메뉴 건너뛰기




Volumn 3, Issue 1, 2018, Pages 38-46

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BACTERIOPHAGE; BACTEROIDETES; CRASSPHAGE; GENE EXPRESSION; GENE REPLICATION; GENE STRUCTURE; GENETIC CONSERVATION; GENETIC DATABASE; GENOMICS; HUMAN; INTESTINE FLORA; METAGENOMICS; MICROBIAL DIVERSITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; VIRUS FORMS; BIOLOGICAL MODEL; CHEMISTRY; CLASSIFICATION; GENETICS; MOLECULAR GENETICS; PHYLOGENY; PROTEIN DATABASE; VIROLOGY; VIRUS GENOME;

EID: 85033594015     PISSN: None     EISSN: 20585276     Source Type: Journal    
DOI: 10.1038/s41564-017-0053-y     Document Type: Article
Times cited : (210)

References (42)
  • 1
    • 0037453721 scopus 로고    scopus 로고
    • Global phage diversity
    • Rohwer, F. Global phage diversity. Cell 113, 141 (2003).
    • (2003) Cell , vol.113 , pp. 141
    • Rohwer, F.1
  • 2
    • 34548792911 scopus 로고    scopus 로고
    • Marine viruses-major players in the global ecosystem
    • Suttle, C. A. Marine viruses-major players in the global ecosystem. Nat. Rev. Microbiol. 5, 801-812 (2007).
    • (2007) Nat. Rev. Microbiol. , vol.5 , pp. 801-812
    • Suttle, C.A.1
  • 3
    • 85008394347 scopus 로고    scopus 로고
    • Consensus statement: Virus taxonomy in the age of metagenomics
    • Simmonds, P. et al. Consensus statement: virus taxonomy in the age of metagenomics. Nat. Rev. Microbiol. 15, 161-168 (2017).
    • (2017) Nat. Rev. Microbiol. , vol.15 , pp. 161-168
    • Simmonds, P.1
  • 4
    • 84905041075 scopus 로고    scopus 로고
    • A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
    • Dutilh, B. E. et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat. Commun. 5, 4498 (2014).
    • (2014) Nat. Commun. , vol.5 , pp. 4498
    • Dutilh, B.E.1
  • 5
    • 84927540709 scopus 로고    scopus 로고
    • Metagenomic ventures into outer sequence space
    • Dutilh, B. E. Metagenomic ventures into outer sequence space. Bacteriophage 4, e979664 (2014).
    • (2014) Bacteriophage , vol.4 , pp. e979664
    • Dutilh, B.E.1
  • 6
    • 84946740229 scopus 로고    scopus 로고
    • The human gut virome: A multifaceted majority
    • Ogilvie, L. A. & Jones, B. V. The human gut virome: a multifaceted majority. Front. Microbiol. 6, 918 (2015).
    • (2015) Front. Microbiol. , vol.6 , pp. 918
    • Ogilvie, L.A.1    Jones, B.V.2
  • 8
    • 85018301376 scopus 로고    scopus 로고
    • Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses
    • Yarygin, K. et al. Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses. PLoS ONE 12, e0176154 (2017).
    • (2017) PLoS ONE , vol.12 , pp. e0176154
    • Yarygin, K.1
  • 9
    • 84987654794 scopus 로고    scopus 로고
    • Healthy human gut phageome
    • Manrique, P. et al. Healthy human gut phageome. Proc. Natl Acad. Sci. USA 113,10400-10405 (2016).
    • (2016) Proc. Natl Acad. Sci. USA , vol.113 , pp. 10400-10405
    • Manrique, P.1
  • 10
    • 85016002937 scopus 로고    scopus 로고
    • 2∗ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences
    • 2∗ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences. Nucleic Acids Res. 45, 39-53 (2017).
    • (2017) Nucleic Acids Res. , vol.45 , pp. 39-53
    • Ahlgren, N.A.1    Ren, J.2    Lu, Y.Y.3    Fuhrman, J.A.4    Sun, F.5
  • 11
    • 85018252210 scopus 로고    scopus 로고
    • An insider's perspective: Bacteroides as a window into the microbiome
    • Wexler, A. G. & Goodman, A. L. An insider's perspective: bacteroides as a window into the microbiome. Nat. Microbiol. 2, 17026 (2017).
    • (2017) Nat. Microbiol. , vol.2 , pp. 17026
    • Wexler, A.G.1    Goodman, A.L.2
  • 12
    • 85018496784 scopus 로고    scopus 로고
    • Tunable expression tools enable single-cell strain distinction in the gut microbiome
    • Whitaker, W. R., Shepherd, E. S. & Sonnenburg, J. L. Tunable expression tools enable single-cell strain distinction in the gut microbiome. Cell 169, 538-546 (2017).
    • (2017) Cell , vol.169 , pp. 538-546
    • Whitaker, W.R.1    Shepherd, E.S.2    Sonnenburg, J.L.3
  • 13
    • 85021345411 scopus 로고    scopus 로고
    • Discovery and complete genome sequence of a bacteriophage from an obligate intracellular symbiont of a cellulolytic protist in the termite gut
    • Pramono, A. K. et al. Discovery and complete genome sequence of a bacteriophage from an obligate intracellular symbiont of a cellulolytic protist in the termite gut. Microbes Environ. 32, 112-117 (2017).
