By Andrea McBeth, ND
In today’s world, we face constant challenges to our health—antibiotics, preservatives in ultra processed foods, environmental toxins, and even societal stressors that disrupt our gut-brain axis. These external pressures act as major perturbations to one of the most sensitive and essential ecosystems within us: the gut microbiome.
Our gut microbiome is not just a collection of bacteria but an interconnected organ system that impacts nearly every aspect of our health. When this system is disrupted—whether by norovirus, repeated antibiotic use, or chronic stress—our ability to bounce back depends on the diversity and resilience of this microbial ecosystem. Without diversity, recovery is hindered, leading to chronic dysbiosis and downstream consequences for immunity, metabolism, and mental health.
Let’s dive deeper into why protecting and restoring microbiome diversity is critical and how postbiotics—along with a balanced gut ecosystem—can help us navigate a world rife with disruptions.
The Anthropocene, the Hygiene Hypothesis, and a Mass Extinction of Microbial Diversity
Our gut microbiome, an organ system honed over millions of years of coevolution, is now facing an unprecedented crisis. Industrialization, urbanization, and modern dietary habits have dramatically altered the environment in which our microbiota evolved, leading to a mass extinction of microbial diversity.
In the Anthropocene—the current epoch marked by human impact on Earth’s ecosystems—our gut microbiome is a reflection of this disruption. The stark contrast between traditional hunter-gatherer populations and industrialized societies illustrates the magnitude of this loss. For example, a study published in Nature found that the Hadza people of Tanzania, who follow a traditional hunter-gatherer lifestyle, harbor an average of 730 gut microbial species. In comparison, the average Californian has only 277 species—nearly a 60% reduction in diversity.
This drastic difference is mirrored in our diets. Hunter-gatherer ancestors consumed between 100 and 150 grams of fiber daily, depending on their habitat, whereas the average American today eats a mere 15 grams. Fiber, the primary fuel for our gut microbes, is essential for maintaining microbial diversity and generating beneficial postbiotics like short-chain fatty acids. Without adequate fiber, microbial populations starve, leading to the extinction of key species.
The hygiene hypothesis offers another perspective on this loss. While reduced exposure to pathogens in industrialized societies has lowered rates of certain infections, it has also deprived our immune system of the microbial diversity it evolved alongside. Babies born in hyper-sanitized environments, delivered via cesarean section, or fed formula instead of breast milk have been shown to develop microbiomes that are less diverse, predisposing them to allergies, autoimmune conditions, and chronic inflammation.
As a result, the microbiome diversity our ancestors relied upon for resilience and health has been eroded over just a few generations. Research by the Sonnenburg Lab at Stanford demonstrated this vividly: in a mouse model, low-fiber diets over multiple generations led to an irreversible loss of microbial diversity. Even after reintroducing fiber-rich diets generations later, the microbial ecosystem failed to recover fully.
Highlighted Takeaway: Modern industrialized lifestyles have caused a mass extinction of gut microbial diversity, leaving us with a fraction of the microbiota our ancestors relied upon for health and resilience. Restoring this diversity requires intentional steps to reintroduce fiber, fermented foods, and other diversity-promoting habits into our daily lives.
The Microbiome as an Organ: A New Perspective
The microbiome functions like an organ—complex, metabolically active, and crucial for maintaining balance in the body. Just as ecosystems like coral reefs or forests require biodiversity to thrive, our gut microbiome relies on a diverse array of microbes to perform its essential functions.
Key functions of the microbiome include:
- Metabolic regulation: Converting fiber and other compounds into beneficial postbiotics like short-chain fatty acids (SCFAs) that regulate inflammation and support brain, liver, and immune function.
- Immune education: Training and modulating immune responses to prevent autoimmune diseases and overactive inflammation.
- Neurological health: Communicating directly with the brain through metabolites, electrical signals via the vagus nerve, and immune pathways.
Highlighted Takeaway: A diverse microbiome acts as a buffer against disruptions, much like a healthy forest can recover from a fire. Without this diversity, our body’s ability to restore balance is compromised.
Perturbations: Threats to Our Internal Ecosystem
From an ecological standpoint, the gut microbiome is sensitive to external insults, or perturbations. These disruptions can strip the microbiome of key species, pushing the system into dysbiosis—a state of imbalance that perpetuates inflammation and disease.
Common perturbations include:
- GI infections: Norovirus or foodborne illnesses can flush out beneficial microbes, leaving gaps in the ecosystem.
