Making Friends with Your Microbiome

Why gut bacteria is vital to your health

An abstract illustration of a bacterial colony represents the microbiome, the healthy bacteria in your gut.

Why gut bacteria is vital to your health

At some level, people have always suspected there’s a relationship between the brain and the stomach. Consider phrases like “gut instinct” or “gut feeling.” An avalanche of research is confirming this intuition, adding terms like “gut-brain axis” to the mix. Every month, new studies offer additional evidence for this profound connection.


But it’s not just two human organs talking to each other. The gut is colonized by around 100 trillion microbes — including thousands of different bacterial, fungal and viral species — that play a critical role in this constant chatter. A balanced microbial ecosystem can support good health, helping our bodies modulate hormones, neurotransmitters, inflammation and even pain.


On the other hand, an imbalanced system may play roles in cancer, diabetes, inflammatory bowel disease, obesity, depression and many other conditions.


“We are recognizing that when we call the gut ‘the second brain,’ it may actually be the first one,” says Robert Bonakdar, MD, director of pain management at Scripps Center for Integrative Medicine. “This is because what we eat — or don’t eat — can have a significant impact on gut inflammation and the makeup of our gut microbiome, which can send signals to the brain that ultimately affect many aspects of our health, our mood and how we deal with stress and pain.”

Diet and disease

Gut microbes have long been pigeonholed as either good or bad, but that’s turning out to be a major oversimplification. Like people, gut microbes have their own self-interests to look after, such as finding food and making more microbes. As long as their interests coincide with ours, everything is in balance — a condition scientists call “homeostasis.” But if the system loses homeostasis, bad things can happen.


“We are beginning to find that people who have less microbial diversity — a reduced overall population and fewer types of bacteria — are more prone to inflammatory conditions, including inflammatory bowel disease and certain types of chronic pain,” Dr. Bonakdar says.


“There is even preliminary research linking the microbiome to neurological conditions, including migraines, Parkinson’s and dementia. There is really no condition that has not been linked in some way to our microbial community, although the evidence is stronger in some areas.”


Many things may impact the gut microbiome: environmental toxins, stress, disease, even loud noises. However, diet — particularly the so-called Western diet, rich in unhealthy fats and carbohydrates — is likely the greatest offender.


“We know that the standard, highly processed American diet typically depletes important micronutrients and fiber,” Dr. Bonakdar says. “A number of studies have demonstrated that the transition to a Western diet in traditional countries begins to increase the occurrence of certain conditions, including inflammatory bowel disease, which is highly linked to both a reduced number of microbes and a loss of microbial diversity.”


On the other hand, a healthy diet may have a positive effect on the microbiome. Early evidence hints that the same strategies that support the cardiovascular system and glucose metabolism may also help keep the microbiome in balance. In other words, exercise; eat lean proteins, fruits, and vegetables; and take steps to mitigate stress.

Probiotics and prebiotics

As people have become more aware of these gut flora, there’s been increased interest in supporting them. Two approaches are to add microbes through diet (probiotics), or to eat nutrients that support these resident microbes (prebiotics).


Some animal studies have shown that targeted probiotics can reduce pain and perform other therapeutic functions; however, the research is in its early days and caution is recommended. While it would be nice to take a pill — or eat a yogurt — to restore microbial balance, probiotic therapies face a number of challenges. The millions of bacteria in yogurt or kimchi may have a tough time integrating into an ecosystem that contains trillions. Also, for economic reasons, many retail probiotics contain only bacteria species that are easily isolated and cultured — not necessarily the most therapeutic strains.


Perhaps most importantly, one-size-fits-all solutions generally fall short. A probiotic that might help in overcoming anxiety may have little effect on inflammation. Any personalized approach should match a targeted probiotic cocktail with a patient’s specific needs.


“I think it is too early to have an absolute take on what individuals should do across the board,” says Dr. Bonakdar. “I tell patients to incorporate many different components in their diet to support good health. This means eating the rainbow of plant foods, which we

know increases our fiber and prebiotic intake, as well as incorporating various fermented foods. Specific probiotic strains may benefit certain conditions. Talk to a health care provider who can clarify the science.”

MLB Hall of Fame pitcher Trevor Hoffman is featured on the cover of the March issue of San Diego Health.

This content appeared in San Diego Health, a publication in partnership between Scripps and San Diego Magazine that celebrates the healthy spirit of San Diego.

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