Searching across hundreds of databases

Our searching services are busy right now. Your search will reload in five seconds.

X
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

X
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.

Nature biotechnology | Sep 11, 2013

Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community's functional capabilities. Here we describe PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this 'predictive metagenomic' approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.

Pubmed ID: 23975157 RIS Download

Mesh terms: Bacteria | Genes, Bacterial | Genetic Markers | High-Throughput Nucleotide Sequencing | Humans | Metagenomics | Microbiota | Phylogeny | RNA, Ribosomal, 16S | Sequence Analysis, DNA

Research resources used in this publication

None found

Research tools detected in this publication

Data used in this publication

None found

Associated grants

  • Agency: NIDDK NIH HHS, Id: P01 DK078669
  • Agency: NIGMS NIH HHS, Id: T32 GM008759
  • Agency: NHGRI NIH HHS, Id: R01HG004872
  • Agency: NHGRI NIH HHS, Id: U01HG004866
  • Agency: NHGRI NIH HHS, Id: U01 HG004866
  • Agency: NIDDK NIH HHS, Id: P01DK078669
  • Agency: NIGMS NIH HHS, Id: T32 GM080177
  • Agency: Canadian Institutes of Health Research, Id: R01 HG004872
  • Agency: Howard Hughes Medical Institute, Id: 1R01HG005969
  • Agency: NHGRI NIH HHS, Id: R01 HG005969
  • Agency: NHGRI NIH HHS, Id:
  • Agency: NHGRI NIH HHS, Id:

Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.

This is a list of tools and resources that we have found mentioned in this publication.


HUMAnN

A pipeline which takes short DNA/RNA reads as inputs and produces gene and pathway summaries as outputs. The pipeline converts sequence reads into coverage and abundance tables summarizing the gene families and pathways in one or more microbial communities.

tool

View all literature mentions

GraPhlAn

Software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. Used for concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation as a high-resolution microbial tree of life with taxonomic annotations.

tool

View all literature mentions