Be thankful for your gut microbes this Thanksgiving

By: Daniel McDonald While you kick back and relax after your Thanksgiving dinner, your gut microbiota – the collection of beneficial microbes, mostly bacteria, that inhabit your lower intestine – will be hard at work breaking down the food you ate and carrying out all kinds of other essential functions. Research on the microbes that call your intestine home has shown they can affect your brain, treat a hospital-acquired condition called Clostridium difficile infection (CDI), and much more. Did you know that you can change them by exercise or travel, and you can change them much more by jetlag? Since 2012, the American Gut Project (AGP) has been collecting gut microbiome data from citizens scientists all over the world to understand the extent of microbial diversity associated with humans. In the five years since the AGP launch, over 10,000 citizen scientists have contributed to our rapidly evolving knowledge of the human microbiome (the bacteria, fungi, archaea, and viruses that inhabit the human body). We’re revolutionizing our understanding of what the microbiome is connected to and what factors may change it. We launched the AGP over Thanksgiving in 2012, a time of the year when a lot of Americans are thinking about their gut. We had been working on the National Institutes of Health-funded Human Microbiome Project (HMP), which had generated a huge amount of public interest, but it was difficult for the public to get involved. To be enrolled in the HMP main cohort, you had to be healthy at every site on the body and examined by a physician in either St. Louis or Houston. So that meant the vast majority of people couldn’t participate. For the AGP, we kept it simple. We asked people to go online and purchase a sampling kit. Much like National Geographic’s Genographic project, the AGP is participant-supported, meaning the purchase covers the cost of processing and analyzing the sample. These financial contributions, as well as the financial support from philanthropies, are fully invested in the research effort, and we have been excited to see participants from all over the globe inspired to join our effort. The AGP is an academic effort run by Knight Lab at the University of California San Diego in coordination with its Center for Microbiome Innovation. We place all of the de-identified data in the public domain at the European Nucleotide Archive or on the Qita platform, and the software to process it is available open source, so if you’re motivated, you can get involved in the analysis as well as the data collection. Our kit looks very low tech – just a couple of swabs, although we spent months figuring out exactly the right ones to use (even forensics-grade swabs, guaranteed free of human DNA, often have a lot of bacteria, which may contaminate our samples and generate inaccurate results). Assuming you want to examine your gut bacteria, you’ll poop, wipe, swab the bathroom tissue – if it’s brown, we have enough DNA for analysis – and mail it back to us. At our lab, the technical part starts using robots and lasers to determine microbial DNA sequences, followed by using supercomputers to generate results. By allowing anyone to send in microbiome samples for analysis – not just from the lower intestine but also their mouth, skin, and even vaginal swabs – we continue to find new types of microbes and microbiome configurations that have never been seen before. In addition, since we ask a wide range of questions, including many suggested by participants, we are able to start connecting changes in the microbiome to differences in health, lifestyle, geography, and many other factors.