-
1
-
-
84910095390
-
Interaction between Campylobacter and intestinal epithelial cells leads to a different proinflammatory response in human and porcine host
-
Aguilar, C., Jiménez-Marín, Á., Martins, R.P., and Garrido, J.J. (2014) Interaction between Campylobacter and intestinal epithelial cells leads to a different proinflammatory response in human and porcine host. Vet Immunol Immunopathol 162: 14–23.
-
(2014)
Vet Immunol Immunopathol
, vol.162
, pp. 14-23
-
-
Aguilar, C.1
Jiménez-Marín, Á.2
Martins, R.P.3
Garrido, J.J.4
-
2
-
-
36649021589
-
Mucosa-associated bacterial diversity in relation to human terminal ileum and colonic biopsy samples
-
Ahmed, S., Macfarlane, G.T., Fite, A., McBain, A.J., Gilbert, P., and Macfarlane, S. (2007) Mucosa-associated bacterial diversity in relation to human terminal ileum and colonic biopsy samples. Appl Environ Microbiol 73: 7435–7442.
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 7435-7442
-
-
Ahmed, S.1
Macfarlane, G.T.2
Fite, A.3
McBain, A.J.4
Gilbert, P.5
Macfarlane, S.6
-
3
-
-
84908306828
-
Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota
-
Albenberg, L., Esipova, T.V., Judge, C.P., Bittinger, K., Chen, J., and Laughlin, A. (2014) Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology 147: 1055–1063.
-
(2014)
Gastroenterology
, vol.147
, pp. 1055-1063
-
-
Albenberg, L.1
Esipova, T.V.2
Judge, C.P.3
Bittinger, K.4
Chen, J.5
Laughlin, A.6
-
4
-
-
0035870985
-
Campylobacter jejuni infections: update on emerging issues and trends
-
Allos, B.M. (2001) Campylobacter jejuni infections: update on emerging issues and trends. Clin Infect Dis 32: 1201–1206.
-
(2001)
Clin Infect Dis
, vol.32
, pp. 1201-1206
-
-
Allos, B.M.1
-
5
-
-
20444373370
-
Prevalences and transmission routes of Campylobacter spp. strains within multiple pig farms
-
Alter, T., Gaull, F., Kasimir, S., Gürtler, M., Mielke, H., Linnebur, M., et al. (2014) Prevalences and transmission routes of Campylobacter spp. strains within multiple pig farms. Vet Microbiol 108: 251–261.
-
(2014)
Vet Microbiol
, vol.108
, pp. 251-261
-
-
Alter, T.1
Gaull, F.2
Kasimir, S.3
Gürtler, M.4
Mielke, H.5
Linnebur, M.6
-
6
-
-
33646827806
-
Multivariate dispersion as a measure of beta diversity
-
Anderson, M.J., Ellingsen, K.E., and McArdle, B.H. (2006) Multivariate dispersion as a measure of beta diversity. Ecol Lett 9: 683–693.
-
(2006)
Ecol Lett
, vol.9
, pp. 683-693
-
-
Anderson, M.J.1
Ellingsen, K.E.2
McArdle, B.H.3
-
7
-
-
0035026232
-
The adherent gastrointestinal mucus gel layer: thickness and physical state in vivo
-
Atuma, C., Strugala, V., Allen, A., and Holm, L. (2001) The adherent gastrointestinal mucus gel layer: thickness and physical state in vivo. Am J Physiol Gastrointest Liver Physiol 280: G922–G929.
-
(2001)
Am J Physiol Gastrointest Liver Physiol
, vol.280
, pp. G922-G929
-
-
Atuma, C.1
Strugala, V.2
Allen, A.3
Holm, L.4
-
8
-
-
40749084834
-
Enteric salmonellosis disrupts the microbial ecology of the murine gastrointestinal tract
-
Barman, M., Unold, D., Shifley, K., Amir, E., Hung, K., Bos, N., et al. (2008) Enteric salmonellosis disrupts the microbial ecology of the murine gastrointestinal tract. Infect Immun 76: 907–915.
-
(2008)
Infect Immun
, vol.76
, pp. 907-915
-
-
Barman, M.1
Unold, D.2
Shifley, K.3
Amir, E.4
Hung, K.5
Bos, N.6
-
9
-
-
84947078803
-
Motility in the epsilon-proteobacteria
-
Beeby, M. (2015) Motility in the epsilon-proteobacteria. Curr Opin Microbiol 28: 115–121.
-
(2015)
Curr Opin Microbiol
, vol.28
, pp. 115-121
-
-
Beeby, M.1
-
10
-
-
85016778725
-
Controlling the false discovery rate: a practical and powerful approach to multiple testing
-
Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B 57: 289–300.
-
(1995)
J R Statist Soc B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
11
-
-
85010197243
-
Whole-genome sequences of two Campylobacter coli isolates from the antimicrobial resistance monitoring program in Colombia
-
Bernal, J.F., Donado-Godoy, P., Valencia, M.F., León, M., Gómez, Y., Rodríguez, F., et al. (2016) Whole-genome sequences of two Campylobacter coli isolates from the antimicrobial resistance monitoring program in Colombia. Genome Announc 4: e00131–16.
