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Gut Microbiome diversity and Diet

A varied diet is good for your gut microbes

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First published: 29.Dec.2018

Healthy Gut Bacteria

In this article, we will explore the relationship between diet and gut microbiome-diversity.

The microorganisms (bacteria, fungus, archaea, and virus) that live in your gut (known as gut microbiome or GM), play an important role in keeping you healthy.

Microbiomes with more diversity are associated with better health, and the loss of species' variety is a sign of disease.

Many factors can disrupt the diversity of gut bacteria, fungus, and archaea, and diet is the most important one.

Our lifestyles and diets define our gut's microbiome diversity.
From McDonald et al.

What is the gut microbiome?

Our gut is an ecosystem where different microorganisms (virus, fungus, bacteria, and archaea) live and interact with each other and us, their host.

We pick these germs up from the moment we are born, during delivery, by oral inoculation with maternal vaginal microbiota. Maternal breast milk also contains bacteria. These microbes colonize our gut and remain with us for the rest of our lives.

Each microbial species in the gut is flooded with energy: partly digested food, undigested fiber, and also fat, alcohol, and drugs such as medicine and supplements.

The gut microorganisms ferment and break down part of these nutrients and absorb some of its energy to keep alive, and at the same time produce different chemical molecules that interact with the host's metabolic systems. (1).

This isn't a "commensal" relationship (meaning it isn't a non-harmful coexistence between host and microbiome), it is a mutualistic one. Both sides benefit from it and depend on the other one to survive.

The approximate weight of your gut microbiota is 4.5 lbs (2 kg) and it has 3 million microbial genes: 150 times more than in the human genome

There are probably 300 to 1,000 different species of bacteria in our gut, but roughly 99% of them belong to some 30 to 40 species.

They weigh around 4.5 pounds (2 kg) and the total genome of these microorganisms is 150 times greater than the genetic information in the human genome.

The most studied microorganisms are bacterial species, but archaea and fungi also play a role in our health though less is known about them.

Factors that influence your microbiota's composition

Your gut microbiota evolves from childhood until adolescence when it stabilizes.

It is influenced by antibiotics, nonsteroidal anti-inflammatory medication, infections, chronic stress, physical activity levels, personal hygiene, and most importantly, by what you eat.

Snacks, alcohol, junk food, skipping breakfast, vitamin supplements, etc. have an important role in your gut microbiome (Mozak, Szulinska and Bogdanski, 2020) (2).

Eating more plant foods increases microbiome diversity

Not all carbohydrates are equal

Carbohydrates are chemical compounds that include different types of sugars, starch, and cellulose. Plants are the main source of dietary carbohydrates.

Sugars and starches are easy to digest and make up a large share of the Western diet. Cellulose, on the other hand, can't be digested but is very good for your digestive system. It comes in two varieties: soluble and insoluble fiber.

The gut microbes thrive on carbohydrates. Sugars such as sucrose and fructose alter their composition and have a negative effect.

Complex carbohydrates known as "Oligosaccharides" (found in fiber) are considered prebiotic and are beneficial for the gut microbiome (2).

Industrial and traditional diets: the plant food factor

Daniel McDonald, et al. (2018) (3) analyzed fecal samples from more than 10,000 contributors in the US, UK, and Australia comparing gut microbiome diversity and the dietary habits of the subjects.

The study found that people eating more than 30 different types of plant foods every week had microbiomes that were much more diverse than those of people eating 10 or fewer types of plant foods.

The authors also compared these samples, which came from industrialized regions with samples of people living traditional lifestyles such as hunter-gatherers or farmers living in remote locations. They found great differences in the types and variety of gut microbes between both groups.

Furthermore, there was more variation within industrial populations than within the traditional ones.

The image further up (from the paper), shows the relative proportions of different types of microorganisms in each type of human population.

More plant diversity in your diet means more microbiome diversity

McDonald's study found that "the number of unique plant species that a subject consumes is associated with microbial diversity, rather than self-reported categories such as 'vegan' or 'omnivore'..."

So it isn't enough to eat veggies (as in a vegan diet) but to eat a diet rich in plant variety.

They explain the reason for this as follows: plant foods are broken down in the gut by microbial fermentation. Different types of bacteria bind to different types of plant carbohydrates in the gut. Each variety of microbe has its specific enzymes to break down specific types of carbohydrates. So a diet with a larger variety of dietary fibers and undigestible starches will promote a more diverse microbial community, each microbe species specializing in a different type of plant fiber.

