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In both human and rodent studies, increasing obesity, insulin resistance, and fasting glucose levels correlate linearly with decreasing distance between gut bacteria and the cells lining the intestine. This invasion of bacteria on the front lines of the gut is called "bacterial encroachment," reminding us that our relationship with our microbiota is best characterized as "frenemies." Andrew Gewirtz leads a team at Penn that published the sobering paper in Nature last year, showing how modest amounts of emulsifying agents nearly universally found in processed food damaged the microbiome and intestinal cells, causing colitis in mice. He made the sensible recommendation to avoid processed food in favor of eating fresh, whole foods.
He's also been able to reverse some damaging effects of more processed, purified diets in mice by adding the fermentable fiber inulin to their chow. The inulin feeds the microbiota and makes them more diverse and robust. However, along the lines of the "frenemies" designation, immune compromised mice got sick when fed inulin, meaning we have to be careful about making recommendations for fiber blooming of our gut microbes. It may make sense to use multiple step treatments, eliminating pathogens with temporary low fermentable fiber diets and possibly antibiotics, then adding in more friendly probiotics, feeding them with fiber. These complex protocols have yet to be studied in a systematic way in humans and remain experimental.
Comment: The cutting edge of gut health and disease