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What does a "Healthy" Microbiome Look Like?

April 08, 2022 5 min read

What does a "Healthy" Microbiome Look Like? - Layer Origin Nutrition

The microbiome has become a hot topic in scientific and medical research over the past decade.

Composed of upwards of 100 trillion bacteria from 500 or more species, the gut microbiome is recognized as a major contributor to immune system regulation, digestion, metabolic health, cognition, and gene regulation within human cells.

Whether these interactions are beneficial or harmful to the host is dependent upon the types and ratios of bacteria present and how they either facilitate or inhibit our ability to interact with our environments.

In other words, a healthy microbiome is one that:

  1. Allows us to interface optimally with our environment
  2. Helps us to be resilient to rapid changes in our environments and exposures
  3. Protects us from illness
  4. Promotes health and longevity.

This brings about the question: what does a healthy microbiome actually look like?

Qualities of a Healthy Microbiome

Interestingly, the research in this space indicates that the specific gut microbiome signature among healthy populations varies widely across individuals.

Factors that influence microbiome composition include:

  • diet
  • environment
  • genetics

Importantly, a healthy microbiome in one individual may not promote health in another individual. 

Microbial Diversity

One quality that does seem to be associated with a beneficial microbiota is microbial diversity. A healthy microbiome is akin to an old growth forest.

The flora and fauna in the forest each contribute something unique to the ecosystem and, together, they create a homeostasis that supports the health of the whole. The dense, water-trapping topsoil prevents fire from spreading, fungi breakdown dead plants and animals into nutrients that go back into the land to support the organisms living within and upon it, bacteria help plants to harvest nutrients from the soil.

In turn, the plants provide food and oxygen to sustain the animals, and the animals provide carbon dioxide and manure to feed the plants.

Likewise, a healthy microbiome contains a wide range of bacteria, fungi, and viruses that are capable of adapting to a variety of conditions. For example, upon exposure to a pathogen like salmonella, a diverse microbiome may inhibit its growth and colonization, and protect the host from illness.

Moreover, a diverse microbiome produces key nutrients, such as short chain fatty acids, that not only directly feed the cells of the colon, but also modulate the immune system to prevent superfluous inflammation throughout the entire body.

Consequences of Low Diversity

Conversely, a low-diversity microbiome is akin to mono-crop agriculture. Mono-crops of plants like soy or corn are highly susceptible to disease, infestation, and malnutrition. They are also extremely vulnerable to changes in their environment.

Accordingly, these crops are sprayed heavily with fungicides, herbicides, rodenticides, and chemical fertilizers to artificially support their survival throughout the growing season.

Similarly, a low-diversity microbiome can be easily overwhelmed by exposures to pathogens, is incapable of effectively mining nutrients from the diet, and fails to protect its environment (i.e., the colon) from inflammation and injury.

Microbial Diversity and Healthy Aging

Indeed, research shows that healthy aged populations possess much higher microbiota diversity compared to aged populations with co-morbidities.

In one study, elderly individuals with high diversity were shown to have more mobility, faster walking pace, and lower mortality during the study period.

Elderly individuals with lower diversity were prescribed significantly more pharmaceutical drugs, had a higher mortality rate, and lower levels of beneficial bacterial metabolites in their bloodstreams.

“Westernized” Microbiome Versus Tribal Microbiome

The “Westernization” of the microbiome is believed to play a major role in the development of chronic diseases of inflammation including cardiovascular disease, type 2 diabetes, obesity, autoimmunity, cancer and cognitive decline.

Microbiome diversity is much lower among Western populations relative to modern day hunter gatherers.

This is largely the result of increasingly sterile indoor environments, lack of interaction with natural outdoor environments, the prevalence of antibiotics, and consumption of processed foods that lack the prebiotics necessary to feed the microbiota.

Studies on the microbiomes of the Hadza hunter gatherer tribe have revealed that the bacteria in the environment strongly influence microbiota composition.

