We are not alone. Trillions of microbes live in our bodies and are concentrated mainly in our gut. Because of the significance of this number, the microbiome is sometimes thought of as an "extra organ" (Tommova et al. 2019).

Interestingly, although humans are about 99.9% identical to each other at the genomic level, their gut microbiome can be up to 80–90% different (Turnbaugh et al., 2009).

But what does the microbiome look like?

Imagine walking through the street in a heavily populated city, let's say, New York City. Then, imagine it’s winter during the height of the holidays and people from everywhere are coming to the city. Some are moving fast while others go slow, but everyone looks different.

This is a good way to picture how the microbiome looks inside your gut.

Both pathogenic and beneficial microbes share the same space in the gut environment. However, the prevalence of one versus others may be the difference between being healthy or sick.

Is there a core microbiome species? What are the good and bad microbes? How do they benefit your body?

crowd of people at a train station - comparible to the diversity of bacteria within the microbiome.

In this article

A close look inside the gut microbiome

The core microbiome

Genus Prevotella

Genus Bacteroides

Genus Ruminococcus

Action mechanisms of gut microbes

Metabolites derived from plant-based resources

Metabolites derived from animal-based resources




A close look inside the gut microbiome

Trillions of microbes live inside the large intestine, among them is a diverse variety of species. So how do these different microbes all live together?

The human microbiota, which is defined as the total of all microbial taxa associated with human beings, is composed of bacteria, viruses, fungi, protozoa, and archaea.

In a healthy person, these microbes coexist peacefully, with the most significant numbers found in the gastrointestinal tract.

Our microbes promote a healthy gut, immune system, bowel movements, metabolism, and hormones and help with appetite regulation when adequately balanced.

A way to keep these microbes under control is through a healthy diet. Multiple studies show the benefits of a plant-based diet (does not exclude meat) for the microbiome, mainly because plant-based foods provide fermentable sugars allowing the growth of beneficial microbes.

Microbes are located in the internal layer of the intestine. They take complex sugars and breakdown into smaller molecules. Then, these small sugars can easily cross the intestinal membrane and are delivered into the bloodstream.how microbes work in the gut, illustration of how complex sugars are broken down into simple sugars by the gut

The process of breaking down sugars into smaller ones by microbes is known as a fermentative process. And the outputs of this process are valuable metabolites needed for homeostasis and nutrition.

These metabolites include short fatty acids (SCFAs), and vitamins like B2, among others.

Furthermore, dysbiosis, which is the imbalance of microbial diversity, has been associated with various gastrointestinal (GI) and non-GI diseases, such as obesity, heart, kidney, and liver-related diseases, cancer, and autism.

However, the dilemma of whether it acts as a cause of disease or a consequence is not yet clear (De Angelis et al. 2020).

The immune system and the microbiome - the microbiome helps the immune system

The core microbiome

Researchers are currently exploring the hypothesis of a stable, core microbiome with similar metabolic traits. Or, another way of describing this is asking the question, “are there common microbes prevalent in most human guts, and how do they relate with the health?”

Before we dive into this hypothesis, we need to define the term bacterial enterotype. A bacterial enterotype is the classification of living organisms based on the bacteriological composition of the gut microbiota.

For now, hypotheses surrounding the concept of a core microbiome have not been confirmed, but three basic bacterial enterotypes have been recognized, the genera Prevotella, Bacteroides, and Ruminococcus.

Enterotypes are made of both pathogenic and nonpathogenic bacteria. They're equally necessary to keep the order and maintain a healthy status. Microbiomes are an ecosystem where both good and bad bacteria work together to keep a balance.

Here’s a familiar situation we can use as an analogy - too many bunnies in a given population would zap resources, and in turn make the bunnies unhealthy. This is where predators come into play, keeping various prey populations in balance.

Likewise, the balance between pathogenic and nonpathogenic must be maintained, not just for the health of our microbiome, but also to ensure the resources within our body remain in balance.

Bacterial enterotypes - organizational chart of various bacteria

Genus Prevotella

Prevotella is considered a beneficial bacteria group with protective and anti-inflammatory functions. Prevotella belongs to Bacteroidetes phylum, and it is significantly richer in a vegan/vegetarian diet.

Genus Bacteroides

The Bacteroides genus also belongs to Bacteroidetes phyla; however, it is considered a pathogenic bacterial genus with pro-inflammatory functions and possibly related to increased risk in metabolic syndrome and other pathological conditions. For instance, Bacteroides have been positively correlated with long-term diets rich in animal protein and saturated fat.

