-
1
-
-
84855245603
-
Antibiotics in feed induce prophages in swine fecal microbiomes
-
Print 2011
-
Allen H.K., Looft T., Bayles D.O., Humphrey S., Levine U.Y., Alt D., Stanton T.B. Antibiotics in feed induce prophages in swine fecal microbiomes. MBio 2011, 2. Print 2011. 10.1128/mBio.00260-11.
-
(2011)
MBio
, vol.2
-
-
Allen, H.K.1
Looft, T.2
Bayles, D.O.3
Humphrey, S.4
Levine, U.Y.5
Alt, D.6
Stanton, T.B.7
-
2
-
-
15544369658
-
Host-bacterial mutualism in the human intestine
-
Backhed F., Ley R.E., Sonnenburg J.L., Peterson D.A., Gordon J.I. Host-bacterial mutualism in the human intestine. Science 2005, 307:1915-1920.
-
(2005)
Science
, vol.307
, pp. 1915-1920
-
-
Backhed, F.1
Ley, R.E.2
Sonnenburg, J.L.3
Peterson, D.A.4
Gordon, J.I.5
-
3
-
-
8644251876
-
Development and evaluation of a quality-controlled ribosomal sequence database for 16S ribosomal DNA-based identification of Staphylococcus species
-
Becker K., Harmsen D., Mellmann A., Meier C., Schumann P., Peters G., von Eiff C. Development and evaluation of a quality-controlled ribosomal sequence database for 16S ribosomal DNA-based identification of Staphylococcus species. J. Clin. Microbiol. 2004, 42:4988-4995.
-
(2004)
J. Clin. Microbiol.
, vol.42
, pp. 4988-4995
-
-
Becker, K.1
Harmsen, D.2
Mellmann, A.3
Meier, C.4
Schumann, P.5
Peters, G.6
von Eiff, C.7
-
4
-
-
0030297089
-
The indigenous gastrointestinal microflora
-
Berg R.D. The indigenous gastrointestinal microflora. Trends Microbiol. 1996, 4:430-435.
-
(1996)
Trends Microbiol.
, vol.4
, pp. 430-435
-
-
Berg, R.D.1
-
5
-
-
77949681033
-
Composition and function of the human-associated microbiota
-
Bik E.M. Composition and function of the human-associated microbiota. Nutr. Rev. 2009, 67(Suppl. 2):S164-S171.
-
(2009)
Nutr. Rev.
, vol.67
, pp. S164-S171
-
-
Bik, E.M.1
-
6
-
-
84901508943
-
Gut microbiota modulation: probiotics, antibiotics or fecal microbiota transplantation?
-
Cammarota G., Ianiro G., Bibbo S., Gasbarrini A. Gut microbiota modulation: probiotics, antibiotics or fecal microbiota transplantation?. Intern. Emerg. Med. 2014, 9:365-373.
-
(2014)
Intern. Emerg. Med.
, vol.9
, pp. 365-373
-
-
Cammarota, G.1
Ianiro, G.2
Bibbo, S.3
Gasbarrini, A.4
-
7
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso J.G., Kuczynski J., Stombaugh J., Bittinger K., Bushman F.D., Costello E.K., Fierer N., Pena A.G., Goodrich J.K., Gordon J.I., Huttley G.A., Kelley S.T., Knights D., Koenig J.E., Ley R.E., Lozupone C.A., McDonald D., Muegge B.D., Pirrung M., Reeder J., Sevinsky J.R., Turnbaugh P.J., Walters W.A., Widmann J., Yatsunenko T., Zaneveld J., Knight R. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 2010, 7:335-336.
-
(2010)
Nat. Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
Kuczynski, J.2
Stombaugh, J.3
Bittinger, K.4
Bushman, F.D.5
Costello, E.K.6
Fierer, N.7
Pena, A.G.8
Goodrich, J.K.9
Gordon, J.I.10
Huttley, G.A.11
Kelley, S.T.12
Knights, D.13
Koenig, J.E.14
Ley, R.E.15
Lozupone, C.A.16
McDonald, D.17
Muegge, B.D.18
Pirrung, M.19
Reeder, J.20
Sevinsky, J.R.21
Turnbaugh, P.J.22
Walters, W.A.23
Widmann, J.24
Yatsunenko, T.25
Zaneveld, J.26
Knight, R.27
more..
-
8
-
-
84863981120
-
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
-
Caporaso J.G., Lauber C.L., Walters W.A., Berg-Lyons D., Huntley J., Fierer N., Owens S.M., Betley J., Fraser L., Bauer M., Gormley N., Gilbert J.A., Smith G., Knight R. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012, 6:1621-1624.
-
(2012)
ISME J.
