-
1
-
-
84890363776
-
Therapeutic fecal microbiota transplantation: current status and future developments
-
Borody, T.J., Brandt, L.J., Paramsothy, S., Therapeutic fecal microbiota transplantation: current status and future developments. Curr Opin Gastroenterol 30 (2014), 97–105.
-
(2014)
Curr Opin Gastroenterol
, vol.30
, pp. 97-105
-
-
Borody, T.J.1
Brandt, L.J.2
Paramsothy, S.3
-
2
-
-
84931295496
-
Update on fecal microbiota transplantation 2015: indications, methodologies, mechanisms, and outlook
-
Kelly, C.R., Kahn, S., Kashyap, P., et al. Update on fecal microbiota transplantation 2015: indications, methodologies, mechanisms, and outlook. Gastroenterology 149 (2015), 223–237.
-
(2015)
Gastroenterology
, vol.149
, pp. 223-237
-
-
Kelly, C.R.1
Kahn, S.2
Kashyap, P.3
-
3
-
-
85048594770
-
The current state of the art for biological therapies and new small molecules in inflammatory bowel disease
-
Paramsothy, S., Rosenstein, A.K., Mehandru, S., et al. The current state of the art for biological therapies and new small molecules in inflammatory bowel disease. Mucosal Immunol 11 (2018), 1558–1570.
-
(2018)
Mucosal Immunol
, vol.11
, pp. 1558-1570
-
-
Paramsothy, S.1
Rosenstein, A.K.2
Mehandru, S.3
-
4
-
-
84931469899
-
Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial
-
Moayyedi, P., Surette, M.G., Kim, P.T., et al. Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial. Gastroenterology 149 (2015), 102–109.
-
(2015)
Gastroenterology
, vol.149
, pp. 102-109
-
-
Moayyedi, P.1
Surette, M.G.2
Kim, P.T.3
-
5
-
-
85012869662
-
Multidonor intensive fecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial
-
Paramsothy, S., Kamm, M.A., Kaakoush, N.O., et al. Multidonor intensive fecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial. Lancet 389 (2017), 1218–1228.
-
(2017)
Lancet
, vol.389
, pp. 1218-1228
-
-
Paramsothy, S.1
Kamm, M.A.2
Kaakoush, N.O.3
-
6
-
-
85041776259
-
Short duration, low intensity pooled fecal microbiota transplantation induces remission in patients with mild-moderately active ulcerative colitis: a randomised controlled trial
-
Costello, S., Waters, O., Bryant, R., et al. Short duration, low intensity pooled fecal microbiota transplantation induces remission in patients with mild-moderately active ulcerative colitis: a randomised controlled trial. Gastroenterology 152:5 Suppl 1 (2017), S198–S199.
-
(2017)
Gastroenterology
, vol.152
, Issue.5
, pp. S198-S199
-
-
Costello, S.1
Waters, O.2
Bryant, R.3
-
7
-
-
85026871259
-
Fecal microbiota transplantation for inflammatory bowel disease: a systematic review and meta-analysis
-
Paramsothy, S., Paramsothy, R., Rubin, D.T., et al. Fecal microbiota transplantation for inflammatory bowel disease: a systematic review and meta-analysis. J Crohns Colitis 11 (2017), 1180–1199.
-
(2017)
J Crohns Colitis
, vol.11
, pp. 1180-1199
-
-
Paramsothy, S.1
Paramsothy, R.2
Rubin, D.T.3
-
8
-
-
85020737567
-
Systematic review with meta-analysis: fecal microbiota transplantation for the induction of remission for active ulcerative colitis
-
Costello, S.P., Soo, W., Bryant, R.V., et al. Systematic review with meta-analysis: fecal microbiota transplantation for the induction of remission for active ulcerative colitis. Aliment Pharmacol Therap 46 (2017), 213–224.
