What They Don't Want You To Know About Microbiome & Your Health

I talk about the gut microbiome the way I talk about an internal ecosystem that literally runs as the core of our health. When your microbiome is strong and diverse, many other systems in the body function better. When it loses diversity you lose functions. The good news is that many of those functions can be restored if we understand what harms the microbiome and what helps it heal.

Where the microbiome begins

Our microbial story likely starts before birth, but the first major inoculation happens during delivery. Babies born vaginally encounter a flood of maternal microbes in the birth canal. Babies born by C-section miss that initial transfer and often start life with a different early microbiome.

From there, diversity grows through breast milk, the first foods a child eats and the host of environmental exposures that follow. The goal throughout life is to increase and maintain diversity so the microbiome can perform as many useful functions as possible.

What depletes microbiome diversity

Diversity can decline for many reasons. Key disruptors include:

• Antibiotics: lifesaving when needed, but they can decimate the microbiome. After a course of antibiotics the reconstituted microbiome is often different and may favor strains that promote weight gain and metabolic disease. Early life antibiotic exposure is linked in studies to higher risks of obesity, type 2 diabetes, allergies, asthma and even autoimmune conditions later in life.

• Poor diet: the food you eat feeds the microbes. Processed foods and low fiber diets starve many beneficial strains.

• Stress and disrupted sleep: high stress and circadian disruption, such as jet lag, reduce diversity.

• Aging and hormonal transitions: diversity naturally declines with age and shifts during menopause, reducing microbial functions tied to metabolism, immunity and gut integrity.

Aerobic versus anaerobic bacteria and why that matters

The gut is not uniform. The distal colon where most gut microbes live is essentially oxygen free. Many important gut microbes are strict anaerobes. They cannot survive in oxygen and require specialized environments to grow.

That detail matters two ways. First, many probiotics on store shelves are not built from strict anaerobes and so miss functions that live only in the oxygen-free colon. Second, growing strict anaerobes for therapeutic use is technically challenging. They need oxygen-free manufacturing and must be kept viable through production, storage and delivery to reach the colon alive.

Meet Akkermansia muciniphila — the keystone microbe

Akkermansia muciniphila is emerging as one of the most important strains you have probably never heard of. Researchers call it a keystone species because it has outsized effects on gut health. Here is what makes it special:

• Mucin regulation: Akkermansia consumes old mucin — the mucus glue that holds the gut lining together — and stimulates production of new mucin. It helps maintain the integrity of the gut barrier and the so-called tight junctions between cells. When the mucus layer thins, “holes” can form and microbial products can cross into the bloodstream, driving inflammation. Akkermansia helps prevent that.

• Metabolic signaling: Akkermansia secretes a protein called P9 and produces short chain fatty acids such as propionate that can be converted to butyrate. P9 and these metabolites stimulate L cells in the gut to release GLP-1, a hormone that promotes satiety and improves blood sugar metabolism.

• Correlation with health: Lower levels of Akkermansia have been associated with conditions ranging from inflammatory bowel disease to type 2 diabetes and even neurodegenerative disorders.

Because Akkermansia is a strict anaerobe that relies on mucin, it is very hard to grow and deliver as a live product. Many products on the market either contain dead cells, no Akkermansia at all, or are not manufactured in oxygen-free conditions. If you are looking for a live Akkermansia product, seek companies that publish sequencing data and describe oxygen-free manufacturing processes.

Prebiotics, probiotics and postbiotics — how they work together

Understanding the difference is simple and vital:

• Prebiotics: are the food for microbes. Examples include fibers such as inulin and a rich variety of polyphenols from fruits, vegetables, tea, coffee, dark chocolate and red wine.

• Probiotics: are live microbial strains you introduce into the gut.

• Postbiotics: are the small molecules and proteins microbes produce — short chain fatty acids like butyrate, propionate, and microbial proteins like P9. These are the signals that integrate with our physiology.