, vol.6
, pp. 1621-1624
-
-
Caporaso, J.G.1
Lauber, C.L.2
Walters, W.A.3
Berg-Lyons, D.4
Huntley, J.5
Fierer, N.6
Owens, S.M.7
Betley, J.8
Fraser, L.9
Bauer, M.10
Gormley, N.11
Gilbert, J.A.12
Smith, G.13
Knight, R.14
-
9
-
-
34147182303
-
A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria
-
Chakravorty S., Helb D., Burday M., Connell N., Alland D. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J. Microbiol. Methods 2007, 69:330-339.
-
(2007)
J. Microbiol. Methods
, vol.69
, pp. 330-339
-
-
Chakravorty, S.1
Helb, D.2
Burday, M.3
Connell, N.4
Alland, D.5
-
10
-
-
35648991375
-
EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences
-
Chun J., Lee J.H., Jung Y., Kim M., Kim S., Kim B.K., Lim Y.W. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int. J. Syst. Evol. Microbiol. 2007, 57:2259-2261.
-
(2007)
Int. J. Syst. Evol. Microbiol.
, vol.57
, pp. 2259-2261
-
-
Chun, J.1
Lee, J.H.2
Jung, Y.3
Kim, M.4
Kim, S.5
Kim, B.K.6
Lim, Y.W.7
-
11
-
-
69249109724
-
Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine
-
Claesson M.J., O'Sullivan O., Wang Q., Nikkila J., Marchesi J.R., Smidt H., de Vos W.M., Ross R.P., O'Toole P.W. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLOS ONE 2009, 4:e6669.
-
(2009)
PLOS ONE
, vol.4
, pp. e6669
-
-
Claesson, M.J.1
O'Sullivan, O.2
Wang, Q.3
Nikkila, J.4
Marchesi, J.R.5
Smidt, H.6
de Vos, W.M.7
Ross, R.P.8
O'Toole, P.W.9
-
12
-
-
78650453707
-
Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions
-
Claesson M.J., Wang Q., O'Sullivan O., Greene-Diniz R., Cole J.R., Ross R.P., O'Toole P.W. Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions. Nucleic Acids Res. 2010, 38:e200.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. e200
-
-
Claesson, M.J.1
Wang, Q.2
O'Sullivan, O.3
Greene-Diniz, R.4
Cole, J.R.5
Ross, R.P.6
O'Toole, P.W.7
-
13
-
-
5644227319
-
Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases
-
table of contents
-
Clarridge J.E. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin. Microbiol. Rev. 2004, 17:840-862. table of contents.
-
(2004)
Clin. Microbiol. Rev.
, vol.17
, pp. 840-862
-
-
Clarridge, J.E.1
-
14
-
-
58149200948
-
The ribosomal database project: improved alignments and new tools for rRNA analysis
-
Cole J.R., Wang Q., Cardenas E., Fish J., Chai B., Farris R.J., Kulam-Syed-Mohideen A.S., McGarrell D.M., Marsh T., Garrity G.M., Tiedje J.M. The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009, 37:D141-D145.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. D141-D145
-
-
Cole, J.R.1
Wang, Q.2
Cardenas, E.3
Fish, J.4
Chai, B.5
Farris, R.J.6
Kulam-Syed-Mohideen, A.S.7
McGarrell, D.M.8
Marsh, T.9
Garrity, G.M.10
Tiedje, J.M.11
-
15
-
-
84865127914
-
Assessment of the probiotic potential of a dairy product fermented by Propionibacterium freudenreichii in piglets
-
Cousin F.J., Foligne B., Deutsch S.M., Massart S., Parayre S., Le Loir Y., Boudry G., Jan G. Assessment of the probiotic potential of a dairy product fermented by Propionibacterium freudenreichii in piglets. J. Agric. Food Chem. 2012, 60:7917-7927.
-
(2012)
J. Agric. Food Chem.
, vol.60
, pp. 7917-7927
-
-
Cousin, F.J.1
Foligne, B.2
Deutsch, S.M.3
Massart, S.4
Parayre, S.5
Le Loir, Y.6
Boudry, G.7
Jan, G.8
-
16
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis T.Z., Hugenholtz P., Larsen N., Rojas M., Brodie E.L., Keller K., Huber T., Dalevi D., Hu P., Andersen G.L. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol. 2006, 72:5069-5072.
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
Huber, T.7
Dalevi, D.8
Hu, P.9
Andersen, G.L.10
-
17
-
-
56849106496
-
The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing
-
Dethlefsen L., Huse S., Sogin M.L., Relman D.A. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 2008, 6:e280.
-
(2008)
PLoS Biol.
