What Is the Microbiome?


Writing in The New Yorker on Oct. 22nd, Michael Specter explains the amazing new discoveries about the bacteria, viruses and fungi that colonize our bodies and affect our health. His article, Germs are Us, starts out with a discussion of the bacterium Helicobacter pylori (H. Pylori), found in the stomach of half the people on earth. While on the one hand it is a principal cause of gastric and peptic ulcers, and is associated with an increased risk of stomach cancer, its longevity in the human species, at least 200,000 years, makes it likely that it also plays a positive role in human evolution. Specter explains that we are inhabited from birth (the birth canal, mother’s skin, other people, all our surroundings) with a hundred trillion or more microorganisms. These microbes are in our mouths, digestive tracts, and skin – some 10,000 bacterial species, with a weight of about 3 pounds. They help us digest our food, manufacture vitamins in the colon (biotin and Vitamin K), and help our immune systems prevent infections. While the genes we inherit play a role in our health and disease, so does the microbiome. The human body can be seen more as a ‘vast, highly mutable ecosystem …. than like an individual assembled from a rulebook of genetic instructions’. Streptococcus mutans, in the mouth, is a principal cause of tooth decay, releasing acid when we eat sugar. Dentists are working on a number of measures to control this bacterium, including chlorhexidine and xylitol chewing gum. The bacterium Lactobacillus sakei may be capable of warding off sinusitis; this bacterium is destroyed by antibiotics. While antibiotics are ‘the signature medical achievement of the 20th century, and have saved millions of lives’, there is a downside to their use in terms of our microbiome. People without H. Pylori in their gut seem to be more sensitive to allergens, and are more likely to have had asthma as children. Children born by C-section lack many microbes transferred in the birth canal. Research from Finland and Germany indicate that these children may have more allergies. There is also a strong relationship between the presence of H. Pylori and two stomach hormones that control appetite. Ghrelin induces eating, and leptin suppresses the appetite. People whose stomachs have H. pylori have less ghrelin after a meal and stop eating; people without it may not get the message to stop and become obese. The reason that animals (poultry, cows and pigs) fed with antibiotics gain weight faster may have more to do with this mechanism than with treatment of illness. About 40% of children treated with broad-spectrum antibiotics develop diarrhea – and treatment with a probiotic (good bacteria for the gut) may prevent this disease. About 10% of people carry a bacterium called Clostridium difficile (C. difficile), which is normally held in check by other bacteria in the gut. When given antibiotics, people with C. difficile can develop severe, life threatening diarrhea and gut inflammation. Researchers are now using a technique called fecal transplant, in which they take intestinal bacteria from healthy donors and place them in the patient’s intestines. Cures have occurred with this treatment when nothing else has worked.






Specter ends his article with cautionary advice on probiotics, which he considers over-advertised without backup research. In the future we may know more about beneficial bacteria, but at present he thinks there is insufficient knowledge to say which bacteria should be used. After reading this, I did a search of current medical research on the use of probiotics. There are considerable findings on the use of beneficial bacteria to decrease antibiotic induced diarrhea, in decreasing childhood allergy, in improving the outcome of patients undergoing surgery for colon cancer, in vaginal infections in women, in the management of adult-onset diabetes, and in many other areas. My own conclusion is that a daily probiotic capsule from a reputable supplement company, with or without the ingestion of high-quality unsweetened yogurt, can help to prevent many gastro-intestinal infections. Use antibiotics when they are needed for serious bacterial infections, but always be mindful of your own beneficial bacteria.


Sadja Greenwood M.D., MPH back issues on this blog