The Microbiome and Health
GENESIS, INFLUENCE, AND EFFECTS The Human Microbiomeâ€™s Many Facets Susan V. Lynch, PhD, and Ariane R. Panzer Traditionally, the medical community has viewed microbes as the cause of illness and sought to eliminate them. This notion, however, is shifting as current re-
search has illustrated that microorganisms living on and within the human body can not only live in harmony with their hosts but are actually necessary for maintenance of human health. The human body is made up of trillions of cells, but for every one of these human cells there are ten times more microbial cells. These microbes exist as part of complex communities composed of bacteria, fungi, and Archaea as well as eukaryotes. The composition of the microbiome varies from site to site across a single human body (for example, the composition of the oral microbiome is distinct from that of the gut); however, at least in healthy subjects, the microbial composition at or in a specific anatomical site is relatively similar from person to person. This entire collection of microbial communities on and within the human body is referred to as the human microbiome. In healthy humans, the relationship that exists between the host and its microbiome is beneficial for both organisms. Humans offer a protected, nutrient-rich environment in which microbes readily colonize and proliferate, while the host is the beneficiary of a wealth of microbial functions that it does not have the capacity to perform by itself. These microbial communities, particularly those resident in the gastrointestinal tract, perform critical functions, such as metabolism of indigestible dietary fibers to produce small-chain fatty acids, an essential energy form for the human cells that lines the gastrointestinal tract. Additionally, they participate in immune development during the critical neonatal stage of development, have been shown to afford protection against infectious microbes, and are associated with maintenance of the immune system in a state of homeostasis.
Variation Across Age and Geography
The composition of microbial communities on and within the human body is influenced by a range of common but variable exposures including diet, local environment, and host genetics, among others. Evidence for this comes from a large study published in 2012 by a group of scientists led by Dr. Jeffrey Gordon of Washington University, St. Louis. The study compared the gut microbiome of Malawian, Amerindian, and U.S. residents aged zero to seventy years and found that the composition differed considerably with age. According to their observations, the gut microbial community undergoes a period of rapid diversification and assembly over the first three years of life, a consistent feature across all three populations. While this had been observed in previous studies with smaller numbers of American children, the multinational study also discovered that U.S. and non-U.S. individuals had distinctive gut bacterial communities WWW.SFMS.ORG
with different functional capacities, which were highly reflective of the distinct diet and geographical residence of these groups.
Antibiotics and Species Loss
Antibiotics also significantly influence the human microbiome. Les Dethlefsen and David Relman from Stanford University found in 2010 that antibiotic administration rapidly decreases gut microbial diversity, and while these bacterial communities are able to rebuild themselves within a relatively short period of time (one to four weeks) following antibiotic exposure, the reassembled communities lacked certain species and did not completely recover to the pretreatment composition. Instead, these communities existed in an alternate yet stable compositional state. While the impact of species loss and the effect of this alternative stable state on long-term health outcomes is currently unknown, significant reductions in community diversity are emerging as a universal characteristic of a range of chronic inflammatory diseases of humans. These observations have led to growing concern that overuse of antibiotics in Western nations may represent a contributory factor to the growing prevalence of chronic inflammatory diseases associated with perturbed gut microbiota.
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SEPTEMBER 2014 SAN FRANCISCO MEDICINE
San Francisco Medicine, Vol. 87, No. 7, September 2014