-
(2016)
Genome Announc
, vol.4
, pp. e00116-e00131
-
-
Bernal, J.F.1
Donado-Godoy, P.2
Valencia, M.F.3
León, M.4
Gómez, Y.5
Rodríguez, F.6
-
12
-
-
79954915318
-
Paneth cells, antimicrobial peptides and maintenance of intestinal homeostasis
-
Bevins, C.L., and Salzman, N.H. (2011) Paneth cells, antimicrobial peptides and maintenance of intestinal homeostasis. Nat Rev Microbiol 9: 356–368.
-
(2011)
Nat Rev Microbiol
, vol.9
, pp. 356-368
-
-
Bevins, C.L.1
Salzman, N.H.2
-
13
-
-
84986300599
-
Microbiota and the gut-brain axis
-
Bienenstock, J., Kunze, W., and Forsythe, P. (2015) Microbiota and the gut-brain axis. Nutr Rev 73 (Suppl 1): 28–31.
-
(2015)
Nutr Rev
, vol.73Suppl 1
, pp. 28-31
-
-
Bienenstock, J.1
Kunze, W.2
Forsythe, P.3
-
14
-
-
31444449652
-
Molecular analysis of the bacterial microbiota in the human stomach
-
Bik, E.M., Eckburg, P.B., Gill, S.R., Nelson, K.E., Purdom, E.A., Francois, F., et al. (2006) Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci USA 103: 732–737.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 732-737
-
-
Bik, E.M.1
Eckburg, P.B.2
Gill, S.R.3
Nelson, K.E.4
Purdom, E.A.5
Francois, F.6
-
15
-
-
62349139719
-
Reduction of thermotolerant Campylobacter species on broiler carcasses following physical decontamination at slaughter
-
Boysen, L., and Rosenquist, H. (2009) Reduction of thermotolerant Campylobacter species on broiler carcasses following physical decontamination at slaughter. J Food Prot 72: 497–502.
-
(2009)
J Food Prot
, vol.72
, pp. 497-502
-
-
Boysen, L.1
Rosenquist, H.2
-
16
-
-
84880708236
-
Prevalence of Campylobacter spp. relative to other enteric pathogens in grow-finish pigs with diarrhea
-
Burrough, E., Terhorst, S., Sahin, O., and Zhang, Q. (2013) Prevalence of Campylobacter spp. relative to other enteric pathogens in grow-finish pigs with diarrhea. Anaerobe 22: 111–114.
-
(2013)
Anaerobe
, vol.22
, pp. 111-114
-
-
Burrough, E.1
Terhorst, S.2
Sahin, O.3
Zhang, Q.4
-
17
-
-
6344229956
-
A European survey of antimicrobial susceptibility among zoonotic and commensal bacteria isolated from food-producing animals
-
Bywater, R., Deluyker, H., Deroover, E., de Jong, A., Marion, H., McConville, M., et al. (2004) A European survey of antimicrobial susceptibility among zoonotic and commensal bacteria isolated from food-producing animals. J Antimicrob Chemother 54: 744–754.
-
(2004)
J Antimicrob Chemother
, vol.54
, pp. 744-754
-
-
Bywater, R.1
Deluyker, H.2
Deroover, E.3
de Jong, A.4
Marion, H.5
McConville, M.6
-
18
-
-
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., et al. (2010a) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 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
-
19
-
-
75249107844
-
PyNAST: a flexible tool for aligning sequences to a template alignment
-
Caporaso, J.G., Bittinger, K., Bushman, F.D., DeSantis, T.Z., Andersen, G.L., and Knight, R. (2010b) PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26: 266–267.
-
(2010)
Bioinformatics
, vol.26
, pp. 266-267
-
-
Caporaso, J.G.1
Bittinger, K.2
Bushman, F.D.3
DeSantis, T.Z.4
Andersen, G.L.5
Knight, R.6
-
20
-
-
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., et al. (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. Isme J 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
-
21
-
-
0001463548
-
Nonparametric estimation of the number of classes in a population
-
Chao, A. (1984) Nonparametric estimation of the number of classes in a population. Scand J Statist 11: 265–270.
-
(1984)
Scand J Statist
, vol.11
, pp. 265-270
-
-
Chao, A.1
-
22
-
-
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., et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 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
-
23
-
-
0037447855
-
Design and evaluation of group-specific oligonucleotide probes for quantitative analysis of intestinal ecosystems: their application to assessment of equine colonic microflora
-
Daly, K., and Shirazi-Beechey, S.P. (2003) Design and evaluation of group-specific oligonucleotide probes for quantitative analysis of intestinal ecosystems: their application to assessment of equine colonic microflora. FEMS Microbiol Ecol 44: 243–252.