, vol.6
, pp. e280
-
-
Dethlefsen, L.1
Huse, S.2
Sogin, M.L.3
Relman, D.A.4
-
18
-
-
18944406651
-
Antibiotic growth promoters in agriculture: history and mode of action
-
Dibner J.J., Richards J.D. Antibiotic growth promoters in agriculture: history and mode of action. Poult. Sci. 2005, 84:634-643.
-
(2005)
Poult. Sci.
, vol.84
, pp. 634-643
-
-
Dibner, J.J.1
Richards, J.D.2
-
19
-
-
49949095159
-
Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs
-
Dowd S.E., Sun Y., Wolcott R.D., Domingo A., Carroll J.A. Bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP) for microbiome studies: bacterial diversity in the ileum of newly weaned Salmonella-infected pigs. Foodborne Pathog. Dis. 2008, 5:459-472.
-
(2008)
Foodborne Pathog. Dis.
, vol.5
, pp. 459-472
-
-
Dowd, S.E.1
Sun, Y.2
Wolcott, R.D.3
Domingo, A.4
Carroll, J.A.5
-
20
-
-
0002537244
-
Indigenous, normal, and autochthonous flora of the gastrointestinal tract
-
Dubos R., Scheduler R.W., Costello R., Hoet P. Indigenous, normal, and autochthonous flora of the gastrointestinal tract. J. Exp. Med. 1965, 122:67-76.
-
(1965)
J. Exp. Med.
, vol.122
, pp. 67-76
-
-
Dubos, R.1
Scheduler, R.W.2
Costello, R.3
Hoet, P.4
-
21
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar R.C., Haas B.J., Clemente J.C., Quince C., Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 2011, 27:2194-2200.
-
(2011)
Bioinformatics
, vol.27
, pp. 2194-2200
-
-
Edgar, R.C.1
Haas, B.J.2
Clemente, J.C.3
Quince, C.4
Knight, R.5
-
22
-
-
0018974560
-
The phylogeny of prokaryotes
-
Fox G.E., Stackebrandt E., Hespell R.B., Gibson J., Maniloff J., Dyer T.A., Wolfe R.S., Balch W.E., Tanner R.S., Magrum L.J., Zablen L.B., Blakemore R., Gupta R., Bonen L., Lewis B.J., Stahl D.A., Luehrsen K.R., Chen K.N., Woese C.R. The phylogeny of prokaryotes. Science 1980, 209:457-463.
-
(1980)
Science
, vol.209
, pp. 457-463
-
-
Fox, G.E.1
Stackebrandt, E.2
Hespell, R.B.3
Gibson, J.4
Maniloff, J.5
Dyer, T.A.6
Wolfe, R.S.7
Balch, W.E.8
Tanner, R.S.9
Magrum, L.J.10
Zablen, L.B.11
Blakemore, R.12
Gupta, R.13
Bonen, L.14
Lewis, B.J.15
Stahl, D.A.16
Luehrsen, K.R.17
Chen, K.N.18
Woese, C.R.19
-
23
-
-
0017325626
-
Deconjugation of bile acids by intestinal lactobacilli
-
Gilliland S.E., Speck M.L. Deconjugation of bile acids by intestinal lactobacilli. Appl. Environ. Microbiol. 1977, 33:15-18.
-
(1977)
Appl. Environ. Microbiol.
, vol.33
, pp. 15-18
-
-
Gilliland, S.E.1
Speck, M.L.2
-
24
-
-
84877765843
-
Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing
-
Guo F., Zhang T. Biases during DNA extraction of activated sludge samples revealed by high throughput sequencing. Appl. Microbiol. Biotechnol. 2013, 97:4607-4616.
-
(2013)
Appl. Microbiol. Biotechnol.
, vol.97
, pp. 4607-4616
-
-
Guo, F.1
Zhang, T.2
-
25
-
-
79952006773
-
Chimeric 16S rRNA sequence formation and detection in sanger and 454-pyrosequenced PCR amplicons
-
Haas B.J., Gevers D., Earl A.M., Feldgarden M., Ward D.V., Giannoukos G., Ciulla D., Tabbaa D., Highlander S.K., Sodergren E., Methe B., DeSantis T.Z., Human Microbiome Consortium, Petrosino J.F., Knight R., Birren B.W. Chimeric 16S rRNA sequence formation and detection in sanger and 454-pyrosequenced PCR amplicons. Genome Res. 2011, 21:494-504.
-
(2011)
Genome Res.
, vol.21
, pp. 494-504
-
-
Haas, B.J.1
Gevers, D.2
Earl, A.M.3
Feldgarden, M.4
Ward, D.V.5
Giannoukos, G.6
Ciulla, D.7
Tabbaa, D.8
Highlander, S.K.9
Sodergren, E.10
Methe, B.11
DeSantis, T.Z.12
Petrosino, J.F.13
Knight, R.14
Birren, B.W.15
-
26
-
-
67650021209
-
Microbial community profiling for human microbiome projects: tools, techniques, and challenges
-
Hamady M., Knight R. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res. 2009, 19:1141-1152.
