Going With The Gut


We all know the importance of the role our DNA plays in our health. But what about the hundreds of thousands of bacteria that live inside us? For example, there are over 1000 species of microbes inside each of us, a total of 10 times more bacterial cells than our own. Our distal gut houses the highest density of these cells in our body; these bacteria  help break down our food as well as harness and store energy from the nutrients we’ve consumed, making it the perfect storm of symbiosis between humans and these bacteria. 

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Image Credit: xkcd.com

This microbial ecosystem has garnered even more attention in the past few years, as research has indicated that these happy helpers also play an unexpectedly large role in immune function. The gut microbiome has been identified as a key player in the maturation and activity of the adaptive and innate immune systems, and changes in microbiome composition are thought to be risk factors for metabolic and inflammatory diseases such as obesity, diabetes, and irritable bowel syndromes. We have only just begun to understand how important this diverse ecosystem can be to our survival and health.

One of the most pertinent biological questions is how perturbing the structure of microbiota affects human health. Antibiotics play a huge role in our society; hundreds of thousands of people around the world take antibiotics chronically. For many, this has led to Clostridium difficile infection (CDI). More commonly known as C. diff, this toxic superbacteria exists on surfaces, especially in hospital settings, and is resistant to heat, ethanol, and most antibiotics. Healthy microbiomes can fight it off with no problem, but antibacterial-compromised gut microbiomes cannot do so, resulting in C. diff taking over and causing debilitating diarrhea. Recently, as a replacement for ineffective bouts of antibiotics, fecal microbial transplants (FMTs) from healthy donors have revolutionized CDI treatment and have been 90% effective. In FMT treatment, microbiomes from donor stool samples are transplanted into CDI patients to repopulate their gut. Almost magically, the donor bacterium takes care of the C. diff and patients see results within a few days. It has been hypothesized that this is due to the release of C. diff growth inhibitors by healthy gut bacteria. Understanding mechanisms like these is critical to developing further safe and efficacious treatments.

OpenBiome, the first stool bank in the world, has been providing hospitals with processed healthy stool from donors for FMT. They are currently supporting clinical research on inflammatory bowel diseases currently considered to be untreatable, such as ulcerative colitis and Crohn’s disease, in order to evaluate if FMT is a viable treatment option. In these clinical trials, and in projects such as the Human Gut Microbiome Initiative, many of the bacterial genomes will be sequenced in order to better understand the roles played by these organisms that literally make us who we are. By studying and understanding the molecular mechanisms behind their function, we can tap into the power and abilities that they can provide for innovative disease treatments.

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