-
(2003)
FEMS Microbiol Ecol
, vol.44
, pp. 243-252
-
-
Daly, K.1
Shirazi-Beechey, S.P.2
-
24
-
-
85028263507
-
Bacterial sensing underlies artificial sweetener-induced growth of gut Lactobacillus
-
Daly, K., Darby, A.C., Hall, N., Wilkinson, M.C., Pongchaikul, P., Bravo, D., et al. (2015) Bacterial sensing underlies artificial sweetener-induced growth of gut Lactobacillus. Environ Microbiol 18: 2159–2171.
-
(2015)
Environ Microbiol
, vol.18
, pp. 2159-2171
-
-
Daly, K.1
Darby, A.C.2
Hall, N.3
Wilkinson, M.C.4
Pongchaikul, P.5
Bravo, D.6
-
25
-
-
84962519537
-
Low calorie sweeteners and gut microbiota
-
Daly, K., Darby, A.C., and Shirazi-Beechey, S.P. (2016) Low calorie sweeteners and gut microbiota. Physiol Behav 164 (Pt B): 494–500.
-
(2016)
Physiol Behav
, vol.164Pt B
, pp. 494-500
-
-
Daly, K.1
Darby, A.C.2
Shirazi-Beechey, S.P.3
-
26
-
-
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., et al. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 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
-
27
-
-
84908115906
-
Hibernation alters the diversity and composition of mucosa-associated bacteria while enhancing antimicrobial defence in the gut of 13-lined ground squirrels
-
Dill-McFarland, K.A., Neil, K.L., Zeng, A., Sprenger, R.J., Kurtz, C.C., Suen, G., et al. (2014) Hibernation alters the diversity and composition of mucosa-associated bacteria while enhancing antimicrobial defence in the gut of 13-lined ground squirrels. Mol Ecol 23: 4658–4669.
-
(2014)
Mol Ecol
, vol.23
, pp. 4658-4669
-
-
Dill-McFarland, K.A.1
Neil, K.L.2
Zeng, A.3
Sprenger, R.J.4
Kurtz, C.C.5
Suen, G.6
-
28
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460–2461.
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
29
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C., and Knight, R. (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 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
-
30
-
-
23044473640
-
Antimicrobial resistance patterns of Campylobacter from feedlot cattle*
-
Englen, M.D., Fedorka-Cray, P.J., Ladely, S.R., and Dargatz, D.A. (2005) Antimicrobial resistance patterns of Campylobacter from feedlot cattle*. J Appl Microbiol 99: 285–291.
-
(2005)
J Appl Microbiol
, vol.99
, pp. 285-291
-
-
Englen, M.D.1
Fedorka-Cray, P.J.2
Ladely, S.R.3
Dargatz, D.A.4
-
31
-
-
84922031840
-
The structures of the colonic mucosa-associated and luminal microbial communities are distinct and differentially affected by a prolonged murine stressor
-
Galley, J.D., Yu, Z., Kumar, P., Dowd, S.E., Lyte, M., and Bailey, M.T. (2014) The structures of the colonic mucosa-associated and luminal microbial communities are distinct and differentially affected by a prolonged murine stressor. Gut Microbes 5: 748–760.
-
(2014)
Gut Microbes
, vol.5
, pp. 748-760
-
-
Galley, J.D.1
Yu, Z.2
Kumar, P.3
Dowd, S.E.4
Lyte, M.5
Bailey, M.T.6
-
32
-
-
0036713151
-
A case-case comparison of Campylobacter coli and Campylobacter jejuni infection: a tool for generating hypotheses
-
Gillespie, I.A., O'brien, S.J., Frost, J.A., Adak, G.K., Horby, P., Swan, A.V., et al. (2002) A case-case comparison of Campylobacter coli and Campylobacter jejuni infection: a tool for generating hypotheses. Emerg Infect Dis 8: 937–942.
-
(2002)
Emerg Infect Dis
, vol.8
, pp. 937-942
-
-
Gillespie, I.A.1
O'brien, S.J.2
Frost, J.A.3
Adak, G.K.4
Horby, P.5
Swan, A.V.6
-
33
-
-
84923860119
-
MPAgenomics: an R package for multi-patient analysis of genomic markers
-
Grimonprez, Q., Celisse, A., Blanck, S., Cheok, M., Figeac, M., and Marot, G. (2014) MPAgenomics: an R package for multi-patient analysis of genomic markers. BMC Bioinform 15: 394.
-
(2014)
BMC Bioinform
, vol.15
, pp. 394
-
-
Grimonprez, Q.1
Celisse, A.2
Blanck, S.3
Cheok, M.4
Figeac, M.5
Marot, G.6
-
34
-
-
28244465760
-
The importance of Campylobacter coli in human campylobacteriosis: prevalence and genetic characterization
-
Gürtler, M., Alter, T., Kasimir, S., and Fehlhaber, K. (2005) The importance of Campylobacter coli in human campylobacteriosis: prevalence and genetic characterization. Epidemiol Infect 133: 1081–1087.
