Expert Commentary

What you need to know about the microbiome

What is the microbiome? We highlight recent research on the unique communities of trillions of bacteria that we all host.

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What is the microbiome?

Like it or not, your body is teeming with trillions of bugs — microbial cells, that is. Thinking about these bacteria and other microorganisms that you host both outside and inside your body might leave you feeling queasy, but they’re actually critical to maintaining your health, from your weight to your mood.

What’s more, this microbial community serves as a unique identifier that contains clues to understanding the past, present and future of its host. That’s why researchers are paying more and more attention to these communities and the genes contained within (commonly called the “microbiome”).

For example, in a letter published in Nature in 2014, Tao Ding and Patrick D. Schloss wrote that there are associations between an individual’s microbiota and various “life-history characteristics,” including whether they were breastfed and what level of education they had attained.

On May 1, 2018, over 20 U.S. government agencies, including the National Science Foundation and several agencies within the Department of Agriculture, released a five-year strategic plan for microbiome research, underscoring the interest in and importance of this work. Beyond just health research, microbiome research has implications in nearly all areas of public policy, including homeland security (“biodefense and biosurveillance”), the environment and criminal justice (forensics).

Agencies like the National Institutes of Health are already funding comprehensive initiatives to document the microbes that inhabit our bodies and their health effects through the Human Microbiome Project, which began in 2007.

This effort, and others, have produced a vast body of research. This explainer will highlight some of the key studies in the field and answer common questions about this buzzy topic.

What does the microbiome of a healthy person look like and do?

A 2016 review published in Genome Medicine by scholars at the Harvard School of Public Health describes various areas where bacteria populate healthy individuals’ bodies and shared features of these communities. A group of 124 healthy people’s gut microbiomes comprised between 1,000-1,500 different species of bacteria; on the individual level, each person had an average of about 160 species. Two families of bacteria were dominant in the guts of most of these individuals, though the ratio of the two varied greatly between subjects.

Other parts of the body, like the skin and mouth, often carry different families of bacteria. Put simply, across healthy individuals, specific areas of the body are often colonized by similar bacteria, and sites located elsewhere carry their own specific strains — your mouth’s bacteria have more in common with a friend’s mouth bacteria than with the communities that populate your skin.

Across the body, bacteria are important to the immune system, but in specific sites their functions can vary drastically. For example, in the mouth, they help to break down carbohydrates and regulate its acidity. They help the skin synthesize vitamin D, and aid digestion in the gut.

The microbiome is relatively stable over time in healthy individuals, according to a 2012 study published by the Human Microbiome Project Consortium in Nature. For more details on what’s known about the ecology of the microbiome, and how it influences health, a  2010 review published in Microbiology and Molecular Biology Reviews provides a comprehensive overview.

How does the microbiome get out of whack?

“Dysbiosis” is a term for changes to the microbiome. A review published in 2014 in Cellular Microbiology by Charisse Petersen of the University of British Columbia and June L. Round of the University of Utah features research showing how diet, infection, medical interventions and an individual’s genetics can alter the microbiome.

Antibiotics offer a clear window into understanding how dysbiosis occurs. The drugs wipe out the harmful bacteria they’re meant to attack as well as benign and helpful microbes. With this loss of diversity, harmful bacteria can grow unchecked, which can result in inflammation and disease. A number of studies published in Nature and Cell Metabolism show how the Western diet, which is low in “microbiota-accessible carbohydrates” can lead to an unhealthy microbiome and subsequent disease.

Which diseases have been linked to the microbiome?

Many studies have established links between dysbiosis and metabolic disease, including type 2 diabetes, obesity and cardiovascular disease. Other diseases linked to the microbiome include Crohn’s disease and inflammatory bowel disease. Low gut microbiome diversity in infancy has been associated with the development of asthma later on, according to a small study published in Clinical & Experimental Allergy in 2013. A study published in Nature Medicine in 2014 indicates that the microbiome influences allergies in mice. A 2011 review published in Dialogues in Clinical Neuroscience by researchers from the University of Colorado describes the “mind-body-microbial continuum,” which presents connections between the microbiome and neurodevelopment. The authors discuss links between microorganisms and conditions with mental and behavioral effects like rabies, toxoplasmosis and autism.

In Science, Harvard School of Public Health Professor Wendy Garrett published a 2015 review of the role of the microbiome in the development of cancer. She writes that about 20 percent of human cancers are linked to microorganisms. While some microbes can spur cancer growth, others offer protective effects. The mechanisms, however, are the same for both functions, which Garrett classifies into three categories: “i) altering the balance of host cell proliferation and death, (ii) guiding immune system function, and (iii) influencing metabolism of host-produced factors, ingested foodstuffs, and pharmaceuticals.” Beyond cancer, scientists have theorized that these basic processes, like bacterially-driven inflammation of the immune system, might also explain why people develop metabolic disease.

Are there ways to right the dysbiotic microbiome?

A review published in Nature in 2012 outlines a few key strategies to promoting healthy microbiota in the gut. Diet, probiotics (“good” bacteria), prebiotics (compounds that encourage the growth of “good” bacteria) and bacteriotherapy (for example, the emerging therapy of fecal transplantation, which is pretty much what it sounds like) have all been shown to help restore healthy microbiota. Research published in April 2018 in Medicine & Science in Sports & Exercise indicates that exercise can improve the microbiome, though the study involved a small sample.

However, certain interventions might be overhyped, especially for healthy adults with diverse microbiota. While yogurt and kombucha tout “live active cultures” and, in some instances, brand themselves as elixirs of health, the science on their effects on the healthy adult’s microbiome isn’t there to match. A 2011 study published in Science Translational Medicine in twins found no significant changes within or between the microbiomes of twins who consumed a commercially available fermented milk product versus those who did not. A spoonful of yogurt is just a drop in the bucket amid the vast community of microbes that flourish in and on your body.

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