How Do Plant-Based Diets Affect Our Gut Microbiota? Part One

What happens “down below” in our intestines is of such vital importance to our health that I’ve previously covered aspects of this subject in relation to a variety of specific subjects, such as alcohol 1 , obstructive sleep apnea 2 , depression 3 , physical activity 4 , and multiple sclerosis 5 . However, a new review 6 just published puts more meat on the bone – or more fruit on the tree!

The review looks at how the food we put in our mouths determines the type and quantity of our gut flora (also known as gut bacteria, microbes, microbiota or microbiome) and, in turn, how these dietary choices affect the direct and indirect actions performed by these vital microscopic inhabitants of our bodies.

This is Part One of a two part blog on this study. Here, we’ll look at the types and activities of microbes found in the intestinal microbiome of those eating plant- and meat-based diets, finally focusing on the microbial effects of consuming the macronutrient, carbohydrate.

In Part Two, we’ll look at the microbial effects of the other two macronutrients (protein and fat), polyphenols, and the influence on human health of microbiome postbiotics7 derived from such things as vitamins and TMAO.

Definition of terms

“Microbiota”and “microbiome” tend to be used interchangeably; however, “microbiota” refers to the total of all microbial taxa associated with humans (including bacteria, viruses, fungi, protozoa and archaea), while “microbiome” refers to the complete catalogue of microbes plus all their genes.

Each human’s gut microbiota is estimated 8 to consist of over 3 trillion microbes – although I don’t know if anyone has actually sat down and counted them…

The human gut microbiome consists of around 3.3 million non-redundant 9 microbial genes. Amazingly, this is much more than our human genome, which only contains around 21,000 genes. So there are around 150 distinct microbial genes in our guts for every one of our human genes 10 .

Omnivore vs plant-based microbiota

Previous blogs 11 12 have looked at the evidence for significant differences between the microbiota of meat eaters and plant eaters. Plant-based diets appear to promote the development of more diverse and stable microbial systems, with significantly more Bacteroidetes-related operational taxonomic units compared to omnivores.

Important components of a plant-based diet include:

Fibre (non-digestible carbohydrates that are only found in plants) increase lactic acid bacteria (e.g. Roseburia, Ruminococcus, and E. rectale) while reducing certain pathogenic bacteria (e.g. Clostridium and Enterococcus species). Lactic acid bacteria can help improve lactose digestion, prevent and treat diarrhoea, and act on the immune system, helping the body to resist and fight infection.

SCFAs (short-chain fatty acids) have a plethora of health benefits. A diet high in fibre encourages species that ferment fibre into metabolites in the form of SCFAs (such as acetate, propionate and buyrate). We previously looked in detail at butyrate 13 and saw how such bacteria-produced SCFAs can improve immunity against pathogens, increase the integrity of the blood–brain barrier, provide energy substrates, and regulate critical intestinal functions.

And it’s not just SCFAs that mark the difference between plant- and meat-based diets –  for instance, the former contains phytoestrogens, and isothiocyanates such as sulforaphane 14 , whilst the latter contains TMAO 15 and secondary bile acids 16 . These and other basic constituents of each diet will determine the type of gut bacteria that can survive within your body. We’ll look at the latter in more detail in Part Two.

Polyphenols (again, only found in plants) increase bacteria species which can provide anti-pathogenic/anti-inflammatory properties as well as cardiovascular protection (e.g. Bifidobacterium and Lactobacillus).

It’s no surprise, then, that a diet which is high in the foregoing will likely result in a diverse ecosystem of beneficial bacteria that supports the health of the host – that is, you and me.

Diversity & distribution matter

Plant-based diets also appear to promote good health by developing a richer, more diverse gut microbial system, and/or by producing an even distribution of a variety of species 17 18 .

Microbiome is a separate “organ”

The range of functions of the human gut microbiome is so wide-ranging (immunity, gastrointestinal, brain, cardiovascular systems, cellular and genetic activity) that it’s increasingly common for researchers to regard it as a distinct “organ” within the human body.