-
(2009)
Genome Res.
, vol.19
, pp. 1141-1152
-
-
Hamady, M.1
Knight, R.2
-
27
-
-
34249015507
-
Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces
-
Hayashi H., Shibata K., Sakamoto M., Tomita S., Benno Y. Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces. Int. J. Syst. Evol. Microbiol. 2007, 57:941-946.
-
(2007)
Int. J. Syst. Evol. Microbiol.
, vol.57
, pp. 941-946
-
-
Hayashi, H.1
Shibata, K.2
Sakamoto, M.3
Tomita, S.4
Benno, Y.5
-
28
-
-
50249099816
-
Metabolic phenotyping in health and disease
-
Holmes E., Wilson I.D., Nicholson J.K. Metabolic phenotyping in health and disease. Cell 2008, 134:714-717.
-
(2008)
Cell
, vol.134
, pp. 714-717
-
-
Holmes, E.1
Wilson, I.D.2
Nicholson, J.K.3
-
29
-
-
84862286169
-
A framework for human microbiome research
-
Human Microbiome Project Consortium A framework for human microbiome research. Nature 2012, 486:215-221.
-
(2012)
Nature
, vol.486
, pp. 215-221
-
-
-
30
-
-
84875805989
-
The intestinal microbiome of the pig
-
Isaacson R., Kim H.B. The intestinal microbiome of the pig. Anim. Health Res. Rev. 2012, 13:100-109.
-
(2012)
Anim. Health Res. Rev.
, vol.13
, pp. 100-109
-
-
Isaacson, R.1
Kim, H.B.2
-
31
-
-
84866551081
-
Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin
-
Kim H.B., Borewicz K., White B.A., Singer R.S., Sreevatsan S., Tu Z.J., Isaacson R.E. Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:15485-15490.
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, pp. 15485-15490
-
-
Kim, H.B.1
Borewicz, K.2
White, B.A.3
Singer, R.S.4
Sreevatsan, S.5
Tu, Z.J.6
Isaacson, R.E.7
-
32
-
-
80052550284
-
Longitudinal investigation of the age-related bacterial diversity in the feces of commercial pigs
-
Kim H.B., Borewicz K., White B.A., Singer R.S., Sreevatsan S., Tu Z.J., Isaacson R.E. Longitudinal investigation of the age-related bacterial diversity in the feces of commercial pigs. Vet. Microbiol. 2011, 153:124-133.
-
(2011)
Vet. Microbiol.
, vol.153
, pp. 124-133
-
-
Kim, H.B.1
Borewicz, K.2
White, B.A.3
Singer, R.S.4
Sreevatsan, S.5
Tu, Z.J.6
Isaacson, R.E.7
-
33
-
-
75549083380
-
Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase
-
Lahr D.J., Katz L.A. Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase. Biotechniques 2009, 47:857-866.
-
(2009)
Biotechniques
, vol.47
, pp. 857-866
-
-
Lahr, D.J.1
Katz, L.A.2
-
34
-
-
79955794476
-
Comparative fecal metagenomics unveils unique functional capacity of the swine gut
-
Lamendella R., Domingo J.W., Ghosh S., Martinson J., Oerther D.B. Comparative fecal metagenomics unveils unique functional capacity of the swine gut. BMC Microbiol. 2011, 11:103.
-
(2011)
BMC Microbiol.
, vol.11
, pp. 103
-
-
Lamendella, R.1
Domingo, J.W.2
Ghosh, S.3
Martinson, J.4
Oerther, D.B.5
-
35
-
-
46249085739
-
Evolution of mammals and their gut microbes
-
Ley R.E., Hamady M., Lozupone C., Turnbaugh P.J., Ramey R.R., Bircher J.S., Schlegel M.L., Tucker T.A., Schrenzel M.D., Knight R., Gordon J.I. Evolution of mammals and their gut microbes. Science 2008, 320:1647-1651.
-
(2008)
Science
, vol.320
, pp. 1647-1651
-
-
Ley, R.E.1
Hamady, M.2
Lozupone, C.3
Turnbaugh, P.J.4
Ramey, R.R.5
Bircher, J.S.6
Schlegel, M.L.7
Tucker, T.A.8
Schrenzel, M.D.9
Knight, R.10
Gordon, J.I.11
-
36
-
-
32944466887
-
Ecological and evolutionary forces shaping microbial diversity in the human intestine
-
Ley R.E., Peterson D.A., Gordon J.I. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 2006, 124:837-848.
