Journal Article

Identifying biologically relevant differences between metagenomic communities

Donovan H. Parks and Robert G. Beiko

in Bioinformatics

Volume 26, issue 6, pages 715-721
Published in print March 2010 | ISSN: 1367-4803
Published online February 2010 | e-ISSN: 1460-2059 | DOI:
Identifying biologically relevant differences between metagenomic communities

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Motivation: Metagenomics is the study of genetic material recovered directly from environmental samples. Taxonomic and functional differences between metagenomic samples can highlight the influence of ecological factors on patterns of microbial life in a wide range of habitats. Statistical hypothesis tests can help us distinguish ecological influences from sampling artifacts, but knowledge of only the P-value from a statistical hypothesis test is insufficient to make inferences about biological relevance. Current reporting practices for pairwise comparative metagenomics are inadequate, and better tools are needed for comparative metagenomic analysis.

Results: We have developed a new software package, STAMP, for comparative metagenomics that supports best practices in analysis and reporting. Examination of a pair of iron mine metagenomes demonstrates that deeper biological insights can be gained using statistical techniques available in our software. An analysis of the functional potential of ‘Candidatus Accumulibacter phosphatis’ in two enhanced biological phosphorus removal metagenomes identified several subsystems that differ between the A.phosphatis stains in these related communities, including phosphate metabolism, secretion and metal transport.

Availability: Python source code and binaries are freely available from our website at


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  5623 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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