    • (2017) Microbes Environ. , vol.32 , pp. 112-117
    • Pramono, A.K.1
  • 14
    • 84881090889 scopus 로고    scopus 로고
    • Twelve previously unknown phage genera are ubiquitous in global oceans
    • Holmfeldt, K. et al. Twelve previously unknown phage genera are ubiquitous in global oceans. Proc. Natl Acad. Sci. USA 110, 12798-12803 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 12798-12803
    • Holmfeldt, K.1
  • 15
    • 84892407267 scopus 로고    scopus 로고
    • Unexplained diarrhoea in HIV-1 infected individuals
    • Oude Munnink, B. B. et al. Unexplained diarrhoea in HIV-1 infected individuals. BMC Infect. Dis. 14, 22 (2014).
    • (2014) BMC Infect. Dis. , vol.14 , pp. 22
    • Oude Munnink, B.B.1
  • 16
    • 84936942726 scopus 로고    scopus 로고
    • Unusual biology across a group comprising more than 15% of domain Bacteria
    • Brown, C. T. et al. Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523, 208-211 (2015).
    • (2015) Nature , vol.523 , pp. 208-211
    • Brown, C.T.1
  • 17
    • 85018184269 scopus 로고    scopus 로고
    • Novel clades of the HU/IHF superfamily point to unexpected roles in the eukaryotic centrosome, chromosome partitioning, and biologic conflicts
    • Burroughs, A. M., Kaur, G., Zhang, D. & Aravind, L. Novel clades of the HU/IHF superfamily point to unexpected roles in the eukaryotic centrosome, chromosome partitioning, and biologic conflicts. Cell Cycle 16, 1093-1103 (2017).
    • (2017) Cell Cycle , vol.16 , pp. 1093-1103
    • Burroughs, A.M.1    Kaur, G.2    Zhang, D.3    Aravind, L.4
  • 18
    • 66349109579 scopus 로고    scopus 로고
    • The P22 tail machine at subnanometer resolution reveals the architecture of an infection conduit
    • Lander, G. C. et al. The P22 tail machine at subnanometer resolution reveals the architecture of an infection conduit. Structure 17, 789-799 (2009).
    • (2009) Structure , vol.17 , pp. 789-799
    • Lander, G.C.1
  • 19
    • 84858166155 scopus 로고    scopus 로고
    • Short noncontractile tail machines: Adsorption and DNA delivery by podoviruses
    • Casjens, S. R. & Molineux, I. J. Short noncontractile tail machines: adsorption and DNA delivery by podoviruses. Adv. Exp. Med. Biol. 726, 143-179 (2012).
    • (2012) Adv. Exp. Med. Biol. , vol.726 , pp. 143-179
    • Casjens, S.R.1    Molineux, I.J.2
  • 20
  • 21
    • 47749144031 scopus 로고    scopus 로고
    • Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail
    • Xiang, Y. et al. Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail. Proc. Natl Acad. Sci. USA 105, 9552-9557 (2008).
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 9552-9557
    • Xiang, Y.1
  • 22
    • 79952072125 scopus 로고    scopus 로고
    • Evolution of mosaically related tailed bacteriophage genomes seen through the lens of phage P22 virion assembly
    • Casjens, S. R. & Thuman-Commike, P. A. Evolution of mosaically related tailed bacteriophage genomes seen through the lens of phage P22 virion assembly. Virology 411, 393-415 (2011).
    • (2011) Virology , vol.411 , pp. 393-415
    • Casjens, S.R.1    Thuman-Commike, P.A.2
  • 23
    • 73649138940 scopus 로고    scopus 로고
    • Molecular evolution of multisubunit RNA polymerases: Sequence analysis
    • Lane, W. J. & Darst, S. A. Molecular evolution of multisubunit RNA polymerases: sequence analysis. J. Mol. Biol. 395, 671-685 (2010).
    • (2010) J. Mol. Biol. , vol.395 , pp. 671-685
    • Lane, W.J.1    Darst, S.A.2
  • 24
    • 85022019380 scopus 로고    scopus 로고
    • Polyvalent proteins, a pervasive theme in the intergenomic biological conflicts of bacteriophages and conjugative elements
    • Iyer, L. M., Burroughs, A. M., Anand, S., de Souza, R. F. & Aravind, L. Polyvalent proteins, a pervasive theme in the intergenomic biological conflicts of bacteriophages and conjugative elements. J. Bacteriol. 199, e00245-17 (2017).
    • (2017) J. Bacteriol. , vol.199 , pp. e00217-e00245
    • Iyer, L.M.1    Burroughs, A.M.2    Anand, S.3    De Souza, R.F.4    Aravind, L.5
  • 25
    • 78650417504 scopus 로고    scopus 로고
    • Temporal regulation of gene expression of the Thermus thermophilus bacteriophage P23-45
    • Berdygulova, Z. et al. Temporal regulation of gene expression of the Thermus thermophilus bacteriophage P23-45. J. Mol. Biol. 405, 125-142 (2011).