-
(2005)
Epidemiol Infect
, vol.133
, pp. 1081-1087
-
-
Gürtler, M.1
Alter, T.2
Kasimir, S.3
Fehlhaber, K.4
-
35
-
-
0000979832
-
Prevalence of Campylobacter spp isolated from the intestinal tract of pigs raised in an integrated swine production system
-
Harvey, R.B., Young, C.R., Ziprin, R.L., Hume, M.E., Genovese, K.J., Anderson, R.C., et al. (1999) Prevalence of Campylobacter spp isolated from the intestinal tract of pigs raised in an integrated swine production system. J Am Vet Med Assoc 215: 1601–1604.
-
(1999)
J Am Vet Med Assoc
, vol.215
, pp. 1601-1604
-
-
Harvey, R.B.1
Young, C.R.2
Ziprin, R.L.3
Hume, M.E.4
Genovese, K.J.5
Anderson, R.C.6
-
36
-
-
34249015507
-
Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces
-
Hayashi, H., Shibata, K., Sakamoto, M., Tomita, S., and Benno, Y. (2007) Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 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
-
37
-
-
0033551085
-
Noninvasive measurement of anatomic structure and intraluminal oxygenation in the gastrointestinal tract of living mice with spatial and spectral EPR imaging
-
He, G., Shankar, R.A., Chzhan, M., Samouilov, A., Kuppusamy, P., and Zweier, J.L. (1999) Noninvasive measurement of anatomic structure and intraluminal oxygenation in the gastrointestinal tract of living mice with spatial and spectral EPR imaging. Proc Natl Acad Sci U S A 96: 4586–4591.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 4586-4591
-
-
He, G.1
Shankar, R.A.2
Chzhan, M.3
Samouilov, A.4
Kuppusamy, P.5
Zweier, J.L.6
-
38
-
-
23044451197
-
Development of real-time PCR and hybridization methods for detection and identification of thermophilic Campylobacter spp. in pig faecal samples
-
Jensen, A.N., Andersen, M.T., Dalsgaard, A., Baggesen, D.L., and Nielsen, E.M. (2005) Development of real-time PCR and hybridization methods for detection and identification of thermophilic Campylobacter spp. in pig faecal samples. J Appl Microbiol 99: 292–300.
-
(2005)
J Appl Microbiol
, vol.99
, pp. 292-300
-
-
Jensen, A.N.1
Andersen, M.T.2
Dalsgaard, A.3
Baggesen, D.L.4
Nielsen, E.M.5
-
39
-
-
54449083567
-
The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria
-
Johansson, M.E., Phillipson, M., Petersson, J., Velcich, A., Holm, L., and Hansson, G.C. (2008) The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. Proc Natl Acad Sci U S A 105: 15064–15069.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 15064-15069
-
-
Johansson, M.E.1
Phillipson, M.2
Petersson, J.3
Velcich, A.4
Holm, L.5
Hansson, G.C.6
-
40
-
-
0034970220
-
The physiology and metabolism of Campylobacter jejuni and Helicobacter pylori
-
Kelly, D.J. (2001) The physiology and metabolism of Campylobacter jejuni and Helicobacter pylori. Symp Ser Soc Appl Microbiol 30: 16S–24S.
-
(2001)
Symp Ser Soc Appl Microbiol
, vol.30
, pp. 16S-24S
-
-
Kelly, D.J.1
-
41
-
-
33745153075
-
Post-natal development of the porcine microbiota composition and activities
-
Konstantinov, S.R., Awati, A.A., Williams, B.A., Miller, B.G., Jones, P., Stokes, C.R., et al. (2006) Post-natal development of the porcine microbiota composition and activities. Environ Microbiol 8: 1191–1199.
-
(2006)
Environ Microbiol
, vol.8
, pp. 1191-1199
-
-
Konstantinov, S.R.1
Awati, A.A.2
Williams, B.A.3
Miller, B.G.4
Jones, P.5
Stokes, C.R.6
-
42
-
-
84929104863
-
Prevalence of Campylobacter spp. in retail chicken, turkey, pork, and beef meat in Poland between 2009 and 2013
-
Korsak, D., Maćkiw, E., Rożynek, E., and Żyłowska, M. (2015) Prevalence of Campylobacter spp. in retail chicken, turkey, pork, and beef meat in Poland between 2009 and 2013. J Food Prot 78: 1024–1028.
-
(2015)
J Food Prot
, vol.78
, pp. 1024-1028
-
-
Korsak, D.1
Maćkiw, E.2
Rożynek, E.3
Żyłowska, M.4
-
43
-
-
34247846235
-
Nutritional management of gut health in pigs around weaning
-
Lallès, J.P., Bosi, P., Smidt, H., and Stokes, C.R. (2007) Nutritional management of gut health in pigs around weaning. Proc Nutr Soc 66: 260–268.
