microorganisms, bacteria in particular, that support our immune system, protect us from viruses and pathogens, and help us absorb nutrients and produce energy. Even after birth, the immune system matures via interactions with microbes in the gut.

Unfortunately, the processed food had a huge impact on its content according to the study of the genome of intestinal microorganisms of over 6,500 individuals from all continents. There is a connection between the microbiome's bacterial content and the increase in obesity, inflammation, autoimmune and gastrointestinal diseases, allergies and other complex conditions. Scientists have grown and catalogued more than 130 bacteria from the human intestine. Imbalances in our gut microbiome cause these complex conditions. Now, at the time of emergence of many diseases, particularly COVID-19, there is an urgent need to better understand how our environment and behaviour can improve human health by shaping healthier microbiomes.

Considering the above, it is pertinent to mention that COVID-19 is primarily a respiratory illness but there is mounting evidence of alteration of gut microbiome composition in patients with COVID-19 compared with non-COVID-19 individuals irrespective of whether patients had received medication. Several gut commensals with known immunomodulatory potential such as faecalibacterium prausnitzii, eubacterium rectale and bifidobacteria were under-represented in patients and remained low in samples collected up to 30 days after disease resolution. Moreover, this perturbed composition exhibited stratification with disease severity concordant with elevated concentrations of inflammatory cytokines and blood markers of tissue damage. Thereby, the gut microbiome is involved in the magnitude of COVID-19 severity, possibly via modulating host immune responses. Furthermore, the dysbiotic gut microbiota composition in patients with COVID-19 persists even after the clearance of the virus.

The differences between western and non-western or prehistoric microbiomes lie in the decrease of some types of bacteria that process complex and vegetal fibres in the intestine on account of the westernisation process. Changes in diet with high fat and low fibre, a sedentary lifestyle in an urban setting and the development of new hygiene habits have brought more comfort to human life. Also, the widespread use of antibiotics and other medical products have, with no doubt, made our lives safer, but impacted the delicate balance of our microbiome. In addition to the change of human behaviour, chronic exposure to some environmental chemicals can impact the gut microbiome. Scientists clearly observed alteration in the composition and function of the microbiome due to perfluorooctanesulfonic acid (PFOS). The US Environmental Protection Agency designated PFOS a "contaminant of emerging concern" and its production was voluntarily ceased in the United States by producers, it is still detected in the blood of up to 99 per cent of the U.S. population.

Similarly, glyphosate was thought to be safe to use but they have a strong impact on bacterial species in the human microbiome and perturbations in the human gut microbiome are connected to many diseases. Therefore, the widespread use of glyphosate may have a strong effect on gut microbiomes as well as on human health. This chemical and perhaps related chemicals have mechanisms of action outside our own cells. In this view, exploring how chemicals impact the microbiome is an important and emerging area of study.

Also, cooking food fundamentally alters the microbiomes of humans because cooking alters the nutrients and other bioactive compounds in both meat and tubers. Raw versus cooked meat had no discernible effect on the animals' gut microbes. In contrast, raw and cooked sweet potatoes significantly altered the composition of the animals' microbiomes, as well as microbes' patterns of gene activity and the biologically crucial metabolic products they produced. Cooked food allows the host to soak up more calories in the small intestine, leaving less for hungry microbes further down the gut; on the other hand, many raw foods contain potent antimicrobial compounds that appear to directly damage certain microbes. But still, no one had studied the fundamental question of how cooking itself alters the composition of the microbial ecosystems in our guts.

Prevotella copri — a microbe — is usually found in our intestine and is present in 30 per cent of western individuals. Most importantly, it is not a monotypic species but is composed of four distinct but similar clades. At least three of these four clades are almost always present in non-westernised populations but are much less prevalent in westernised individuals. The critical process of westernisation had a considerable impact on the gradual disappearance of this bacterium. Presence of the four clades in fossilised stool samples from Mexico, that are more than one thousand years old revealed the disappearance of microbes in the gut intestine. This may be attributed to the change of lifestyle of human beings. However, we still do not know what are the biomedical consequences of these changes of the microbiomes which have evolved considerably in recent decades while the human body it colonises has remained genetically and practically unchanged for centuries. The relation between the evolution of the human species and the diversity of intestinal microorganisms is still rather unexplored but can yield important results in the future.

Considering the disappearance of gut microbes on account of diet change, scientists are pushing to restore human health in western countries by changing the diet to restore the microbes in the gut intestine. It is reported that the gut microbiome of healthy Indians is different from those of healthy people from China, the US, and Denmark. The western diet is high in fat and protein, whereas the Indian diet is high in carbohydrates and fibre. Hence, there are

different sets of microbiota determining the functioning of the western and Indian gut. This difference may be compared to the difference between flora and fauna in different ecosystems. Similarly, the gut microbiota is easily influenced by diet, environment and genetics. However, there is no scientific evidence to suggest that western probiotic-rich foods will not work as well for the Indian gut or vice versa. But it will take longer for the stomach to adjust to an unfamiliar foodstuff well enough for it.

Now, there is an emergent need to eat more whole-grain wheat, oats, millets and bajra for fibre; green vegetables like kale, spinach, and broccoli; a bowl of curd or a glass of buttermilk every day, and/or 'haldi doodh' (hot milk with turmeric) to maintain the ecological health of the gut microbiome. In addition, adding spices like coriander, cumin, fennel seeds, ginger and garlic to soups and gravies will also boost gut health. Traditional fermented foods like idlis, dosas, and dhoklas are rich in probiotics — living microorganisms that help restore gut flora. Most importantly, we must minimise the consumption of processed food if we are really concerned about promoting microbiome growth of microbiomes in the gut intestine.

The writer is a former Senior Scientist, Central Pollution Control Board. Views expressed are personal