Ron Polk for Mtn Medicine

‘When we eat, so do they. When we travel, they come along. When we die, they consume us.”

—From “I Contain Multitudes,” by Ed Yong.

Today’s Mountain Medicine Column is an introduction (Part 1) to the human microbiome. This introduction will summarize “What is the microbiome all about, and why is it important?” and in subsequent columns, “Where is it going?”

Among many of the profound changes in scientific thinking that have had major impact on our daily lives is the realization that the world of microbes is not always to be feared and conquered. Those that live happily in our gut and body are known as our microbiome. They provide many functions that keep us healthy and are essential — though unseen — partners in our lives.

The old attitudes of “Just take an antibiotic,” and the heavy promotion and use of over-the-counter antibacterial soaps, body washes and hand washes are rapidly changing. Earlier this year, the federal Food and Drug Administration announced that most “antibacterial” soaps and washes are overkill, since plain soap and water are equally effective used properly.

The reasons for these new approaches are twofold. First, antibiotic resistance continues to increase, in part from exposure to unnecessary antibiotics. Second, it is increasingly realized that most of the bacteria that normally reside within and on our bodies — our microbiome — are the products of evolution; they are “normal,” they often have a protective effect to prevent diseases and, most intriguing, these bacteria interact with our bodies, such as our immune system, in ways that appear to be essential for human health.

Most of the bacteria that compose our microbiome live in the gastrointestinal tract. That they serve a protective effect is most evident when antibiotics are taken for treatment of infection. Antibiotics cannot distinguish between the bacteria causing the infection and the microbiome bacteria, and the death of a significant number of the protecting bacteria can result in resistant and pathogenic microorganisms taking over. The most dramatic of these is the unwelcome bacterium Clostridium difficile, or “C. diff”. Clostridium difficile infection (CDI) is the most common cause of hospital acquired infection.

Therapy for CDI usually requires antibiotics to kill Clostridium difficile, but relapse of CDI after a course of antibiotics is not uncommon. Attempts to replace the normal, protective bacteria by fecal transplantation (via enema or capsules) are increasingly used and appear to be effective. However there are potential downsides to this approach. You may have heard of the report in October of two patients who received fecal transplants that contained antibiotic-resistant bacteria and that subsequently caused a new infection. We still have a lot to learn about improving strategies to prevent and treat CDI.

CDI may not be the only adverse consequence of an altered microbiome, called “dysbiosis.” Much of the material to follow is selected from the April 2018 issue of the journal, Nature Medicine: “Current understanding of the human microbiome.” The authors (Gilbert et al.) are leading U.S. scientists in microbiome research. Nature Medicine is a highly regarded peer-reviewed journal.

The composition of an individual’s microbiome is complex, and differed from individual human to individual human. The specific bacteria, their numbers, their locations, as well as nonbacterial microorganisms, including fungi and viruses, are determined by the conditions of birth (vaginal vs. cesarean section), diet (including breast milk vs. formula), exposure to antibiotics, exposure to probiotics, various diseases, lifestyle (e.g., pet ownership. livestock exposure, exercise and stress) and other factors. The microbiome tends to be relatively constant for each individual over their lifetime unless one or more of the preceding variables are introduced.

Differences in microbiome composition have been shown to correlate to, for example, obesity, possibly autism spectrum disorder and depression, childhood onset allergies and asthma, inflammatory bowel disease and Type 1 diabetes. While many of these conditions may include genetics and environmental factors, the microbiome contributes to development and maintenance of the immune system in ways only recently discovered.

Why might a person’s microbiome have an effect on medical conditions that are anatomically distant from the gastrointestinal tract? It appears that microbiome bacteria communicate with one-another and the brain via existing neural pathways. Bacteria produce compounds that may influence the central and peripheral nervous systems, and thus provide feedback to the microbiome. This is very strange stuff.

Human microbiome science is a new, rapidly evolving science. Whether taking tablets of various microorganisms to establish a healthy microbiome or eating yogurt will be effective in preventing or treating the multiple medical conditions affected by our microbiomes is currently unknown. These topics will be explored in future columns.

Finally, a disclaimer. The broad generalizations discussed above are not patient specific and may not be applicable to your specific medical condition. As always, your health care practitioner is in the best position to advise you regarding diagnosis and treatment, including a discussion of the role of the issues just reviewed. However the microbiome story is just beginning. Subsequent research will impact us in ways that will be profound and difficult to predict.

Mountain Medicine is edited by Lostine resident Ron Polk (Google, “Ron Polk SHEA”), with frequent contributions from Wallowa County medical practitioners.

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