-
1
-
-
0035843908
-
Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis
-
Ochman H, Moran NA. Genes lost and genes found: evolution of bacterial pathogenesis and symbiosis. Science. 2001;292:1096-9.
-
(2001)
Science
, vol.292
, pp. 1096-1099
-
-
Ochman, H.1
Moran, N.A.2
-
2
-
-
84860265013
-
Microbial lifestyle and genome signatures
-
Dutta C, Paul S. Microbial lifestyle and genome signatures. Curr Genomics. 2012;13:153-62.
-
(2012)
Curr Genomics
, vol.13
, pp. 153-162
-
-
Dutta, C.1
Paul, S.2
-
3
-
-
77953809752
-
Evolutionary microbial genomics: insights into bacterial host adaptation
-
Toft C, Andersson SG. Evolutionary microbial genomics: insights into bacterial host adaptation. Nat Rev Genet. 2010;11:465-75.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 465-475
-
-
Toft, C.1
Andersson, S.G.2
-
5
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature. 2000;405:299-304.
-
(2000)
Nature
, vol.405
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.G.2
Groisman, E.A.3
-
6
-
-
77954143123
-
Impact of recombination on bacterial evolution
-
Didelot X, Maiden MC. Impact of recombination on bacterial evolution. Trends Microbiol. 2010;18:315-22.
-
(2010)
Trends Microbiol
, vol.18
, pp. 315-322
-
-
Didelot, X.1
Maiden, M.C.2
-
7
-
-
67650074198
-
Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter
-
Lefebure T, Stanhope MJ. Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter. Genome Res. 2009;19:1224-32.
-
(2009)
Genome Res
, vol.19
, pp. 1224-1232
-
-
Lefebure, T.1
Stanhope, M.J.2
-
8
-
-
68149175229
-
The consequences of genetic drift for bacterial genome complexity
-
Kuo CH, Moran NA, Ochman H. The consequences of genetic drift for bacterial genome complexity. Genome Res. 2009;19:1450-4.
-
(2009)
Genome Res
, vol.19
, pp. 1450-1454
-
-
Kuo, C.H.1
Moran, N.A.2
Ochman, H.3
-
9
-
-
77949441084
-
Distinct, ecotype-specific genome and proteome signatures in the marine cyanobacteria Prochlorococcus
-
Paul S, Dutta A, Bag SK, Das S, Dutta C. Distinct, ecotype-specific genome and proteome signatures in the marine cyanobacteria Prochlorococcus. BMC Genomics. 2010;11:103.
-
(2010)
BMC Genomics
, vol.11
, pp. 103
-
-
Paul, S.1
Dutta, A.2
Bag, S.K.3
Das, S.4
Dutta, C.5
-
10
-
-
55249124606
-
The origins of ecological diversity in prokaryotes
-
Cohan FM, Koeppel AF. The origins of ecological diversity in prokaryotes. Curr Biol. 2008;18:R1024-34.
-
(2008)
Curr Biol
, vol.18
, pp. R1024-R1034
-
-
Cohan, F.M.1
Koeppel, A.F.2
-
11
-
-
32944466887
-
Ecological and evolutionary forces shaping microbial diversity in the human intestine
-
Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell. 2006;124:837-48.
-
(2006)
Cell
, vol.124
, pp. 837-848
-
-
Ley, R.E.1
Peterson, D.A.2
Gordon, J.I.3
-
12
-
-
80051856839
-
The human gut microbiome: ecology and recent evolutionary changes
-
Walter J, Ley R. The human gut microbiome: ecology and recent evolutionary changes. Annu Rev Microbiol. 2011;65:411-29.
-
(2011)
Annu Rev Microbiol
, vol.65
, pp. 411-429
-
-
Walter, J.1
Ley, R.2
-
13
-
-
78449296237
-
Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors
-
Benson AK, Kelly SA, Legge R, Ma F, Low SJ, Kim J, et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci U S A. 2010;107:18933-8.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 18933-18938
-
-
Benson, A.K.1
Kelly, S.A.2
Legge, R.3
Ma, F.4
Low, S.J.5
Kim, J.6
Zhang, M.7
Oh, P.L.8
Nehrenberg, D.9
Hua, K.10
Kachman, S.D.11
Moriyama, E.N.12
Walter, J.13
Peterson, D.A.14
Pomp, D.15
-
14
-
-
72949091232
-
Bacterial community variation in human body habitats across space and time
-
Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science. 2009;326:1694-7.