-
(2006)
Cell
, vol.124
, pp. 837-848
-
-
Ley, R.E.1
Peterson, D.A.2
Gordon, J.I.3
-
37
-
-
33745884382
-
Effects of live yeast on the performance, nutrient digestibility, gastrointestinal microbiota and concentration of volatile fatty acids in weanling pigs
-
Li J., Li D., Gong L., Ma Y., He Y., Zhai H. Effects of live yeast on the performance, nutrient digestibility, gastrointestinal microbiota and concentration of volatile fatty acids in weanling pigs. Arch. Anim. Nutr. 2006, 60:277-288.
-
(2006)
Arch. Anim. Nutr.
, vol.60
, pp. 277-288
-
-
Li, J.1
Li, D.2
Gong, L.3
Ma, Y.4
He, Y.5
Zhai, H.6
-
38
-
-
84864920004
-
Comparison of next-generation sequencing systems
-
Liu L., Li Y., Li S., Hu N., He Y., Pong R., Lin D., Lu L., Law M. Comparison of next-generation sequencing systems. J. Biomed. Biotechnol. 2012, 2012:251364.
-
(2012)
J. Biomed. Biotechnol.
, vol.2012
, pp. 251364
-
-
Liu, L.1
Li, Y.2
Li, S.3
Hu, N.4
He, Y.5
Pong, R.6
Lin, D.7
Lu, L.8
Law, M.9
-
39
-
-
54549106898
-
Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers
-
Liu Z., DeSantis T.Z., Andersen G.L., Knight R. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Res. 2008, 36:e120.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. e120
-
-
Liu, Z.1
DeSantis, T.Z.2
Andersen, G.L.3
Knight, R.4
-
40
-
-
35549007148
-
Short pyrosequencing reads suffice for accurate microbial community analysis
-
Liu Z., Lozupone C., Hamady M., Bushman F.D., Knight R. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acids Res. 2007, 35:e120.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. e120
-
-
Liu, Z.1
Lozupone, C.2
Hamady, M.3
Bushman, F.D.4
Knight, R.5
-
41
-
-
84904999639
-
Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations
-
Looft T., Allen H.K., Cantarel B.L., Levine U.Y., Bayles D.O., Alt D.P., Henrissat B., Stanton T.B. Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations. ISME J. 2014, 8:1566-1576.
-
(2014)
ISME J.
, vol.8
, pp. 1566-1576
-
-
Looft, T.1
Allen, H.K.2
Cantarel, B.L.3
Levine, U.Y.4
Bayles, D.O.5
Alt, D.P.6
Henrissat, B.7
Stanton, T.B.8
-
42
-
-
84905162859
-
Carbadox has both temporary and lasting effects on the swine gut microbiota
-
Looft T., Allen H.K., Casey T.A., Alt D.P., Stanton T.B. Carbadox has both temporary and lasting effects on the swine gut microbiota. Front. Microbiol. 2014, 5:276.
-
(2014)
Front. Microbiol.
, vol.5
, pp. 276
-
-
Looft, T.1
Allen, H.K.2
Casey, T.A.3
Alt, D.P.4
Stanton, T.B.5
-
43
-
-
84857135712
-
In-feed antibiotic effects on the swine intestinal microbiome
-
Looft T., Johnson T.A., Allen H.K., Bayles D.O., Alt D.P., Stedtfeld R.D., Sul W.J., Stedtfeld T.M., Chai B., Cole J.R., Hashsham S.A., Tiedje J.M., Stanton T.B. In-feed antibiotic effects on the swine intestinal microbiome. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:1691-1696.
-
(2012)
Proc. Natl. Acad. Sci. U. S. A.
, vol.109
, pp. 1691-1696
-
-
Looft, T.1
Johnson, T.A.2
Allen, H.K.3
Bayles, D.O.4
Alt, D.P.5
Stedtfeld, R.D.6
Sul, W.J.7
Stedtfeld, T.M.8
Chai, B.9
Cole, J.R.10
Hashsham, S.A.11
Tiedje, J.M.12
Stanton, T.B.13
-
44
-
-
0032790494
-
Bacterial species identification after DNA amplification with a universal primer pair
-
McCabe K.M., Zhang Y.H., Huang B.L., Wagar E.A., McCabe E.R. Bacterial species identification after DNA amplification with a universal primer pair. Mol. Genet. Metab. 1999, 66:205-211.
-
(1999)
Mol. Genet. Metab.
