The Dirt on Immunity: How Soil, Sauerkraut, and Whole Foods Feed Your Gut

The immune system is a network of biological processes that protects an organism from diseases. It detects and responds to a wide variety of pathogens, from viruses to parasitic worms, as well as cancer cells and objects such as wood splinters, distinguishing them from the organism’s own healthy tissue.

Scientists have found that microbiomes are essential in shaping the development of innate and adaptive immunity and, in turn, the immune system shapes the microbiome.

So how can we improve our microbiome, which is primarily located in the gut, and thus improve our immune system?

The immune system and microbiome connection: This bidirectional relationship is well documented — roughly 70–80% of the body’s immune cells reside in gut-associated tissue, and the gut microbiota actively shapes the development of T-cells, antibody-producing B-cells, and other immune components, while the immune system in turn helps regulate which microbial species thrive. Disruption of this balance — called dysbiosis — has been linked not just to digestive issues but to autoimmune disorders, inflammatory disease, and even cardiovascular and neurological conditions.

Gardening and soil contact: Have you heard of this microbe? Mycobacterium vaccae is a harmless bacterium common in healthy soil. Research associated with Dr. Christopher Lowry has found that contact with it (through skin contact or inhalation while gardening) can stimulate serotonin production in ways that mirror the effect of certain antidepressants, while also helping regulate immune function. Lowry has noted that as societies have urbanized and lost regular contact with soil-based bacteria that once helped calibrate our immune systems, this may be contributing to rising rates of inflammatory disease.

Eat Prebiotic Foods: Many people waste money (and health) by neglecting the link between prebiotics and probiotics. Prebiotics are food for the probiotics, so if your diet is poor on prebiotics, your expensive probiotic pills will not make much of an improvement in your gut microbiome. Hence, eat these prebiotic foods regularly: leeks, asparagus, oats, bananas, and chicory root; the skin of vegetables and fruits; beans; artichokes; and apricots are all rich prebiotic sources. They work by feeding beneficial bacteria that produce short-chain fatty acids important for gut-lining integrity.

Eat Probiotic Foods: Eating sauerkraut daily, either homemade or from the cooler in the market, since the one on the store shelves is pasteurized and thus contains very few probiotics, will dramatically improve your microbiome. Similarly, yogurt (from animals or plants) will also improve your microbiome. Also eat kimchi, kombucha, miso, and kefir, all of which introduce live Lactobacillus and Bifidobacterium strains.

Avoid processed/factory-farmed foods: Emulsifiers and artificial sweeteners common in processed foods have been shown in studies to erode the protective mucus layer of the gut lining, while antibiotic residues in factory-farmed meat can directly reduce microbial diversity.

Sleep and stress management also significantly shape the microbiome — chronic stress alters gut bacterial composition and increases intestinal permeability (“leaky gut”). Thus, practice yoga and meditation regularly to reduce stress.

A Dramatic Study on How Quickly Diet Changes the Microbiome

A striking 2015 study published in Nature Communications by researcher Stephen O’Keefe put this connection to microbiomes and diet. Colon cancer rates are more than ten times higher in African Americans than in rural South Africans, and researchers suspected diet was the reason. So, for two weeks, under close supervision, they had a group of African Americans eat a high-fiber, low-fat African-style diet, while a group of rural South Africans ate a high-fat, low-fiber Western-style diet.

The results were dramatic and reversed for each group. The African Americans’ guts shifted toward more fiber-fermenting bacteria and produced more butyrate, a compound that protects against colon cancer, while their cancer-risk biomarkers dropped.

The rural Africans saw the opposite. Their protective short-chain fatty acid production fell, harmful secondary bile acids rose, and their cancer-risk markers climbed. In just two weeks, diet alone reshaped both groups’ microbiomes and disease risk, thus showing strong evidence that what we eat, far more than genetics, determines gut health.

About The Author

Ramesh Bjonnes

Ramesh Bjonnes has been teaching and writing about yoga philosophy and history for the past 25 years. He is the co-founder of the Prama Institute, a yoga retreat center in the Blue Ridge Mountains of North Carolina, USA, where he is director of the Prama Wellness Center. He is the author of three books on yoga and Tantra, including A Brief History of Yoga. His forthcoming book is titled The Lost Teachings of Tantra. Websites: www.prama.org  www.rameshbjonnes.org