Ask the doctors: Trusting your gut on gut health

Dear Doctor: I read with interest your column about how sugar likely affects the gut, and I now have questions concerning antibiotic treatment. Are all gut bacteria eliminated? Can they be restored? Do probiotic supplements help the gut return to normal? I thought the body produces its own.

Dear Reader: In the same way that the discovery of penicillin launched a medical revolution in the late 1920s, the near-daily discoveries about the power and potential of the gut microbiome are now transforming our understanding of both health and disease.

The 10 trillion to 100 trillion microorganisms that each of us harbors in our digestive tract consist of more than a thousand species with more than 3 million genes. Not only do they play significant roles in digestion, synthesize vitamins and other nutrients, and coordinate with the immune system, research shows that our gut flora has a hand in regulating mood, weight, inflammation and certain disease processes.

So what happens to the gut microbiome after antibiotic treatment? Two well-regarded studies into the question, one performed in mice and one in healthy men, had similar answers. An outcome common to both studies was that, following antibiotic therapy, the numbers and diversity of the microbial communities were vastly reduced. The other was that once antibiotic therapy concluded, the gut microbiome began to quickly repopulate. However, in both the mouse and human studies, a comparison of pre- and post-therapy fecal samples revealed that the landscape of the new gut microbiomes had changed significantly.

The mouse study found that in addition to nearly eradicating the native microbes, antibiotic therapy reduced the metabolic rate of those that managed to survive. The antibiotics also caused certain changes to the environment of the gut itself. These two factors opened the door to repopulation of the mouse guts by new species, some of them potentially harmful.

The human study found that although the gut had repopulated the majority of its original species six months after antibiotic therapy, nine common beneficial bacteria failed to return. At the same time, several potentially harmful bacteria made an appearance. The takeaway is that while the gut microbiome in most healthy adults is resilient in the face of antibiotics, the breadth and diversity of our microscopic partners do take a hit.

One new area of research is the use of fecal transplants to both restore the original ecosystem of the gut and protect against colonization by undesirable species. This was done in a recent study in patients undergoing intense cancer treatment. Using fecal samples that were frozen and stored prior to their procedures, patients recovered a significant portion of their pre-treatment gut flora.

When it comes to countering the effects of antibiotics with probiotic supplements, though, the jury is still out. One study found that while probiotic supplements successfully colonized the gut, they also delayed the return of native flora. Until we have definitive answers, time and diet look like best approach for gut recovery. That means eating from a wide range of fermented, cultured and fiber-rich foods, and limiting sugar and red meat, all of which have been shown to contribute to gut health.