, vol.66
, pp. 205-211
-
-
McCabe, K.M.1
Zhang, Y.H.2
Huang, B.L.3
Wagar, E.A.4
McCabe, E.R.5
-
45
-
-
84862491799
-
Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits
-
McKnite A.M., Perez-Munoz M.E., Lu L., Williams E.G., Brewer S., Andreux P.A., Bastiaansen J.W., Wang X., Kachman S.D., Auwerx J., Williams R.W., Benson A.K., Peterson D.A., Ciobanu D.C. Murine gut microbiota is defined by host genetics and modulates variation of metabolic traits. PLOS ONE 2012, 7:e39191.
-
(2012)
PLOS ONE
, vol.7
, pp. e39191
-
-
McKnite, A.M.1
Perez-Munoz, M.E.2
Lu, L.3
Williams, E.G.4
Brewer, S.5
Andreux, P.A.6
Bastiaansen, J.W.7
Wang, X.8
Kachman, S.D.9
Auwerx, J.10
Williams, R.W.11
Benson, A.K.12
Peterson, D.A.13
Ciobanu, D.C.14
-
46
-
-
84904575496
-
Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing
-
S16-2164-14-S5-S16. Epub 2013 Oct 16
-
Mitra S., Forster-Fromme K., Damms-Machado A., Scheurenbrand T., Biskup S., Huson D.H., Bischoff S.C. Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing. BMC Genomics 2013, 14(Suppl. 5). S16-2164-14-S5-S16. Epub 2013 Oct 16.
-
(2013)
BMC Genomics
, vol.14
-
-
Mitra, S.1
Forster-Fromme, K.2
Damms-Machado, A.3
Scheurenbrand, T.4
Biskup, S.5
Huson, D.H.6
Bischoff, S.C.7
-
47
-
-
3142757153
-
Molecular analysis of the microflora associated with dental caries
-
Munson M.A., Banerjee A., Watson T.F., Wade W.G. Molecular analysis of the microflora associated with dental caries. J. Clin. Microbiol. 2004, 42:3023-3029.
-
(2004)
J. Clin. Microbiol.
, vol.42
, pp. 3023-3029
-
-
Munson, M.A.1
Banerjee, A.2
Watson, T.F.3
Wade, W.G.4
-
48
-
-
84928828318
-
Nature, End sequence
-
Nature End sequence. Nature 2013, 502:414-415.
-
(2013)
Nature
, vol.502
, pp. 414-415
-
-
-
49
-
-
34547579868
-
Genotypic microbial community profiling: a critical technical review
-
Nocker A., Burr M., Camper A.K. Genotypic microbial community profiling: a critical technical review. Microb. Ecol. 2007, 54:276-289.
-
(2007)
Microb. Ecol.
, vol.54
, pp. 276-289
-
-
Nocker, A.1
Burr, M.2
Camper, A.K.3
-
50
-
-
0022462668
-
Microbial ecology and evolution: a ribosomal RNA approach
-
Olsen G.J., Lane D.J., Giovannoni S.J., Pace N.R., Stahl D.A. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 1986, 40:337-365.
-
(1986)
Annu. Rev. Microbiol.
, vol.40
, pp. 337-365
-
-
Olsen, G.J.1
Lane, D.J.2
Giovannoni, S.J.3
Pace, N.R.4
Stahl, D.A.5
-
51
-
-
0022523096
-
Ribosomal RNA phylogeny and the primary lines of evolutionary descent
-
Pace N.R., Olsen G.J., Woese C.R. Ribosomal RNA phylogeny and the primary lines of evolutionary descent. Cell 1986, 45:325-326.
-
(1986)
Cell
, vol.45
, pp. 325-326
-
-
Pace, N.R.1
Olsen, G.J.2
Woese, C.R.3
-
52
-
-
84908087729
-
Assessment of fecal bacterial diversity among healthy piglets during the weaning transition
-
Pajarillo E.A., Chae J., Balolong M.P., Kim H.B., Kang D. Assessment of fecal bacterial diversity among healthy piglets during the weaning transition. J. Gen. Appl. Microbiol. 2014, 60:140-146.
-
(2014)
J. Gen. Appl. Microbiol.
, vol.60
, pp. 140-146
-
-
Pajarillo, E.A.1
Chae, J.2
Balolong, M.P.3
Kim, H.B.4
Kang, D.5
-
53
-
-
84905701221
-
Pyrosequencing-based analysis of fecal microbial communities in three purebred pig lines
-
Pajarillo E.A., Chae J.P., Balolong M.P., Kim H.B., Seo K.S., Kang D.K. Pyrosequencing-based analysis of fecal microbial communities in three purebred pig lines. J. Microbiol. 2014, 52:646-651.