-
(2017)
Aliment Pharmacol Therap
, vol.46
, pp. 213-224
-
-
Costello, S.P.1
Soo, W.2
Bryant, R.V.3
-
9
-
-
85029748331
-
The current landscape and lessons from fecal microbiota transplantation for inflammatory bowel disease: past, present, and future
-
Allegretti, J., Eysenbach, L.M., El-Nachef, N., et al. The current landscape and lessons from fecal microbiota transplantation for inflammatory bowel disease: past, present, and future. Inflamm Bowel Dis 23 (2017), 1710–1717.
-
(2017)
Inflamm Bowel Dis
, vol.23
, pp. 1710-1717
-
-
Allegretti, J.1
Eysenbach, L.M.2
El-Nachef, N.3
-
10
-
-
84931423571
-
Findings from a randomized controlled trial of fecal transplantation for patients with ulcerative colitis
-
Rossen, N.G., Fuentes, S., van der Spek, M.J., et al. Findings from a randomized controlled trial of fecal transplantation for patients with ulcerative colitis. Gastroenterology 149 (2015), 110–118.
-
(2015)
Gastroenterology
, vol.149
, pp. 110-118
-
-
Rossen, N.G.1
Fuentes, S.2
van der Spek, M.J.3
-
11
-
-
85017473671
-
Microbial shifts and signatures of long-term remission in ulcerative colitis after fecal microbiota transplantation
-
Fuentes, S., Rossen, N.G., van der Spek, M.J., et al. Microbial shifts and signatures of long-term remission in ulcerative colitis after fecal microbiota transplantation. ISME J 11 (2017), 1877–1889.
-
(2017)
ISME J
, vol.11
, pp. 1877-1889
-
-
Fuentes, S.1
Rossen, N.G.2
van der Spek, M.J.3
-
12
-
-
85014315210
-
Efficacy of sterile fecal filtrate transfer for treating patients with Clostridium difficile infection
-
Ott, S.J., Waetzig, G.H., Rehman, A., et al. Efficacy of sterile fecal filtrate transfer for treating patients with Clostridium difficile infection. Gastroenterology 152 (2017), 799–811.
-
(2017)
Gastroenterology
, vol.152
, pp. 799-811
-
-
Ott, S.J.1
Waetzig, G.H.2
Rehman, A.3
-
13
-
-
72949107142
-
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss, P.D., Westcott, S.L., Ryabin, T., et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75 (2009), 7537–7541.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
-
14
-
-
84884251320
-
Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform
-
Kozich, J.J., Westcott, S.L., Baxter, N.T., et al. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 79 (2013), 5112–5120.
-
(2013)
Appl Environ Microbiol
, vol.79
, pp. 5112-5120
-
-
Kozich, J.J.1
Westcott, S.L.2
Baxter, N.T.3
-
15
-
-
84873739311
-
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
-
Quast, C., Pruesse, E., Yilmaz, P., et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41 (2013), D590–D596.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D590-D596
-
-
Quast, C.1
Pruesse, E.2
Yilmaz, P.3
-
16
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar, R.C., Haas, B.J., Clemente, J.C., et al. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27 (2011), 2194–2200.
-
(2011)
Bioinformatics
, vol.27
, pp. 2194-2200
-
-
Edgar, R.C.1
Haas, B.J.2
Clemente, J.C.3
-
17
-
-
34548293679
-
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang, Q., Garrity, G.M., Tiedje, J.M., et al. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73 (2007), 5261–5267.
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
-
18
-
-
85030973816
-
OptiClust, an improved method for assigning amplicon-based sequence data to operational taxonomic units
-
pii: e00073-17
-
Westcott, S.L., Schloss, P.D., OptiClust, an improved method for assigning amplicon-based sequence data to operational taxonomic units. mSphere, 2, 2017 pii: e00073-17.
-
(2017)
mSphere
, vol.2
-
-
Westcott, S.L.1
Schloss, P.D.2
-
19
-
-
79952390994
-
Fast identification and removal of sequence contamination from genomic and metagenomic datasets
-
Schmieder, R., Edwards, R., Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PLoS One, 6, 2011, e17288.