-
(2007)
Proc Nutr Soc
, vol.66
, pp. 260-268
-
-
Lallès, J.P.1
Bosi, P.2
Smidt, H.3
Stokes, C.R.4
-
44
-
-
69949088176
-
Better living through microbial action: the benefits of the mammalian gastrointestinal microbiota on the host
-
Leser, T.D., and Molbak, L. (2009) Better living through microbial action: the benefits of the mammalian gastrointestinal microbiota on the host. Environ Microbiol 11: 2194–2206.
-
(2009)
Environ Microbiol
, vol.11
, pp. 2194-2206
-
-
Leser, T.D.1
Molbak, L.2
-
45
-
-
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., et al. (2014) Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations. Isme J 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
-
46
-
-
77950789269
-
Acquisition, evolution and maintenance of the normal gut microbiota
-
Macfarlane, G.T., and Macfarlane, L.E. (2009) Acquisition, evolution and maintenance of the normal gut microbiota. Dig Dis 27 (Suppl 1): 90–98.
-
(2009)
Dig Dis
, vol.27Suppl 1
, pp. 90-98
-
-
Macfarlane, G.T.1
Macfarlane, L.E.2
-
47
-
-
79960923900
-
Mucosal biofilm communities in the human intestinal tract
-
Macfarlane, S., Bahrami, B., and Macfarlane, G.T. (2011) Mucosal biofilm communities in the human intestinal tract. Adv Appl Microbiol 75: 111–143.
-
(2011)
Adv Appl Microbiol
, vol.75
, pp. 111-143
-
-
Macfarlane, S.1
Bahrami, B.2
Macfarlane, G.T.3
-
48
-
-
80054913451
-
FLASH: fast length adjustment of short reads to improve genome assemblies
-
Magoč, T., and Salzberg, S.L. (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27: 2957–2963.
-
(2011)
Bioinformatics
, vol.27
, pp. 2957-2963
-
-
Magoč, T.1
Salzberg, S.L.2
-
49
-
-
0037178771
-
Helicobacter pylori SabA adhesin in persistent infection and chronic inflammation
-
Mahdavi, J., Sondén, B., Hurtig, M., Olfat, F.O., Forsberg, L., Roche, N., et al. (2002) Helicobacter pylori SabA adhesin in persistent infection and chronic inflammation. Science 297: 573–578.
-
(2002)
Science
, vol.297
, pp. 573-578
-
-
Mahdavi, J.1
Sondén, B.2
Hurtig, M.3
Olfat, F.O.4
Forsberg, L.5
Roche, N.6
-
50
-
-
84899813808
-
Mucosa-associated bacterial microbiome of the gastrointestinal tract of weaned pigs and dynamics linked to dietary calcium-phosphorus
-
Mann, E., Schmitz-Esser, S., Zebeli, Q., Wagner, M., Ritzmann, M., and Metzler-Zebeli, B.U. (2014) Mucosa-associated bacterial microbiome of the gastrointestinal tract of weaned pigs and dynamics linked to dietary calcium-phosphorus. PLoS One 9: e86950.
-
(2014)
PLoS One
, vol.9
-
-
Mann, E.1
Schmitz-Esser, S.2
Zebeli, Q.3
Wagner, M.4
Ritzmann, M.5
Metzler-Zebeli, B.U.6
-
51
-
-
78651440997
-
Breathing life into pathogens: the influence of oxygen on bacterial virulence and host responses in the gastrointestinal tract
-
Marteyn, B., Scorza, F.B., Sansonetti, P.J., and Tang, C. (2010) Breathing life into pathogens: the influence of oxygen on bacterial virulence and host responses in the gastrointestinal tract. Cell Microbiol 13: 171–176.
-
(2010)
Cell Microbiol
, vol.13
, pp. 171-176
-
-
Marteyn, B.1
Scorza, F.B.2
Sansonetti, P.J.3
Tang, C.4
-
52
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Martin, M. (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17: 10–12.
-
(2011)
EMBnet J
, vol.17
, pp. 10-12
-
-
Martin, M.1
-
53
-
-
84924085783
-
Gut/brain axis and the microbiota
-
Mayer, E.A., Tillisch, K., and Gupta, A. (2015) Gut/brain axis and the microbiota. J Clin Investig 125: 926–938.
-
(2015)
J Clin Investig
, vol.125
, pp. 926-938
-
-
Mayer, E.A.1
Tillisch, K.2
Gupta, A.3
-
54
-
-
79952756170
-
Mucin dynamics and enteric pathogens
-
McGuckin, M.A., Lindén, S.K., Sutton, P., and Florin, T.H. (2011) Mucin dynamics and enteric pathogens. Nat Rev Microbiol 9: 265–278.
-
(2011)
Nat Rev Microbiol
, vol.9
, pp. 265-278
-
-
McGuckin, M.A.1
Lindén, S.K.2
Sutton, P.3
Florin, T.H.4
-
55
-
-
84876427223
-
phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data
-
McMurdie, P.J., and Holmes, S. (2013) phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8: e61217.
