Strain-level dissection of the contribution of the gut microbiome to human metabolic disease

Chenhong Zhang, Liping Zhao

Research output: Contribution to journalArticlepeer-review

44 Scopus citations


The gut microbiota has been linked with metabolic diseases in humans, but demonstration of causality remains a challenge. The gut microbiota, as a complex microbial ecosystem, consists of hundreds of individual bacterial species, each of which contains many strains with high genetic diversity. Recent advances in genomic and metabolomic technologies are facilitating strain-level dissection of the contribution of the gut microbiome to metabolic diseases. Interventional studies and correlation analysis between variations in the microbiome and metabolome, captured by longitudinal sampling, can lead to the identification of specific bacterial strains that may contribute to human metabolic diseases via the production of bioactive metabolites. For example, high-quality draft genomes of prevalent gut bacterial strains can be assembled directly from metagenomic datasets using a canopy-based algorithm. Specific metabolites associated with a disease phenotype can be identified by nuclear magnetic resonance-based metabolomics of urine and other samples. Such multi-omics approaches can be employed to identify specific gut bacterial genomes that are not only correlated with detected metabolites but also encode the genes required for producing the precursors of those metabolites in the gut. Here, we argue that if a causative role can be demonstrated in follow-up mechanistic studies-for example, using gnotobiotic models-such functional strains have the potential to become biomarkers for diagnostics and targets for therapeutics.

Original languageEnglish (US)
Article number41
JournalGenome Medicine
Issue number1
StatePublished - Apr 20 2016

All Science Journal Classification (ASJC) codes

  • Molecular Medicine
  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Fingerprint Dive into the research topics of 'Strain-level dissection of the contribution of the gut microbiome to human metabolic disease'. Together they form a unique fingerprint.

Cite this