-
(2009)
Science
, vol.326
, pp. 1694-1697
-
-
Costello, E.K.1
Lauber, C.L.2
Hamady, M.3
Fierer, N.4
Gordon, J.I.5
Knight, R.6
-
15
-
-
77149149718
-
Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution
-
Oh PL, Benson AK, Peterson DA, Patil PB, Moriyama EN, Roos S, et al. Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution. Isme J. 2010;4:377-87.
-
(2010)
Isme J
, vol.4
, pp. 377-387
-
-
Oh, P.L.1
Benson, A.K.2
Peterson, D.A.3
Patil, P.B.4
Moriyama, E.N.5
Roos, S.6
Walter, J.7
-
16
-
-
77953050946
-
A catalog of reference genomes from the human microbiome
-
Nelson KE, Weinstock GM, Highlander SK, Worley KC, Creasy HH, Wortman JR, et al. A catalog of reference genomes from the human microbiome. Science. 2010;328:994-9.
-
(2010)
Science
, vol.328
, pp. 994-999
-
-
Nelson, K.E.1
Weinstock, G.M.2
Highlander, S.K.3
Worley, K.C.4
Creasy, H.H.5
Wortman, J.R.6
Rusch, D.B.7
Mitreva, M.8
Sodergren, E.9
Chinwalla, A.T.10
Feldgarden, M.11
Gevers, D.12
Haas, B.J.13
Madupu, R.14
Ward, D.V.15
Birren, B.W.16
Gibbs, R.A.17
Methe, B.18
Petrosino, J.F.19
Strausberg, R.L.20
Sutton, G.G.21
White, O.R.22
Wilson, R.K.23
Durkin, S.24
Giglio, M.G.25
Gujja, S.26
Howarth, C.27
Kodira, C.D.28
Kyrpides, N.29
Mehta, T.30
more..
-
17
-
-
0025344613
-
Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides
-
Shah HN, Collins DM. Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides. Int J Syst Bacteriol. 1990;40:205-8.
-
(1990)
Int J Syst Bacteriol
, vol.40
, pp. 205-208
-
-
Shah, H.N.1
Collins, D.M.2
-
18
-
-
80053618114
-
Linking long-term dietary patterns with gut microbial enterotypes
-
Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011;334:105-8.
-
(2011)
Science
, vol.334
, pp. 105-108
-
-
Wu, G.D.1
Chen, J.2
Hoffmann, C.3
Bittinger, K.4
Chen, Y.Y.5
Keilbaugh, S.A.6
Bewtra, M.7
Knights, D.8
Walters, W.A.9
Knight, R.10
Sinha, R.11
Gilroy, E.12
Gupta, K.13
Baldassano, R.14
Nessel, L.15
Li, H.16
Bushman, F.D.17
Lewis, J.D.18
-
19
-
-
77957075815
-
Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa
-
De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A. 2010;107:14691-6.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 14691-14696
-
-
Filippo, C.1
Cavalieri, D.2
Paola, M.3
Ramazzotti, M.4
Poullet, J.B.5
Massart, S.6
Collini, S.7
Pieraccini, G.8
Lionetti, P.9
-
20
-
-
77951774144
-
Quantitative PCR assessments of bacterial species in women with and without bacterial vaginosis
-
Zozaya-Hinchliffe M, Lillis R, Martin DH, Ferris MJ. Quantitative PCR assessments of bacterial species in women with and without bacterial vaginosis. J Clin Microbiol. 2010;48:1812-9.
-
(2010)
J Clin Microbiol
, vol.48
, pp. 1812-1819
-
-
Zozaya-Hinchliffe, M.1
Lillis, R.2
Martin, D.H.3
Ferris, M.J.4
-
21
-
-
77649119443
-
Disordered microbial communities in asthmatic airways
-
Hilty M, Burke C, Pedro H, Cardenas P, Bush A, Bossley C, et al. Disordered microbial communities in asthmatic airways. PLoS One. 2010;5:e8578.
