-
1
-
-
70350343544
-
Induction of intestinal Th17 cells by segmented filamentous bacteria
-
Ivanov, I. I. et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139, 485-498 (2009).
-
(2009)
Cell
, vol.139
, pp. 485-498
-
-
Ivanov, I.I.1
-
2
-
-
85027947787
-
Induction of colonic regulatory T cells by indigenous Clostridium species
-
Atarashi, K. et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science 331, 337-341 (2011).
-
(2011)
Science
, vol.331
, pp. 337-341
-
-
Atarashi, K.1
-
3
-
-
77954738601
-
Inducible Foxp3 regulatory T-cell development by a commensal bacterium of the intestinal microbiota
-
Round, J. L. & Mazmanian, S. K. Inducible Foxp3 regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc. Natl Acad. Sci. USA 107, 12204-12209 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 12204-12209
-
-
Round, J.L.1
Mazmanian, S.K.2
-
4
-
-
84883478660
-
Gut microbiota from twins discordant for obesity modulate metabolism in mice
-
Ridaura, V. K. et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 341, 1241214 (2013).
-
(2013)
Science
, vol.341
, pp. 1241214
-
-
Ridaura, V.K.1
-
5
-
-
84905968786
-
Fecal microbiota transplantation for the treatment of Clostridium difficile infection: A systematic review
-
Cammarota, G., Ianiro, G. & Gasbarrini, A. Fecal microbiota transplantation for the treatment of Clostridium difficile infection: a systematic review. J. Clin. Gastroenterol. 48, 693-702 (2014).
-
(2014)
J. Clin. Gastroenterol.
, vol.48
, pp. 693-702
-
-
Cammarota, G.1
Ianiro, G.2
Gasbarrini, A.3
-
6
-
-
84904384753
-
Foxp3() T cells regulate immunoglobulin A selection and facilitate diversification of bacterial species responsible for immune homeostasis
-
Kawamoto, S. et al. Foxp3() T cells regulate immunoglobulin A selection and facilitate diversification of bacterial species responsible for immune homeostasis. Immunity 41, 152-165 (2014).
-
(2014)
Immunity
, vol.41
, pp. 152-165
-
-
Kawamoto, S.1
-
7
-
-
84923587206
-
Host adaptive immunity alters gut microbiota
-
Zhang, H., Sparks, J. B., Karyala, S. V., Settlage, R. & Luo, X. M. Host adaptive immunity alters gut microbiota. ISME J. 9, 770-781 (2015).
-
(2015)
ISME J.
, vol.9
, pp. 770-781
-
-
Zhang, H.1
Sparks, J.B.2
Karyala, S.V.3
Settlage, R.4
Luo, X.M.5
-
8
-
-
52049092682
-
Worlds within worlds: Evolution of the vertebrate gut microbiota
-
Ley, R. E., Lozupone, C. A., Hamady, M., Knight, R. & Gordon, J. I. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat. Rev. Microbiol. 6, 776-788 (2008).
-
(2008)
Nat. Rev. Microbiol.
, vol.6
, pp. 776-788
-
-
Ley, R.E.1
Lozupone, C.A.2
Hamady, M.3
Knight, R.4
Gordon, J.I.5
-
9
-
-
84926080075
-
Mycobiota in gastrointestinal diseases
-
Mukherjee, P. K. et al. Mycobiota in gastrointestinal diseases. Nat. Rev. Gastroenterol. Hepatol. 12, 77-87 (2015).
-
(2015)
Nat. Rev. Gastroenterol. Hepatol.
, vol.12
, pp. 77-87
-
-
Mukherjee, P.K.1
-
11
-
-
84897389131
-
The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps
-
Barroso-Batista, J. et al. The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps. PLoS Genet. 10, e1004182 (2014).
-
(2014)
PLoS Genet.
, vol.10
, pp. e1004182
-
-
Barroso-Batista, J.1
-
13
-
-
0028832576
-
Physiological state of Escherichia coli BJ4 growing in the large intestines of streptomycintreated mice
-
Poulsen, L. K., Licht, T. R., Rang, C., Krogfelt, K. A. & Molin, S. Physiological state of Escherichia coli BJ4 growing in the large intestines of streptomycintreated mice. J. Bacteriol. 177, 5840-5845 (1995).