Three basic bacterial enterotypes

Several studies 19 20 have suggested that there are three basic bacterial enterotypes 21 :

  1. genus Prevotella (largely anti-inflammatory and protective)
  2. genus Bacteroides (more pro-inflammatory and possible associations with heightened risk of metabolic syndrome and other pathological conditions)
  3. genus Ruminococcus (whose biological significance is still largely unclear)

The effects of imbalanced gut microbiota

Imbalanced gut microbiota has been linked 22 23 24 25 with a surprisingly large number of conditions, including the following:

  • acid reflux 26
  • peptic ulcers 27
  • irritable bowel syndrome 28
  • non-alcoholic liver disease 29
  • inflammatory bowel disease 30
  • obesity 31
  • atherosclerosis 32
  • type 2 diabetes 33
  • cancer
  • Alzheimer’s 34
  • Parkinson’s 35
  • motor neurone disease 36
  • lateral sclerosis 37
  • autism spectrum disorder 38 39
  • atopy40 41

Microbiota and personalised nutrition

Because of the amount of evidence being accumulated in support of the role of our gut microbiota in acting as a mediator of dietary impact on the host metabolic status, an increasing amount of research is being focused on establishing causal relationships in individual people between the food they eat, what it does to their gut microbiota and the consequent effects on their overall health. It’s anticipated that this will allow for the development of therapeutic interventions such as personalised nutrition (18).

One such study concludes: “Convincing accumulating evidence shows that the human gut microbiota contributes to many aspects of human health via molecular pathways that we only begin to understand. The GI microbiota entertains deep mutualistic relationships and co-evolves with the human host, albeit at a much faster rate and demonstrates deep ecological links with the host which are being studied at the interface between Biology, Ecology, and Medicine. Experimental probing of the deep and reciprocal ties characterizing the microbiota-host relationship constitutes a formidable challenge, yet holds the promise to shed light on unknown aspects of human and microbial physiology and novel therapeutic possibilities in the manipulation of microbiota composition via antibiotics, probiotics, and microbial transplantation.” 42

Microbiota and postbiotics

The term “postbiotics” is relatively new. It refers to the vast range of compounds (metabolites) produced by the metabolic activity of our gut bacteria depending, to a large extent, on what nutrients they receive from the diet we eat. These probiotic-produced postbiotic compounds play vital roles in the regulation, not only of the host’s health, but also in the maintenance of a healthy gut microbiome.

The postbiotics produced by probiotic bacteria appear to be responsible for many of the beneficial effects claimed for probiotics.

N.B. In most cases, it can be argued that a healthy and balanced WFPB diet will provide all the natural probiotics you need without having to resort to commercially-produced stuff with dubious effectiveness or, indeed, safety. 43 44 Whole plants are covered with bacteria that have been interacting effectively with our bodies for millions of years; and the postbiotics produced by microbes inside vegetarians/vegans have been shown 45 to be particularly effective in reducing various risk factors for chronic inflammation and chronic degenerative diseases.

What determines gut microbiota composition?

Variations in microbiota composition from one person to another are likely to be a combination of the following:

  • different directly-consumed foodborne bacteria 46
  • differences in the substrates 47
  • variations in transit time through the GI tract 48
  • pH level 49
  • host secretion influenced by dietary patterns 50
  • regulation of gene expression of the host and/or his/her microbiota 51 45

Gut Microbiota – Why diversity matters

Microbial diversity associated with plant-based diets – particularly seen in research on long-term fruit, vegetable and whole grain intake 52 53 – appears to have important associations with many health indicators, including:

  • reduced BMI
  • reduced risk of obesity
  • improved vascular compliance 54 55

It takes time to achieve optimal gut health

Dietary changes are shown 56 to have relatively rapid impact (within a week) on microbial composition and, hence, on the effects of their metabolites. However, it’s important to note that these effects can be modest and reversible if the individual reverts to their prior dietary habits 51 .

One study showed 57 that changes in microbiota and associated immune parameters after just 3 months on a vegetarian (not a WFPB or vegan) diet can be pretty significant; but these changes pale into comparison when compared with the degree of change that occurs with a long-term plant-based diet.

Microbial “stress” and high-fibre diets

Whilst high-fibre diets are excellent for gut health, there is a suggestion that microbes may experience stress at the point when a sudden change from low- to high-fibre diets takes place. One indicator of such stress is an increase in Enterobacteriaceae, known as a pathogenic species of bacteria. Short-term dietary interventions which increase fibre consumption were shown to cause a slight but significant decrease in diversity, possibly associated with a slight but, once again, significant increase in Enterobacteriaceae – a species which is typically lower in vegan compared with omnivorous diets 58 .

This is probably the case because of the fact that longer-term dietary habits that favour high-fibre foods are known to produce greater amounts of butyrate-producing bacteria, which lower the colonic pH and, thus, prevent the growth of pathogenic bacteria, such as Enterobacteriaceae 59 .

Obesity & reduced microbial diversity

Studies have shown 60 reduced microbial diversity in obese individuals. In addition, it was shown that obese individuals have a reduction in the Bacteriodetes:Firmicutes ratio – that is, increased numbers of Bacteriodetes and decreased numbers of Firmicutes (more on this ratio below), an increase in Proteobacteria (a pro-inflammatory phylum), and an increase in C-reactive protein (which is inversely correlated with a healthy Bacteriodetes:Firmicutes ratio – that is, more C-reactive protein means a less favourable Bacteriodetes:Firmicutes ratio).