But what are the benefits of eating more plant foods?

The study found that people eating more than 30 different types of plants each week had a gut microbiome with fewer bacterial genes that promote antibiotic resistance.

Meaning that antibiotics will probably have better infection-fighting power on you, should you need to take them.

Take-Home Point

Eat a large variety of plant foods (high in fiber) to diversify your gut bacteria.

Carbohydrates fungus and archaea

Weight gain and archaea microbes

Besides bacteria, fungi and archaea are also found in the gut. Archaea are microbes that look like bacteria but are very different.

The archaea Methanobrevibacter is the most common genus and is the most prevalent one found in people eating diets high in carbohydrates.

It is not so common among people eating diets high in protein, amino acids, and fatty acids (oils and fats) (4).

So it shouldn't surprise us to find out that children that have higher Body Mass Index (or BMI) scores and are overweight have higher counts of a Methanobrevibacter species (M. smithii) (5).

A study using rats (6) concluded that "the levels and extent of small intestinal colonization with M. smithii correlated with, and were predictive of, the degree of weight gain, irrespective of dietary fat content.... suggesting that methanogens ... may contribute to weight gain and obesity."

"Good" archaea

On the other hand, Nitrososphaera archaea have a positive effect. They can oxidize ammonia and degrade urea providing nutrients for the rest of the gut microbiome.

They seem to be mutually exclusive with Methanobrevibacter and they thrive in the presence of ingested proteins and amino acids.


Gut fungi such as the pathogen Candida albicans follow the same trend as Methanobrevibacter. They thrive after the ingestion of carbs.

Candida albicans can cause infections (candidiasis) in immunocompromised subjects yet is a normal part of the gut microflora in healthy subjects where the bacterial microbiome keeps it in check producing substances that inhibit its growth or its transition into a virulent form known as hyphae.

Fungi in general can harm health. Mice genetically sensitive to them suffer from intestinal inflammation (4).

Take-Home Point

Regulate (reduce) your carbs intake (Have you considered a Ketogenic diet?) to keep archaea and fungi under control.

Fiber a key prebiotic

Food with a high fiber content (seeds, whole-grain, fruit, and vegetables) have a positive influence on GM composition. It promotes the growth of Bifidobacterium and Lactobacillus species.

Certain varieties of fiber, like the resistant starch and plant cell-wall polysaccharides, are broken down in the gut by Firmicutes and Bacteroidetes, to produce short-chain fatty acids (SCFAs) like butyrate, propionate, and acetate.

Butyrate helps promote the integrity of the intestinal barrier, protecting you from "leaky gut", and has an important role in brain function (2).

Experimental studies have proven that regular consumption of fiber (especially the soluble fraction) in the optimal amount, i.e., about 30 g per day, is positively correlated with the production of butyrate by multiple bacteria.   Moszak, Szulinska, and Bogdanski (2020)

Butyrate has beneficial effects such as killing colon cancer cells and maintains the oxygen balance in the gut, keeping the microbiota stable.

Propionate is used by the liver to regulate glucose production and it also helps promote satiety. Acetate seems to regulate appetite and plays a beneficial role in cholesterol metabolism and the formation of fatty tissues (3).

The higher the production of SCFAs, the lower is diet-induced obesity and insulin resistance. In mice, both propionate and butyrate reduce appetite and food intake by acting on gut-produced hormones (7).

Gut microbes also produce indolepropionic acid (more dietary fiber intake promotes more output of this acid), which is a potent antioxidant and seems to reduce the risk of type 2 diabetes.

Lifestyle influences your microbiome

A study by Jha et al. (2018) (8) compared the gut microbiome (GM) in four different populations in the same geographic region, Nepal.

Their goal was to eliminate any influence that geography and genetics may have on the gut microbiomes.

They found that the main difference between the groups was due to their traditional lifestyles.

One group was a traditional forager, the others were farmers that adopted farming and abandoned their seminomadic hunter-gathering lifestyle 100 to 300 years ago.

Jha's team reported that the transition from foraging to farming was accompanied by noticeable shifts in the gut microbiome.

They found the greatest difference between the most "advanced" farmers (the ones who shifted to farming around 300 years ago) and the foragers.