-
(1995)
J. Bacteriol.
, vol.177
, pp. 5840-5845
-
-
Poulsen, L.K.1
Licht, T.R.2
Rang, C.3
Krogfelt, K.A.4
Molin, S.5
-
14
-
-
0031771290
-
Oxygen-insensitive nitroreductases: Analysis of the roles of nfsA and nfsB in development of resistance to 5-nitrofuran derivatives in Escherichia coli
-
Whiteway, J. et al. Oxygen-insensitive nitroreductases: analysis of the roles of nfsA and nfsB in development of resistance to 5-nitrofuran derivatives in Escherichia coli. J. Bacteriol. 180, 5529-5539 (1998).
-
(1998)
J. Bacteriol.
, vol.180
, pp. 5529-5539
-
-
Whiteway, J.1
-
15
-
-
84880474099
-
Analysis of microbiota alterations in inflammasome-deficient mice
-
Elinav, E., Thaiss, C. A. & Flavell, R. A. Analysis of microbiota alterations in inflammasome-deficient mice. Methods Mol. Biol. 1040, 185-194 (2013).
-
(2013)
Methods Mol. Biol.
, vol.1040
, pp. 185-194
-
-
Elinav, E.1
Thaiss, C.A.2
Flavell, R.A.3
-
16
-
-
84874691463
-
Temporal stability of the mouse gut microbiota in relation to innate and adaptive immunity
-
Dimitriu, P. A. et al. Temporal stability of the mouse gut microbiota in relation to innate and adaptive immunity. Environ. Microbiol. Rep. 5, 200-210 (2013).
-
(2013)
Environ. Microbiol. Rep.
, vol.5
, pp. 200-210
-
-
Dimitriu, P.A.1
-
17
-
-
84897388020
-
Immune mediated shaping of microflora community composition depends on barrier site
-
Scholz, F., Badgley, B. D., Sadowsky, M. J. & Kaplan, D. H. Immune mediated shaping of microflora community composition depends on barrier site. PLoS ONE 9, e84019 (2014).
-
(2014)
PLoS ONE
, vol.9
, pp. e84019
-
-
Scholz, F.1
Badgley, B.D.2
Sadowsky, M.J.3
Kaplan, D.H.4
-
18
-
-
1242296822
-
Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut
-
Suzuki, K. et al. Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut. Proc. Natl Acad. Sci. USA 101, 1981-1986 (2004).
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 1981-1986
-
-
Suzuki, K.1
-
19
-
-
84911873660
-
Composition of intestinal microbiota in immunedeficient mice kept in three different housing conditions
-
Thoene-Reineke, C. et al. Composition of intestinal microbiota in immunedeficient mice kept in three different housing conditions. PLoS ONE 9, e113406 (2014).
-
(2014)
PLoS ONE
, vol.9
, pp. e113406
-
-
Thoene-Reineke, C.1
-
20
-
-
84856083002
-
Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut
-
Shulzhenko, N. et al. Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut. Nat. Med. 17, 1585-1593 (2011).
-
(2011)
Nat. Med.
, vol.17
, pp. 1585-1593
-
-
Shulzhenko, N.1
-
21
-
-
84925600482
-
Manipulation of the quorum sensing signal AI-2 affects the antibiotic-treated gut microbiota
-
Thompson, J. A., Oliveira, R. A., Djukovic, A., Ubeda, C. & Xavier, K. B. Manipulation of the quorum sensing signal AI-2 affects the antibiotic-treated gut microbiota. Cell Rep. 10, 1861-1871 (2015).
-
(2015)
Cell Rep.
, vol.10
, pp. 1861-1871
-
-
Thompson, J.A.1
Oliveira, R.A.2
Djukovic, A.3
Ubeda, C.4
Xavier, K.B.5
-
22
-
-
28444483927
-
Mouse intestine selects nonmotile flhDC mutants of Escherichia coli MG1655 with increased colonizing ability and better utilization of carbon sources
-
Leatham, M. P. et al. Mouse intestine selects nonmotile flhDC mutants of Escherichia coli MG1655 with increased colonizing ability and better utilization of carbon sources. Infect. Immun. 73, 8039-8049 (2005).
