-
1
-
-
84944755228
-
A metagenomic investigation of the duodenal microbiota reveals links with obesity
-
Angelakis, E. et al. A Metagenomic Investigation of the Duodenal Microbiota Reveals Links with Obesity. PloS One. 10, e0137784 (2015).
-
(2015)
PloS One.
, vol.10
, pp. e0137784
-
-
Angelakis, E.1
-
2
-
-
84555197106
-
The relationship between gut microbiota and weight gain in humans
-
Angelakis, E., Armougom, F., Million, M. & Raoult, D. The relationship between gut microbiota and weight gain in humans. Future. Microbiol 7, 91-109 (2012).
-
(2012)
Future. Microbiol
, vol.7
, pp. 91-109
-
-
Angelakis, E.1
Armougom, F.2
Million, M.3
Raoult, D.4
-
3
-
-
84884370038
-
Related actions of probiotics and antibiotics on gut microbiota and weight modification
-
Angelakis, E., Merhej, V. & Raoult, D. Related actions of probiotics and antibiotics on gut microbiota and weight modification. Lancet Infect Dis 13, 889-899 (2013).
-
(2013)
Lancet Infect Dis
, vol.13
, pp. 889-899
-
-
Angelakis, E.1
Merhej, V.2
Raoult, D.3
-
4
-
-
84883864245
-
Meta-analyses of studies of the human microbiota
-
Lozupone, C. A. et al. Meta-analyses of studies of the human microbiota. Genome Res. 23, 1704-1714 (2013).
-
(2013)
Genome Res.
, vol.23
, pp. 1704-1714
-
-
Lozupone, C.A.1
-
5
-
-
84878120468
-
Human gut microbiota: Repertoire and variations
-
Lagier, J. C., Million, M., Hugon, P., Armougom, F. & Raoult, D. Human gut microbiota: repertoire and variations. Front Cell Infect Microbiol 2, 136 (2012).
-
(2012)
Front Cell Infect Microbiol
, vol.2
, pp. 136
-
-
Lagier, J.C.1
Million, M.2
Hugon, P.3
Armougom, F.4
Raoult, D.5
-
6
-
-
84939179628
-
Temporal and technical variability of human gut metagenomes
-
Voigt, A. Y. et al. Temporal and technical variability of human gut metagenomes. Genome Biol. 16, 73 (2015).
-
(2015)
Genome Biol.
, vol.16
, pp. 73
-
-
Voigt, A.Y.1
-
7
-
-
84892586947
-
Microbial diversity in fecal samples depends on DNA extraction method: EasyMag DNA extraction compared to QIAamp DNA stool mini kit extraction
-
Mirsepasi, H. et al. Microbial diversity in fecal samples depends on DNA extraction method: easyMag DNA extraction compared to QIAamp DNA stool mini kit extraction. BMC. Res. Notes 7, 50 (2014).
-
(2014)
BMC. Res. Notes
, vol.7
, pp. 50
-
-
Mirsepasi, H.1
-
8
-
-
84893848394
-
Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities
-
Henderson, G. et al. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities. PloS One. 8, e74787 (2013).
-
(2013)
PloS One.
, vol.8
, pp. e74787
-
-
Henderson, G.1
-
9
-
-
0036242883
-
A comparison of five methods for extraction of bacterial DNA from human faecal samples
-
McOrist, A. L., Jackson, M. & Bird, A. R. A comparison of five methods for extraction of bacterial DNA from human faecal samples. J. Microbiol Methods 50, 131-139 (2002).
-
(2002)
J. Microbiol Methods
, vol.50
, pp. 131-139
-
-
McOrist, A.L.1
Jackson, M.2
Bird, A.R.3
-
10
-
-
79955812835
-
Optimising bacterial DNA extraction from faecal samples: Comparison of three methods
-
Smith, B., Li, N., Andersen, A. S., Slotved, H. C. & Krogfelt, K. A. Optimising bacterial DNA extraction from faecal samples: comparison of three methods. Open. Microbiol J. 5, 14-17 (2011).
-
(2011)
Open. Microbiol J.
