Host-associated and free-living phage communities differ profoundly in phylogenetic composition

PLoS ONE

Volumn 6, Issue 2, 2011, Pages

  Caporaso, J Gregory ^a   Knight, Rob ^a,b   Kelley, Scott T ^c  

^a UNIVERSITY OF COLORADO   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^c SAN DIEGO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIOPHAGE; BIOINFORMATICS; COMMUNITY DYNAMICS; COMMUNITY LIVING; CONTROLLED STUDY; HOST; METAGENOME; MICROBIAL COMMUNITY; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; VIRUS GENOME; BIODIVERSITY; BIOTA; COMPARATIVE STUDY; ECOSYSTEM; GENETIC VARIABILITY; GENETICS; HOST PATHOGEN INTERACTION; HUMAN; NUCLEOTIDE SEQUENCE; PHYSIOLOGY;

BACTERIA (MICROORGANISMS);

BACTERIOPHAGES; BASE SEQUENCE; BIODIVERSITY; BIOTA; ECOSYSTEM; GENETIC VARIATION; HOST-PATHOGEN INTERACTIONS; HUMANS; METAGENOME; PHYLOGENY;

EID: 79952082506     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016900     Document Type: Article

References (16)

1. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI, (2008) Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6: 776-788.
2. Allen B, Willner D, Oechel WC, Lipson D, (2009) Top-down control of microbial activity and biomass in an Arctic soil ecosystem. Environ Microbiol 12: 642-648.
3. Sandaa RA, Gomez-Consarnau L, Pinhassi J, Riemann L, Malits A, et al. (2009) Viral control of bacterial biodiversity-evidence from a nutrient-enriched marine mesocosm experiment. Environ Microbiol 11: 2585-2597.
4. Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, et al. (2008) Functional metagenomic profiling of nine biomes. Nature 452: 629-632.
5. Rohwer F, Edwards R, (2002) The Phage Proteomic Tree: a genome-based taxonomy for phage. J Bacteriol 184: 4529-4535.
6. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
7. Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, et al. (2010) Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466: 334-338.
8. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480-484.
9. Gower JC, (1975) Generalized Procrustes Analysis. Psychometrika 40.
10. Kuczynski J, Liu Z, Lozupone C, McDonald D, Fierer N, et al. (2010) Microbial community resemblance methods differ in their ability to detect biologically relevant patterns. Nat Methods 7: 813-819.
11. Breitbart M, Haynes M, Kelley S, Angly F, Edwards RA, et al. (2008) Viral diversity and dynamics in an infant gut. Res Microbiol 159: 367-373.
12. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO, (2007) Development of the human infant intestinal microbiota. PLoS Biol 5: e177.
13. Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M, (2007) CAMERA: a community resource for metagenomics. PLoS Biol 5: e75.
14. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, et al. (2008) The metagenomics RAST server- a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
15. Hamady M, Lozupone C, Knight R, (2009) Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data. ISME J.
16. Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG, et al. (2007) PyCogent: a toolkit for making sense from sequence. Genome Biol 8: R171.