-
(2005)
Infect. Immun.
, vol.73
, pp. 8039-8049
-
-
Leatham, M.P.1
-
23
-
-
84859697972
-
The streptomycin-treated mouse intestine selects Escherichia coli envZ missense mutants that interact with dense and diverse intestinal microbiota
-
Leatham-Jensen, M. P. et al. The streptomycin-treated mouse intestine selects Escherichia coli envZ missense mutants that interact with dense and diverse intestinal microbiota. Infect. Immun. 80, 1716-1727 (2012).
-
(2012)
Infect. Immun.
, vol.80
, pp. 1716-1727
-
-
Leatham-Jensen, M.P.1
-
24
-
-
13244279408
-
Multiple regulators control expression of the Entner-Doudoroff Aldolase (Eda) of Escherichia coli
-
Murray, E. L. & Conway, T. Multiple regulators control expression of the Entner-Doudoroff Aldolase (Eda) of Escherichia coli. J. Bacteriol. 187, 991-1000 (2005).
-
(2005)
J. Bacteriol.
, vol.187
, pp. 991-1000
-
-
Murray, E.L.1
Conway, T.2
-
25
-
-
0032464663
-
Whats for dinner?: Entner-Doudoroff metabolism in Escherichia coli
-
Peekhaus, N. & Conway, T. Whats for dinner?: Entner-Doudoroff metabolism in Escherichia coli. J. Bacteriol. 180, 3495-3502 (1998).
-
(1998)
J. Bacteriol.
, vol.180
, pp. 3495-3502
-
-
Peekhaus, N.1
Conway, T.2
-
26
-
-
38649127863
-
Regulation of the yjjQ-bglJ operon, encoding LuxR-Type transcription factors, and the divergent yjjP gene by H-NS and LeuO
-
Stratmann, T., Madhusudan, S. & Schnetz, K. Regulation of the yjjQ-bglJ operon, encoding LuxR-Type transcription factors, and the divergent yjjP gene by H-NS and LeuO. J. Bacteriol. 190, 926-935 (2008).
-
(2008)
J. Bacteriol.
, vol.190
, pp. 926-935
-
-
Stratmann, T.1
Madhusudan, S.2
Schnetz, K.3
-
27
-
-
35649003869
-
Activation of yeaR-yoaG operon transcription by the nitrate-responsive regulator NarL is independent of oxygen- responsive regulator Fnr in Escherichia coli K-12
-
Lin, H.-Y., Bledsoe, P. J. & Stewart, V. Activation of yeaR-yoaG operon transcription by the nitrate-responsive regulator NarL is independent of oxygen- responsive regulator Fnr in Escherichia coli K-12. J. Bacteriol. 189, 7539-7548 (2007).
-
(2007)
J. Bacteriol.
, vol.189
, pp. 7539-7548
-
-
Lin, H.-Y.1
Bledsoe, P.J.2
Stewart, V.3
-
28
-
-
0035933597
-
Quinones as the redox signal for the arc two-component system of bacteria
-
Georgellis, D., Kwon, O. & Lin, E. C. C. Quinones as the redox signal for the arc two-component system of bacteria. Science 292, 2314-2316 (2001).
-
(2001)
Science
, vol.292
, pp. 2314-2316
-
-
Georgellis, D.1
Kwon, O.2
Lin, E.C.C.3
-
29
-
-
0037044736
-
Identification of a pathway for the utilization of the amadori product fructoselysine in Escherichia coli
-
Wiame, E., Delpierre, G., Collard, F. & Schaftingen, E. V. Identification of a pathway for the utilization of the amadori product fructoselysine in Escherichia coli. J. Biol. Chem. 277, 42523-42529 (2002).