-
(2011)
PLoS One
, vol.6
, pp. e17288
-
-
Schmieder, R.1
Edwards, R.2
-
20
-
-
77957151956
-
SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data
-
Cox, M.P., Peterson, D.A., Biggs, P.J., SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics, 11, 2010, 485.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 485
-
-
Cox, M.P.1
Peterson, D.A.2
Biggs, P.J.3
-
21
-
-
84964994621
-
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
-
Truong, D.T., Franzosa, E.A., Tickle, T.L., et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods 12 (2015), 902–903.
-
(2015)
Nat Methods
, vol.12
, pp. 902-903
-
-
Truong, D.T.1
Franzosa, E.A.2
Tickle, T.L.3
-
22
-
-
85035359870
-
A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients
-
Hall, A.B., Yassour, M., Sauk, J., et al. A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Genome Med, 9, 2017, 103.
-
(2017)
Genome Med
, vol.9
, pp. 103
-
-
Hall, A.B.1
Yassour, M.2
Sauk, J.3
-
23
-
-
85063383542
-
-
Vegan: community ecology package Available at
-
Oksanen J, Blanchet FG, Friendly M, et al. Vegan: community ecology package, 2017. Available at: https://cran.r-project.org/web/packages/vegan/vegan.pdf.
-
(2017)
-
-
Oksanen, J.1
Blanchet, F.G.2
Friendly, M.3
-
24
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love, M.I., Huber, W., Anders, S., Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol, 15, 2014, 550.
-
(2014)
Genome Biol
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
25
-
-
79959383523
-
Metagenomic biomarker discovery and explanation
-
Segata, N., Izard, J., Waldron, L., et al. Metagenomic biomarker discovery and explanation. Genome Biol, 12, 2011, R60.
-
(2011)
Genome Biol
, vol.12
, pp. R60
-
-
Segata, N.1
Izard, J.2
Waldron, L.3
-
26
-
-
84973539413
-
The common gut microbe Eubacterium hallii also contributes to intestinal propionate formation
-
Engels, C., Ruscheweyh, H.J., Beerenwinkel, N., et al. The common gut microbe Eubacterium hallii also contributes to intestinal propionate formation. Front Microbiol, 7, 2016, 713.
-
(2016)
Front Microbiol
, vol.7
, pp. 713
-
-
Engels, C.1
Ruscheweyh, H.J.2
Beerenwinkel, N.3
-
27
-
-
33646824923
-
ppGpp: stringent response and survival
-
Jain, V., Kumar, M., Chatterji, D., ppGpp: stringent response and survival. J Microbiol 44 (2006), 1–10.
-
(2006)
J Microbiol
, vol.44
, pp. 1-10
-
-
Jain, V.1
Kumar, M.2
Chatterji, D.3
-
28
-
-
0017646836
-
Ansamycins. Chemistry, biosynthesis and biological activity
-
Wehrli, W., Ansamycins. Chemistry, biosynthesis and biological activity. Top Curr Chem 72 (1977), 21–49.
-
(1977)
Top Curr Chem
, vol.72
, pp. 21-49
-
-
Wehrli, W.1
-
29
-
-
85046437053
-
Role of bile acids in inflammatory bowel disease
-
Tiratterra, E., Franco, P., Porru, E., et al. Role of bile acids in inflammatory bowel disease. Ann Gastroenterol 31 (2018), 266–272.
-
(2018)
Ann Gastroenterol
, vol.31
, pp. 266-272
-
-
Tiratterra, E.1
Franco, P.2
Porru, E.3
-
30
-
-
0037214339
-
Induction of experimental ulcerative colitis by Fusobacterium varium isolated from colonic mucosa of patients with ulcerative colitis
-
Ohkusa, T., Okayasu, I., Ogihara, T., et al. Induction of experimental ulcerative colitis by Fusobacterium varium isolated from colonic mucosa of patients with ulcerative colitis. Gut 52 (2003), 79–83.
