Article

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

ABSTRACT

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
    • "Composition of microbiota from nasal passages, oral cavities, skin, and gastrointestinal and urogenital tracts was determined and classified into various phylogenetic and taxonomical groups using the traditional Sanger method and 16S ribosomal RNA gene sequencing. Sophisticated computational algorithms combined with bioinformatics tools were employed to interpret the massive amounts of data (Gevers et al., 2012; Methé, 2012 ). New innovative technologies are currently under development to improve isolation and analysis of unculturable and uncharacterized bacteria, differentiate species, and rapidly sort cells. "
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    ABSTRACT: Abstract Multidisciplinary approaches enabled a better understanding of the connection between human gut microbes and health. This knowledge is rapidly changing how we think about probiotics and related -biotics (prebiotics, synbiotics, pharmabiotics, and postbiotics). Functional -omics approaches are very important tools used to understand interindividual diversity of gut microbiota. Despite diverse gut microbial composition, individuals demonstrated similar microbial metabolic pathways, emphasizing the importance of functional genes. Dysbiosis observed in chronic illnesses such as obesity, diabetes, and inflammatory bowel disease could be an important therapeutic target. Commensal bacteria delivered in the form of fecal transplant, stress-adapted probiotic bacteria, pharmabiotic agents derived from beneficial bacteria, and postbiotic bioactive compounds have enormous potential in the therapeutics and supplement industries for targeting dysbiosis. Several relevant questions are raised in this chapter that will provide a framework to evaluate exponentially increasing data related to the gut microbiome and human health.
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    • "However, this technique does not provide direct evidence of functional capabilities (Gill et al. 2006;Pruesse et al. 2007;Ley et al. 2008). Introduction of next generation sequencing (NGS) allows more extensive analysis of small-subunit 16S ribosomal RNA gene sequences and also WHOle genome shotgun sequencing of microbes to catalogue the bacterial genome (Turnbaugh et al. 2007;Shendure & Ji 2008;Gevers et al. 2012;Weinstock 2012). Since their introduction in 2005, NGS technologies can be classifi ed into two main categories; PCR-based technologies and single-molecule sequencing (SMS) technologies (Shokralla et al. 2012) (Table 2). "

    Full-text · Article · Jun 2015
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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:// bit.ly/1d86hy2, 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.
    Full-text · Article · May 2014 · Omics: a journal of integrative biology
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