-
(2010)
PLoS One
, vol.5
, pp. e8578
-
-
Hilty, M.1
Burke, C.2
Pedro, H.3
Cardenas, P.4
Bush, A.5
Bossley, C.6
Davies, J.7
Ervine, A.8
Poulter, L.9
Pachter, L.10
Moffatt, M.F.11
Cookson, W.O.12
-
22
-
-
84887323708
-
Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis
-
Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C, et al. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. Elife. 2013;2:e01202.
-
(2013)
Elife
, vol.2
, pp. e01202
-
-
Scher, J.U.1
Sczesnak, A.2
Longman, R.S.3
Segata, N.4
Ubeda, C.5
Bielski, C.6
Rostron, T.7
Cerundolo, V.8
Pamer, E.G.9
Abramson, S.B.10
Huttenhower, C.11
Littman, D.R.12
-
23
-
-
84878553340
-
Chapter 20: anaerobic gram-negative bacilli
-
In: Baron S, editor. Medical microbiology. 4th ed. Galveston (TX): University of Texas Medical Branch at Galveston;
-
Finegold SM. Chapter 20: anaerobic gram-negative bacilli. In: Baron S, editor. Medical microbiology. 4th ed. Galveston (TX): University of Texas Medical Branch at Galveston; 1996 [http://www.ncbi.nlm.nih.gov/books/NBK8438/]
-
(1996)
-
-
Finegold, S.M.1
-
24
-
-
0029070612
-
Prevotella and Porphyromonas infections in children
-
Brook I. Prevotella and Porphyromonas infections in children. J Med Microbiol. 1995;42:340-7.
-
(1995)
J Med Microbiol
, vol.42
, pp. 340-347
-
-
Brook, I.1
-
25
-
-
27444438599
-
The microbial pan-genome
-
Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R. The microbial pan-genome. Curr Opin Genet Dev. 2005;15:589-94.
-
(2005)
Curr Opin Genet Dev
, vol.15
, pp. 589-594
-
-
Medini, D.1
Donati, C.2
Tettelin, H.3
Masignani, V.4
Rappuoli, R.5
-
27
-
-
77958479691
-
Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept
-
Lefebure T, Bitar PD, Suzuki H, Stanhope MJ. Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept. Genome Biol Evol. 2010;2:646-55.
-
(2010)
Genome Biol Evol
, vol.2
, pp. 646-655
-
-
Lefebure, T.1
Bitar, P.D.2
Suzuki, H.3
Stanhope, M.J.4
-
29
-
-
84875273263
-
Horizontal gene transfer and the evolution of bacterial and archaeal population structure
-
Polz MF, Alm EJ, Hanage WP. Horizontal gene transfer and the evolution of bacterial and archaeal population structure. Trends Genet. 2013;29:170-5.
-
(2013)
Trends Genet
, vol.29
, pp. 170-175
-
-
Polz, M.F.1
Alm, E.J.2
Hanage, W.P.3
-
30
-
-
84897944457
-
Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria
-
Zhang Y, Sievert SM. Pan-genome analyses identify lineage- and niche-specific markers of evolution and adaptation in Epsilonproteobacteria. Front Microbiol. 2014;5:110.
-
(2014)
Front Microbiol
, vol.5
, pp. 110
-
-
Zhang, Y.1
Sievert, S.M.2
-
31
-
-
84938977002
-
Bergey's Manual of Systematic Bacteriology Volume Four The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes)
-
Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. 0: Springer; 2010.
-
Noel RK, James TS, Daniel RB, Brian PH, Bruce JP, Naomi LW, et al. Bergey's Manual of Systematic Bacteriology Volume Four The Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae, and Planctomycetes. 0: Springer; 2010.
-
(2010)
-
-
Noel, R.K.1
James, T.S.2
Daniel, R.B.3
Brian, P.H.4
Bruce, J.P.5
Naomi, L.W.6
Wolfgang, L.7
William, B.W.8
-
32
-
-
33745634395
-
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
-
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658-9.
-
(2006)
Bioinformatics
, vol.22
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
34
-
-
84876080407
-
Description of Alloprevotella rava gen. nov., sp. nov., isolated from the human oral cavity, and reclassification of Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov
-
Downes J, Dewhirst FE, Tanner AC, Wade WG. Description of Alloprevotella rava gen. nov., sp. nov., isolated from the human oral cavity, and reclassification of Prevotella tannerae Moore et al. 1994 as Alloprevotella tannerae gen. nov., comb. nov. Int J Syst Evol Microbiol. 2013;63:1214-8.