Genus Ruminococcus

Ruminococcus belongs to Firmicutes phylum. The biological significance of this genus is less evident, and some species exert a positive effect and are associated with long-term fruit and vegetable consumption. However, some other species are linked to diseases.

Ruminococcus microbes degrade dietary fibers, producing butyrate, a short fatty acid, which is an anti-inflammatory compound. Also, a significant enrichment of Ruminococcus bacteria has been associated with plant-based foods, particularly walnut consumption.

Furthermore, a recurrent topic in microbiome research is the Bacteroidetes: Firmicutes ratio. These are the two dominant phyla in the human microbiota, and their ratio has been suggested to be an indicator of health.

For instance, a lower ratio Bacteroidetes: Firmicutes is observed in obese participants, leading to a higher abundance of Proteobacteria, a pro-inflammatory phylum (Verdam et al., 2013).

An increased Bacteroidetes: Firmicutes ratio has been seen in plant-based diets. However, controversial results also have been found regarding this ratio. So, more research is needed to verify if the Bacteroidetes: Firmicutes ratio indeed can work as an effective indicator of health.

Action mechanisms of gut microbes

Microbes exert their effects on human health through the metabolites they produce by fermentation of food. These metabolites are commonly known as "postbiotics." Consequently, these metabolites affect our digestive and immune systems, organs, and genes.

For instance, metabolites like short fatty acids (SCFAs), phytoestrogens, and vitamins are more linked with plant-based food. In contrast, trimethylamine N-oxide (TMAO) and secondary bile acids are associated with the meat-based diet. First metabolites are indicators of good health while the second are related with an unhealthy status.

Metabolites derived from plant-based resources

Short fatty acids (SCFAs)

SFAs include acetate, propionate, and butyrate. Microbes like Prevotella spp. produce acetate; Bacteroides spp. produce acetate and propionate, and Clostridium spp. produce butyrate.

These metabolites are derived from fermented fibers and other carbohydrates, with a small fraction derived from proteins.

They are essential energy sources for the body and benefit gut health.

SCFAs promote immunity against pathogens and have roles in intestinal homeostasis and mitigation of inflammation (Singh et al., 2017).

SCFAs also increase thermogenesis, preventing and or treating obesity. Plant sources promoting SCFA production include grain legumes (also known as pulses).

Phytoestrogens subproducts

Phytoestrogens are polyphenols derived from plant sources. Phytoestrogens are used by species like Bifidobacterium, Lactobacillus sp., Clostridium sp., and Bacteroides to produce equol, urolithins, and enterolignans.

These transformed metabolites serve as prebiotics, promoting the gut bacteria's growth.

Particularly urolithins promote the development of Lactobacillus and Bifidobacterium species (Tomas-Berberan et al. 2016).

Maybe one of the most critical functions of the gut microbiota is the production of vitamins essentials for humans.

These vitamins are needed for tissue maintenance, the nervous system, and as cofactors in producing DNA, fatty acids, and amino acids (Girones-Vilaplana et al., 2017).

For instance, vitamin K2 (menaquinone), vitamin B9 (folate), vitamin B12 (cobalamin), and vitamin B2 (riboflavin) are all produced by gut microbes.

Species like Bifidobacterium produce vitamins K, B12, biotin, folate, and thiamine. Bacillus subtilis and Escherichia coli synthesize riboflavin, and Lactobacillus produce cobalamin.

Metabolites derived from animal-based resources

Secondary Bile Acids and Coprostanol
Good microbes convert cholesterol and bile acids into coprostanol and secondary bile acids, respectively. These metabolites are poorly absorbed by the intestines and decrease the risk of cardiovascular diseases. In this way, these postbiotics are involved in equilibrium health/disease statuses.

Trimethylamine N-Oxide (TMAO) metabolites
Contrary to the previously described postbiotics, the trimethylamine N-oxide metabolites are associated with adverse effects on human health, including cardiovascular and neurological disorders.

They are commonly derived from carnitine and choline, compounds primarily found in foods of animal origin like beef and pork.

Some species from Ruminococcus transform carnitine and choline precursors into TMAO metabolites (De Filippis et al., 2015).

A vegetarian diet generates low TMAO levels in plasma, which support a plant-based diet for human health.

mechanism of action of the gut microbiome


  • Microbiome research suggests that although inter-individual variability is evident, dietary patterns significantly influences microbial composition.
  • To promote health, an appropriate balance for gut microbiota should exist.
  • A healthy microbiome is a diverse microbiome, and a plant-based diet is a good choice to achieve this.
  • A plant-based diet promotes the production of postbiotics which contribute to human health.


Microbiome, postbiotics, gut microbiota, core microbiome.


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