- Antibiotics: While lifesaving, antibiotics are a double-edged sword, wiping out both harmful and beneficial microbes.
- Dietary choices: Ultraprocessed foods, preservatives, and low-fiber diets fail to nourish our microbial communities.
- Stress: Chronic psychological and physical stress alters gut motility and microbial metabolism, leading to inflammation.
- Environmental toxins: Chlorinated water, pesticides, poor air quality, and microplastics disrupt microbial diversity and function.
Each of these stressors diminishes the resilience of the microbiome, making it harder for the system to recover after a disruption.
Highlighted Takeaway: Once microbial diversity is lost, it’s difficult—if not impossible—to restore fully. Protecting what diversity we have left is vital.
Why Diversity Matters: Lessons from Ecology
Ecological principles teach us that biodiversity fosters resilience. In the microbiome, a diverse array of species provides redundancy, ensuring that essential functions—like producing SCFAs in order to modulate the immune system—continue even if one species is temporarily knocked out.
However, losing keystone species—microbes with outsized roles—can destabilize the entire system. A powerful analogy is the reintroduction of wolves to Yellowstone National Park: Though few in number, wolves transformed the ecosystem by regulating prey populations and reshaping the landscape. Similarly, microbes like Akkermansia muciniphila or Bifidobacterium infantis play pivotal roles in gut health, despite their small population sizes. When these keystone species are lost due to diet, antibiotics, or other perturbations, the microbiome’s ability to recover diminishes, leading to chronic dysbiosis and long-term health consequences.
Highlighted Takeaway: Diversity is not just about numbers—it’s about having the right microbes in the right balance to maintain a healthy ecosystem.
The Postbiotic Advantage: A Path to Resilience
Postbiotics—metabolites produced by gut bacteria—are the active players in many of the microbiome’s health benefits. These include SCFAs like butyrate, acetate, and propionate, as well as polyphenol metabolites and bile acids.Research shows that postbiotics:
- Reduce inflammation and oxidative stress
- Strengthen the gut barrier, preventing “leaky gut”
- Modulate brain function and behavior
- Improve metabolic health, including blood sugar regulation and lipid profiles
For those with low microbial diversity, introducing postbiotics directly—through fermented foods or targeted supplements—can bypass the need for the microbiome to produce them, offering a lifeline to restore balance.
Highlighted Takeaway: Postbiotics are the microbiome’s way of communicating with the body, translating diet into health outcomes.
Practical Steps to Support Microbiome Resilience
Given the challenges of our modern environment, restoring and protecting microbiome diversity requires a multi-pronged approach:
- Eat fiber-rich foods: Aim for 30–40 grams daily from a variety of sources (fruits, vegetables, legumes, whole grains).
- Incorporate fermented foods: Kimchi, kefir, yogurt, and sauerkraut introduce beneficial microbes and postbiotics.
- Avoid unnecessary antibiotics: Use only when medically necessary and follow with microbiome-supportive care.
- Filter your water: Chlorine and other chemicals in tap water can disrupt the microbiome.
- Use a HEPA air filter in your bedroom to reduce airborne pollutants, improve air quality, and support restful sleep and overall health.
- Manage stress: Practices like mindfulness, exercise, and adequate sleep support gut-brain communication and motility.
- Consider postbiotic supplements: In cases of severe dysbiosis, targeted postbiotics can jumpstart recovery.
A Call to Action: Ecologists of Our Inner World
As stewards of our own internal ecosystems, we must take proactive steps to protect what remains of our microbial diversity. Just as we advocate for rewilding natural environments to combat climate change, we must “rewild” our guts through conscious dietary and lifestyle choices. The microbiome is a fragile yet powerful organ system, uniquely poised to adapt and thrive if given the right tools. By prioritizing diversity—through diet, fermented foods, and postbiotic support—we can build resilience not only in our gut but in our overall health.
Highlighted Takeaway: The health of your microbiome is the foundation of your resilience. Protect it, nourish it, and it will support you through life’s inevitable disruptions.
To conclude, I will leave you with this thought: Our gut microbiome is the ultimate survivalist, capable of adapting to the most hostile environments. But even survivalists need a strong foundation. Let’s give it the care and attention it deserves to thrive in the Anthropocene era.
*If you are interested in learning more, I invite you to check out my lecture at the upcoming Environmental Medicine Conference: Harmony Heals happening virtually February 1-2, 2025. My talk on Environmental Medicine and the Microbiome takes place at 3:30pm PST on Saturday, February 1.