Microbes from the animals that the men hunt are present within their gut microbiota.

In contrast, the women within the tribe, who consume more fibrous plant matter, have markedly different microbiomes that are more capable of breaking down the plants and extracting nutrients and energy.

Increasing Microbiota Diversity

Fermented Foods 

Although fiber is an important food source for the microbiota, a 2021 study out of the Sonnenburg lab at Stanford showed that a high-fiber diet alone is not sufficient to increase diversity.

While the high-fiber diet did alter microbiome function and metabolism, a fermented food diet was uniquely capable of increasing microbial diversity and exerting anti-inflammatory effects within the body.

Fermented foods have been consumed by cultures around the world for millennia, and their consumption has been linked to benefits including improved weight management, and reduced risk of diabetes, cancer, and cardiovascular disease.

Examples of fermented foods include yogurt, kefir, sauerkraut, kimchi, natto, and kombucha.

Even though fermented foods themselves contains probiotics (i.e., beneficial species of bacteria), the Sonnenburg study showed that these species were not directly resulting in the enhancements in diversity observed.

Instead, these probiotic strains likely create metabolites during the fermentation process that, upon consumption, can promote the growth of other bacteria in the gut.

The process by which metabolic products made by one species of bacteria are consumed by other species of bacteria is known as a cross-feeding interaction.


In addition to fermented foods, prebiotics like human milk oligosaccharides (HMOs) are also likely effective at enhancing microbial diversity in the gut.

HMOs, alongside dark fruits and resistant starches, are particularly effective at feeding Bifidobacteria in the gut.

Bifidobacteria play an important role in gut health because they are major producers of the metabolites lactate and acetate, which are key substrates in cross-feeding interactions.

In other words, the lactate and acetate made by Bifidobacteria subsequently support the growth of many other species in the gut.

Thus, by focusing on supporting Bifidobacteria populations in the gut, we can improve overall microbiota diversity and health.

Indeed, higher levels of Bifidobacteria are associated with healthy aging, lower systemic inflammation, and decreased risk of developing age-related diseases.

The Takeaway

Although the specifics of a healthy microbiome may look quite different across individuals, key features of the microbiome that are associated with improved health outcomes across individuals include:

  • Richness of key probiotic bacteria 
  • Microbial diversity

Individuals can support key probiotic bacteria, e.g. Bifidobacteria, through the consumption of more prebiotic foods or supplements. The production of the key metabolites acetate and lactate by Bifidobacteria subsequently support the growth of many other health-bolstering species in the gut.

Microbial diversity is largely influenced by both diet and environment, and individuals can improve their diversity by both regularly spending time in natural outdoor environments as well as through daily consumption of fiber-rich foods and fermented foods.



Dr. Alexis Cowan, a Princeton-trained PhD specializing in the metabolic physiology of nutritional and exercise interventions.

Follow Dr. Cowan on Instagram: @dralexisjazmyn 




Eisenstein M. The hunt for a healthy microbiome. Nature. 2020 Jan;577(7792):S6-S8. doi: 10.1038/d41586-020-00193-3. PMID: 31996823.

Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature. 2012;489(7415):220-230. doi:10.1038/nature11550

Deng F, Li Y, Zhao J. The gut microbiome of healthy long-living people. Aging (Albany NY). 2019;11(2):289-290. doi:10.18632/aging.101771

Schnorr, S. The Diverse Microbiome of the Hunter-Gatherer. Nature 518, S14–S15 (2015).

Wastyk HC, Fragiadakis GK, Perelman D, Dahan D, Merrill BD, Yu FB, Topf M, Gonzalez CG, Van Treuren W, Han S, Robinson JL, Elias JE, Sonnenburg ED, Gardner CD, Sonnenburg JL. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021 Aug 5;184(16):4137-4153.e14. doi: 10.1016/j.cell.2021.06.019. Epub 2021 Jul 12. PMID: 34256014.

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