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Protocols

HMP specifications

Information


Unique identifier OMICS_25873
Name HMP
Alternative name Human Microbiome Project
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Joseph Petrosino

Publications for Human Microbiome Project

HMP citations

 (254)
library_books

Small RNA profiling of low biomass samples: identification and removal of contaminants

2018
BMC Biol
PMCID: 5952572
PMID: 29759067
DOI: 10.1186/s12915-018-0522-7

[…] t. The collapsed reads were mapped against the human genome (GRCh37), including RefSeq exon junction sequences, as well as prokaryotic, viral, fungal, plant and animal genomes from GenBank [] and the Human Microbiome Project [] using Novoalign V2.08.02 (Additional file : Tables S3 to S5) []. These organisms were selected based on their presence in the human microbiome, human nutrition and the publ […]

library_books

Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia

2018
PMCID: 5943399
PMID: 29743478
DOI: 10.1038/s41398-018-0107-9

[…] icrobial communities and possible confounders.To compare the inferred microbial composition found in blood with that in other body sites, we used taxonomic composition of 499 metagenomic samples from Human Microbiome Project (HMP) obtained by MetaPhlAn or five major body habitats (gut, oral, airways, and skin). Of the 23 phyla discovered in our sample, 15 were also found in HMP samples, of which 1 […]

library_books

Gut microbiomes of wild great apes fluctuate seasonally in response to diet

2018
Nat Commun
PMCID: 5934369
PMID: 29725011
DOI: 10.1038/s41467-018-04204-w

[…] s. 2010) for WLG and chimpanzee groups, suggesting that length of time for storage of older samples did not adversely impact diversity in our samples (Supplementary Fig. ).US human sequences from the Human Microbiome Project QIIME community profiling (HMPQCP) dataset were downloaded. Only stool samples sequenced over the V1–V3 region of bacterial 16S rDNA were selected for analysis (175 individual […]

call_split

A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults

2018
mSystems
PMCID: 5915698
PMID: 29719871
DOI: 10.1128/mSystems.00044-18
call_split See protocol

[…] trimming and removal of duplicate reads or of reads of substandard quality were performed with Picard and SAM tools. Functional profiling of high-quality processed reads was facilitated by use of the Human Microbiome Project (HMP) Unified Metabolic Analysis Network (HUMAnN2 V.0.99) pipeline (). Models of microbial metabolic pathways produced by HUMAnN2 were derived from the MetaCyc database () and […]

library_books

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

2018
mSystems
PMCID: 5893860
PMID: 29657970
DOI: 10.1128/mSystems.00039-18

[…] s on the complete data sets available [], not subsamples as in the case of Nd; see Materials and Methods for details.)Next, we evaluated paired metagenomic and 16S rRNA gene amplicon samples from the Human Microbiome Project (HMP) (set II) and observed a similarly high correlation between median Nd and median H′ values per body site (r = 0.93), as well as between Nd and H′ values per data set (r = […]

library_books

Reproducible protocols for metagenomic analysis of human faecal phageomes

2018
Microbiome
PMCID: 5892011
PMID: 29631623
DOI: 10.1186/s40168-018-0446-z

[…] RS013158, SRS013215, SRS014613, SRS014923, SRS015854, SRS016095, SRS016753, SRS017521, SRS018575, SRS018656, SRS019601, SRS020328, SRS022137, SRS024549, SRS045645, SRS053398, SRS054956) deriving from Human Microbiome Project was used for comparisons. […]


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HMP institution(s)
Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
HMP funding source(s)
Supported by grant 2 U54 HG003273 from NIH/NHGRI.

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