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Microbiome Diversity: Is it Clinically Meaningful?

by Melissa Blake, ND and Noelle Patno, PhD


The human microbiome and its impact on health has become a hot topic and potent interest for clinicians and researchers alike. The interest should not come as a surprise, as research and clinical evidence have repeatedly demonstrated the significance of a healthy microbiome. Disruptions, specifically in the gut microbiome, have been linked to a plethora of diseases and conditions ranging from obesity to cognitive decline.1

The microbiome plays an essential role in maintaining homeostasis within the host, offering protection from invading microbes, providing cells with essential nutrients, regulating inflammation, and supporting a healthy immune response.2

It is these clinical implications that continue to drive our interest in the potential ability to target and manipulate the state of the microbiome.

This article reviews the concept of microbiome diversity as one of the potential therapeutic targets and reviews the available evidence to support its clinical application.

What is diversity? Is it clinically important or a myth?

Microbiome diversity and balance play an important role in human health over the course of the entire lifecycle.  Diversity is defined as “the condition of having or being composed of differing elements”.3 As it relates to microbiome diversity, the field of research has not yet established a uniform agreement on a standard quantifiable definition since multiple measurement indices may be used to describe diversity.4 Most measurements of microbiome diversity refer to structural diversity. Structural diversity measures the types of bacteria that are present. Functional diversity, as in what the bacteria do, is usually calculated by inference, based on the abundances of genes with known functions.4,5

How is diversity measured?

Until the development of DNA-based culture-independent methods, our knowledge of the bacteria that we play host to was limited to those that grew well in the laboratory.6 The ability to identify and quantify bacterial strains has led to significant improvement in our understanding of microbiome diversity as well as the overall function of the microbiome.3

Sequencing and mapping have allowed for identification of bacteria abundances. The identified sequences are mapped to known microbial taxa (such as genera or phyla) and quantified. Researchers can then apply mathematical models to determine diversity indices. These indices may include Shannon’s index, Simpson index, Inverse Simpson index and/or Chao1.4,5 These models help estimate two aspects of diversity: 1) richness, the number of unique strains and 2) evenness, how equally or evenly are the relative abundance of those strains distributed.4,5

Measurement of microbiome diversity, when applied to one sample, is known as alpha diversity, the diversity within a specific location or individual (also called, “local diversity”).4 Beta diversity compares the microbial composition of one environment, or population, to another, for example between healthy individuals and those with a chronic condition.4

Even with these remarkable advancements, we are not yet able to answer the question of what an optimal microbiome looks like. The human gut microbiome is like a fingerprint, so intimately related to the individual that no two are exactly alike. The highly personalized and always changing composition of the microbiome make it difficult to study and interpret.6

Diversity and disease

Evidence suggests diversity is a marker of a healthy intestinal microbiome.  Normal variations of microbiome diversity are related to age, genetics, the environment and diet among healthy people.5 Generally, microbiome diversity is relatively lower in diseased individuals compared to healthy individuals.7,8

For example, a study comparing the composition of fecal samples found healthy individuals had substantially more microbiome diversity compared to individuals with Crohn’s disease (CD). This example evaluated diversity at the phylum level (most general or lowest resolution of measurement), called “phylogenetic diversity.” Specifically, there was a significantly lower relative abundance of Firmicutes, a phylum of Gram positive anaerobic bacteria that usually account for a large percentage of the fecal microbiome of healthy subjects.8 There was also a global loss of microbial diversity (alpha diversity) in patients with CD.8

A study done in China associated lower microbiome diversity in fecal samples from individuals with Parkinson’s disease (PD). Samples from patients with PD displayed lower species richness, beta diversity and phylogenetic diversity of their gut microbiota relative to those of healthy individuals.9

A similar phenomenon has been observed in patients with psoriatic arthritis as well as in patients with psoriasis. Both groups had lower microbiome diversity (as evaluated by two diversity measurement indices) compared to healthy controls.10

It appears that understanding microbiome diversity, what affects it and how it is measured, are clinically relevant questions to answer.

