What Is the Microbiome?

By Dr. Jay

The gut hosts trillions of residents with different DNA and structures. Billions of years ago, multicellular organisms lacked the means to process food efficiently and produce enough energy for survival. At some point, we made a trade—allowing different bacteria to become our guests if they could help us digest food. Over time, this symbiotic relationship has allowed us to survive and thrive.

This community of microorganisms is called the microbiome. The microbiota are the living members that make up the microbiome. Some researchers even consider the microbiome a newly discovered organ due to its profound impact on human health.

Why Is the Microbiome Important?

The microbiome plays a vital role in our health. Different communities within it produce chemicals—called metabolites—that influence the body. Some of these are neurotransmitters that directly affect brain function, such as serotonin and dopamine.

It also plays a role in the development of autoimmune diseases. The gut microbiota forms a biofilm along the intestinal wall, protecting its lining. These bacteria promote homeostasis and reduce intestinal permeability. Together, the biofilm forms “ecological niches.” However, inflammation can reduce the thickness of this biofilm, increase intestinal permeability (commonly known as “leaky gut”), and trigger autoimmune conditions.

The Gut as the “Second Brain”

Remarkably, the gut lining produces over 100 million neurotransmitters—similar to those in the central nervous system. This system, called the enteric nervous system (ENS), operates independently of the brain. Because of this independence, the gut is often referred to as the “second brain.”

A close association exists between the gut and brain through the vagus nerve, forming what’s known as the gut-brain connection. Many brain diseases are linked to the enteric nervous system. For instance, Parkinson’s disease is associated with deficiencies in dopamine, which may originate in the gut.

One specific probiotic, Lactobacillus plantarum SP128, is critical for neurological health. Its destruction—often following antibiotic use—can result in reduced dopamine and serotonin levels. This may lead to tremors, depression, and anxiety if not restored.

Probiotics and Mental Health

Even conditions like Alzheimer’s disease have shown related lesions in the enteric nervous system. Another important probiotic, Lactobacillus rhamnosus, produces metabolites that influence the brain. A deficiency in this bacterium may lead to stress, anxiety, and depression.

Lactobacillus rhamnosus is also found in the healthy female genitourinary tract and helps regulate conditions like bacterial vaginosis and small intestinal bacterial overgrowth (SIBO).

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