Microbial community resemblance methods differ in their ability to detect biologically relevant patterns View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2010-09-05

AUTHORS

Justin Kuczynski, Zongzhi Liu, Catherine Lozupone, Daniel McDonald, Noah Fierer, Rob Knight

ABSTRACT

High-throughput sequencing methods enable characterization of microbial communities in a wide range of environments on an unprecedented scale. However, insight into microbial community composition is limited by our ability to detect patterns in this flood of sequences. Here we compare the performance of 51 analysis techniques using real and simulated bacterial 16S rRNA pyrosequencing datasets containing either clustered samples or samples arrayed across environmental gradients. We found that many diversity patterns were evident with severely undersampled communities and that methods varied widely in their ability to detect gradients and clusters. Chi-squared distances and Pearson correlation distances performed especially well for detecting gradients, whereas Gower and Canberra distances performed especially well for detecting clusters. These results also provide a basis for understanding tradeoffs between number of samples and depth of coverage, tradeoffs that are important to consider when designing studies to characterize microbial communities. More... »

PAGES

813-819

References to SciGraph publications

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  • 2008-11-30. A core gut microbiome in obese and lean twins in NATURE
  • 2010-05-06. Soil bacterial and fungal communities across a pH gradient in an arable soil in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 1987-04. Compositional dissimilarity as a robust measure of ecological distance in PLANT ECOLOGY
  • 2008-10. Worlds within worlds: evolution of the vertebrate gut microbiota in NATURE REVIEWS MICROBIOLOGY
  • 1987-04. An evaluation of the relative robustness of techniques for ecological ordination in PLANT ECOLOGY
  • 2007-10-17. The Human Microbiome Project in NATURE
  • 2008-02-10. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex in NATURE METHODS
  • 2010-02-11. Characterisation of microbial communities colonising the hyphal surfaces of arbuscular mycorrhizal fungi in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2005-07-31. Genome sequencing in microfabricated high-density picolitre reactors in NATURE
  • 2007-08-21. PyCogent: a toolkit for making sense from sequence in GENOME BIOLOGY
  • 1980-10. Detrended correspondence analysis: An improved ordination technique in PLANT ECOLOGY
  • 2010-05-05. Direct sequencing of the human microbiome readily reveals community differences in GENOME BIOLOGY
  • 2001-10-01. Ecologically meaningful transformations for ordination of species data in OECOLOGIA
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nmeth.1499

    DOI

    http://dx.doi.org/10.1038/nmeth.1499

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1006708540

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/20818378


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