-
(2003)
Gut
, vol.52
, pp. 79-83
-
-
Ohkusa, T.1
Okayasu, I.2
Ogihara, T.3
-
31
-
-
79959474060
-
Invasive potential of gut mucosa-derived Fusobacterium nucleatum positively correlates with IBD status of the host
-
Strauss, J., Kaplan, G.G., Beck, P.L., et al. Invasive potential of gut mucosa-derived Fusobacterium nucleatum positively correlates with IBD status of the host. Inflamm Bowel Dis 17 (2011), 1971–1978.
-
(2011)
Inflamm Bowel Dis
, vol.17
, pp. 1971-1978
-
-
Strauss, J.1
Kaplan, G.G.2
Beck, P.L.3
-
32
-
-
4143069158
-
High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease
-
Darfeuille-Michaud, A., Boudeau, J., Bulois, P., et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology 127 (2004), 412–421.
-
(2004)
Gastroenterology
, vol.127
, pp. 412-421
-
-
Darfeuille-Michaud, A.1
Boudeau, J.2
Bulois, P.3
-
33
-
-
0036056366
-
Update on the taxonomy and clinical aspects of the genus Fusobacterium
-
Citron, D.M., Update on the taxonomy and clinical aspects of the genus Fusobacterium. Clin Infect Dis 35 (2002), S22–S27.
-
(2002)
Clin Infect Dis
, vol.35
, pp. S22-S27
-
-
Citron, D.M.1
-
34
-
-
84882354326
-
Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment
-
Kostic, A.D., Chun, E., Robertson, L., et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe 14 (2013), 207–215.
-
(2013)
Cell Host Microbe
, vol.14
, pp. 207-215
-
-
Kostic, A.D.1
Chun, E.2
Robertson, L.3
-
35
-
-
85010756263
-
Fusobacterium nucleatum and T cells in colorectal carcinoma
-
Mima, K., Sukawa, Y., Nishihara, R., et al. Fusobacterium nucleatum and T cells in colorectal carcinoma. JAMA Oncol 1 (2015), 653–661.
-
(2015)
JAMA Oncol
, vol.1
, pp. 653-661
-
-
Mima, K.1
Sukawa, Y.2
Nishihara, R.3
-
36
-
-
84940055522
-
Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis
-
Mima, K., Nishihara, R., Qian, Z.R., et al. Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis. Gut 65 (2016), 1973–1980.
-
(2016)
Gut
, vol.65
, pp. 1973-1980
-
-
Mima, K.1
Nishihara, R.2
Qian, Z.R.3
-
37
-
-
85034809112
-
Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer
-
Bullman, S., Pedamallu, C.S., Sicinska, E., et al. Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer. Science 358 (2017), 1443–1448.
-
(2017)
Science
, vol.358
, pp. 1443-1448
-
-
Bullman, S.1
Pedamallu, C.S.2
Sicinska, E.3
-
38
-
-
85039789170
-
Fusobacterium's link to colorectal neoplasia sequenced: a systematic review and future insights
-
Hussan, H., Clinton, S.K., Roberts, K., et al. Fusobacterium's link to colorectal neoplasia sequenced: a systematic review and future insights. World J Gastroenterol 23 (2017), 8626–8650.
-
(2017)
World J Gastroenterol
, vol.23
, pp. 8626-8650
-
-
Hussan, H.1
Clinton, S.K.2
Roberts, K.3
-
39
-
-
78651254481
-
Acute appendicitis is characterised by local invasion with Fusobacterium nucleatum/necrophorum
-
Swidsinski, A., Dorffel, Y., Loening-Baucke, V., et al. Acute appendicitis is characterised by local invasion with Fusobacterium nucleatum/necrophorum. Gut 60 (2011), 34–40.
-
(2011)
Gut
, vol.60
, pp. 34-40
-
-
Swidsinski, A.1
Dorffel, Y.2
Loening-Baucke, V.3
-
40
-
-
84857801101
-
Local appendiceal dysbiosis: the missing link between the appendix and ulcerative colitis?