-
(2014)
J. Microbiol.
, vol.52
, pp. 646-651
-
-
Pajarillo, E.A.1
Chae, J.P.2
Balolong, M.P.3
Kim, H.B.4
Seo, K.S.5
Kang, D.K.6
-
54
-
-
34547129847
-
Development of the human infant intestinal microbiota
-
Palmer C., Bik E.M., DiGiulio D.B., Relman D.A., Brown P.O. Development of the human infant intestinal microbiota. PLoS Biol. 2007, 5:e177.
-
(2007)
PLoS Biol.
, vol.5
, pp. e177
-
-
Palmer, C.1
Bik, E.M.2
DiGiulio, D.B.3
Relman, D.A.4
Brown, P.O.5
-
55
-
-
84874245287
-
Characterisation of gut microbiota in Ossabaw and Gottingen minipigs as models of obesity and metabolic syndrome
-
Pedersen R., Ingerslev H.C., Sturek M., Alloosh M., Cirera S., Christoffersen B.O., Moesgaard S.G., Larsen N., Boye M. Characterisation of gut microbiota in Ossabaw and Gottingen minipigs as models of obesity and metabolic syndrome. PLOS ONE 2013, 8:e56612.
-
(2013)
PLOS ONE
, vol.8
, pp. e56612
-
-
Pedersen, R.1
Ingerslev, H.C.2
Sturek, M.3
Alloosh, M.4
Cirera, S.5
Christoffersen, B.O.6
Moesgaard, S.G.7
Larsen, N.8
Boye, M.9
-
56
-
-
37549027613
-
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
-
Pruesse E., Quast C., Knittel K., Fuchs B.M., Ludwig W., Peplies J., Glockner F.O. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007, 35:7188-7196.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 7188-7196
-
-
Pruesse, E.1
Quast, C.2
Knittel, K.3
Fuchs, B.M.4
Ludwig, W.5
Peplies, J.6
Glockner, F.O.7
-
57
-
-
69549112742
-
Accurate determination of microbial diversity from 454 pyrosequencing data
-
Quince C., Lanzen A., Curtis T.P., Davenport R.J., Hall N., Head I.M., Read L.F., Sloan W.T. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods 2009, 6:639-641.
-
(2009)
Nat. Methods
, vol.6
, pp. 639-641
-
-
Quince, C.1
Lanzen, A.2
Curtis, T.P.3
Davenport, R.J.4
Hall, N.5
Head, I.M.6
Read, L.F.7
Sloan, W.T.8
-
58
-
-
0021262688
-
Production of menaquinones by intestinal anaerobes
-
Ramotar K., Conly J.M., Chubb H., Louie T.J. Production of menaquinones by intestinal anaerobes. J. Infect. Dis. 1984, 150:213-218.
-
(1984)
J. Infect. Dis.
, vol.150
, pp. 213-218
-
-
Ramotar, K.1
Conly, J.M.2
Chubb, H.3
Louie, T.J.4
-
59
-
-
84857164927
-
Effect of Lactobacillus salivarius bacteriocin Abp118 on the mouse and pig intestinal microbiota
-
Riboulet-Bisson E., Sturme M.H., Jeffery I.B., O'Donnell M.M., Neville B.A., Forde B.M., Claesson M.J., Harris H., Gardiner G.E., Casey P.G., Lawlor P.G., O'Toole P.W., Ross R.P. Effect of Lactobacillus salivarius bacteriocin Abp118 on the mouse and pig intestinal microbiota. PLOS ONE 2012, 7:e31113.
-
(2012)
PLOS ONE
, vol.7
, pp. e31113
-
-
Riboulet-Bisson, E.1
Sturme, M.H.2
Jeffery, I.B.3
O'Donnell, M.M.4
Neville, B.A.5
Forde, B.M.6
Claesson, M.J.7
Harris, H.8
Gardiner, G.E.9
Casey, P.G.10
Lawlor, P.G.11
O'Toole, P.W.12
Ross, R.P.13
-
60
-
-
0017341656
-
Microbial ecology of the gastrointestinal tract
-
Savage D.C. Microbial ecology of the gastrointestinal tract. Annu. Rev. Microbiol. 1977, 31:107-133.
-
(1977)
Annu. Rev. Microbiol.
, vol.31
, pp. 107-133
-
-
Savage, D.C.1
-
61
-
-
72949107142
-
Introducing mothur: open source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.F. Introducing mothur: open source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 2009.
-
(2009)
Appl. Environ. Microbiol.
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
Hall, J.R.4
Hartmann, M.5
Hollister, E.B.6
Lesniewski, R.A.7
Oakley, B.B.8
Parks, D.H.9
Robinson, C.J.10
Sahl, J.W.11
Stres, B.12
Thallinger, G.G.13
Van Horn, D.J.14
Weber, C.F.15
-
62
-
-
37749031255
-
Next-generation sequencing transforms today's biology
-
Schuster S.C. Next-generation sequencing transforms today's biology. Nat. Methods 2008, 5:16-18.
