The Prevalence of Species and Strains in the Human Microbiome: A Resource for Experimental Efforts

Abstract

Experimental efforts to characterize the human microbiota often use bacterial strains that were chosen for historical rather than biological reasons. Here, we report an analysis of 380 whole-genome shotgun samples from 100 subjects from the NIH Human Microbiome Project. By mapping their reads to 1,751 reference genome sequences and analyzing the resulting relative strain abundance in each sample we present metrics and visualizations that can help identify strains of interest for experimentalists. We also show that approximately 14 strains of 10 species account for 80% of the mapped reads from a typical stool sample, indicating that the function of a community may not be irreducibly complex. Some of these strains account for >20% of the sequence reads in a subset of samples but are absent in others, a dichotomy that could underlie biological differences among subjects. These data should serve as an important strain selection resource for the community of researchers who take experimental approaches to studying the human microbiota.

Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species

“…Accordingly, the true functional potential of a microbiome cannot be inferred from species composition alone, and species-level comparative analyses may fail to capture important functional differences across samples. Recent efforts to catalog the relative abundance of known strains in human microbiome samples (Kraal et al, 2014) may recover some of these differences but are limited to sequenced reference genomes and are not be able to identify novel, yet to be sequenced, variation. Gene-centric shotgun metagenomic studies on the other hand, may identify genes or pathways that are differentially abundant across samples, but cannot necessarily attribute these shifts to specific species or strains.…”

Neisseria cinerea isolates can adhere to human epithelial cells by type IV pilus-independent mechanisms

“…These commensal species can be isolated from humans and various animals (Berger, 1962) although they rarely cause disease. Several of the commensal Neisseria species can be found in the human oral cavity or nasopharynx (Gold et al, 1978;Knapp & Hook, 1988;Kraal et al, 2014;Kristiansen et al, 2012;Sheikhi et al, 2015) and must therefore be able to associate with cells of the human airways. This has been shown in vitro for some species, such as Neisseria lactamica (Green et al, 2011); however, relatively little is known about the molecular mechanisms that mediate interaction of the non-pathogenic Neisseria with the human host.…”

Discovery of MRSA active antibiotics using primary sequence from the human microbiome

“…While R. equi has historically been regarded as an opportunistic pathogen seen in animals and immune-compromised patients, 20 R. erythropolis is found as a part of the normal human nasal, mouth and eye microbiota. 21,22 Interestingly, the occurrence of Rhodococcus species in the gut increases dramatically to a median of 30% in some patients diagnosed with ulcerative colitis (UC).…”