-
1
-
-
84864778682
-
Defning the human microbiome
-
Ursell, L. K., Metcalf, J. L., Parfrey, L. W. & Knight, R. Defning the human microbiome. Nutr Rev 70 Suppl 1, S38-S44 (2012).
-
(2012)
Nutr Rev 70 Suppl
, vol.1
, pp. S38-S44
-
-
Ursell, L.K.1
Metcalf, J.L.2
Parfrey, L.W.3
Knight, R.4
-
2
-
-
83755185513
-
Experimental and analytical tools for studying the human microbiome
-
Kuczynski, J. et al. Experimental and analytical tools for studying the human microbiome. Nat Rev Genet 13, 47-58 (2011).
-
(2011)
Nat Rev Genet
, vol.13
, pp. 47-58
-
-
Kuczynski, J.1
-
3
-
-
84959453255
-
Mucosal immunity to pathogenic intestinal bacteria
-
Perez-Lopez, A., Behnsen, J., Nuccio, S. P. & Rafatellu, M. Mucosal immunity to pathogenic intestinal bacteria. Nat Rev Immunol 16, 135-148, doi: 10.1038/nri.2015.17 (2016).
-
(2016)
Nat Rev Immunol
, vol.16
, pp. 135-148
-
-
Perez-Lopez, A.1
Behnsen, J.2
Nuccio, S.P.3
Rafatellu, M.4
-
4
-
-
84867074831
-
A metagenome-wide association study of gut microbiota in type 2 diabetes
-
Qin, J. et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55-60 (2012).
-
(2012)
Nature
, vol.490
, pp. 55-60
-
-
Qin, J.1
-
5
-
-
84894118144
-
Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders
-
Hsiao, E. Y. et al. Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders. Cell 155, 1451-1463 (2013).
-
(2013)
Cell
, vol.155
, pp. 1451-1463
-
-
Hsiao, E.Y.1
-
6
-
-
76349111356
-
Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice
-
Zhang, C. et al. Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice. ISME J 4, 232-241 (2010).
-
(2010)
ISME J
, vol.4
, pp. 232-241
-
-
Zhang, C.1
-
8
-
-
84862276328
-
Structure function and diversity of the healthy human microbiome
-
Consortium, H. M. P. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214 (2012).
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
Consortium, H.M.P.1
-
9
-
-
78049240050
-
The efects of alignment quality, distance calculation method, sequence fltering, and region on the analysis of 16S rRNA gene-based studies
-
Schloss, P. D. The efects of alignment quality, distance calculation method, sequence fltering, and region on the analysis of 16S rRNA gene-based studies. PLoS Comput Biol 6, e1000844 (2010).
-
(2010)
PLoS Comput Biol
, vol.6
, pp. e1000844
-
-
Schloss, P.D.1
-
10
-
-
53649108801
-
The potential and challenges of nanopore sequencing
-
Branton, D. et al. The potential and challenges of nanopore sequencing. Nat Biotechnol 26, 1146-1153 (2008).
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1146-1153
-
-
Branton, D.1
-
11
-
-
84946557268
-
Oxford Nanopore sequencing hybrid error correction and de novo assembly of a eukaryotic genome
-
Goodwin, S. et al. Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res 25, 1750-1756 (2015).
-
(2015)
Genome Res
, vol.25
, pp. 1750-1756
-
-
Goodwin, S.1
-
12
-
-
84938421951
-
A complete bacterial genome assembled de novo using only nanopore sequencing data
-
Loman, N. J., Quick, J. & Simpson, J. T. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods 12, 733-735 (2015).
-
(2015)
Nat Methods
, vol.12
, pp. 733-735
-
-
Loman, N.J.1
Quick, J.2
Simpson, J.T.3
-
13
-
-
84936764311
-
Scafolding of a bacterial genome using MinION nanopore sequencing
-
Karlsson, E., Lärkeryd, A., Sjödin, A., Forsman, M. & Stenberg, P. Scafolding of a bacterial genome using MinION nanopore sequencing. Sci Rep 5, 11996 (2015).
-
(2015)
Sci Rep
, vol.5
, pp. 11996
-
-
Karlsson, E.1
Lärkeryd, A.2
Sjödin, A.3
Forsman, M.4
Stenberg, P.5
-
14
-
-
84934284959
-
Rapid draf sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella
-
Quick, J. et al. Rapid draf sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol 16, 114 (2015).
-
(2015)
Genome Biol
, vol.16
, pp. 114
-
-
Quick, J.1
-
15
-
-
84938851187
-
MinION nanopore sequencing of an infuenza genome
-
Wang, J., Moore, N. E., Deng, Y.-M., Eccles, D. A. & Hall, R. J. MinION nanopore sequencing of an infuenza genome. Front Microbiol 6, 766 (2015).