Unsurprisingly, the gut microbiome composition in all four Nepalese groups also differed from that of industrialized countries (such as America).

These differences were the following.

"The Himalayan populations were characterized by higher abundance of Proteobacteria, while abundances of Actinobacteria, Firmicutes, and Verrucomicrobia were highest in the Americans, intermediate in the farmers..., and lowest in the ... foragers."

However, the species richness, or diversity of microbial species, was the same in all groups, including the Americans.

Regardless of lifestyle, the GM richness is similar but the species that compose the gut microbiomes are different.

Water and Honey

They also found that drinking water was the main factor associated with the human gut microbiome differences.

This is quite reasonable because the water in Nepal isn't the tap water that you drink in the Western world, it has contaminants and is not purified. So it has its unique load of microorganisms (not necessarily pathogens). Jha also speculated that the minerals in the water also influence the GM.

Read More about water quality in the US:

> > Tap or Bottled Water?

Surprisingly, the other factor that influences gut microbes was honey consumption. But why, or how it does so remains a mystery.

Food Variety and Microbiome Diversity

Different food choices provide different substrates for these gut microorganisms to thrive on, and this promotes gut microbiome diversity and species richness.

Over the last 50 years. the plants and animal sources in our diet have narrowed. Out of some 300,000 edible plant species we consume around 200. Seventy-five percent of the world's food comes from 12 plant species and 5 animal species (1).

Foragers eat a wide variety of locally harvested foods such as tubers, fruits, nuts, fish, and legumes. While those living in industrialized nations eat more wheat, corn, beef, and poultry. Most of it with added fats and sugars, and highly processed.

To make matters worse, adults also tend to become more rigid as they age, eating a narrow variety of foods. They become less curious and shun different foods and tastes.

Gut Microbiota's diversity and health

Further up, we mentioned the health benefits of "short-chain fatty acids" (SCFAs) such as butyrate, propionate, and acetate and their link to fiber and a diverse GM.

Gut bacteria also intervene in the synthesis of vitamin B and vitamin K.

Diet and Gut Microbiome

Many factors influence the microbes in your gut such as the diet itself, excessive intake of salt, coffee, tea, and alcohol, vitamin supplements, probiotics, and polyphenols.


Polyphenols from your diet are well-known antioxidants and you get them from veggies, fruit (berries), tea, red wine, cocoa, and dark chocolate.

cranberries and blueberries

Berries: Packed with antioxidants

Berries, full of antioxidants such as flavonoids and anthocyanins, are great for your health, improving: diabetes, hypertension, obesity, cholesterol levels, and even cancer and neurodegenerative diseases


Polyphenols have a positive impact on GM as it promotes the growth of Bifidobacteria and Lactobacillus, the production of SCFAs, and reduces the population of pathogens like Clostridium histolyticum (2).


Food like yogurt, kefir or kimchi, contain live microorganisms and is good for your health. Probiotic foods reduce the population of harmful microorganisms like Helicobacter pylori and increase the growth of Bifidobacterium and Lactobacillus (2).

the Lactobacillus casei bacteria in yogurt

Yogurt and its health benefits

Probiotics like yogurt have many health benefits: weight loss, anti-inflammatory action, control of diabetes type 2. Learn how they promote a healthy gut


The Mediterranean Diet

There is strong evidence that the Mediterranean Diet has a beneficial effect on health and GM diversity, it increases SCFAs and increases certain varieties of gut microbes (Bacteroidetes, Faecalibacterium prausnitzii, Lactobacillus, and Bifidobacteria (2).

The Downside of Western Diet

On the other hand, there is also strong evidence that the Western diet upsets the balance of the gut microbiota, promotes inflammation and metabolic disorders.

The negative influence on gut microbes may be due to the high proportion of ultra-processed foods in the Western-style diet. These foods contain non-digestible trans-fats, synthetic chemicals such as emulsifiers (polysorbates), and thickeners (carboxymethylcellulose), and non-caloric artificial sweeteners, all of which alter the gut microbiome (2).

three packets of zero calorie sweeteners

Artificial Sweeteners and obesity

Sugar substitutes alter your gut microbiome, increase appetite and glucose intolerance, promoting weight gain. Artificial sweeteners are not risk-free


Alcohol abuse

Drinking too much alcohol is harmful to your health, and it also damages your GM. Different studies have shown that it depletes Akkermansia muciniphila, Faecalibacterium prausnitzii, Proteobacteria, and other SCFAs-producing microbial species.