All three are important. Prebiotics feed and select for beneficial species. Probiotics can reintroduce missing functions. Postbiotics are the actionable chemicals that alter metabolism, immunity, inflammation and gut-brain signaling.

Why butyrate matters

Butyrate is one of the most important postbiotics. Colon cells prefer butyrate as their fuel. It supports colonic health and has been linked to reduced colon cancer risk in studies. Butyrate also stimulates L cells to release GLP-1.

One major caveat: taking butyrate as an oral supplement often fails to deliver meaningful results. The molecule gets consumed by other cells along the intestine before it reaches the target L cells in sufficient amounts. Producing butyrate in situ via live microbes that colonize near L cells is a much more effective strategy because it creates a direct handoff.

Fecal transplants — why they matter

Fecal microbiota transplants are exactly what they sound like: transfer of stool from a healthy donor to a patient. They proved highly effective for recurrent Clostridioides difficile infection where antibiotics have wiped out ecosystem competitors and C. difficile takes over.

For C. difficile the success rates are dramatic and often lifesaving. That success showed scientists that components of a healthy microbiome can cure disease and shifted thinking toward identifying the active parts of stool that confer benefit. Because of safety concerns about transmitting pathogens, researchers are working to isolate the beneficial components and recreate them in manufactured therapies.

Gut brain, vagus nerve and neurological links

There is a direct highway between gut and brain: the vagus nerve. The gut produces large amounts of neurotransmitters such as serotonin, dopamine and GABA. Interestingly, the gut houses neurons that constantly renew, unlike many brain neurons.

Research shows that signs of neurodegenerative disease, such as plaques linked to Parkinson’s, can appear in gut neurons before the brain. Dietary changes that alter the microbiome can impact neurological symptoms in some conditions, including reports of symptom changes in autism with diet modifications. The gut is not only digestion. It is communication.

Practical, evidence-based tips you can use today

• Be judicious with antibiotics: They save lives but use them only when necessary and under guidance.

• Prioritize fiber and polyphenol-rich foods: Fruits, vegetables, beans, whole grains, berries, pomegranate, artichokes, asparagus and leafy greens feed beneficial microbes. If whole foods are hard to access, greens powders or polyphenol supplements can be useful stepping stones.

• Introduce fiber gradually

  . If your microbiome has been depleted you may feel bloated when reintroducing fiber. Start slow, pair with targeted probiotics, and increase over weeks.

• Consider targeted probiotics: For strains like Akkermansia you want products that demonstrate viable, oxygen-free manufacturing and published sequencing evidence.

• During travel: keep consuming fiber- and polyphenol-rich foods, prioritize sleep to avoid sugar cravings, and continue any probiotic supplement you use.

• Use pre and postbiotics together: Feeding the microbes you introduce helps them colonize and produce the signals you want.

"The gut is at your core. If you can have a strong gut microbiome it will really impact all these other systems in your body."

The gut is at your core. If you can have a strong gut microbiome it will really impact all these other systems in your body.

How long does it take to feel changes?

It depends. Some people notice GI symptom improvement in days. Others need months. A practical benchmark is 90 days. Microbiome shifts after major dietary change often stabilize around eight weeks, and key metabolic markers like hemoglobin A1c reflect changes over roughly 90 days. Give targeted interventions time and combine them with dietary changes for the best chance of durable results.

Final thoughts and next steps:

Microbiome science is young but rapidly evolving. Many simple, practical steps powerfully influence your gut — and by extension your metabolism, immune health and even mood. Feed your microbes well, be careful with antibiotics, prioritize sleep and diversity in the diet, and consider evidence-backed targeted probiotics when appropriate. These are the levers that can restore lost functions and help you feel better from the inside out.

If you want to learn more about targeted products and the science behind them visit pendulumlife.com where you can explore formulations and clinical resources. If you are a healthcare practitioner look for the professional science section and clinical trial information.

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