What Causes Diversity in a Person's Microbiome?

November 30, 2025 •

4 min read

An estimated 100 trillion microbial cells, including bacteria, fungi, and viruses, reside within the human body, forming a complex and unique ecosystem known as the microbiome. A highly diverse microbiome is often associated with better health outcomes, leading many to question: what causes diversity in a person's microbiome? A combination of inherited and environmental factors shapes this microbial community from birth and throughout a person's life.

Quick Summary

The diversity of a person's microbiome is shaped by a complex interplay of diet, genetics, environmental exposures, and lifestyle choices. Factors like birth mode, medication use, geography, and diet profoundly influence the composition and richness of microbial communities.

Key Points

Early Life Factors: Mode of birth and infant feeding methods, like breastfeeding, establish the foundational diversity of a person's microbiome from the beginning.
Dietary Influence: A varied, plant-based diet rich in fiber and prebiotics is one of the most powerful ways to cultivate a diverse microbial community, while processed foods decrease diversity.
Medication and Toxins: Antibiotics and other medications can act as major disruptors, wiping out beneficial bacteria and negatively impacting diversity, with environmental toxins also playing a role.
Lifestyle Choices: Regular exercise, managing stress, and adequate sleep patterns contribute positively to microbiome diversity, supporting overall metabolic and immune health.
Genetics and Geography: While genetics play a smaller, non-modifiable role, geographical location and associated lifestyles contribute to observable differences in microbial composition across populations.
A Dynamic Ecosystem: The microbiome is not static but a dynamic ecosystem influenced by continuous interactions between our environment, lifestyle, and inherited traits throughout our entire lives.

The Foundational Role of Early Life

Your microbiome's journey begins at birth, with initial colonization profoundly influenced by the circumstances of your arrival.

Mode of Delivery: Infants born vaginally are exposed to the mother's vaginal and gut microbes, which provides a rich initial microbial seeding. This differs significantly from infants born via Cesarean section, whose first colonizers are typically skin-associated bacteria from the operating room environment. This early divergence can have lasting effects on the developing microbiome.
Infant Feeding: The feeding method also plays a critical role. Breastfeeding provides beneficial bacteria and prebiotic compounds that promote the growth of specific microbes, such as Bifidobacterium, which is crucial for early immune system development. Formula-fed infants develop a different microbial profile, which some studies associate with a lower overall diversity compared to breastfed infants.
Maternal Microbiome: Beyond delivery, the mother's own microbiome, even during pregnancy, influences the developing fetus. The mother's diet, stress levels, and antibiotic use can all affect the microbial landscape inherited by the infant.

The Power of Diet and Nutrition

As a person ages, diet becomes one of the most powerful and modifiable factors influencing microbiome diversity. What you eat directly feeds the trillions of microorganisms in your gut, shaping which types thrive and which do not.

Dietary Fiber and Prebiotics: A diet rich in plant-based, fibrous foods provides fermentable fibers and starches that serve as fuel for a wide variety of beneficial bacteria. Prebiotics, which are non-digestible components that promote microbial growth, are found in foods like fruits, vegetables, and whole grains. A diverse intake of these foods helps maintain a diverse microbial ecosystem.
Processed Foods and Sugar: Conversely, a Western-style diet, typically high in processed foods, sugar, and saturated fats, is associated with a reduction in overall microbial diversity. This type of diet can starve the beneficial fiber-loving microbes while promoting the growth of less desirable species.
Probiotics and Fermented Foods: Consuming fermented foods like yogurt, sauerkraut, and kimchi introduces live microorganisms into the gut, potentially boosting diversity. Similarly, probiotic supplements offer a targeted approach to introducing specific beneficial bacterial strains.

Lifestyle and Environmental Influences

Beyond the plate, numerous other factors from daily life to our surroundings leave an imprint on our internal ecosystem.

