The gut microbiome, a complex system of trillions of microorganisms, plays a crucial role in human health beyond digestion.
Modern food systems, particularly ultra-processed foods, disrupt this balance, leading to health issues.
Food systems must prioritise diversity, reduce chemical use, focus on sustainable practices that support gut health.
New research on gut microbiome is uncovering how the chemicals in food are connected to human health. The bacteria-dominant gut microbiome plays a bigger role than digestion; it is a multi-organ system which can disrupt metabolism, immunity and hormonal response if imbalanced.
Food is a key influencer of the gut microbiome health. In addition to chemicals, its the diversity, fibre content and pathogens play a big role. For example, chemicals used in production, processing or storage (such as pesticides and fertilisers, antibiotics or preservatives), contamination due to heavy metals and bacterial pathogens in food and water.
The gut or the gastrointestinal tract is home to a staggering microbial community (microbiota) composed of trillions of bacteria, fungi, viruses and archaea.
Dominated by bacterial cells (~38 trillion), this microbial population exists in a nearly 1:1 ratio with our own human cells. Gut microbiome encompasses a larger entity, including microbiota, genetic elements and metabolites.
The microbiome is said to weigh about 1-2 kg — almost same as the human brain — and contains 2-20 million bacterial genes, much higher than the 20,000 genes in human genome. It is because of this high genetic diversity, that the gut microbiome is able to perform functions which otherwise human body cannot.
About 2,000 different bacterial species have been reported, most of it populating the colon. Some 90 per cent of these are good bacteria such as Bacteriodetes sp and Firmicutes sp. The gut microbiome of an individual is unique much like fingerprints.
Multiple factors influence gut microbiome’s diversity such as birth and infancy, food and diet, exposure to antibiotics, habitat, lifestyle factors, ethnicity and culture.
When the delicate balance between ‘good’ and ‘bad’ bacteria is lost — a condition called dysbiosis — the protective gut barrier can fail, leading to a ‘leaky gut’ that can lead to systemic inflammation impacting multiple organs.
The gut microbiome perform functions beyond digestion. It acts as a metabolic hub, synthesizing essential vitamins (e.g., vitamin K, certain vitamin B), and digesting complex fibers. It is also the body’s primary immune trainer influencing autoimmune responses, provides protection against pathogens, and heps main gut barrier integrity.
The gut microbiome also plays endocrine and neurological roles, synthesizing neurotransmitters that regulate mood, sleep, stress and anxiety, or hormones that control hunger and satiety. While the bi-directional communication — the ‘gut-brain axis’ — is often talked about but similar communication channels exist with the lung, endocrine systems.
The modern and industrial way of producing food impacts the diversity of food, soil and the gut in multiple ways.
For example, in the case of ultra-processed foods (UPF) which are factory-made ‘products’ high in fat, salt and sugar (HFSS) rather than kitchen-made wholesome meals, there are three key linkages.
First, the ‘low fibre’ connection. These foods lack a ‘real food’ matrix, they are pre-digested and lack fibre content on which beneficial gut bacteria thrive. Starved of fibre, the good bacteria may die off or even begin to consume the gut’s protective mucus lining, leading to dysbiosis and reduced production of short-chain fatty acids (SCFA) that are anti-inflammatory, help in maintaining intestinal wall lining thereby preventing leaky gut. They also help in preventing cancer of the colon.
Second is the ‘high chemical’ connection. Chemicals in these ‘junk foods’ act as hidden disruptors. For instance, emulsifiers through their detergent effect can wash off the gut lining; artificial sweeteners can trick bacteria and promote glucose intolerance. Preservatives meant to prevent microbial growth in packages can even kill beneficial microbes, and food colours can trigger immune system and allergic responses.
Third and most concerning is the ‘high sugar’ connection. Sugar acts as a readily available ‘fast fuel’ for opportunistic pathogens like E coli and Candida sp, which can outgrow beneficial Bifidobacteria sp, Lactobacilli sp, leading to non-alcoholic fatty liver disease, through dysbiosis, leaky gut, drop in SCFA levels, rise in ethanol and acetaldehyde levels. Studies also point to the ability of opportunistic bacteria to biologically ‘hack’ the brain to crave for more sugar, making UPFs addictive, which explains the aggressive marketing and misleading labelling of these bad foods.
The intensive rearing of animals for food involves antibiotic use which is a big concern. Indiscriminate antibiotic use in poultry, dairy, and aquaculture can lead to residues of antibiotics in fish, meat, milk, and eggs. This chronic, low-level exposure on one hand kills beneficial gut bacteria (yielding into dysbiosis, reduced bacteria diversity), and on the other, allows for selection pressure to dominate making bacteria resistant — contributing to the ‘no-longer silent pandemic’ of antimicrobial resistance (AMR).
In the case of agriculture, pesticide residues on crops are known to be linked to gut imbalances and endocrine disruption. Certain pesticides are known to interfere with the estrobolome, the specific collection of gut bacteria that regulates estrogen metabolism, leading to hormonal imbalances.
There are also reports of increased cortisol, decreased thyroid (T3), insulin resistance through pathways of low-grade inflammation. Combination of food and water with pathogens (such as Salmonella sp, Campylobacter sp) can significantly disturb the gut microbiome leading to dysbiosis.
Health of the gut microbiome is known to be directly linked with the health of the people. Fixing the food systems to make them more sustainable will go a long-way in not just providing food with less chemicals but more diversity and nutrition.
Diversity in food becomes important, because only then different bacteria within our gut microbiome, that perform different and important functions for the body, will be able to feed on different food sources and thrive. It is therefore often said that we must eat to feed the gut, and not ourselves.
Making our food systems sustainable will also help with co-benefits like improving livelihoods, improving soil health, and preventing damage to environment and climate.
This needs rethinking and transition as sustainability in food systems is linked to who grows our food. Is it made in factories, comes to us from far-off distances or is grown locally. It is about how we grow our food such as in a chemical-intensive way characterised by monocropping, excessive water uses and soil degradation.
It is also about what we grow — rich in diversity or otherwise — and, most importantly, what we eat — ultra-processed and packaged or fresh and colorful plate filled with nutrition. Such a transition needs a reform and systems-based long-term approach.