A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Structure, function and diversity of the healthy human microbiome

Author Posting. © The Authors, 2012. This article is posted here by permission of Nature Publishing Group. The definitive version was published in Nature 486 (2012): 207-214, doi:10.1038/nature11234.Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.This research was supported in part by National Institutes of Health grants U54HG004969 to B.W.B.; U54HG003273 to R.A.G.; U54HG004973 to R.A.G., S.K.H. and J.F.P.; U54HG003067 to E.S.Lander; U54AI084844 to K.E.N.; N01AI30071 to R.L.Strausberg; U54HG004968 to G.M.W.; U01HG004866 to O.R.W.; U54HG003079 to R.K.W.; R01HG005969 to C.H.; R01HG004872 to R.K.; R01HG004885 to M.P.; R01HG005975 to P.D.S.; R01HG004908 to Y.Y.; R01HG004900 to M.K.Cho and P. Sankar; R01HG005171 to D.E.H.; R01HG004853 to A.L.M.; R01HG004856 to R.R.; R01HG004877 to R.R.S. and R.F.; R01HG005172 to P. Spicer.; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.V.; M.J.B. was supported by UH2AR057506; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); S.M.H. was supported by UH3DK083993 (V. B. Young, E. B. Chang, F. Meyer, T. M. S., M. L. Sogin, J. M. Tiedje); K.P.R. was supported by UH2DK083990 (J. V.); J.A.S. and H.H.K. were supported by UH2AR057504 and UH3AR057504 (J.A.S.); DP2OD001500 to K.M.A.; N01HG62088 to the Coriell Institute for Medical Research; U01DE016937 to F.E.D.; S.K.H. was supported by RC1DE0202098 and R01DE021574 (S.K.H. and H. Li); J.I. was supported by R21CA139193 (J.I. and D. S. Michaud); K.P.L. was supported by P30DE020751 (D. J. Smith); Army Research Office grant W911NF-11-1-0473 to C.H.; National Science Foundation grants NSF DBI-1053486 to C.H. and NSF IIS-0812111 to M.P.; The Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231 for P.S. C.; LANL Laboratory-Directed Research and Development grant 20100034DR and the US Defense Threat Reduction Agency grants B104153I and B084531I to P.S.C.; Research Foundation - Flanders (FWO) grant to K.F. and J.Raes; R.K. is an HHMI Early Career Scientist; Gordon&BettyMoore Foundation funding and institutional funding fromthe J. David Gladstone Institutes to K.S.P.; A.M.S. was supported by fellowships provided by the Rackham Graduate School and the NIH Molecular Mechanisms in Microbial Pathogenesis Training Grant T32AI007528; a Crohn’s and Colitis Foundation of Canada Grant in Aid of Research to E.A.V.; 2010 IBM Faculty Award to K.C.W.; analysis of the HMPdata was performed using National Energy Research Scientific Computing resources, the BluBioU Computational Resource at Rice University

The “Most Wanted” Taxa from the Human Microbiome for Whole Genome Sequencing

<div><p>The goal of the Human Microbiome Project (HMP) is to generate a comprehensive catalog of human-associated microorganisms including reference genomes representing the most common species. Toward this goal, the HMP has characterized the microbial communities at 18 body habitats in a cohort of over 200 healthy volunteers using 16S rRNA gene (16S) sequencing and has generated nearly 1,000 reference genomes from human-associated microorganisms. To determine how well current reference genome collections capture the diversity observed among the healthy microbiome and to guide isolation and future sequencing of microbiome members, we compared the HMP’s 16S data sets to several reference 16S collections to create a ‘most wanted’ list of taxa for sequencing. Our analysis revealed that the diversity of commonly occurring taxa within the HMP cohort microbiome is relatively modest, few novel taxa are represented by these OTUs and many common taxa among HMP volunteers recur across different populations of healthy humans. Taken together, these results suggest that it should be possible to perform whole-genome sequencing on a large fraction of the human microbiome, including the ‘most wanted’, and that these sequences should serve to support microbiome studies across multiple cohorts. Also, in stark contrast to other taxa, the ‘most wanted’ organisms are poorly represented among culture collections suggesting that novel culture- and single-cell-based methods will be required to isolate these organisms for sequencing.</p> </div

Phenotypic, genomic, and transcriptional characterization of Streptococcus pneumoniae interacting with human pharyngeal cells.