-
(2013)
PLoS One
, vol.8
-
-
McMurdie, P.J.1
Holmes, S.2
-
56
-
-
84930276082
-
The role of microbiota on the gut immunology
-
Min, Y.W., and Rhee, P.L. (2015) The role of microbiota on the gut immunology. Clin Ther 37: 968–975.
-
(2015)
Clin Ther
, vol.37
, pp. 968-975
-
-
Min, Y.W.1
Rhee, P.L.2
-
57
-
-
84929035714
-
Intestinal events and nutritional dynamics predispose Clostridium perfringens virulence in broilers
-
Moran, E.T. Jr (2014) Intestinal events and nutritional dynamics predispose Clostridium perfringens virulence in broilers. Poult Sci 93: 3028–3036.
-
(2014)
Poult Sci
, vol.93
, pp. 3028-3036
-
-
Moran, E.T.1
-
58
-
-
84880696355
-
Divergent mechanisms of interaction of Helicobacter pylori and Campylobacter jejuni with mucus and mucins
-
Naughton, J.A., Mariño, K., Dolan, B., Reid, C., Gough, R., Gallagher, M.E., et al. (2013) Divergent mechanisms of interaction of Helicobacter pylori and Campylobacter jejuni with mucus and mucins. Infect Immun 81: 2838–2850.
-
(2013)
Infect Immun
, vol.81
, pp. 2838-2850
-
-
Naughton, J.A.1
Mariño, K.2
Dolan, B.3
Reid, C.4
Gough, R.5
Gallagher, M.E.6
-
59
-
-
79953025268
-
Spatial organization of intestinal microbiota in the mouse ascending colon
-
Nava, G.M., Friedrichsen, H.J., and Stappenbeck, T.S. (2011) Spatial organization of intestinal microbiota in the mouse ascending colon. Isme J 5: 627–638.
-
(2011)
Isme J
, vol.5
, pp. 627-638
-
-
Nava, G.M.1
Friedrichsen, H.J.2
Stappenbeck, T.S.3
-
60
-
-
84855676758
-
Genotypes and antibiotic resistances of Campylobacter jejuni and Campylobacter coli isolates from domestic and travel-associated human cases
-
Niederer, L., Kuhnert, P., Egger, R., Büttner, S., Hächler, H., and Korczak, B.M. (2012) Genotypes and antibiotic resistances of Campylobacter jejuni and Campylobacter coli isolates from domestic and travel-associated human cases. Appl Environ Microbiol 78: 288–291.
-
(2012)
Appl Environ Microbiol
, vol.78
, pp. 288-291
-
-
Niederer, L.1
Kuhnert, P.2
Egger, R.3
Büttner, S.4
Hächler, H.5
Korczak, B.M.6
-
61
-
-
84887602582
-
The core faecal bacterial microbiome of Irish Thoroughbred racehorses
-
O'Donnell, M.M., Harris, H.M., Jeffery, I.B., Claesson, M.J., Younge, B., O' Toole, P.W., et al. (2013) The core faecal bacterial microbiome of Irish Thoroughbred racehorses. Lett Appl Microbiol 57: 492–501.
-
(2013)
Lett Appl Microbiol
, vol.57
, pp. 492-501
-
-
O'Donnell, M.M.1
Harris, H.M.2
Jeffery, I.B.3
Claesson, M.J.4
Younge, B.5
O' Toole, P.W.6
-
62
-
-
67649327176
-
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix
-
Price, M.N., Dehal, P.S., and Arkin, A.P. (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26: 1641–1650.
-
(2009)
Mol Biol Evol
, vol.26
, pp. 1641-1650
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
63
-
-
80052970180
-
Evidence for a core gut microbiota in the zebrafish
-
Roeselers, G., Mittge, E.K., Stephens, W.Z., Parichy, D.M., Cavanaugh, C.M., Guillemin, K., et al. (2011) Evidence for a core gut microbiota in the zebrafish. Isme J 5: 1595–1608.
-
(2011)
Isme J
, vol.5
, pp. 1595-1608
-
-
Roeselers, G.1
Mittge, E.K.2
Stephens, W.Z.3
Parichy, D.M.4
Cavanaugh, C.M.5
Guillemin, K.6
-
65
-
-
11144353967
-
Epidemiology of sporadic Campylobacter infection in the United States and declining trend in incidence, FoodNet 1996-1999
-
Samuel, M.C., Vugia, D.J., Shallow, S., Marcus, R., Segler, S., McGivern, T., et al. (2004) Epidemiology of sporadic Campylobacter infection in the United States and declining trend in incidence, FoodNet 1996-1999. Clin Infect Dis 38 (Suppl 3): S165–S174.
-
(2004)
Clin Infect Dis
, vol.38Suppl 3
, pp. S165-S174
-
-
Samuel, M.C.1
Vugia, D.J.2
Shallow, S.3
Marcus, R.4
Segler, S.5
McGivern, T.6
-
66
-
-
84871630781
-
Intestinal microbes in inflammatory bowel diseases
-
Sartor, R.B., and Mazmanian, S.K. (2012) Intestinal microbes in inflammatory bowel diseases. Am J Gastro Suppl 1: 15–21.
