Evolution of symbiotic bacteria in the distal human intestine

Jian Xu^1,2*, Michael A. Mahowald^1*, Ruth E. Ley¹, Catherine A. Lozupone³, Micah Hamady⁴, Eric C. Martens¹, Bernard Henrissat⁵, Pedro M. Coutinho⁴, Patrick Minx², Philippe Latreille², Holland Cordum², Andrew Van Brunt², Kyung Kim², Robert S. Fulton², Lucinda A. Fulton², Sandra W. Clifton², Richard K. Wilson^1,2, Robin D. Knight⁶, and Jeffrey I. Gordon^1,2

¹Center for Genome Sciences and ²Genome Sequencing Center, Washington University School of Medicine, St. Louis, MO 63108, ³Department of Molecular, Cellular and Developmental Biology and ⁴Department of Computer Science, University of Colorado, Boulder, CO 80309, ⁵CNRS-UMR6098, UniversitŽs Aix-Marseille I & II, Marseille, France, and ⁶Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309

*Contributed equally

Additional files:

Gene Ontology hierarchy file used in the study (zip file)

Raw output from InterProScan (zip archive of tab delimited text files)

Complete lists of numbers of genes assigned to each GO term (zip archive of tab delimited text files)

Parsed list of InterPro ID, InterProScan hits and GO term assignments for each genome (zip archive of tab delimited text files)

Figure 5A with locus tags and bootstrap values (PDF)

Table of SusC/SusD homologs (xls file)

Table of SusC/SusD-linked genes (xls file)

The complete classification of the origin of all protein-coding genes in the gut Bacteroidetes and Porphyromonas gingivalis (xls file)