The human microbiome is the community of microorganisms, including bacteria, fungi, and viruses, that inhabits the body, primarily residing in the gut. Microbial diversity refers to both the richness (total species present) and the evenness (relative abundance of species). Studies consistently find that individuals in industrialized societies exhibit a significantly lower variety of gut microbes compared to traditional populations. Scientists believe this reduction in biodiversity represents a loss of our “ancestral” microbial heritage, driven by modern lifestyle factors. This decrease is a major concern because a diverse microbial community is associated with resilience and proper bodily function.
The Industrialized Diet
The shift toward highly processed, Western-style diets is a primary factor driving the reduction in microbial diversity. These modern diets are low in fermentable fiber, or microbiota-accessible carbohydrates (MACs), the essential fuel source for many beneficial gut bacteria. When MACs are scarce, fiber-degrading microbes, such as Ruminococcus, cannot thrive and disappear.
This population reduction is a generational loss that can be irreversible. This is evident when comparing industrialized microbiomes to traditional communities, where taxa like Prevotellaceae are abundant in traditional populations but nearly absent in Westernized guts. High consumption of processed ingredients, fats, and sugars can also favor the growth of less-beneficial organisms.
Artificial sweeteners and emulsifiers, ubiquitous in processed foods, directly disrupt the gut’s mucosal layer. This creates an environment less favorable for the complex, anaerobic bacteria that constitute a diverse microbiome. When fiber-fermenting microbes are depleted, the community’s ability to produce beneficial metabolites is compromised.
Medical Interventions and Hygiene
Modern medical and hygiene practices, while improving life expectancy, disrupt the establishment and maintenance of microbial communities. The widespread use of broad-spectrum antibiotics causes “collateral damage” by killing targeted pathogens and beneficial bystand species. A single course of antibiotics can lead to the death of over half of common gut bacterial strains, resulting in diversity loss.
This acute disturbance, known as dysbiosis, allows opportunistic pathogens, such as Clostridioides difficile, to quickly colonize the vacant space. Although the microbiome may partially recover, full restoration can take months or years, and some ancestral strains may be permanently lost. Repeated courses of antibiotics, particularly in early childhood, compound this effect.
Early Life Colonization
The rising rate of cesarean section (C-section) deliveries interferes with the natural microbial seeding process of vaginal birth. Vaginally born infants are exposed to the mother’s microbes, providing initial colonization of species like Lactobacillus and Bacteroides. C-section infants are colonized by microbes from the mother’s skin and hospital environment, often resulting in lower diversity and higher abundance of opportunistic species.
Infant formula use further exacerbates this difference. Breast milk contains specific microbes and human milk oligosaccharides (HMOs) that act as prebiotics to selectively promote the growth of beneficial species. Formula lacks these components, hindering the establishment of a diverse microbial community during the critical developmental window of infancy.
Loss of Environmental Exposure
Modern urban living limits exposure to the diverse microbial sources necessary for a resilient microbiome. Spending less time outdoors, especially in natural green spaces or soil, reduces the input of new microbes. Traditional populations show greater diversity due to their close contact with soil, animals, and natural food sources.
This lack of environmental input supports the “hygiene hypothesis,” suggesting that reduced microbial exposure during early life impairs immune system development. The immune system relies on diverse microbial signals to differentiate between harmless environmental microbes and pathogens. Insufficient training, due to hyper-sanitized indoor environments, can lead to immune dysregulation.
High sanitation and the use of antimicrobial products further reduce microbial dispersal in the home. This limits the variety of strains that can diversify the gut community, resulting in a more uniform microbial profile among individuals in industrialized settings.
Observed Health Consequences of Low Diversity
The concern about decreasing microbial diversity stems from its correlation with non-communicable diseases prevalent in industrialized nations. A low diversity microbiome is characterized by dysbiosis, where beneficial anaerobic bacteria are replaced by a simpler, less stable community dominated by opportunistic species. This shift compromises the microbiome’s functional capacity, including its ability to produce short-chain fatty acids (SCFAs), essential for gut health and immune regulation.
This loss of functional capacity and stability is linked to an increased incidence of immune-related and metabolic disorders. Reduced diversity correlates with conditions such as obesity and Type 2 diabetes due to altered energy extraction and signaling pathways.
A less diverse gut community weakens the body’s defenses, increasing susceptibility to severe infections. The loss of SCFA-producing bacteria, which maintain the gut barrier, can lead to increased gut permeability and chronic low-grade inflammation. This systemic inflammation plays a role in links between low diversity and other chronic conditions.
Associated Health Conditions
Low microbial diversity is associated with an increased risk of:
- Allergies and asthma
- Inflammatory bowel disease (IBD)
- Eczema in childhood
- Metabolic syndromes (obesity and Type 2 diabetes)
- Certain central nervous system disorders
- Chronic fatigue