Medication Use: Antibiotics are a major disruptor of microbial diversity, often wiping out beneficial bacteria along with harmful ones. Other medications, such as acid blockers, can also alter the gut's environment, thereby affecting the microbial community. The long-term effects can be significant and may require specific interventions to restore balance.
Geography and Lifestyle: Studies have shown significant differences in the microbiomes of people living in different regions, influenced by diet, culture, sanitation, and exposure to different microbes in the local environment. People in industrialized nations often show less microbial diversity compared to those in more rural or non-Western regions.
Exercise and Physical Activity: Regular physical activity has been linked to increased microbial diversity and the promotion of beneficial bacteria that produce short-chain fatty acids. A sedentary lifestyle, in contrast, may contribute to reduced diversity.
Stress and Sleep: Chronic stress and disrupted sleep patterns can also negatively impact microbiome composition through hormonal and neurological pathways known as the gut-brain axis. Maintaining good mental health is therefore linked to a healthy gut.

The Immutable Role of Genetics

While environmental factors are highly influential and modifiable, a person's genetics also play a foundational, though smaller, role in shaping their microbiome. Twin studies, for example, have shown that while family members share more similar microbial compositions than unrelated individuals, the environment accounts for the majority of variation. Host genetics can influence factors like immune function, nutrient processing, and the composition of gut-mucus, all of which provide unique niches for microbial colonization. These innate predispositions set a baseline, but the dynamic influence of a person's life and environment constantly builds upon this genetic foundation.

Comparison of Key Factors Influencing Microbiome Diversity


Factor	Impact on Diversity	Influence Level	Example	Notes
Diet	High (Varied plant-based food increases, processed food decreases)	High & Modifiable	Eating a diverse range of fruits, vegetables, and whole grains enhances beneficial microbes.	Long-term and short-term dietary habits can alter microbiota.
Genetics	Medium (Sets a baseline susceptibility and environment)	Inherent & Non-modifiable	Twin studies show a small but definite heritable component.	Host genes influence immune pathways and nutrient metabolism.
Environment & Lifestyle	High (Significant long-term effects)	Modifiable	Living in a rural vs. urban area, exposure to toxins, and exercise levels matter.	Impacts can change over time based on shifts in living conditions.
Medications (e.g., Antibiotics)	Very High (Potent disruptor)	Modifiable	A course of antibiotics can drastically reduce microbial richness.	Recovery is possible, but may require specific probiotic or dietary support.
Early Life Events	High (Foundational)	Inherent & Non-modifiable	Mode of delivery and infant feeding (breastfeeding vs. formula) create initial microbial differences.	These early seeds can influence health trajectories later in life.

Conclusion

Understanding what causes diversity in a person's microbiome reveals a complex interplay of early life events, genetics, and ongoing environmental and lifestyle factors. While we have no control over our genetics or how we were born, we hold significant influence over our diet and lifestyle choices. By prioritizing a diverse, plant-rich diet, exercising regularly, and using medications judiciously, we can foster a rich and resilient internal microbial community. This intentional cultivation of our microbiome is not just about gut health, but an investment in our overall metabolic, immune, and neurological well-being. The research continues to uncover new connections, emphasizing the profound and dynamic relationship between our daily choices and the trillions of organisms that call us home.

For more in-depth information on the human microbiome and its impact on health, including the effects of modern lifestyles, you can explore peer-reviewed articles on the National Institutes of Health website at https://www.ncbi.nlm.nih.gov/.

Frequently Asked Questions

While many factors contribute, diet is widely considered the most powerful and modifiable influence on microbiome diversity. A varied diet rich in plant-based fibers and fermented foods directly supports a wider variety of microbial species.

Yes, genetics do play a role, but it is less significant than environmental factors like diet. Host genes can influence immune responses and gut environment, providing a baseline upon which environmental factors build.

Antibiotics are a major disruptor of the microbiome, as they kill off beneficial bacteria along with harmful pathogens. This can lead to a significant, though often temporary, reduction in microbial diversity.

Yes, research shows a positive correlation between regular physical activity and increased microbial diversity. Exercise is associated with higher levels of beneficial bacteria and improved gut health.

Studies indicate that geography and environment have a notable impact on microbiome diversity. People in industrialized, urban areas tend to have less microbial diversity than those living in rural or more traditional settings.

Early life events, such as birth mode and infant feeding, have a foundational impact on initial microbiome colonization. While this early seeding is important, the microbiome remains dynamic and is continuously shaped by ongoing diet and lifestyle choices.

There is a bidirectional relationship, known as the gut-brain axis, between stress and the microbiome. Chronic stress can negatively impact the composition and diversity of gut bacteria through hormonal and neurological signals.