, vol.5
, pp. 14-17
-
-
Smith, B.1
Li, N.2
Andersen, A.S.3
Slotved, H.C.4
Krogfelt, K.A.5
-
11
-
-
84907948695
-
Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for faecal and swab samples
-
Vo, A. T. & Jedlicka, J. A. Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for faecal and swab samples. Mol. Ecol. Resour. 14, 1183-1197 (2014).
-
(2014)
Mol. Ecol. Resour.
, vol.14
, pp. 1183-1197
-
-
Vo, A.T.1
Jedlicka, J.A.2
-
12
-
-
84880286399
-
Assessing the fecal microbiota: An optimized ion torrent 16S rRNA gene-based analysis protocol
-
Milani, C. et al. Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol. PloS One. 8, e68739 (2013).
-
(2013)
PloS One.
, vol.8
, pp. e68739
-
-
Milani, C.1
-
13
-
-
84867711039
-
PCR inhibitors - Occurrence, properties and removal
-
Schrader, C., Schielke, A., Ellerbroek, L. & Johne, R. PCR inhibitors - occurrence, properties and removal. J. Appl. Microbiol. 113, 1014-1026 (2012).
-
(2012)
J. Appl. Microbiol.
, vol.113
, pp. 1014-1026
-
-
Schrader, C.1
Schielke, A.2
Ellerbroek, L.3
Johne, R.4
-
14
-
-
77952441809
-
Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens
-
Ariefdjohan, M. W., Savaiano, D. A. & Nakatsu, C. H. Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens. Nutr J. 9, 23 (2010).
-
(2010)
Nutr J.
, vol.9
, pp. 23
-
-
Ariefdjohan, M.W.1
Savaiano, D.A.2
Nakatsu, C.H.3
-
15
-
-
60449119254
-
PCR inhibition in stool samples in relation to age of infants
-
Oikarinen, S. et al. PCR inhibition in stool samples in relation to age of infants. J. Clin. Virol. 44, 211-214 (2009).
-
(2009)
J. Clin. Virol.
, vol.44
, pp. 211-214
-
-
Oikarinen, S.1
-
16
-
-
84921532911
-
Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis
-
Wesolowska-Andersen, A. et al. Choice of bacterial DNA extraction method from fecal material influences community structure as evaluated by metagenomic analysis. Microbiome. 2, 19 (2014).
-
(2014)
Microbiome
, vol.2
, pp. 19
-
-
Wesolowska-Andersen, A.1
-
17
-
-
84905364439
-
Life on the outside: Role of biofilms in environmental persistence of Shiga-toxin producing Escherichia coli
-
Vogeleer, P., Tremblay, Y. D., Mafu, A. A., Jacques, M. & Harel, J. Life on the outside: role of biofilms in environmental persistence of Shiga-toxin producing Escherichia coli. Front Microbiol 5, 317 (2014).
-
(2014)
Front Microbiol
, vol.5
, pp. 317
-
-
Vogeleer, P.1
Tremblay, Y.D.2
Mafu, A.A.3
Jacques, M.4
Harel, J.5
-
18
-
-
84898918386
-
Influence of isolate origin and presence of various genes on biofilm formation by Enterococcus faecium
-
Almohamad, S., Somarajan, S. R., Singh, K. V., Nallapareddy, S. R. & Murray, B. E. Influence of isolate origin and presence of various genes on biofilm formation by Enterococcus faecium. FEMS Microbiol Lett. 353, 151-156 (2014).
-
(2014)
FEMS Microbiol Lett.
, vol.353
, pp. 151-156
-
-
Almohamad, S.1
Somarajan, S.R.2
Singh, K.V.3
Nallapareddy, S.R.4
Murray, B.E.5
-
19
-
-
65549099539
-
Tropheryma whipplei glycosylation in the pathophysiologic profile of Whipple's disease
-
Bonhomme, C. J. et al. Tropheryma whipplei glycosylation in the pathophysiologic profile of Whipple's disease. J. Infect. Dis. 199, 1043-1052 (2009).
-
(2009)
J. Infect. Dis.
, vol.199
, pp. 1043-1052
-
-
Bonhomme, C.J.1
-
20
-
-
0033591467
-
Bacterial biofilms: A common cause of persistent infections
-
Costerton, J. W., Stewart, P. S. & Greenberg, E. P. Bacterial biofilms: a common cause of persistent infections. Science 284, 1318-1322 (1999).
