HMD: HUMAN MICROBIOME DATABASE


Human body is harbored by tens of trillions of microbes. These tiny creatures have been living and evolving with us for all of our history, but we still know little about them. Thanks to the explosion of sequencing techniques and big data technology, now we get the chance to have a close look of these familiar strangers

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Note: you can enter sample ID, Project ID, Phylogenetic level name as key words.

Three major characteristics of the site


1  Microorganism

Accurated classification and nomenclature for all of the organisms in the public gut microbiota.

2  Query

Identification of microbiota and community structures typical of a condition or disease state of interest that could be suitable susceptibility biomarkers or bacteriotherapy candidates; identification of conditions or communities where genes or functional capability exist such as conditions with a dominance or absence of antimicrobial resistance or important metabolic pathways; identification and investigation of conditions where species or phylogenetic groups of interest are dominant or absent to further biological and functional understandings of important or poorly described species.

3  BLAST

Identification of unknown sequence.

Basic users groups


1  Microbiology researchers

Identification and investigation of conditions where species or phylogenetic groups of interest are dominant or absent to further biological and functional understandings of important or poorly described species.

2  Clinical and disease based researchers

Identification of microbiota and community structures typical of a condition or disease state of interest that could be suitable susceptibility biomarkers or bacteriotherapy candidates

3  Genetics and Genomics based researchers

Identification of conditions or communities where genes or functional capability exist such as conditions with a dominance or absence of antimicrobial resistance or important metabolic pathways.

Gene Statistics


# ORFS% Complete ORFSTotal length (bp)Average length (bp)N50 (bp)N90 (bp)Max lengthMin length% annotated on Phylum level% annotated on Genus level% annotated on KO% annotated on eggNOG
9,879,89657.74%7,436,156,0557531,03538488,23010021.3%16.3%42.1%60.4%

*ORFs: open reading frame

*N50: it is the length for which the collection of all contigs of that length or longer contains at least half of the total of the lengths of the contigs

*N90: it is the length for which the collection of all contigs of that length or longer contains at least 90% of the total of the lengths of the contigs

KO: KEGG orthologue group

*eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups)

See our paper for details.

Statistics