Viruses in the faecal microbiota of monozygotic twins and their mothers (original) (raw)
Kunin, V. et al. A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome Res.18, 293–297 (2008) ArticleCAS Google Scholar
Tyson, G. W. & Banfield, J. F. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ. Microbiol.10, 200–207 (2008) CAS Google Scholar
Angly, F. et al. Genomic analysis of multiple Roseophage SIO1 strains. Environ. Microbiol.11, 2863–2873 (2009) ArticleCAS Google Scholar
Oliver, K. M., Degnan, P. H., Hunter, M. S. & Moran, N. A. Bacteriophages encode factors required for protection in a symbiotic mutualism. Science325, 992–994 (2009) ArticleCASADS Google Scholar
Schuch, R. & Fischetti, V. A. The secret life of the anthrax agent Bacillus anthracis: bacteriophage-mediated ecological adaptations. PLoS ONE4, e6532 (2009) ArticleADS Google Scholar
Casjens, S. Prophages and bacterial genomics: what have we learned so far? Mol. Microbiol.49, 277–300 (2003) ArticleCAS Google Scholar
Tettelin, H. et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc. Natl Acad. Sci. USA102, 13950–13955 (2005) ArticleCASADS Google Scholar
Finkbeiner, S. R. et al. Metagenomic analysis of human diarrhea: viral detection and discovery. PLoS Pathog.4, e1000011 (2008) Article Google Scholar
Breitbart, M. et al. Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol.185, 6220–6223 (2003) ArticleCAS Google Scholar
Zhang, T. et al. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol.4, e3 (2006) Article Google Scholar
Breitbart, M. et al. Viral diversity and dynamics in an infant gut. Res. Microbiol.159, 367–373 (2008) ArticleCAS Google Scholar
Turnbaugh, P. J. et al. A core gut microbiome in obese and lean twins. Nature457, 480–484 (2009) ArticleCASADS Google Scholar
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics22, 1658–1659 (2006) ArticleCAS Google Scholar
Turnbaugh, P. J. et al. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc. Natl Acad. Sci. USA107, 7503–7508 (2010) ArticleCASADS Google Scholar
Qin, J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature464, 59–65 (2010) ArticleCAS Google Scholar
Angly, F. E. et al. The marine viromes of four oceanic regions. PLoS Biol.4, e368 (2006) Article Google Scholar
Rodriguez-Brito, B. et al. Viral and microbial community dynamics in four aquatic environments. ISME J.4, 739–751 (2010) Article Google Scholar
White, J. R., Nagarajan, N. & Pop, M. Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput. Biol.5, e1000352 (2009) ArticleADS Google Scholar
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res.32, 1792–1797 (2004) ArticleCAS Google Scholar
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol.26, 1641–1650 (2009) ArticleCAS Google Scholar
Sharon, I. et al. Photosystem I gene cassettes are present in marine virus genomes. Nature461, 258–262 (2009) ArticleCASADS Google Scholar
Rodriguez-Valera, F. et al. Explaining microbial population genomics through phage predation. Nature Rev. Microbiol.7, 828–836 (2009) ArticleCAS Google Scholar
Rey, F. E. et al. Dissecting the in vivo metabolic potential of two human gut acetogens. J. Biol. Chem.285, 22082–22090 (2010) ArticleCAS Google Scholar
Magnuson, R. D. Hypothetical functions of toxin-antitoxin systems. J. Bacteriol.189, 6089–6092 (2007) ArticleCAS Google Scholar
DeShazer, D. Genomic diversity of Burkholderia pseudomallei clinical isolates: subtractive hybridization reveals a _Burkholderia mallei_-specific prophage in B.pseudomallei 1026b. J. Bacteriol.186, 3938–3950 (2004) ArticleCAS Google Scholar
Heath, A. C. et al. Ascertainment of a mid-western US female adolescent twin cohort for alcohol studies: assessment of sample representativeness using birth record data. Twin Res.5, 107–112 (2002) Article Google Scholar
