30 November 2020; updated 23 October 2023
In Part 1 of this series on the gut microbiome, I discussed the intriguing history of gut microbiota research, and summarised the known functions of our microscopic co-residents.
Now, let’s delve deeper into the research on the myriad of ways in which what we eat affects our gut microbiota, and how this influences our health.
Remarkably, although about one third of the bacterial species that inhabit our guts are common to most people, the remaining two thirds are unique to each individual – as unique as their fingerprint. Although we are about 99.9% identical to each other in terms of our human genome, our gut microbiomes can differ by up to 90%.
Our core microbiota is inherited from our mother, and remains more similar to hers than to unrelated people’s for our entire lifespan.
However, our diet, exercise, lifestyle habits and medication use shape our complex microbial communities and their gene expression throughout life, so that even identical twins, who share the exact same human genome, end up with distinct microbial profiles – although more similar to each other’s than either non-identical twins, or non-twin siblings.
What we eat, in particular, powerfully and rapidly influences the composition of our gut bacteria, and their gene expression. In a landmark study published in 2014, researchers fed 10 volunteers on two different diets – a ‘plant-based diet’ rich in grains, legumes, fruits, and vegetables; and an ‘animal-based diet’ comprising meats, eggs, and cheeses – for 5 days each.
The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of species that metabolise dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii) – in just two days!
Furthermore, on the animal-based diet, bacteria expressed more genes involved in synthesising a bile acid that is known to promote liver cancer, and hydrogen sulphide, a gas linked to inflammatory bowel disease and bowel cancer.
Fortunately for the participants, their gut microbiota reverted to their original structure two days after the all-animal food diet ended and they resumed their normal eating pattern. But just imagine the damage they would do if they ate such a diet over the long term!
Actually, you don’t have to imagine. Extensive studies have found that people who habitually eat a Western-style diet – high in meat, fat and refined carbohydrate, and low in fibre and other forms of complex carbohydrate found in whole plant foods – have been found to have a microbiota profile dominated by Bacteroides species. This is associated with increased inflammation, weight gain and impaired blood sugar control.
High fat diets have been found to suppress beneficial bacteria including Lactobacilli, Bifidobacteria, Bacteroidetes and Akkermansia muciniphila, all of which help to maintain a healthy gut barrier; and fuel the growth of Oscillibacter and Desulfovibrio species, which increase intestinal permeability and hence, inflammation.
Saturated fat – found primarily in animal products including meat, poultry, dairy products, eggs and some species of oily fish, as well as coconut oil and palm oil – is the biggest culprit in enriching the gut microflora with bacteria that contain lipopolysaccharide (LPS), also known as endotoxin. LPS is a bacterial component that damages the gut barrier and drives up systemic inflammation levels.
Hence, the typical Western diet creates the perfect storm for generating both dysbiosis (an unhealthy change in microbial composition) and increased gut permeability (‘leaky gut’). Together, dysbiosis and leaky gut play pivotal roles in a host of human maladies including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), coeliac disease, diabetes, asthma, depression, anxiety, and autism.
On the other hand, diets rich in fibre and unrefined carbohydrates have been linked to a Prevotella-predominant microbiota profile.
This cluster of bacterial species ferments the types of carbohydrates that humans are unable to digest – fibre, resistant starch and oligosaccharides, collectively known as microbiota-accessible carbohydrates, or MACs – into beneficial short chain fatty acids (SCFAs), including butyrate, acetate and propionate.
These SCFAs bestow a bounty of health benefits, including reducing inflammation both in the gut itself and throughout the entire body, strengthening and repairing the gut barrier, tamping down cholesterol synthesis, improving insulin sensitivity (and thus reducing blood glucose levels), promoting immunity, regulating our appetite, increasing fat-burning, and stimulating the production of brain-derived neurotrophic factor (BDNF), the so-called ‘Miracle-Gro for the brain’.
Unsurprisingly, people who eat plant-centric diets have been shown to have greater gut microbial diversity and richness of species, which is associated with better digestive health and lower risk of obesity and metabolic disease (such as diabetes).
Researchers describe the link between diet, gut bugs and obesity with a colourful analogy:
“The obese gut microbiota is not like a rainforest or reef, which are adapted to high energy flux and are highly diverse, but rather may be more like a fertilizer runoff where a reduced diversity microbial community blooms with abnormal energy input.”
A core gut microbiome in obese and lean twins
But ultraprocessed vegan junk food, stripped of its fibre and complex carbohydrates and laced with fat, sugar and simple starches, just doesn’t cut the microbial mustard. To cultivate your garden of healthy gut bugs, you must feed them a variety of whole and minimally-processed plant foods, rich in microbiota-accessible carbohydrates – big MACs such as legumes (dried lentils, peas and beans), whole grains, vegetables, fruits and nuts, not Big Macs (even vegan ones!).
Why does variety matter? The American Gut Project – a crowdsourced, global citizen science effort which has sequenced the gut bacteria of more humans than any organisation on Earth – found that people who ate 30 or more different plant foods per week had the most diverse gut microbiota.
‘Eating the rainbow’ ensures that your gut bugs have access to a plethora of polyphenols, plant compounds which boost the growth of beneficial bacteria, such as:
- Resveratrol (found in grapes, peanuts, pistachios, blueberries, cranberries, and cocoa);
- Curcumin (turmeric);
- Lignans (flax and sesame seeds);
- Quercetin (onions, apples, grapes, berries, broccoli, citrus fruits, cherries, tea, and capers);
- EGCG (green and white tea); and
- Isoflavones (soy).
Plants produce polyphenols to defend themselves against stress caused by poor soil, fungal disease and insect predation. These powerful plant compounds pass through our upper gut largely intact, but once they reach our colons, gut bacteria begin to metabolise them into active compounds that we can absorb through the colon wall. These compounds deliver a stunning array of health benefits including antioxidant, anticancer and antimicrobial activity, and hormone modulation.
As far as we know, we are not “being watched keenly and closely by intelligences greater than man’s”, as H.G. Wells imaginatively speculated in the opening lines of The War of the Worlds.
It’s not Wells’ hostile Martians that we have to fear, after all. It’s ourselves. Our “infinite complacency” has caused up to disrupt the harmonious relationship between our human and microbial selves – a relationship which supported the health, growth and development of our species over the long march of evolutionary time, allowing humans to adapt to seasonal and geographic changes in food supply.
However, in the last few decades, we have relentlessly carpet-bombed our gut microbiota with antibiotics; disrupted their normal transmission from mother to infant with caesarean sections and formula feeding; and starved the most beneficial species of the MACs they need, while overfeeding the most disease-causing ones on excess calories, fat and protein.
In their article ‘The ancestral and industrialized gut microbiota and implications for human health’, pioneering gut microbiota researchers Drs Justin and Erica Sonnenburg argue that due to the damage we have inflicted on them, for the first time in our millennia-long partnership our gut microbiota are no longer acting in our best interests:
“The microbiota associated with humans in the industrialized world has diverged in its compatibility with the less malleable human genome.”
The ancestral and industrialized gut microbiota and implications for human health
The “infusoria under the microscope” adapt in order to survive and thrive. It is up to us to provide them with an environment in which those that thrive, also support our own thriving. And the best way to do that, is with a diet centred on a rich abundance of whole and minimally processed plant foods.
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