-
(1999)
Science
, vol.284
, pp. 1318-1322
-
-
Costerton, J.W.1
Stewart, P.S.2
Greenberg, E.P.3
-
21
-
-
0020553319
-
Influences of anionic polysaccharides on DNA synthesis in isolated nuclei and by DNA polymerase alpha: Correlation of observed effects with properties of the polysaccharides
-
Furukawa, K. & Bhavanandan, V. P. Influences of anionic polysaccharides on DNA synthesis in isolated nuclei and by DNA polymerase alpha: correlation of observed effects with properties of the polysaccharides. Biochim. Biophys. Acta 740, 466-475 (1983).
-
(1983)
Biochim. Biophys. Acta
, vol.740
, pp. 466-475
-
-
Furukawa, K.1
Bhavanandan, V.P.2
-
22
-
-
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
-
23
-
-
0030909382
-
Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model
-
Monteiro, L. et al. Complex polysaccharides as PCR inhibitors in feces: Helicobacter pylori model. J. Clin. Microbiol. 35, 995-998 (1997).
-
(1997)
J. Clin. Microbiol.
, vol.35
, pp. 995-998
-
-
Monteiro, L.1
-
24
-
-
84889102325
-
Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags
-
Peng, X. et al. Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags. J. Microbiol Methods 95, 455-462 (2013).
-
(2013)
J. Microbiol Methods
, vol.95
, pp. 455-462
-
-
Peng, X.1
-
25
-
-
0033988456
-
Use of macroporous polypropylene filter to allow identification of bacteria by PCR in human fecal samples
-
Cavallini, A., Notarnicola, M., Berloco, P., Lippolis, A. & De Leo, A. Use of macroporous polypropylene filter to allow identification of bacteria by PCR in human fecal samples. J. Microbiol. Methods 39, 265-270 (2000).
-
(2000)
J. Microbiol. Methods
, vol.39
, pp. 265-270
-
-
Cavallini, A.1
Notarnicola, M.2
Berloco, P.3
Lippolis, A.4
De Leo, A.5
-
26
-
-
84878869719
-
A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples
-
Claassen, S. et al. A comparison of the efficiency of five different commercial DNA extraction kits for extraction of DNA from faecal samples. J. Microbiol Methods 94, 103-110 (2013).
-
(2013)
J. Microbiol Methods
, vol.94
, pp. 103-110
-
-
Claassen, S.1
-
27
-
-
84869113067
-
Microbial culturomics: Paradigm shift in the human gut microbiome study
-
Lagier, J. C. et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 18, 1185-93 (2012).
-
(2012)
Clin Microbiol Infect
, vol.18
, pp. 1185-1193
-
-
Lagier, J.C.1
-
28
-
-
84904812959
-
Motility activity, slime production, biofilm formation and genetic typing by ERIC-PCR for Pseudomonas aeruginosa strains isolated from bovine and other sources (human and environment)
-
Wolska, K. et al. Motility activity, slime production, biofilm formation and genetic typing by ERIC-PCR for Pseudomonas aeruginosa strains isolated from bovine and other sources (human and environment). Pol. J. Vet. Sci. 17, 321-329 (2014).
-
(2014)
Pol. J. Vet. Sci.
, vol.17
, pp. 321-329
-
-
Wolska, K.1
-
30
-
-
33947211934
-
Succession in the intestinal microbiota of preadolescent turkeys
-
Scupham, A. J. Succession in the intestinal microbiota of preadolescent turkeys. FEMS Microbiol Ecol. 60, 136-147 (2007).
-
(2007)
FEMS Microbiol Ecol.
, vol.60
, pp. 136-147
-
-
Scupham, A.J.1
-
31
-
-
84924187224
-
The gut microbiota of Colombians differs from that of Americans, Europeans and Asians
-
Escobar, J. S., Klotz, B., Valdes, B. E. & Agudelo, G. M. The gut microbiota of Colombians differs from that of Americans, Europeans and Asians. BMC. Microbiol 14, 311 (2014).