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 42523-42529
-
-
Wiame, E.1
Delpierre, G.2
Collard, F.3
Schaftingen, E.V.4
-
30
-
-
0023427972
-
Cloning and nucleotide sequencing of the genes rimI and rimJ which encode enzymes acetylating ribosomal proteins S18 and S5 of Escherichia coli K12
-
Yoshikawa, A., Isono, S., Sheback, A. & Isono, K. Cloning and nucleotide sequencing of the genes rimI and rimJ which encode enzymes acetylating ribosomal proteins S18 and S5 of Escherichia coli K12. Mol. Gen. Genet. 209, 481-488 (1987).
-
(1987)
Mol. Gen. Genet.
, vol.209
, pp. 481-488
-
-
Yoshikawa, A.1
Isono, S.2
Sheback, A.3
Isono, K.4
-
31
-
-
84874672692
-
Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization
-
Ubeda, C. et al. Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization. Infect. Immun. 81, 965-973 (2013).
-
(2013)
Infect. Immun.
, vol.81
, pp. 965-973
-
-
Ubeda, C.1
-
32
-
-
84941647683
-
BALB/c and C57BL/6 mice differ in polyreactive IgA abundance, which impacts the generation of antigen-specific IgA and microbiota diversity
-
Fransen, F. et al. BALB/c and C57BL/6 mice differ in polyreactive IgA abundance, which impacts the generation of antigen-specific IgA and microbiota diversity. Immunity 43, 527-540 (2015).
-
(2015)
Immunity
, vol.43
, pp. 527-540
-
-
Fransen, F.1
-
33
-
-
84893370250
-
Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice
-
Faith, J. J., Ahern, P. P., Ridaura, V. K., Cheng, J. & Gordon, J. I. Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice. Sci. Transl. Med. 6, 220ra11 (2014).
-
(2014)
Sci. Transl. Med.
, vol.6
, pp. 220ra11
-
-
Faith, J.J.1
Ahern, P.P.2
Ridaura, V.K.3
Cheng, J.4
Gordon, J.I.5
-
34
-
-
0028176507
-
Transport of C4-dicarboxylates by anaerobically grown Escherichia coli. Energetics and mechanism of exchange, uptake and efflux
-
Engel, P., Krämer, R. & Unden, G. Transport of C4-dicarboxylates by anaerobically grown Escherichia coli. Energetics and mechanism of exchange, uptake and efflux. Eur. J. Biochem. 222, 605-614 (1994).
-
(1994)
Eur. J. Biochem.
, vol.222
, pp. 605-614
-
-
Engel, P.1
Krämer, R.2
Unden, G.3
-
35
-
-
84920621547
-
Gut microbiota-produced succinate promotes C. Difficile infection after antibiotic treatment or motility disturbance
-
Ferreyra, J. A. et al. Gut microbiota-produced succinate promotes C. difficile infection after antibiotic treatment or motility disturbance. Cell Host Microbe 16, 770-777 (2014).
-
(2014)
Cell Host Microbe
, vol.16
, pp. 770-777
-
-
Ferreyra, J.A.1
-
36
-
-
80855136527
-
Anaerobic respiration of Escherichia coli in the mouse intestine
-
Jones, S. A. et al. Anaerobic respiration of Escherichia coli in the mouse intestine. Infect. Immun. 79, 4218-4226 (2011).
-
(2011)
Infect. Immun.
, vol.79
, pp. 4218-4226
-
-
Jones, S.A.1
-
37
-
-
2442611939
-
Carbon nutrition of Escherichia coli in the mouse intestine
-
Chang, D. E. et al. Carbon nutrition of Escherichia coli in the mouse intestine. Proc. Natl Acad. Sci. USA 101, 7427-7432 (2004).
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 7427-7432
-
-
Chang, D.E.1
-
38
-
-
0029842584
-
Escherichia coli F-18 and E. Coli K-12 eda mutants do not colonize the streptomycin-treated mouse large intestine
-
Sweeney, N. J., Laux, D. C. & Cohen, P. S. Escherichia coli F-18 and E. coli K-12 eda mutants do not colonize the streptomycin-treated mouse large intestine. Infect. Immun. 64, 3504-3511 (1996).
-
(1996)
Infect. Immun.