It increases Enterobacteriaceae, Bacteroidetes, Firmicutes (Clostridiales), and pro-inflammatory species (2).

Risks: oxidized trimethylamine

Oxidized trimethylamine or TMAOA is a microbial chemical with negative effects. TMAOA is linked to an increased risk of atherosclerosis and major adverse cardiovascular events (9).

However, it is interesting to point out that compared with vegans and vegetarians, omnivores exhibited higher levels of TMAO. Plant foods therefore would help promote the growth of microbes that produce less TMAO.

Sporobacter and Lachnospira and not abundant in omnivores, but Clostridiaceae and Peptostreptococcaceae are plentiful. Prevotella also seems to promote an increase in TMAO concentration (8).

Lower bacterial diversity in sick people

People with conditions such as psoriatic arthritis, type 1 diabetes, type 2 diabetes, atopic eczema, inflammatory bowel disease, coeliac disease, and obesity have lower bacterial diversity than control groups.

The beneficial health mechanism of having a greater gut microbial diversity seems to be the following: in the event of negative environmental influences, a richer microbiome can compensate for the loss of some species and cover their function while people with less diversity will lose those functions and their health will suffer.

Tip: Don't go overboard with it

Valdes reported that a major increase in dietary fiber intake "can temporarily reduce diversity, as the microbes that digest fibre become specifically enriched, leading to a change in composition and, through competitive interactions, reduced diversity." (7)

So any deliberate changes in your diet aimed at modifying your gut microbiome should be gradual. Increase plant foods slowly, let your body adapt, don't rush.

The microbiome's balance is delicate: stress, surgery, or a dose of antibiotics can upset it very easily.

References and Further Reading

(1) Heiman M. and Greenway F., (2016). A healthy gastrointestinal microbiome is dependent on dietary diversity. Mol Metab. 2016 Mar 5;5(5):317-320

(2) Moszak, M., Szulinska, M., & Bogdanski, P. (2020). You Are What You Eat-The Relationship between Diet, Microbiota, and Metabolic Disorders-A Review. Nutrients, 12(4), 1096.

(3) McDonald D. et al. (2018). American Gut: an Open Platform for Citizen Science Microbiome Research. Systems, Journal of the American Society for Microbiology, May 15, 2018. DOI: 10.1128/mSystems.00031-18

(4) Hoffmann C, et al. (2013). Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents. PLoS ONE 8(6): e66019

(5) Mbakwa CA., et al., (2015). Gut colonization with methanobrevibacter smithii is associated with childhood weight development. Obesity (Silver Spring). 2015 Dec;23(12):2508-16. doi: 10.1002/oby.21266. Epub 2015 Nov 2

(6) Ruchi Mathur et al., (2013). Intestinal Methanobrevibacter smithii but Not Total Bacteria Is Related to Diet-Induced Weight Gain in Rats. Obesity 21(4):748-754. April 2013 doi: 10.1002/oby.20277

(7) Valdes A., Walter J., Segal E., and Spector T., (2018). Role of the gut microbiota in nutrition and health. BMJ 2018; 361 doi: (Published 13 June 2018)

(8) Jha AR, Davenport ER, Gautam Y, Bhandari D, Tandukar S, Ng KM, et al. (2018). Gut microbiome transition across a lifestyle gradient in Himalaya. PLoS Biol 16(11): e2005396.

(9) Tian-Xing Liu, Hai-Tao Niu, and Shu-Yang Zhang, (2015). Intestinal Microbiota Metabolism and Atherosclerosis. Chin Med J (Engl). 2015 Oct 20; 128(20): 2805-2811. doi: 10.4103/0366-6999.167362

About this Article

Gut microbiome diversity and diet, A. Whittall

©2018, 29.Dec.2018. Updated. 27.Dec.2020.

Tags: polyphenols, gut microbiome, GM, gut bacteria, microbiome diversity, diet and gut microbiome, prebiotics, probiotics, C. albicans, gut flora, gut microbiota.

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Subject: Gut microbiome diversity and diet. A species-rich gut microbiome (or GM), with a diversity of microorganisms, is critical for good health. Eating a varied plant food diet, rich in fiber, cutting back on carbs, and diversifying food sources helps enrich your gut bacteria and promote good health.

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