The Microbes We Should Be Thankful For

Thomas Kim, Wesleyan class of 2016

Antibiotics have prevented deadly pathogens from killing us for many decades now. However, widespread abuse of antibiotics has led to antibiotic resistance in our pathogens, causing at least 2 million deaths per year. Moreover, the repercussions of antibiotic abuse appear to go way beyond resistance. In his book Missing Microbes, Martin Blaser of New York University proposes that antibiotic abuse has caused our modern plagues of obesity, allergies, asthma, and various gut issues in the United States.

In order to understand the long-term effects of antibiotics, Blaser and his lab use a ‘metagenomic’ approach to study the microbiomes of mice under different antibiotic treatments. That is, his group sequences DNA from the gut to characterize and compare whole microbial communities without the need to cultivate bacteria in the lab. Metagenomics of the gut microbiome is particularly important because it identifies the microbial communities in our bodies and how these microbes affect our health.

In one study, Blaser characterized the gut microbiomes of mouse populations that were exposed to low-doses of penicillin before weaning and found that the microbial community differed from the penicillin-free group. In particular, the microbes Lactobacillus and Allobaculum, both of which play important roles in human digestion, were missing in the antibiotic-treated populations. The mice also showed physical changes, including increased mass and fat.  The same effects are likely in the millions of humans who are treated with antibiotics–note that the typical child in the US has received 10-20 courses of antibiotics by the time he or she is 18 years old.

Blaser has also found that some pathogenic microbes may actually benefit their human hosts. The stomach pathogen Helicobacter pylori has infected humans for many thousands of years and causes ulcers and gastric cancer. It was prominent in the human gut until the mid-twentieth century but is now present in less than 6% of children in the US, Sweden, and Germany due to antibiotics. Beyond its harmful properties, H. pylori appears to confer the benefit of preventing gastroesophageal reflux disease (GERD).

People who take a regimen of antibiotics may become susceptible to chronic Clostridium difficile infection of the gut. One solution, in the form of fecal transplants, has successfully restored and repopulated the gut with healthful bacteria, even eliminating C. difficile pests. However, there are limitations to fecal transplants. The specific microbes needed for good health are not well known, but a few, such as Faecalibacterium prausnitzii have been identified. Researchers hope to identify the specific microbes needed for a healthy microbiome so that the messy transplants won’t be necessary.

Thanksgiving Day is now right around the corner. Most people take time out of their Thanksgiving Day to be thankful for all that they take for granted. Yes, we are grateful for family, food, and maybe football, but we should be especially grateful for the (really!) little things we do not acknowledge on an everyday basis. Perhaps starting on Turkey Day, we can include the microbes that inhabit our bodies to the list of ‘little things’ that we are thankful for, not only because these guys are really little, but also because they play a vital role in our physiology and development. We may be tempted too often to remedy our lesser illnesses with antibiotics, but wholesale elimination of many beneficial microbes is likely to harm us in the long run.