It’s possible to see quite the opposite results when looking at the ~60,000 participants in the Adventist Health Study-2 61 . The individuals who followed a vegan diet shown the lowest BMI values when compared with vegetarians or omnivores. The suggestion followed that the lower body weight associated with vegan diets might produce a microbial diversity which protects against systemic inflammation.

Why the Bacteroidetes:Firmicutes ratio matters

Out of thousands of bacterial species-level phylotypes 62 inhabiting the human gut, the majority belong to two dominant phyla, the Bacteroidetes and Firmicutes . Members of the Bacteroidetes in particular have been associated with human metabolic diseases.” 63 So, even taking into account the wide range of inter-individual variations in human intestinal microbiomes, it’s known 64 65 that these Bacteroidetes and Firmicutes phyla dominate healthy human microbiomes.

However, it’s the actual ratio between them that seems to matter most. Diets heavier in animal fat and protein than in whole grains and plant-based foods (rich in starch, fibre and plant protein) have been shown 66 to cause a significant decrease in Bacteroidetes and increase in Firmicutes.

See the following video by Dr Greger for more information on this important ratio:

In the video, Dr Greger offers a useful way of remembering which bacterial phyla is associated with which body type: Bacteroidetes for bony, and Firmicutes for fat!

Bacteroidetes:Firmicutes ratio and obesity

As the above video explained, a decrease in Firmicutes levels usually favours an increase in Bacteroidetes and Bifidobacteria – something that happens when you eat lots of resistant starches 67 . The typical result of this is that obesity/high BMI can be prevented and treated 68 .

A decreased Bacteroidetes:Firmicutes ratio has a strong negative correlation with BMI 60 . This may be explained by the observation that a 20% increase in Firmicutes with a corresponding decrease in Bacteroidetes abundance is associated with a 150 kcal/day increase in energy harvest 69 – something which would, over time, result in weight gain. Thus, an increased Bacteroidetes:Firmicutes ratio (as seen in high-fibre, plant-based diets) could result in weight loss by causing a reduction in the amount of energy being extracted from the diet.

Additional studies are required to decide whether increased energy harvest is caused by the Bacteroidetes:Firmicutes ratio promoting adiposity or by a host-mediated adaptive response to limit energy uptake 70 .

Nothing is plain and simple in the world of microbes, and there are sufficient conflicting results from various studies on the Bacteroidetes:Firmicutes ratio to support the argument that making wide-sweeping statements about which phyla are good and which are bad is likely to be inaccurate and over-generalised. Increased awareness is growing about a need to appreciate the complexity of dynamic interactions between microbes within the microbiome, rather than trying to match one microbe with one health outcome 71 52 72 73 .

How gut bacteria enterotypes are affected by diet

As mentioned above, there are three main enterotypes observed in human microbiomes:

1. Prevotella

2. Bacteroides

3. Ruminococcus

1. Prevotella is a genus of the Bacteroidetes phyla. Studies suggest 74 75 76 77 that it’s significantly richer in the microbiome of vegans.


Studies with mice have suggested 78 that Prevotella improves glucose metabolism by improving glycogen storage. It has also been observed 79  to confer anti-inflammatory effects, and additional research suggests 80 that it can decrease the growth of other bacteria by competing for fibre as an energy substrate.

2. Bacteroides is another main enterotype and genus of the Bacteroidetes phyla. Whilst still appearing to be affected by the type of diet eaten, Bacteroidetes has been positively associated 81 52 with long-term diets high in saturated fat and animal protein.


An explanation of this is that such bacteria are better able to tolerate bile – something common in the gut environments of meat-eaters. It’s no surprise, therefore, that high proportions of Bacteroides are found 76 in the intestinal environments of those who eat the modern Western diet, while the opposite is the case for those eating lots of legumes, fruits and fibre.

3. Ruminococcus is an enterotype and genus also associated with long-term fruit and vegetable consumption. An explanation of this is that species of this genus are specialists in degrading complex carbohydrates (e.g. cellulose and resistant starch which are only found in plants) and, thereby, producing butyrate, an anti-inflammatory SCFA56 .


Increased communities of Ruminococcus have been associated with the following:

  • low BMI and healthy lipid profiles 52
  • lower endotoxemia82 and lower arterial stiffness 55

“A high fat diet increases the absorption of LPS [lipopolysaccharides or LPS are an integral component of Gram negative microorganisms], which, in turn, has been found to be associated with metabolic endotoxemia and to induce inflammation resulting in obesity.” 83

Walnuts, refined grains and Ruminococcus

Studies have shown 65 that eating walnuts appears to enrich the Ruminococcus community within our gut environment.

