The convergence of carbohydrate active gene repertoires in human gut microbes

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 39, 2008, Pages 15076-15081

  Lozupone, Catherine A ^a,b   Hamady, Micah ^c   Cantarel, Brandi L ^d,e   Coutinho, Pedro M ^d,e   Henrissat, Bernard ^d,e   Gordon, Jeffrey I ^b   Knight, Rob ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UCB 450   (United States)

^d CNRS   (France)

^e AIX MARSEILLE UNIVERSITY   (France)

Author keywords

Comparative genomics; Glycoside hydrolases; Glycosyltransferases; Gut ecosystem; Microbial genome evolution

Indexed keywords

CARBOHYDRATE; GLYCOSIDASE; GLYCOSYLTRANSFERASE;

ARTICLE; GENE FUNCTION; GENE SEQUENCE; GENE TRANSFER; INTESTINE FLORA; MICROBIAL GENETICS; PHYLOGENY; PRIORITY JOURNAL; ARCHAEBACTERIUM; BACTERIAL GENE; BACTERIUM; BIOSYNTHESIS; CLASSIFICATION; CLUSTER ANALYSIS; GENE; GENETIC VARIABILITY; GENETICS; HORIZONTAL GENE TRANSFER; HUMAN; INTESTINE; ISOLATION AND PURIFICATION; MICROBIOLOGY; MULTIGENE FAMILY;

BACTERIA (MICROORGANISMS);

ARCHAEA; BACTERIA; CARBOHYDRATES; CLUSTER ANALYSIS; GENE TRANSFER, HORIZONTAL; GENES, ARCHAEAL; GENES, BACTERIAL; GLYCOSIDE HYDROLASES; GLYCOSYLTRANSFERASES; HUMANS; INTESTINES; MULTIGENE FAMILY; PHYLOGENY; VARIATION (GENETICS);

EID: 54449097150     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0807339105     Document Type: Article

References (33)

1. Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102:2567-2572.
2. Willenbrock H, Hallin PF, Wassenaar TM, Ussery DW (2007) Characterization of probiotic Escherichia coli isolates with a novel pan- genomemicroarray. Genome Biol 8:R267.
3. Fraser-Liggett CM (2005) Insights on biology and evolution from microbial genome sequencing. Genome Res 15:1603-1610.
4. Nakamura Y, Itoh T, Matsuda H, Gojobori T (2004) Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nat Genet 36:760-766.
5. Ohno S (1970) Evolution by Gene Duplication (Springer, New York).
6. Mira A, Ochman H, Moran NA (2001) Deletional bias and the evolution of bacterial genomes. Trends Genet 17:589-596.
7. Sonnenburg JL, et al. (2005) Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307:1955-1959.
8. White O, et al. (1999) Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science 286:1571-1577.
9. Turnbaugh PJ, et al. (2007) The human microbiome project. Nature 449:804-810.
10. Snel B, Huynen MA, Dutilh BE (2005) Genome trees and the nature of genome evolution. Annu Rev Microbiol 59:191-209.
11. Dutilh BE, Huynen MA, Bruno WJ, Snel B (2004) The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. J Mol Evol 58:527-539.
12. Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ (2001) Universal trees based on large combined protein sequence data sets. Nat Genet 28:281-285.
13. Daubin V, Gouy M, Perriere G (2002) A phylogenomic approach to bacterial phylogeny: Evidence of a core of genes sharing a common history. Genome Res 12:1080-1090.
14. Ren Q, Paulsen IT (2007) Large-scale comparative genomic analyses of cytoplasmic membrane transport systems in prokaryotes. J Mol Microbiol Biotechnol 12:165-179.
15. Mazmanian SK, Round JL, Kasper DL (2008) A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 453:620-625.
16. Walter J, Schwab C, Loach DM, Ganzle MG, Tannock GW (2008) Glucosyltransferase A (GtfA) and inulosucrase (Inu) of Lactobacillus reuteri TMW1106 contribute to cell aggregation, in vitro biofilm formation, and colonization of the mouse gastrointestinal tract. Microbiology 154:72-80.
17. Xu J, et al. (2003) A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 299:2074-2076.
18. Xu J, et al. (2007) Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 5:1574-1586.
19. Lozupone C, Knight R (2005) UniFrac: A new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228-8235.
20. Lozupone CA, Hamady M, Kelley ST, Knight R (2007) Quantitative and qualitative β diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73:1576-1585.
21. Lozupone C, Hamady M, Knight R (2006) UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7:371-385.
22. Coutinho PM, Henrissat B (1999) Carbohydrate-active enzymes: An integrated database approach. Recent Advances in Carbohydrate Bioengineering, eds Gilbert HJ, Davies G, Henrissat B, Svensson B (Royal Society of Chemistry, Cambridge), pp 3-12.
23. Pupko T, Huchon D, Cao Y, Okada N, Hasegawa M (2002) Combining multiple data sets in a likelihood analysis: Which models are the best? Mol Biol Evol 19:2294-2307.
24. Saitou N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425.
25. Felsenstein J (2004) Inferring Phylogenies (Sinauer, Sunderland, MA).
26. Penny D, Hendy MD (1985) The use of tree comparison metrics. Syst Zool 34:75-82.
27. Larkin JM (1989) Nonphotosynthetic, nonfruiting gliding bacteria. Bergey's Manual of Systematic Bacteriology, eds Staley JT, Bryant MP, Pfenning N, Holt JG (Williams and Wilkins, Baltimore), pp 2010-2138.
28. Stanier RY (1947) Studies on non-fruiting myxobacteria I Cytophaga Johnsonae, N Sp, a chitin-decomposing myxobacterium. J Bacteriol 53:297-315.
29. Warnick TA, Methe BA, Leschine SB (2002) Clostridium phytofermentans sp. nov., a cellulolytic mesophile from forest soil. Int J Syst Evol Microbiol 52:1155-1160.
30. Lerat E, Daubin V, Ochman H, Moran NA (2005) Evolutionary origins of genomic repertoires in bacteria. PLoS Biol 3:807-814.
31. Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797.
32. Chenna R, et al. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31:3497-3500.
33. Knight R, et al. (2007) PyCogent: A toolkit for making sense from sequence. Genome Biol 8:R171.