-
(2013)
Int J Syst Evol Microbiol
, vol.63
, pp. 1214-1218
-
-
Downes, J.1
Dewhirst, F.E.2
Tanner, A.C.3
Wade, W.G.4
-
35
-
-
85019215135
-
-
NCBI Genome. [ http://www.ncbi.nlm.nih.gov/genome ].
-
-
-
-
36
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207-14.
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
37
-
-
85019266109
-
-
The NIH Human Microbiome Project. [ http://www.hmpdacc.org/ ]
-
-
-
-
38
-
-
85019224242
-
-
Microbial Reference Genomes. [ http://www.hmpdacc.org/reference:genomes/reference:genomes.php ]
-
-
-
-
39
-
-
84891822155
-
RefSeq microbial genomes database: new representation and annotation strategy
-
Tatusova T, Ciufo S, Fedorov B, O'Neill K, Tolstoy I. RefSeq microbial genomes database: new representation and annotation strategy. Nucleic Acids Res. 2014;42(Database issue):D553. 559.
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.DATABASE ISSUE
, pp. D553
-
-
Tatusova, T.1
Ciufo, S.2
Fedorov, B.3
O'Neill, K.4
Tolstoy, I.5
-
40
-
-
84876266928
-
QUAST: quality assessment tool for genome assemblies
-
Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072-5.
-
(2013)
Bioinformatics
, vol.29
, Issue.8
, pp. 1072-1075
-
-
Gurevich, A.1
Saveliev, V.2
Vyahhi, N.3
Tesler, G.4
-
41
-
-
77949601825
-
CD-HIT Suite: a web server for clustering and comparing biological sequences
-
Huang Y, Niu B, Gao Y, Fu L, Li W. CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics. 2010;26:680-2.
-
(2010)
Bioinformatics
, vol.26
, pp. 680-682
-
-
Huang, Y.1
Niu, B.2
Gao, Y.3
Fu, L.4
Li, W.5
-
42
-
-
84897951003
-
PanGP: a tool for quickly analyzing bacterial pan-genome profile
-
Zhao Y, Jia X, Yang J, Ling Y, Zhang Z, Yu J, et al. PanGP: a tool for quickly analyzing bacterial pan-genome profile. Bioinformatics. 2014;30:1297-9.
-
(2014)
Bioinformatics
, vol.30
, pp. 1297-1299
-
-
Zhao, Y.1
Jia, X.2
Yang, J.3
Ling, Y.4
Zhang, Z.5
Yu, J.6
Wu, J.7
Xiao, J.8
-
43
-
-
84890330527
-
MEGA6: molecular evolutionary genetics analysis version 6.0
-
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725-9.
-
(2013)
Mol Biol Evol
, vol.30
, Issue.12
, pp. 2725-2729
-
-
Tamura, K.1
Stecher, G.2
Peterson, D.3
Filipski, A.4
Kumar, S.5
-
44
-
-
75149150388
-
TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses
-
Stover BC, Muller KF. TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics. 2010;11:7.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 7
-
-
Stover, B.C.1
Muller, K.F.2
-
45
-
-
80052606131
-
WebMGA: a customizable web server for fast metagenomic sequence analysis
-
Wu S, Zhu Z, Fu L, Niu B, Li W. WebMGA: a customizable web server for fast metagenomic sequence analysis. BMC Genomics. 2011;12:444.
-
(2011)
BMC Genomics
, vol.12
, pp. 444
-
-
Wu, S.1
Zhu, Z.2
Fu, L.3
Niu, B.4
Li, W.5
-
46
-
-
84856503492
-
The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms
-
Beck C, Knoop H, Axmann IM, Steuer R. The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms. BMC Genomics. 2012;13:56.
-
(2012)
BMC Genomics
, vol.13
, pp. 56
-
-
Beck, C.1
Knoop, H.2
Axmann, I.M.3
Steuer, R.4
-
47
-
-
0031897964
-
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
-
Yang Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol. 1998;15:568-73.
-
(1998)
Mol Biol Evol
, vol.15
, pp. 568-573
-
-
Yang, Z.1
|