Interestingly, however, one study showed 84 an increase of Ruminococcus in college students who had low dietary fibre intake in their diets. This may be explained by the ability of these bacteria to also break down resistant starches in the many refined grain products eaten by this group.

How plant food components influence gut microbiota

This final section will look at both nutrient bioavailability and the microbial responses to the consumption of carbohydrates.

Nutrient Bioavailability

It may seem counter-intuitive, but less is more when it comes to certain aspects of nutrient bioavailability85 . When you consume food nutrients with low bioavailability (normally found in intact plant cell walls, larger food particles, and the latter foods without thermal treatment), more nutrients are able to pass through the stomach and small intestine to reach lower in the gastrointestinal tract. This is important since it allows our gut microbiota, lurking down in the colon, to receive a delivery of rich nutrients 86 .

A rich supply of nutrients will help support the normal development and functions of gut microbiota. The modern Western diet has loads of ultra-processed foods and acellular nutrients87 . The small intestine can more easily absorb these components and, thus, deprive the colon of important nutrients. Eating acellular food has been shown 88 to alter the composition and metabolism of the gut microbiota, and induce inflammation in young infants, adolescents, women of child-bearing age, and older adults.

On the other hand, whole plant foods have protective effects, and favour the growth of beneficial fibre-degrading bacteria in the colon.


Both digestible and non-digestible carbohydrates appear able to influence gut microbiota.

Digestible carbohydrates (e.g. glucose, sucrose, and fructose from fruits) have been shown 89 to reduce the following:

  • Bacteroides 90
  • Clostridia 91 .

The following diagram 92 provides more detail on the absorption of digestible carbohydrates:

Non-digestible carbohydrates (NDCs) generally:

  • increase the following:
    • lactic acid bacteria
    • Ruminococcus
    • Eubacterium rectale
    • Roseburia,
  • reduce the following:
    • Clostridium
    • Enterococcus

The following diagram 93 provides a little more in-depth detail on NDCs.

Both digestible and non-digestible carbohydrates have been shown to increase Bifidobacteria (a genus of the Actinobacteria phylum)

Bifidobacteria are some of the good guys. As a butyrate-producing genus, with known protective properties for the human gut barrier, Bifidobacteria provide effective defences against pathogens and diseases, and increase in number when “fed” with health-giving short-chain fructooligosaccharides (scFOS) and fibre – both forms of carbohydrate found in abundance in natural plant foods, such as bananas, artichokes, onions, etc 94 . On the other hand, high consumption of cholesterol (only found in animal foods), was strongly associated with a lower abundance of Bifidobacteria 95 .

Prebiotic fibres

A recent study found 96 that the following fibres have differing prebiotic effects on gut microbiota:

  • inulin
  • alpha-linked galacto-oligosaccharides
  • beta-linked galacto-oligosaccharides
  • xylo-oligosaccharides (from corn cobs and high-fibre sugar cane)
  • beta-glucan (from oats)

Inulin and all oligosaccharides have a strong bifidogenic effect 97 .

Beta-glucan induces Prevotella and Roseburia growth with associated increase in production of the SCFA, propionate – a good thing, since it’s known 98 99  to promote weight loss and provide many other health benefits, including being anti-carcinogenic and anti-inflammatory.

All natural sugars, especially non-digestible forms like inulin and oligosaccharides, increase SCFA levels 100 101 .

Prebiotic effects vary depending on which type of bacteria breaks down which type of fibre. The specificity of bacterial activity in relation to fibre is determined by specific gene clusters within the bacterial genome that dictate which saccharolytic 102 enzymes the bacteria can produce and, hence, whether they can metabolise the particular prebiotic substrate 103  .

Other protective effects of non-digestible carbohydrates

NDCs don’t just act as prebiotics by promoting the growth of beneficial microorganisms, they are also shown 89 to do the following:

  • reduce proinflammatory cytokine 104 production
  • reduce concentrations of serum triglycerides
  • reduce total cholesterol
  • reduce LDL-cholesterol

It can be seen from the above that NDCs are, thus, likely to confer significant protective effects against cardiovascular disease as well as central nervous system disorders.

Final thoughts

An increasing body of research indicates that diet is the essential factor when it comes to the composition of human gut microbiota. These microbes are then responsible for converting nutrients into active postbiotics that we (the hosts) absolutely need. The weight of evidence is favoured towards a plant-based diet being the most effective way in which we can ensure a diverse ecosystem of beneficial microbes is promoted within us, so that they can support overall health.

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