Diversity vs dysbiosis

Much of the focus in the clinic as well as in the literature has been on dysbiosis as it relates to disease. Diversity and dysbiosis are different but they do share similarities and connections.

Dysbiosis refers to a change in the balance between commensal bacteria and pathogenic strains, typically a loss of beneficial organisms and an increase in harmful ones.9 A disruption in microbiome homeostasis may contribute to a long list of health concerns. Above and beyond gastrointestinal conditions, dysbiosis has been associated with allergies, asthma, metabolic syndrome, cardiovascular disease, immune-mediated conditions, metabolic disease, obesity, and cognitive dysfunction.1

Microbiome diversity relates to the number of unique bacterial strains that are dominant within a specific environment. Not only does the overall number of strains contribute to a diverse microbiome (richness), but also the relative distribution of the strains (evenness).4 Dysbiosis often leads to a reduction in overall microbiome diversity.

As already discussed, studies on Crohn’s patients typically report reduced proportions of Firmicutes. The loss of commensal strains, strains that promote microbiome diversity and symbiosis, may create an environment that allows for the growth of opportunistic bacteria that otherwise would be kept in check. Research has confirmed this, as patients with Crohn’s showed higher levels of pro-inflammatory Gram negative species of the Porphyromonadaceae family.8 Pathogenic strains often will quickly crowd out other bacteria to become the predominant species, contributing to dysbiosis and reduced microbiome diversity.

Is more diversity always better?

Although it appears that microbiome diversity is desirable for health, there are several examples in humans when more diversity is associated with the disease or risk state compared to the healthy controls. As with most things, diversity is relative.  Although a “perfect” microbiome has yet to be identified, we are now able to compare diversity measures to determine the impact various factors have on an individual’s microbiome.

Microbiome diversity starts low at birth and increases over time.11Early determinants of microbiota composition include mother’s health status, delivery method, feeding patterns, and antibiotics.12 An interesting area of research is not only how these factors influence the microbiome but also what the short- and long-term health implications are.

For example, we now know that full-term babies, born vaginally and exclusively breastfed, are host to higher levels of health-promoting gut microbiota, specifically bifidobacteria, and lower numbers of C. difficile and E. coli.13  The microbiome of formula-fed infants is very distinct from exclusively breastfed infants, and also generally higher in diversity. 14

While breastfeeding has been associated with a variety of health benefits,14 formula feeding has been associated with higher rates of infant and childhood obesity.13  In a study to better understand the implications of feeding methods on the microbiome, formula-fed infants were found to have higher diversity and quantity of Lachnospiraceae bacteria at 3 months and higher diversity and quantity of Bacteroidaceae at the 12 month mark.14 Formula feeding in this study was associated with increased risk of being overweight and contributed to a specific gut microbial profile with overall higher diversity relative to the breastfed infants.14

The female reproductive tract is another example when more diversity may not be the optimal state. A healthy female reproductive tract has generally been associated with a “homogeneous Lactobacillus-dominated microbiome”.16 Although composition differs across ethnic groups, a highly diverse vaginal environment has been linked to increased rates of pre-term births in pregnant women, inflammation, and infection.16

Diversity is a relative measurement that research will continue to explore. When evaluating microbiome diversity, it is important to know more than the one measurement.  Consider this analogy. An organization is thought to be diverse when people within the organization belong to each of several ethnic and racial categories. Diversity is generally celebrated and organizations that emphasize diversity are often seen in a positive light. However, diversity does not equal impact or influence. Simply because an organization is high in diversity will not ensure its success. The individuals within the organization need to be engaged, show up to meetings, complete their work, and make progress. The same goes for the microbiome. Diversity can be a positive indication if it’s reflecting more than just representation but rather is evaluating the impact of the individual strains. A microbiota made up of “bad employees” could still measure high in diversity but have overall negative consequences.

Said another way, more or less diversity is a relative measurement. Disruptions in composition that are associated with disease can occur while still maintaining diversity of the microbiota.

