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LiteratureArticle Details
PMID: 17337554
Published · ppublish
English
Journal Article
Research Support, Non-U.S. Gov't
Alignment-independent comparisons of human gastrointestinal tract microbial communities in a multidimensional 16S rRNA gene evolutionary space.
Abstract
We present a novel approach for comparing 16S rRNA gene clone libraries that is independent of both DNA sequence alignment and definition of bacterial phylogroups. These steps are the major bottlenecks in current microbial comparative analyses. We used direct comparisons of taxon density distributions in an absolute evolutionary coordinate space. The coordinate space was generated by using alignment-independent bilinear multivariate modeling. Statistical analyses for clone library comparisons were based on multivariate analysis of variance, partial least-squares regression, and permutations. Clone libraries from both adult and infant gastrointestinal tract microbial communities were used as biological models. We reanalyzed a library consisting of 11,831 clones covering complete colons from three healthy adults in addition to a smaller 390-clone library from infant feces. We show that it is possible to extract detailed information about microbial community structures using our alignment-independent method. Our density distribution analysis is also very efficient with respect to computer operation time, meeting the future requirements of large-scale screenings to understand the diversity and dynamics of microbial communities.
MeSH Terms
Bacteria/classification,genetics
Computational Biology/methods
DNA, Bacterial/chemistry,genetics
DNA, Ribosomal/chemistry,genetics
Evolution, Molecular
Feces/microbiology
Gastrointestinal Tract/microbiology
Genes, rRNA
Humans
Infant
Infant, Newborn
Molecular Sequence Data
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Sequence Homology, Nucleic Acid
Chemicals
DNA, Bacterial
DNA, Ribosomal
RNA, Ribosomal, 16S
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Article Info
Journal
Applied and environmental microbiology
Abbr.
Appl Environ Microbiol
ISSN
0099-2240
Email
Published
2007-04-00
Epub
2007-00-02
Pages
2727-34
Language
English
Region
United States
NLM ID
7605801
PMCID
PMC1855614
Subset
IM
Databases
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