Nowhere in the body does the theme of ecology, balance and interconnectedness find more resonance than in the gastrointestinal system. Much has been made of the importance of probiotics, or supplemental beneficial bacteria—and rightly so, in this era of overuse of antibiotics. Then came pre-biotics, and now “synbiotics,” or prebiotics in the same capsule as probiotics.

We now know that the community of bacteria in our beings, known as the microbiome, is responsible for all sorts of important functions, from the creation and absorption of vitamins to the regulation of inflammation and even the modulation of our hormones, cognitive function and mood. Our interrelatedness with these smallest of beings, when in harmonious and healthy balance, yields a happier mood, less heart disease, smooth digestive function and elimination, mental clarity and optimized weight. At least that’s what the research suggests.

In our classically Western, interventionist and consumer product-oriented approach to health, we have researched and marketed probiotic preparations in light of this understanding. Doctors recommend the scientifically validated brands and products that are believed to be most helpful. Often times these probiotics help. A recent study published in the journal “Clinical and Translational Gastroenterology” elucidates what many have experienced, however: that sometimes taking probiotics, especially those containing lactobacillus, leads to abdominal pain and bloating.

The study’s author, Dr. Satish Rao, and his colleagues link the experience of abdominal pain and bloating to the presence of bacteria in the small intestine—also known as small intestinal bacterial overgrowth—and the fermentation processes creating lactic acid buildup. Dr. Rao describes how probiotics can sometimes further “dysbiosis,” or an imbalance of the gut flora. Restoring balance always requires a more nuanced approach than taking a pill.

How, then, do we support our gastrointestinal microbiome, our gastrointestinal function, and thus our whole beings? The answer lies in bringing ourselves into balance with the natural world and that which we have evolved to require.

Our gastrointestinal system—think esophagus, stomach, and small and large intestines—is our interface between the inner and outer worlds. What we swallow has the potential to nourish or inflame, to support healthy bacteria or those that are less helpful and even harmful. Our food sources, the soil in which our vegetables are grown, and the emotional state in which we approach our food preparation all contribute to digestive function in fascinating ways.

The more we elevate our consciousness through the choices we make, the behaviors we cultivate and the community relationships we support—think local farmers—the better our systems function.

Just as an ecologist observes which conditions lead to degraded habitat, loss of biodiversity or the collapse of a system, so, too, can we track what triggers symptoms and what helps them. Has our intestinal habitat been degraded by excessive sugar, gluten, GMO-containing food products, weird chemicals and antibiotics? Do we feel better or worse on probiotics? Tests that zero in on our own gut flora and the presence of gas—which can indicate the presence of bacteria in the small intestine—might help increase our understanding. Do we feel better on diets that support our microbiome? Are we at risk for slowed gut motility, as happens with diabetes or under chronic stress? Do we notice an alleviation of symptoms when we eat fewer gas-forming foods? These observations provide clues to our underlying imbalances, and a path forward.

We know that our bodies were not evolved to take in processed, chemical-laden food through the delicate villi and microvilli in our small intestines; trying to do so causes inflammation at this interface. We know that stress shifts our bodies out of the gastrointestinal-supportive parasympathetic nervous system and into fight or flight mode. (Evolutionary rationale: there is no time to stop to eliminate when you are fighting or fleeing.) Mindfulness and nourishing whole foods support every system in our body, especially the gastrointestinal system.

Eating a whole-foods diet with natural sources of beneficial bacteria, and the fiber they need to thrive, is a solid strategy to support your microbiome. This has been borne out in research as the most reliable, sustainable way to a healthy gut flora.

Our beings, and the worlds within worlds therein, are marvelously complex and wise. Cultivating a harmonious relationship with our inner and outer ecologies is a rich practice. If you’d like to deepen your engagement with this process and cultivate a practice community with fellow beings, please come to my Community Medicine Circles in the Commonweal Garden. They are free of charge, supported by Coastal Health Alliance, and open to all.


Anna O’Malley, M.D., is an integrative-family and community-medicine physician at the Coastal Health Alliance. She also practices reciprocal healing at Natura Institute for Ecology and Medicine in the Commonweal Garden, in Bolinas. For more information, visit