Does optimal diversity exist?

Advanced quantification techniques, as well as an increase in studies that include people from broader ranges of age groups, ethnic backgrounds, and living conditions have weakened the idea of a universal optimal microbiota composition.7 The microbiome is highly variable, complex, and influenced by many factors, further complicating the definition of what an optimal state may be.7,17 Although we may see crossover and redundancies when comparing composition at higher taxonomic levels, variations in the dominant phyla are seen across healthy individuals.7

In vitro as well as in vivo along with clinical evidence suggests that various biological effects are associated with specific strains within a species. That evidence has been used to identify pathogens as well as to determine specific strains of probiotics that show clinical effects.

The benefits of commensal bacteria are related to their ability to produce various biological effects. Likely the impact is through both unique and overlapping effects associated with specific strains within a species. For example, several core benefits, such as supporting barrier function18-21 or producing antimicrobial and beneficial metabolites,22-25 are shared by several different strains. This may suggest that function is driven not by the higher taxonomic level but rather by the species and strains that comprise the individual’s microbiota.7,17  In reality, there may be an unlimited number of “healthy normals” in terms of microbial composition, emphasizing the importance for healthcare practitioners to personalize care.

Is diversity clinically relevant?

Measuring the “health” of a person’s microbiome has several limitations. An individual’s microbiome is highly dynamic and changes in response to various factors including diet, stress, and medications.7 Guidelines and parameters for comparison have not yet been established, creating a challenge in interpreting results. However, the enormous progress in our knowledge of microbiome, and its relationship to health, has generated significant interest in how we can apply this information clinically.

Currently, the most reasonable way in clinic to assess microbiome status is a whole stool sample.26  Most panels available to practitioners target a specific number of bacteria, toxins, viruses, and parasites and can provide the absolute abundance of each. Typically, these organisms are identified using a    combination of polymerase chain reaction (PCR), culture, DNA sequencing, mass spectrometry, and microscopic methods. Higher level analyses, such as alpha and beta diversity, can be analyzed. Fecal biomarkers and metabolites may also be included in stool panels and, together, can help a practitioner individualize treatment plans. This type of testing is limited in scope to known and selected organisms on the panel.

Interpreting the results is another challenge as various sequencing methods can produce completely different results. This makes it difficult to compare outcomes in studies with a patient’s sample. There are many determinants of microbiota composition, including age, which also make it difficult to apply study results to a specific patient. Lastly, the idea of a “core” microbiota is unlikely, considering the extreme variability within and between healthy populations.7 Therefore, it is awkward to attempt to find a healthy normal standard for comparison.

Although stool testing may provide some helpful information to help guide treatment plans, it is essential healthcare providers not rely on this data alone but rather in the context of the whole patient.


With so many possible combinations contributing to health and slight variations leading to disease, it is essential that healthcare providers take a personalized approach to optimizing gut health. Emerging technology is developing tools to evaluate microbiome diversity in a clinically-meaningful way that is connected to research showing a link between diversity and health. Evaluating diet and lifestyle factors associated with microbiome diversity and dysbiosis lend a way for the clinician to address adoption of healthy habits that promote an intestinal microbiome associated with health.


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Melissa Blake, ND  completed her pre-medical studies at Dalhousie University in Halifax, Nova Scotia and obtained her naturopathic medical training from the Canadian College of Naturopathic Medicine. Dr. Blake has over 10 years of clinical experience, specializing in the integrative and functional management of chronic diseases.

Noelle Patno, PhD received her PhD in Molecular Metabolism and Nutrition and Masters in Translational Science from the University of Chicago, studying the role of microbial components in intestinal epithelial cell survival related to inflammatory bowel disease. Prior to her graduate studies, Dr. Patno received a chemical engineering degree from Stanford University and worked as an engineer. She has personal experience and interest in preventive nutrition and nutritional therapies for chronic disease, and her current role involves researching and developing probiotics, prebiotics, and other nutritional programs for the promotion of digestive and overall health.

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