MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome

Bioinformatics. 2015 Oct 15;31(20):3368-70. doi: 10.1093/bioinformatics/btv382. Epub 2015 Jun 22.


Microbiome researchers frequently want to know how abundant a particular microbial gene or pathway is across different human hosts, including its association with disease and its co-occurrence with other genes or microbial taxa. With thousands of publicly available metagenomes, these questions should be easy to answer. However, computational barriers prevent most researchers from conducting such analyses. We address this problem with MetaQuery, a web application for rapid and quantitative analysis of specific genes in the human gut microbiome. The user inputs one or more query genes, and our software returns the estimated abundance of these genes across 1267 publicly available fecal metagenomes from American, European and Chinese individuals. In addition, our application performs downstream statistical analyses to identify features that are associated with gene variation, including other query genes (i.e. gene co-variation), taxa, clinical variables (e.g. inflammatory bowel disease and diabetes) and average genome size. The speed and accessibility of MetaQuery are a step toward democratizing metagenomics research, which should allow many researchers to query the abundance and variation of specific genes in the human gut microbiome.

Availability and implementation:

Contact: snayfach@gmail.comS UPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Diabetes Mellitus / microbiology
  • Feces / microbiology
  • Gastrointestinal Microbiome / genetics*
  • Genes, Bacterial
  • Humans
  • Inflammatory Bowel Diseases / microbiology
  • Internet
  • Metagenomics / methods*
  • Molecular Sequence Annotation
  • Software*