Thurber, R. V., Haynes, M., Breitbart, M., Wegley, L. & Rohwer, F. Laboratory procedures to generate viral metagenomes. Nature Protocols4, 470–483 (2009) ArticleCAS Google Scholar
Becker, A., Kuster, H., Niehaus, K. & Puhler, A. Extension of the Rhizobium meliloti succinoglycan biosynthesis gene cluster: identification of the exsA gene encoding an ABC transporter protein, and the exsB gene which probably codes for a regulator of succinoglycan biosynthesis. Mol. Gen. Genet.249, 487–497 (1995) ArticleCAS Google Scholar
Gon, S., Faulkner, M. J. & Beckwith, J. In vivo requirement for glutaredoxins and thioredoxins in the reduction of the ribonucleotide reductases of Escherichia coli. Antioxid. Redox Signal.8, 735–742 (2006) ArticleCAS Google Scholar
Padovani, D., Thomas, F., Trautwein, A. X., Mulliez, E. & Fontecave, M. Activation of class III ribonucleotide reductase from E.coli. The electron transfer from the iron-sulfur center to S-adenosylmethionine. Biochemistry40, 6713–6719 (2001) ArticleCAS Google Scholar
Garriga, X. et al. nrdD and nrdG genes are essential for strict anaerobic growth of Escherichia coli. Biochem. Biophys. Res. Commun.229, 189–192 (1996) ArticleCAS Google Scholar
Tabor, C. W. & Tabor, H. 1,4-Diaminobutane (putrescine), spermidine, and spermine. Annu. Rev. Biochem.45, 285–306 (1976) ArticleCAS Google Scholar
Gomez-Alvarez, V., Teal, T. K. & Schmidt, T. M. Systematic artifacts in metagenomes from complex microbial communities. ISME J.3, 1314–1317 (2009) Article Google Scholar
Hamady, M., Walker, J. J., Harris, J. K., Gold, N. J. & Knight, R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nature Methods5, 235–237 (2008) ArticleCAS Google Scholar
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods7, 335–336 (2010) ArticleCAS Google Scholar
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol.73, 5261–5267 (2007) ArticleCAS Google Scholar
Fouts, D. E. Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res.34, 5839–5851 (2006) ArticleCAS Google Scholar
Angly, F. E. et al. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput. Biol.5, e1000593 (2009) ArticleMathSciNet Google Scholar
Angly, F. et al. PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics6, 41 (2005) Article Google Scholar
Breitbart, M. et al. Genomic analysis of uncultured marine viral communities. Proc. Natl Acad. Sci. USA99, 14250–14255 (2002) ArticleCASADS Google Scholar
Delcher, A. L., Bratke, K. A., Powers, E. C. & Salzberg, S. L. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics23, 673–679 (2007) ArticleCAS Google Scholar
Jensen, L. J. et al. STRING 8–a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res.37, D412–D416 (2009) ArticleCAS Google Scholar
Finn, R. D. et al. The Pfam protein families database. Nucleic Acids Res.36, D281–D288 (2008) ArticleCAS Google Scholar
Haft, D. H., Selengut, J. D. & White, O. The TIGRFAMs database of protein families. Nucleic Acids Res.31, 371–373 (2003) ArticleCAS Google Scholar
Faith, J. J., Olson, A. J., Gardner, T. S. & Sachidanandam, R. Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context. BMC Bioinformatics8, 344 (2007) Article Google Scholar
Rohwer, F., Seguritan, V., Choi, D. H., Segall, A. M. & Azam, F. Production of shotgun libraries using random amplification. Biotechniques31, 108–112, 114–106 118 (2001) ArticleCAS Google Scholar
Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol.5, R12 (2004) Article Google Scholar
Grissa, I., Vergnaud, G. & Pourcel, C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res.35, W52–W57 (2007) Article Google Scholar
Gordon, D., Desmarais, C. & Green, P. Automated finishing with Autofinish. Genome Res.11, 614–625 (2001) ArticleCAS Google Scholar
R Development Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna) 〈http://www.r-project.org〉 (2009)