    • (2011) J. Mol. Biol. , vol.405 , pp. 125-142
    • Berdygulova, Z.1
  • 26
    • 84865194444 scopus 로고    scopus 로고
    • Insights from the architecture of the bacterial transcription apparatus
    • Iyer, L. M. & Aravind, L. Insights from the architecture of the bacterial transcription apparatus. J. Struct. Biol. 179, 299-319 (2012).
    • (2012) J. Struct. Biol. , vol.179 , pp. 299-319
    • Iyer, L.M.1    Aravind, L.2
  • 27
    • 84964531764 scopus 로고    scopus 로고
    • A non-canonical multisubunit RNA polymerase encoded by a giant bacteriophage
    • Yakunina, M. et al. A non-canonical multisubunit RNA polymerase encoded by a giant bacteriophage. Nucleic Acids Res. 43, 10411-10420 (2015).
    • (2015) Nucleic Acids Res. , vol.43 , pp. 10411-10420
    • Yakunina, M.1
  • 28
    • 84969835514 scopus 로고    scopus 로고
    • The genome of AR9, a giant transducing Bacillus phage encoding two multisubunit RNA polymerases
    • Lavysh, D. et al. The genome of AR9, a giant transducing Bacillus phage encoding two multisubunit RNA polymerases. Virology 495, 185-196 (2016).
    • (2016) Virology , vol.495 , pp. 185-196
    • Lavysh, D.1
  • 29
    • 77955814228 scopus 로고    scopus 로고
    • Non-canonical DNA transcription enzymes and the conservation of two-barrel RNA polymerases
    • Ruprich-Robert, G. & Thuriaux, P. Non-canonical DNA transcription enzymes and the conservation of two-barrel RNA polymerases. Nucleic Acids Res. 38, 4559-4569 (2010).
    • (2010) Nucleic Acids Res. , vol.38 , pp. 4559-4569
    • Ruprich-Robert, G.1    Thuriaux, P.2
  • 30
    • 85016110780 scopus 로고    scopus 로고
    • Multiple origins of viral capsid proteins from cellular ancestors
    • Krupovic, M. & Koonin, E. V. Multiple origins of viral capsid proteins from cellular ancestors. Proc. Natl Acad. Sci. USA 114, E2401-E2410 (2017).
    • (2017) Proc. Natl Acad. Sci. USA , vol.114 , pp. E2401-E2410
    • Krupovic, M.1    Koonin, E.V.2
  • 31
    • 84946594594 scopus 로고    scopus 로고
    • Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters
    • Barr, J. J. et al. Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters. Proc. Natl Acad. Sci. USA 112, 13675-13680 (2015).
    • (2015) Proc. Natl Acad. Sci. USA , vol.112 , pp. 13675-13680
    • Barr, J.J.1
  • 32
    • 84953298206 scopus 로고    scopus 로고
    • Taxonomy of prokaryotic viruses: Update from the ICTV bacterial and archaeal viruses subcommittee
    • Krupovic, M. et al. Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee. Arch. Virol. 161, 1095-1099 (2016).
    • (2016) Arch. Virol. , vol.161 , pp. 1095-1099
    • Krupovic, M.1
  • 33
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 34
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • Soding, J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21, 951-960 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 951-960
    • Soding, J.1
  • 35
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004).
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 36
    • 23144452801 scopus 로고    scopus 로고
    • GeneMark: Web software for gene finding in prokaryotes, eukaryotes and viruses
    • Besemer, J. & Borodovsky, M. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 33, W451-454 (2005).
    • (2005) Nucleic Acids Res. , vol.33 , pp. W451-W454
    • Besemer, J.1    Borodovsky, M.2
  • 37
    • 84855258501 scopus 로고    scopus 로고
    • Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering
    • Kelley, D. R., Liu, B., Delcher, A. L., Pop, M. & Salzberg, S. L. Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering. Nucleic Acids Res. 40, e9 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. e9
    • Kelley, D.R.1    Liu, B.2    Delcher, A.L.3    Pop, M.4    Salzberg, S.L.5
  • 39
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-approximately maximum-likelihood trees for large alignments
    • Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
    • (2010) PLoS ONE , vol.5 , pp. e9490
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 40
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximumlikelihood phylogenies: Assessing the performance of PhyML 3.0
    • Guindon, S. et al. New algorithms and methods to estimate maximumlikelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59,307-321 (2010).
    • (2010) Syst. Biol. , vol.59 , pp. 307-321
    • Guindon, S.1
  • 41
    • 33747823564 scopus 로고    scopus 로고
    • MEME: Discovering and analyzing DNA and protein sequence motifs
    • Bailey, T. L., Williams, N., Misleh, C. & Li, W. W. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res. 34, W369-373 (2006).
    • (2006) Nucleic Acids Res. , vol.34 , pp. W369-W373
    • Bailey, T.L.1    Williams, N.2    Misleh, C.3    Li, W.W.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.