Repost: Diversity Matters in Microbiota

Diversity enriches our global ecosystems. It appears to be no different for many sites of the human body hosting microbial populations — albeit with at least one striking exception. For example, vaginal microbiota is distinct in that greater bacterial diversity is seen in women with bacterial vaginosis, which goes against the assumption that higher diversity is always better. Therefore, appraisal of the merits of diversity must be considered in context of the setting; a microbial stew may include a mix of probiotics, commensals and pathogens…it is all about balance.

That said, researchers in the last several decades observed loss of microbial diversity (LOMD) in numerous disorders and diseases.

Although the means by which LOMD is linked to these diseases are complicated, restoring optimum microbial diversity with prebiotic and/or probiotic foods and supplements may have a role in prevention and possibly treatments of these often intractable problems.

Intestinal dysbiosis and loss of microbial diversity

The concept of dysbiosis is often defined as an imbalance in the gut microbial community that is associated with gastrointestinal symptoms, which can lead to a disease. This imbalance is characterized by a decrease in microbial diversity and an increase in pro-inflammatory species.

LOMD appears as the most constant finding of intestinal dysbiosis. Several studies comparing microbiota of people in developing countries with Western counterparts reveal less diversity in the latter groups.

Notably, LOMD appears to be a key factor that links lifestyle in higher income countries with higher rates of chronic diseases.

An excellent table from recent research provides a list of diseases associated with LOMD in higher income countries. Some of these include:

  • Immune diseases: Crohn’s disease, ulcerative colitis, Type 1 diabetes mellitus, celiac disease and allergy
  • Metabolic disease: obesity
  • Cancer: colorectal 
  • Autism

Are these links pointing to a cause or effect of disease? Newer observations strongly argue for a causal relationship. The commensal microbiota can be qualitatively and quantitatively modulated by the environment according to data from the Human Microbiome Project

Loss of microbial diversity and environmental influences

Some of the first clues to variations in microbial diversity came from studies comparing the microbiota of individuals in less developed countries to that of counterparts in Western countries.

LOMD is a feature of industrialized countries. Among the many candidate risk factors causing LOMD, some of them can be highlighted, such as lifestyle, eating behaviors, disruption of biological clock and antibiotic and other drug consumption. This list is not exhaustive.

Lifestyle practices

One notable trend is the dramatic increase in the use of cesarean sections in more developed countries in the last few decades. While lifesaving when complications arise during pregnancy and labor, C-section surgeries are often employed well beyond what is medically necessary. The most recent data reveal that by sub-region, rates range from 3% in West Africa — less than the advised 10% (to reduce mortality)— to a lofty 42% in South America.

While reasons are multifactorial, the trend is worrisome for its implications for maternal and perinatal health. For example, one study showed that children born by C-section have lower total microbial diversity when compared to infants born vaginally. A later systematic review concluded that mode of delivery affects the diversity of the gut microbiota during the first year of the infant’s life with potential long-term effects on the child’s immune system and increased risks to illnesses such as asthma and allergies.


A fiber-rich diet enhances gut microbiota diversity. Unfortunately, Western-style diets are often low in fermentable prebiotic fibers, which can lead to a harmful reduction in beneficial microbes, which normally produce important health-regulating compounds known as postbiotic metabolites. One example is short-chain fatty acids, which provide anti-inflammatory benefits and also compete with pathogens. The result is significantly different microbiota compositions (i.e. less microbiome diversity) than seen in cultures with an intake of traditional high-fiber diets.

Disruption of biological clock

Stress, jet lag, and shift work have been shown to disrupt the biological clock, which can have consequences for the host and the microbiota. The intestinal microbiota in both mice and humans has been shown to exhibit diurnal oscillations, that when disrupted, leads to a LOMD and dysbiosis.


These potent medications fight bacterial infections, which cause disease. But one significant downside —in addition to the development of bacterial resistance — to the current over usage is that antibiotics reduce bacterial diversity of the human intestinal microbiota. Notably, antibiotic use during infancy and childhood is associated with increased incidences of asthma, atopic dermatitis, obesity and other disorders.

Restoring gut microbiota diversity

Changing habits is never easy. But clearly, many modern dietary practices such as high sugar, low fiber and processed foods should be reconsidered.  As we have seen, these foods are detrimental to gut microbiota diversity.

Cesarean sections for convenience or to minimize malpractice should not be allowed. Processed foods should be substituted with fiber-rich fresh fruits, vegetables and grains. Stress should be managed. Antibiotics must only be used when absolutely necessary.


Restoring optimum gut microbiota diversity is an important clinical target for health promotion and disease prevention. Probiotics with high anti-oxidant and anti-inflammatory potential can help. Also, it is important to remember that fiber is the “food” for your probiotic bacteria. Consuming a wide diversity of different fiber-rich foods is critical to create and maintain a healthy microbiome.

Key references

Fredricks, David N et al. “Molecular identification of bacteria associated with bacterial vaginosis.” The New England journal of medicine vol. 353,18 (2005): 1899-911. doi:10.1056/NEJMoa043802

Guarner, Francisco. Translating Microbiome Science: Gut Microbial Diversity and Chronic Disease. Probiota 2020 Presentation.

Human Microbiome Project Consortium. “Structure, function and diversity of the healthy human microbiome.” Nature vol. 486,7402 207-14. 13 Jun. 2012, doi:10.1038/nature11234

Mosca, Alexis et al. “Gut Microbiota Diversity and Human Diseases: Should We Reintroduce Key Predators in Our Ecosystem?” Frontiers in microbiology vol. 7 455. 31 Mar. 2016, doi:10.3389/fmicb.2016.00455

Shade, Ashley. “Diversity is the question, not the answer.” The ISME journal vol. 11,1 (2017): 1-6. doi:10.1038/ismej.2016.118

Leave a comment