Grant: Travel Awards - Institute Community Support

Mycobacteria are a group of bacteria found in many places, such as soil, water, and dust. Some species can cause diseases in humans, like tuberculosis, while others are harmless and commonly found in the environment. Whether healthy people can carry mycobacteria in their bodies without becoming sick, as we do for other types of bacteria, is not clear. The question underlying this research project is whether there is a human mycobacteriome as part of our microbiome. To investigate this question, we used advanced computer-based methods to identify bacteria directly from complex samples that have undergone DNA sequencing, a process known as shotgun metagenomics. However, identifying specific mycobacterial species from these data is challenging because many species have very similar genetic sequences and reference genome databases are incomplete. We compared three new computer programs, called sylph, metapresence, and YACHT, to see how well they could detect mycobacteria in metagenomic samples. Using simulated datasets, we found that sylph performed best: it was highly accurate, worked even when reference genome information was incomplete, and could reliably identify a species when only small numbers of DNA sequence fragments were present. We then applied sylph to samples from the Human Microbiome Project, a comprehensive database of DNA sequencing from various sites in healthy people. Mycobacteria were rarely found on the skin, in the nose, and in the vagina, but were not found in the mouth or gut. Most detected species were environmental rather than those known to be human-associated. Overall, our findings suggest that there is little consistent evidence for a healthy human mycobacteriome.