-
(2012)
Am J Gastro Suppl
, vol.1
, pp. 15-21
-
-
Sartor, R.B.1
Mazmanian, S.K.2
-
67
-
-
78650979311
-
Foodborne illness acquired in the United States–major pathogens
-
Scallan, E., Hoekstra, R.M., Angulo, F.J., Tauxe, R.V., Widdowson, M.A., Roy, S.L., et al. (2011) Foodborne illness acquired in the United States–major pathogens. Emerg Infect Dis 17: 7–15.
-
(2011)
Emerg Infect Dis
, vol.17
, pp. 7-15
-
-
Scallan, E.1
Hoekstra, R.M.2
Angulo, F.J.3
Tauxe, R.V.4
Widdowson, M.A.5
Roy, S.L.6
-
68
-
-
0036319829
-
Gastrointestinal transit times in mice and humans measured with 27Al and 19F nuclear magnetic resonance
-
Schwarz, R., Kaspar, A., Seelig, J., and Künnecke, B. (2002) Gastrointestinal transit times in mice and humans measured with 27Al and 19F nuclear magnetic resonance. Magn Reson Med 48: 255–261.
-
(2002)
Magn Reson Med
, vol.48
, pp. 255-261
-
-
Schwarz, R.1
Kaspar, A.2
Seelig, J.3
Künnecke, B.4
-
69
-
-
0025344613
-
Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides
-
Shah, H.N., and Collins, D.M. (1990) Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides. Int J Syst Bacteriol 40: 205–208.
-
(1990)
Int J Syst Bacteriol
, vol.40
, pp. 205-208
-
-
Shah, H.N.1
Collins, D.M.2
-
71
-
-
0037267246
-
Aerotolerance of human clinical isolates of Prevotella spp
-
Silva, V.L., Carvalho, M.A., Nicoli, J.R., and Farias, L.M. (2003) Aerotolerance of human clinical isolates of Prevotella spp. J Appl Microbiol 94: 701–707.
-
(2003)
J Appl Microbiol
, vol.94
, pp. 701-707
-
-
Silva, V.L.1
Carvalho, M.A.2
Nicoli, J.R.3
Farias, L.M.4
-
72
-
-
84859747964
-
Bacterial biogeography of the human digestive tract
-
Stearns, J.C., Lynch, M.D., Senadheera, D.B., Tenenbaum, H.C., Goldberg, M.B., Cvitkovitch, D.G., et al. (2011) Bacterial biogeography of the human digestive tract. Sci Rep 1: 170.
-
(2011)
Sci Rep
, vol.1
, pp. 170
-
-
Stearns, J.C.1
Lynch, M.D.2
Senadheera, D.B.3
Tenenbaum, H.C.4
Goldberg, M.B.5
Cvitkovitch, D.G.6
-
73
-
-
55849133415
-
Effects of sweeteners on individual feed intake characteristics and performance in group-housed weanling pigs
-
Sterk, A., Schlegel, P., Mul, A.J., Ubbink-Blanksma, M., and Bruininx, E.M. (2008) Effects of sweeteners on individual feed intake characteristics and performance in group-housed weanling pigs. J Anim Sci 86: 2990–2997.
-
(2008)
J Anim Sci
, vol.86
, pp. 2990-2997
-
-
Sterk, A.1
Schlegel, P.2
Mul, A.J.3
Ubbink-Blanksma, M.4
Bruininx, E.M.5
-
74
-
-
0028884686
-
Campylobacter jejuni motility and invasion of Caco-2 cells
-
Szymanski, C.M., King, M., Haardt, M., and Armstrong, G.D. (1995) Campylobacter jejuni motility and invasion of Caco-2 cells. Infect Immun 63: 4295–4300.
-
(1995)
Infect Immun
, vol.63
, pp. 4295-4300
-
-
Szymanski, C.M.1
King, M.2
Haardt, M.3
Armstrong, G.D.4
-
75
-
-
0037481812
-
Campylobacter coli - an important foodborne pathogen
-
Tam, C.C., O'brien, S.J., Adak, G.K., Meakins, S.M., and Frost, J.A. (2003) Campylobacter coli - an important foodborne pathogen. J Infect 47: 28–32.
-
(2003)
J Infect
, vol.47
, pp. 28-32
-
-
Tam, C.C.1
O'brien, S.J.2
Adak, G.K.3
Meakins, S.M.4
Frost, J.A.5
-
76
-
-
70349233883
-
Towards the human intestinal microbiota phylogenetic core
-
Tap, J., Mondot, S., Levenez, F., Pelletier, E., Caron, C., Furet, J.P., et al. (2009) Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 11: 2574–2584.
-
(2009)
Environ Microbiol
, vol.11
, pp. 2574-2584
-
-
Tap, J.1
Mondot, S.2
Levenez, F.3
Pelletier, E.4
Caron, C.5
Furet, J.P.6
-
77
-
-
84978115999
-
The microbiome and innate immunity
-
Thaiss, C.A., Zmora, N., Levy, M., and Elinav, E. (2016) The microbiome and innate immunity. Nature 535: 65–74.
