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Applied and Environmental Microbiology, April 2007, p. 2727-2734, Vol. 73, No. 8
0099-2240/07/$08.00+0     doi:10.1128/AEM.01205-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Alignment-Independent Comparisons of Human Gastrointestinal Tract Microbial Communities in a Multidimensional 16S rRNA Gene Evolutionary Space{triangledown}

Knut Rudi,1,2* Monika Zimonja,2,7 Bente Kvenshagen,3 Jarle Rugtveit,4 Tore Midtvedt,5 and Merete Eggesbø6

Hedmark University College, Hamar, Norway,1 Norwegian Food Research Institute (MATFORSK), Ås, Norway,2 Østfold Hospital Trust, Fredrikstad, Norway,3 Ullevål University Hospital, Oslo, Norway,4 Karolinska Institute, Stockholm, Sweden,5 Norwegian National Public Health Institute, Oslo, Norway,6 University of Oslo, Oslo, Norway7

Received 24 May 2006/ Accepted 4 February 2007

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.

* Corresponding author. Mailing address: Hedmark University College, Holsetgt. 31, 2306 Hamar, Norway. Phone: 47 62 51 78 53. Fax: 47 62 43 00 01. E-mail: knut.rudi{at}hihm.no

{triangledown} Published ahead of print on 2 March 2007.

Applied and Environmental Microbiology, April 2007, p. 2727-2734, Vol. 73, No. 8
0099-2240/07/$08.00+0     doi:10.1128/AEM.01205-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.





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