The Landscape of Genetic Content in the Human Microbiome
29 Pages
Posted: 26 Feb 2019
Sneak Peek Status: Published
See all articles by Braden T. TierneyJoslin Diabetes Center - Section on Pathophysiology and Molecular Pharmacology; Joslin Diabetes Center - Section on Islet Cell and Regenerative Biology; Harvard University - Department of Microbiology and Immunobiology; Harvard University - Department of Biomedical Informatics
Joslin Diabetes Center - Section on Pathophysiology and Molecular Pharmacology; Joslin Diabetes Center - Section on Islet Cell and Regenerative Biology; Harvard University - Department of Microbiology and Immunobiology; University of Waterloo - Department of Combinatorics and Optimization
Joslin Diabetes Center - Section on Pathophysiology and Molecular Pharmacology; Joslin Diabetes Center - Section on Islet Cell and Regenerative Biology; Harvard University - Department of Microbiology and Immunobiology; Harvard University - Department of Biomedical Informatics
Joslin Diabetes Center - Section on Pathophysiology and Molecular Pharmacology; Joslin Diabetes Center - Section on Islet Cell and Regenerative Biology; Harvard University - Department of Microbiology and Immunobiology; University of Alberta - Faculty of Medicine & Denistry
Joslin Diabetes Center - Section on Pathophysiology and Molecular Pharmacology; Joslin Diabetes Center - Section on Islet Cell and Regenerative Biology; Harvard University - Department of Microbiology and Immunobiology
University of California, Berkeley - Department of Electrical Engineering & Computer Sciences (EECS)
Harvard University - Department of Biomedical Informatics
Joslin Diabetes Center - Section on Pathophysiology and Molecular Pharmacology; Joslin Diabetes Center - Section on Islet Cell and Regenerative Biology; Harvard University - Department of Microbiology and Immunobiology
More...
Abstract
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 21 studies. We found staggering genetic heterogeneity in our dataset, identifying that 50% of the genes in both datasets were “singletons”, meaning they were unique to specific individuals. We found that singletons arose from individual-specific, instransient, and extremely rare microbial strains. Further, we estimated that the oral and gut microbiomes universally contain 91 and 239 million unique genes, respectively, and that adequately sampling these spaces, such that each new metagenome contains 1% undiscovered genes, will take 6,000 and 20,000 samples. Overall, these results serve as a potential explanation for the large, unexplained heterogeneity observed in microbiome-derived human phenotypes.
Suggested Citation:
Suggested Citation
Tierney, Braden T. and Yang, Zhen and Luber, Jacob M. and Beaudin, Marc and Wibowo, Marsha C. and Baek, Christina and Patel, Chirag J. and Kostic, Aleksandar D., The Landscape of Genetic Content in the Human Microbiome (January 19, 2019). Available at SSRN:
https://ssrn.com/abstract=3318927 or
http://dx.doi.org/10.2139/ssrn.3318927
This is a paper under consideration at Cell Press and has not been peer-reviewed.