The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome

The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.
PLoS Biology (Impact Factor: 9.34). 08/2012; 10(8):e1001377. DOI: 10.1371/journal.pbio.1001377
Source: PubMed


This manuscript describes the NIH Human Microbiome Project, including a brief review of human microbiome research, a history of the project, and a comprehensive overview of the consortium's recent collection of publications analyzing the human microbiome.

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Available from: Dirk Gevers,
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    • "The international effort grew fast, pioneered by the European Metagenomics of the Human Intestinal Tract (MetaHIT) consortium, who, in 2010, published a catalogue of the gut microbiome (Qin et al., 2010). Soon after, in 2012, the HMP published a full description of the composition and diversity of the microbiomes of five human body sites (gut, skin, nares, oral cavity, and vagina) (Human Microbiome Project Consortium , 2012) in addition to a growing collection of articles with more specific microbiome-related projects (URL: http://, eg., Gevers et al., 2012). So far, most of the published data describing the so-called healthy human microbiome come from volunteers in Western countries. "
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    ABSTRACT: Abstract The Human Microbiome Project (HMP) is a global initiative undertaken to identify and characterize the collection of human-associated microorganisms at multiple anatomic sites (skin, mouth, nose, colon, vagina), and to determine how intra-individual and inter-individual alterations in the microbiome influence human health, immunity, and different disease states. In this review article, we summarize the key findings and applications of the HMP that may impact pharmacology and personalized therapeutics. We propose a microbiome cloud model, reflecting the temporal and spatial uncertainty of defining an individual's microbiome composition, with examples of how intra-individual variations (such as age and mode of delivery) shape the microbiome structure. Additionally, we discuss how this microbiome cloud concept explains the difficulty to define a core human microbiome and to classify individuals according to their biome types. Detailed examples are presented on microbiome changes related to colorectal cancer, antibiotic administration, and pharmacomicrobiomics, or drug-microbiome interactions, highlighting how an improved understanding of the human microbiome, and alterations thereof, may lead to the development of novel therapeutic agents, the modification of antibiotic policies and implementation, and improved health outcomes. Finally, the prospects of a collaborative computational microbiome research initiative in Africa are discussed.
    Omics: a journal of integrative biology 05/2014; 18(7). DOI:10.1089/omi.2014.0018 · 2.36 Impact Factor
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    • "These genera, namely, Roseburia, Faecalibacterium, Butyrivibrio, Eubacterium and Phascolarctobacterium, have been suggested to have positive influence on the nutritional status of the children. These genera have earlier been reported to be a part of the normal commensal microflora of the human gut [26]–[32]. Several studies have indicated the beneficial and probiotic properties of these genera in either nutrition harvest from the food or in maintaining the immune stability of the gut. For example, genera like Roseburia and Butyrivibrio are known producers of short chain fatty acids (SCFA) in the intestine [27], [28]. "
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    ABSTRACT: Malnutrition is a global health problem affecting more than 300 million pre-school children worldwide. It is one of the major health concerns in India since around 50% of children below the age of two suffer from various forms of malnutrition. The gut microbiome plays an important role in nutrient pre-processing, assimilation and energy harvest from food. Consequently, dysbiosis of the gut microbiota has been implicated in malnutrition. Metagenomics approach was adopted to investigate the gut microbiome sampled from 20 rural Indian children with varying nutritional status. The changes in the abundances of various taxonomic and functional groups were investigated across these gut microbiomes. A core set of 23 genera were observed across samples, with some showing differential abundances with varying nutritional status. One of the findings of the current study is the positive/negative associations of specific taxonomic and functional groups with the nutritional status of the children. Notable alterations in the architecture of the inter-microbial co-occurrence networks were also observed with changes in nutritional status. A key example is the clustering of potentially pathogenic groups into a distinct hub in severely malnourished gut. Our data does not demonstrate causality with the microbiome patterns that we observed, rather a description of some interesting patterns, whose underlying mechanism remains to be uncovered. The present study envisioned interrelationships between the pattern of gut microbiome and the nutritional status of children. The cause of this pattern needs to be explored. However, insights obtained from the present study form the basis for further metagenomic investigations on larger population of children. Results of such studies will be useful in identifying the key microbial groups that can be utilized for targeted therapeutic interventions for managing severe acute malnutrition.
    PLoS ONE 04/2014; 9(4):e95547. DOI:10.1371/journal.pone.0095547 · 3.23 Impact Factor
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    • "Recently, together with the rapid development of the Human Microbiome Project, numerous computational tools and methodologies have been developed for effective interpretation and visualization of taxonomic and metabolic profiling of complex microbial communities [19], [20] and could be applied to the analysis of the soil microbiota. Particularly, some outstanding computational techniques that could better explain the complexity and heterogeneity of microbial communities are still less applied in the study of the soil microbiota, e.g. "
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    ABSTRACT: As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment) and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function.
    PLoS ONE 04/2014; 9(4):e93445. DOI:10.1371/journal.pone.0093445 · 3.23 Impact Factor
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