, vol.64
, pp. 3504-3511
-
-
Sweeney, N.J.1
Laux, D.C.2
Cohen, P.S.3
-
39
-
-
15444350252
-
The complete genome sequence of Escherichia coli K-12
-
Blattner, F. R. et al. The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1462 (1997).
-
(1997)
Science
, vol.277
, pp. 1453-1462
-
-
Blattner, F.R.1
-
41
-
-
84879354995
-
Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization
-
Skinner, S. O., Sepulveda, L. A., Xu, H. & Golding, I. Measuring mRNA copy number in individual Escherichia coli cells using single-molecule fluorescent in situ hybridization. Nat. Protoc. 8, 1100-1113 (2013).
-
(2013)
Nat. Protoc.
, vol.8
, pp. 1100-1113
-
-
Skinner, S.O.1
Sepulveda, L.A.2
Xu, H.3
Golding, I.4
-
42
-
-
72949107142
-
Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss, P. D. et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75, 7537-7541 (2009).
-
(2009)
Appl. Environ. Microbiol.
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
-
43
-
-
83355173006
-
Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies
-
Schloss, P. D., Gevers, D. & Westcott, S. L. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 6, e27310 (2011).
-
(2011)
PLoS ONE
, vol.6
, pp. e27310
-
-
Schloss, P.D.1
Gevers, D.2
Westcott, S.L.3
-
44
-
-
37549027613
-
SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
-
Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188-7196 (2007).
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 7188-7196
-
-
Pruesse, E.1
-
45
-
-
33750983947
-
Clearcut: A fast implementation of relaxed neighbor joining
-
Sheneman, L., Evans, J. & Foster, J. A. Clearcut: a fast implementation of relaxed neighbor joining. Bioinforma. Oxf. Engl 22, 2823-2824 (2006).
-
(2006)
Bioinforma. Oxf. Engl
, vol.22
, pp. 2823-2824
-
-
Sheneman, L.1
Evans, J.2
Foster, J.A.3
-
46
-
-
0001463548
-
Nonparametric estimation of the number of classes in a population
-
Chao, A. Nonparametric estimation of the number of classes in a population. Scand. J. Stat. 11, 265-270 (1984).
-
(1984)
Scand. J. Stat.
, vol.11
, pp. 265-270
-
-
Chao, A.1
-
47
-
-
84940644968
-
A mathematical theory of communication
-
Shannon, C. E. A mathematical theory of communication. Bell Syst. Tech. J. 27, 379-423 (1948).
-
(1948)
Bell Syst. Tech. J.
, vol.27
, pp. 379-423
-
-
Shannon, C.E.1
-
48
-
-
0000286531
-
An ordination of the upland forest communities of southern Wisconsin
-
Bray, J. R. & Curtis, J. T. An ordination of the upland forest communities of southern Wisconsin. Ecol. Monogr. 27, 326-349 (1957).
-
(1957)
Ecol. Monogr.
, vol.27
, pp. 326-349
-
-
Bray, J.R.1
Curtis, J.T.2
-
49
-
-
33947269742
-
Quantitative and qualitative b diversity measures lead to different insights into factors that structure microbial communities
-
Lozupone, C. A., Hamady, M., Kelley, S. T. & Knight, R. Quantitative and qualitative b diversity measures lead to different insights into factors that structure microbial communities. Appl. Environ. Microbiol. 73, 1576-1585 (2007).
-
(2007)
Appl. Environ. Microbiol.
, vol.73
, pp. 1576-1585
-
-
Lozupone, C.A.1
Hamady, M.2
Kelley, S.T.3
Knight, R.4
-
50
-
-
78751575501
-
UniFrac: An effective distance metric for microbial community comparison
-
Lozupone, C., Lladser, M. E., Knights, D., Stombaugh, J. & Knight, R. UniFrac: an effective distance metric for microbial community comparison. ISME J. 5, 169-172 (2011).
-
(2011)
ISME J.
, vol.5
, pp. 169-172
-
-
Lozupone, C.1
Lladser, M.E.2
Knights, D.3
Stombaugh, J.4
Knight, R.5
|