-
(2008)
Nat. Methods
, vol.5
, pp. 16-18
-
-
Schuster, S.C.1
-
63
-
-
0034961194
-
Use of antimicrobials in veterinary medicine and mechanisms of resistance
-
Schwarz S., Chaslus-Dancla E. Use of antimicrobials in veterinary medicine and mechanisms of resistance. Vet. Res. 2001, 32:201-225.
-
(2001)
Vet. Res.
, vol.32
, pp. 201-225
-
-
Schwarz, S.1
Chaslus-Dancla, E.2
-
64
-
-
23744440709
-
A dynamic partnership: celebrating our gut flora
-
Sears C.L. A dynamic partnership: celebrating our gut flora. Anaerobe 2005, 11:247-251.
-
(2005)
Anaerobe
, vol.11
, pp. 247-251
-
-
Sears, C.L.1
-
66
-
-
53649106195
-
Next-generation DNA sequencing
-
Shendure J., Ji H. Next-generation DNA sequencing. Nat. Biotechnol. 2008, 26:1135-1145.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 1135-1145
-
-
Shendure, J.1
Ji, H.2
-
67
-
-
84885141191
-
The effect of dietary supplementation with spent cider yeast on the swine distal gut microbiome
-
Upadrasta A., O'Sullivan L., O'Sullivan O., Sexton N., Lawlor P.G., Hill C., Fitzgerald G.F., Stanton C., Ross R.P. The effect of dietary supplementation with spent cider yeast on the swine distal gut microbiome. PLOS ONE 2013, 8:e75714.
-
(2013)
PLOS ONE
, vol.8
, pp. e75714
-
-
Upadrasta, A.1
O'Sullivan, L.2
O'Sullivan, O.3
Sexton, N.4
Lawlor, P.G.5
Hill, C.6
Fitzgerald, G.F.7
Stanton, C.8
Ross, R.P.9
-
68
-
-
0029789623
-
A quantitative map of nucleotide substitution rates in bacterial rRNA
-
Van de Peer Y., Chapelle S., De Wachter R. A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucleic Acids Res. 1996, 24:3381-3391.
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 3381-3391
-
-
Van de Peer, Y.1
Chapelle, S.2
De Wachter, R.3
-
70
-
-
34548293679
-
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
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. 2007, 73:5261-5267.
-
(2007)
Appl. Environ. Microbiol.
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
71
-
-
70350527180
-
Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies
-
Wang Y., Qian P.Y. Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. PLoS One 2009, 4:e7401.
-
(2009)
PLoS One
, vol.4
, pp. e7401
-
-
Wang, Y.1
Qian, P.Y.2
-
72
-
-
84921532911
-
Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis
-
eCollection 2014
-
Wesolowska-Andersen A., Bahl M.I., Carvalho V., Kristiansen K., Sicheritz-Ponten T., Gupta R., Licht T.R. Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis. Microbiome 2014, 2:19-2618. eCollection 2014.
-
(2014)
Microbiome
, vol.2
, pp. 19-2618
-
-
Wesolowska-Andersen, A.1
Bahl, M.I.2
Carvalho, V.3
Kristiansen, K.4
Sicheritz-Ponten, T.5
Gupta, R.6
Licht, T.R.7
-
73
-
-
84867613923
-
Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform
-
Whiteley A.S., Jenkins S., Waite I., Kresoje N., Payne H., Mullan B., Allcock R., O'Donnell A. Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. J. Microbiol. Methods 2012, 91:80-88.
-
(2012)
J. Microbiol. Methods
, vol.91
, pp. 80-88
-
-
Whiteley, A.S.1
Jenkins, S.2
Waite, I.3
Kresoje, N.4
Payne, H.5
Mullan, B.6
Allcock, R.7
O'Donnell, A.8
-
74
-
-
0001271789
-
Phylogenetic structure of the prokaryotic domain: the primary kingdoms
-
Woese C.R., Fox G.E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. U. S. A. 1977, 74:5088-5090.
-
(1977)
Proc. Natl. Acad. Sci. U. S. A.
, vol.74
, pp. 5088-5090
-
-
Woese, C.R.1
Fox, G.E.2
-
76
-
-
0017073762
-
Influence of certain indigenous gastrointestinal microorganisms on duodenal alkaline phosphatase in mice
-
Yolton D.P., Savage D.C. Influence of certain indigenous gastrointestinal microorganisms on duodenal alkaline phosphatase in mice. Appl. Environ. Microbiol. 1976, 31:880-888.
-
(1976)
Appl. Environ. Microbiol.
, vol.31
, pp. 880-888
-
-
Yolton, D.P.1
Savage, D.C.2
|