All data on this site is taken from the following publication:
The Landscape of Genetic Content in the Human Microbiome
Braden T. Tierney, Zhen Yang, Jacob M. Luber, Marc Beaudin, Marsha C. Wibowo, Christina Baek, Eleanor Mehlenbacher, Chirag J. Patel, Aleksandar D. Kostic

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Chirag J. Patel
10 Shattuck St.
Boston, MA. 02115

Aleksandar D. Kostic
Joslin Diabetes Center
One Joslin Place
Boston, MA 02215


Despite substantial interest in the species diversity of the human microbiome and its role in human disease, we have not quantitated the scale of human microbiome genetic diversity, an instrumental task for understanding human-microbe interactions. Here, to do so, we conducted a cross-study meta-analysis of metagenomes from two niches, the mouth and gut, amassing 3,655 samples from 13 studies. We found staggering genetic heterogeneity in our dataset, identifying, at the 95% identity level, a total of 45,666,334 non-redundant genes (23,961,508 in the oral, 22,254,436 in the gut). We found that 50% of the genes in both datasets were “singletons”, meaning they were unique to a single metagenomic sample. We identified that singletons were enriched for discrete functions (compared to non-singletons) and arose from sub-population specific and extremely rare microbial strains. Overall, these results serve as a potential explanation for the large, unexplained heterogeneity observed in microbiome-derived human phenotypes.