BACKGROUND: Streptococcus pneumoniae is a leading cause of childhood morbidity and mortality worldwide, despite the availability of effective pneumococcal vaccines. Understanding the molecular interactions between the bacterium and the host will contribute to the control and prevention of pneumococcal disease. RESULTS: We used a combination of adherence assays, mutagenesis and functional genomics to identify novel factors involved in adherence. By contrasting these processes in two pneumococcal strains, TIGR4 and G54, we showed that adherence and invasion capacities vary markedly by strain. Electron microscopy showed more adherent bacteria in association with membranous pseudopodia in the TIGR4 strain. Operons for cell wall phosphorylcholine incorporation (lic), manganese transport (psa) and phosphate utilization (phn) were up-regulated in both strains on exposure to epithelial cells. Pneumolysin, pili, stress protection genes (adhC-czcD) and genes of the type II fatty acid synthesis pathway were highly expressed in the naturally more invasive strain, TIGR4. Deletion mutagenesis of five gene regions identified as regulated in this study revealed attenuation in adherence. Most strikingly, ∆SP_1922 which was predicted to contain a B-cell epitope and revealed significant attenuation in adherence, appeared to be expressed as a part of an operon that includes the gene encoding the cytoplasmic pore-forming toxin and vaccine candidate, pneumolysin. CONCLUSION: This work identifies a list of novel potential pneumococcal adherence determinants

Rank Abundance curves for V1–V3 (black symbols) and V3–V5 (gray symbols) OTUs.

<p>(A) The number of sequences in each OTU. (B) Cumulative rank abundance. For both V1–V3 and V3–V5, on the order of 10–15 OTUs captured half of all individual sequences.</p

Body habitat distribution of non-chimeric and most wanted HMP OTUs.

<p>The distributions of 1,468 non-chimeric HMP OTUs (left panel) and 119 most wanted OTUs (right panel) are shown as phyla (outer circle) and genera (inner circle) at each of the 5 sampled body habitats. Distribution profiles were based on the habitat in which the HMP OTU was found most frequently. Bar graphs illustrate the relative proportion of HMP OTUs from each 16S variable region, shown as phyla. Color codes for all phyla and ‘most wanted’ genera with more than one representative are shown in left and right figure legends, respectively.</p

There were few novel, but many uncultured and unsequenced taxa within the HMP OTUs.

<p>Panels A through F present results from aligning HMP OTUs to six separate 16S sequence databases, indicated. For each HMP OTU, the y-axis of each panel shows the percent identity for the best matching sequence from the queried database, as determined by the program align.seqs in Mothur <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041294#pone.0041294-Schloss1" target="_blank">[30]</a>. The x-axis of each panel shows the fraction of samples in which the OTU was present, at the body site of its highest prevalence. For example, a value of 0.5 means that the OTU was present in, at most, 50% of samples from a particular body site. The colors in all panels indicate assignment to priority groups for whole genome sequencing: red = highest priority, blue = medium priority, gray = low priority. Horizontal lines indicate 98% and 90% sequence identity.</p

Nearly all sequenced taxa have been cultured but not all cultured taxa have been sequenced.

<p>For each taxa, the percent identity from the best match to a human sequenced database (GOLD-Human or HMP-strains) versus the best match to a sequence database of cultured organisms (named or unnamed). The colors in all panels indicate assignment to priority groups for whole genome sequencing: red = highest priority, blue = medium priority, gray = low priority. (A) OTUs that are present in at least 20% of all samples in at least one body habitat; (B) all HMP OTUs.</p

The most prevalent HMP OTUs were also present in other human cohorts.

<p>Databases were created from non-HMP enrolled healthy volunteers in which stool (4A), saliva (4B) and vaginal (4C) microbiomes were characterized (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041294#pone.0041294.s005" target="_blank">Table S2</a>). For each HMP OTU, the y-axis of each panel shows the percent identity for the best matching sequence from the queried database, as determined by the program align.seqs in Mothur <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041294#pone.0041294-Schloss1" target="_blank">[30]</a>. The colors in all panels indicate assignment to priority groups for whole genome sequencing: red = highest priority, blue = medium priority, gray = low priority. Horizontal lines indicate 98% and 90% sequence identity.</p