-
Roblin, X., Neut, C., Darfeuille-Michaud, A., et al. Local appendiceal dysbiosis: the missing link between the appendix and ulcerative colitis?. Gut 61 (2012), 635–636.
-
(2012)
Gut
, vol.61
, pp. 635-636
-
-
Roblin, X.1
Neut, C.2
Darfeuille-Michaud, A.3
-
41
-
-
84956660868
-
Gut microbiota in 2015: Prevotella in the gut: choose carefully
-
Ley, R.E., Gut microbiota in 2015: Prevotella in the gut: choose carefully. Nat Rev Gastroenterol Hepatol 13 (2016), 69–70.
-
(2016)
Nat Rev Gastroenterol Hepatol
, vol.13
, pp. 69-70
-
-
Ley, R.E.1
-
42
-
-
0035997382
-
Lipopolysaccharide endotoxins
-
Raetz, C.R., Whitfield, C., Lipopolysaccharide endotoxins. Annu Rev Biochem 71 (2002), 635–700.
-
(2002)
Annu Rev Biochem
, vol.71
, pp. 635-700
-
-
Raetz, C.R.1
Whitfield, C.2
-
43
-
-
84962694827
-
Heme synthesis and acquisition in bacterial pathogens
-
Choby, J.E., Skaar, E.P., Heme synthesis and acquisition in bacterial pathogens. J Mol Biol 428 (2016), 3408–3428.
-
(2016)
J Mol Biol
, vol.428
, pp. 3408-3428
-
-
Choby, J.E.1
Skaar, E.P.2
-
44
-
-
0032919364
-
KEGG: Kyoto Encyclopedia of Genes and Genomes
-
Ogata, H., Goto, S., Sato, K., et al. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 27 (1999), 29–34.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 29-34
-
-
Ogata, H.1
Goto, S.2
Sato, K.3
-
45
-
-
85032492045
-
Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation
-
Atarashi, K., Suda, W., Luo, C., et al. Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation. Science 358 (2017), 359–365.
-
(2017)
Science
, vol.358
, pp. 359-365
-
-
Atarashi, K.1
Suda, W.2
Luo, C.3
-
46
-
-
85053680468
-
Predicting recurrence of Clostridium difficile infection following encapsulated fecal microbiota transplantation
-
Staley, C., Kaiser, T., Vaughn, B.P., et al. Predicting recurrence of Clostridium difficile infection following encapsulated fecal microbiota transplantation. Microbiome, 6, 2018, 166.
-
(2018)
Microbiome
, vol.6
, pp. 166
-
-
Staley, C.1
Kaiser, T.2
Vaughn, B.P.3
-
47
-
-
85029744525
-
Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease
-
Khanna, S., Vazquez-Baeza, Y., González, A., et al. Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease. Microbiome, 5, 2017, 55.
-
(2017)
Microbiome
, vol.5
, pp. 55
-
-
Khanna, S.1
Vazquez-Baeza, Y.2
González, A.3
-
48
-
-
85044337697
-
Strain tracking reveals the determinants of bacterial engraftment in the human gut following fecal microbiota transplantation
-
Smillie, C.S., Sauk, J., Gevers, D., et al. Strain tracking reveals the determinants of bacterial engraftment in the human gut following fecal microbiota transplantation. Cell Host Microbe 23 (2018), 229–240.
-
(2018)
Cell Host Microbe
, vol.23
, pp. 229-240
-
-
Smillie, C.S.1
Sauk, J.2
Gevers, D.3
-
49
-
-
85045908393
-
Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection
-
Seekatz, A.M., Theriot, C.M., Rao, K., et al. Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection. Anaerobe 53 (2018), 64–73.
-
(2018)
Anaerobe
, vol.53
, pp. 64-73
-
-
Seekatz, A.M.1
Theriot, C.M.2
Rao, K.3
|