-
(2016)
Nature
, vol.535
, pp. 65-74
-
-
Thaiss, C.A.1
Zmora, N.2
Levy, M.3
Elinav, E.4
-
78
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A., Ley, R.E., et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480–484.
-
(2009)
Nature
, vol.457
, pp. 480-484
-
-
Turnbaugh, P.J.1
Hamady, M.2
Yatsunenko, T.3
Cantarel, B.L.4
Duncan, A.5
Ley, R.E.6
-
79
-
-
84960798719
-
Species shift and multidrug resistance of Campylobacter from chicken and swine, China, 2008-14
-
Wang, Y., Dong, Y., Deng, F., Liu, D., Yao, H., Zhang, Q., et al. (2016) Species shift and multidrug resistance of Campylobacter from chicken and swine, China, 2008-14. J Antimicrob Chemother 71: 666–669.
-
(2016)
J Antimicrob Chemother
, vol.71
, pp. 666-669
-
-
Wang, Y.1
Dong, Y.2
Deng, F.3
Liu, D.4
Yao, H.5
Zhang, Q.6
-
80
-
-
66249145772
-
Statistical methods for detecting differentially abundant features in clinical metagenomic samples
-
White, J.R., Nagarajan, N., and Pop, M. (2009) Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5: e1000352.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
White, J.R.1
Nagarajan, N.2
Pop, M.3
-
81
-
-
84881005763
-
Aquacultured rainbow trout (Oncorhynchus mykiss) possess a large core intestinal microbiota that is resistant to variation in diet and rearing density
-
Wong, S., Waldrop, T., Summerfelt, S., Davidson, J., Barrows, F., Kenney, P.B., et al. (2013) Aquacultured rainbow trout (Oncorhynchus mykiss) possess a large core intestinal microbiota that is resistant to variation in diet and rearing density. Appl Environ Microbiol 79: 4974–4984.
-
(2013)
Appl Environ Microbiol
, vol.79
, pp. 4974-4984
-
-
Wong, S.1
Waldrop, T.2
Summerfelt, S.3
Davidson, J.4
Barrows, F.5
Kenney, P.B.6
-
82
-
-
0034284024
-
Prevotella enzymes involved in mucin oligosaccharide degradation and evidence for a small operon of genes expressed during growth on mucin
-
Wright, D.P., Rosendale, D.I., and Robertson, A.M. (2000) Prevotella enzymes involved in mucin oligosaccharide degradation and evidence for a small operon of genes expressed during growth on mucin. FEMS Microbiol Lett 190: 73–79.
-
(2000)
FEMS Microbiol Lett
, vol.190
, pp. 73-79
-
-
Wright, D.P.1
Rosendale, D.I.2
Robertson, A.M.3
-
83
-
-
84926248729
-
Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque
-
Yasuda, K., Oh, K., Ren, B., Tickle, T.L., Franzosa, E.A., Wachtman, L.M., et al. (2015) Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque. Cell Host Microbe 17: 385–391.
-
(2015)
Cell Host Microbe
, vol.17
, pp. 385-391
-
-
Yasuda, K.1
Oh, K.2
Ren, B.3
Tickle, T.L.4
Franzosa, E.A.5
Wachtman, L.M.6
-
84
-
-
84928902097
-
The dynamic distribution of porcine microbiota across different ages and gastrointestinal tract segments
-
Zhao, W., Wang, Y., Liu, S., Huang, J., Zhai, Z., He, C., et al. (2015) The dynamic distribution of porcine microbiota across different ages and gastrointestinal tract segments. PLoS One 10: e0117441.
-
(2015)
PLoS One
, vol.10
-
-
Zhao, W.1
Wang, Y.2
Liu, S.3
Huang, J.4
Zhai, Z.5
He, C.6
-
85
-
-
0036300743
-
Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces
-
Zoetendal, E.G., von Wright, A., Vilpponen-Salmela, T., Ben-Amor, K., Akkermans, A.D., and de Vos, W.M. (2002) Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol 68: 3401–3407.
-
(2002)
Appl Environ Microbiol
, vol.68
, pp. 3401-3407
-
-
Zoetendal, E.G.1
von Wright, A.2
Vilpponen-Salmela, T.3
Ben-Amor, K.4
Akkermans, A.D.5
de Vos, W.M.6
-
86
-
-
84862590343
-
The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates
-
Zoetendal, E.G., Raes, J., van den Bogert, B., Arumugam, M., Booijink, C.C., and Troost, F.J. (2012) The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. Isme J 6: 1415–1426.
-
(2012)
Isme J
, vol.6
, pp. 1415-1426
-
-
Zoetendal, E.G.1
Raes, J.2
van den Bogert, B.3
Arumugam, M.4
Booijink, C.C.5
Troost, F.J.6
|