-
(2014)
BMC. Microbiol
, vol.14
, pp. 311
-
-
Escobar, J.S.1
Klotz, B.2
Valdes, B.E.3
Agudelo, G.M.4
-
32
-
-
84923080032
-
Gut microbiome of the Hadza hunter-gatherers
-
Schnorr, S. L. et al. Gut microbiome of the Hadza hunter-gatherers. Nat. Commun. 5, 3654 (2014).
-
(2014)
Nat. Commun.
, vol.5
, pp. 3654
-
-
Schnorr, S.L.1
-
33
-
-
84929074103
-
Comparison of the gut microbiota of people in France and Saudi Arabia
-
Yasir, M. et al. Comparison of the gut microbiota of people in France and Saudi Arabia. Nutr. Diabetes 5, e153 (2015).
-
(2015)
Nutr. Diabetes
, vol.5
, pp. e153
-
-
Yasir, M.1
-
34
-
-
84939267295
-
Inter- and intra-individual variations in seasonal and daily stabilities of the human gut microbiota in Japanese
-
Hisada, T., Endoh, K. & Kuriki, K. Inter- and intra-individual variations in seasonal and daily stabilities of the human gut microbiota in Japanese. Arch Microbiol 197, 919-934 (2015).
-
(2015)
Arch Microbiol
, vol.197
, pp. 919-934
-
-
Hisada, T.1
Endoh, K.2
Kuriki, K.3
-
35
-
-
33847226411
-
Isolation of RNA from bacterial samples of the human gastrointestinal tract
-
Zoetendal, E. G. et al. Isolation of RNA from bacterial samples of the human gastrointestinal tract. Nat. Protoc. 1, 954-959 (2006).
-
(2006)
Nat. Protoc.
, vol.1
, pp. 954-959
-
-
Zoetendal, E.G.1
-
36
-
-
84871108136
-
Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities
-
Oldham, A. L., Drilling, H. S., Stamps, B. W., Stevenson, B. S. & Duncan, K. E. Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities. AMB. Express 2, 60 (2012).
-
(2012)
AMB. Express
, vol.2
, pp. 60
-
-
Oldham, A.L.1
Drilling, H.S.2
Stamps, B.W.3
Stevenson, B.S.4
Duncan, K.E.5
-
37
-
-
58749112734
-
A core gut microbiome in obese and lean twins
-
Turnbaugh, P. J. et al. A core gut microbiome in obese and lean twins. Nature 457, 480-484 (2009).
-
(2009)
Nature
, vol.457
, pp. 480-484
-
-
Turnbaugh, P.J.1
-
38
-
-
84857011001
-
PANDAseq: Paired-end assembler for illumina sequences
-
Masella, A. P., Bartram, A. K., Truszkowski, J. M., Brown, D. G. & Neufeld, J. D. PANDAseq: paired-end assembler for illumina sequences. BMC. Bioinformatics. 13, 31 (2012).
-
(2012)
BMC. Bioinformatics.
, vol.13
, pp. 31
-
-
Masella, A.P.1
Bartram, A.K.2
Truszkowski, J.M.3
Brown, D.G.4
Neufeld, J.D.5
-
39
-
-
84874552495
-
Midgut microbiota of the malaria mosquito vector Anopheles gambiae and interactions with Plasmodium falciparum infection
-
Boissiere, A. et al. Midgut microbiota of the malaria mosquito vector Anopheles gambiae and interactions with Plasmodium falciparum infection. PloS Pathog. 8, e1002742 (2012).
-
(2012)
PloS Pathog.
, vol.8
, pp. e1002742
-
-
Boissiere, A.1
-
40
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 26, 2460-2461 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 2460-2461
-
-
Edgar, R.C.1
-
41
-
-
84873739311
-
The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools
-
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590-D596 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D590-D596
-
-
Quast, C.1
-
42
-
-
0344898137
-
Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample
-
Chao, A. & Shen, T. J. Nonparametric estimation of Shannon's index of diversity when there are unseen species in sample. Environmental and Ecological Statistics 10, 429-443 (2003).
-
(2003)
Environmental and Ecological Statistics
, vol.10
, pp. 429-443
-
-
Chao, A.1
Shen, T.J.2
-
43
-
-
77952243141
-
QIIME allows analysis of high-throughput community sequencing data
-
Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7, 335-336 (2010).
-
(2010)
Nat. Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
|