-
(2015)
Front Microbiol
, vol.6
, pp. 766
-
-
Wang, J.1
Moore, N.E.2
Deng, Y.-M.3
Eccles, D.A.4
Hall, R.J.5
-
16
-
-
84942518081
-
Rapid metagenomic identifcation of viral pathogens in clinical samples by real-time nanopore sequencing analysis
-
Greninger, A. L. et al. Rapid metagenomic identifcation of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med 7, 99 (2015).
-
(2015)
Genome Med
, vol.7
, pp. 99
-
-
Greninger, A.L.1
-
17
-
-
84938850442
-
Bacterial and viral identifcation and diferentiation by amplicon sequencing on the MinION nanopore sequencer
-
Kilianski, A. et al. Bacterial and viral identifcation and diferentiation by amplicon sequencing on the MinION nanopore sequencer. GigaScience 4, 12 (2015).
-
(2015)
GigaScience
, vol.4
, pp. 12
-
-
Kilianski, A.1
-
18
-
-
84949664420
-
Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing
-
Hargreaves, A. D. & Mulley, J. F. Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing. Peer J 3, e1441 (2015).
-
(2015)
Peer J
, vol.3
, pp. e1441
-
-
Hargreaves, A.D.1
Mulley, J.F.2
-
19
-
-
84942602825
-
Determining exon connectivity in complex mRNAs by nanopore sequencing
-
Bolisetty, M. T., Rajadinakaran, G. & Graveley, B. R. Determining exon connectivity in complex mRNAs by nanopore sequencing. Genome Biol 16, 1-12 (2015).
-
(2015)
Genome Biol
, vol.16
, pp. 1-12
-
-
Bolisetty, M.T.1
Rajadinakaran, G.2
Graveley, B.R.3
-
20
-
-
84924388692
-
MinION nanopore sequencing identifes the position and structure of a bacterial antibiotic resistance island
-
Ashton, P. M. et al. MinION nanopore sequencing identifes the position and structure of a bacterial antibiotic resistance island. Nat Biotechnol 33, 296-300 (2014).
-
(2014)
Nat Biotechnol
, vol.33
, pp. 296-300
-
-
Ashton, P.M.1
-
21
-
-
85006184217
-
Species-level resolution of 16S rRNA gene amplicons sequenced through the MinIONTM portable nanopore sequencer
-
Benítez-Páez, A., Portune, K. J. & Sanz, Y. Species-level resolution of 16S rRNA gene amplicons sequenced through the MinIONTM portable nanopore sequencer. GigaScience 1-9 (2016).
-
(2016)
GigaScience
, pp. 1-9
-
-
Benítez-Páez, A.1
Portune, K.J.2
Sanz, Y.3
-
22
-
-
84917735497
-
An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform
-
Fadrosh, D. W. et al. An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome 2, 6, doi: 10.1186/2049-2618-2-6 (2014).
-
(2014)
Microbiome
, vol.2
, pp. 6
-
-
Fadrosh, D.W.1
-
23
-
-
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, doi: 10.1038/ nmeth.f.303 (2010).
-
(2010)
Nat Methods
, vol.7
, pp. 335-336
-
-
Caporaso, J.G.1
-
24
-
-
84871808499
-
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
-
Klindworth, A. et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41, e1 (2013).
-
(2013)
Nucleic Acids Res
, vol.41
, pp. e1
-
-
Klindworth, A.1
-
25
-
-
84926472171
-
Improved data analysis for the MinION nanopore sequencer
-
Jain, M. et al. Improved data analysis for the MinION nanopore sequencer. Nat Methods 12, 351-356 (2015).
-
(2015)
Nat Methods
, vol.12
, pp. 351-356
-
-
Jain, M.1
-
26
-
-
84943637090
-
De novo sequencing and variant calling with nanopores using PoreSeq
-
Szalay, T. & Golovchenko, J. A. De novo sequencing and variant calling with nanopores using PoreSeq. Nat Biotechnol 33, 1087-1091 (2015).
-
(2015)
Nat Biotechnol
, vol.33
, pp. 1087-1091
-
-
Szalay, T.1
Golovchenko, J.A.2
-
27
-
-
77649140807
-
Parameters for accurate genome alignment
-
Frith, M. C., Hamada, M. & Horton, P. Parameters for accurate genome alignment. BMC Bioinf 11, 80 (2010).
-
(2010)
BMC Bioinf
, vol.11
, pp. 80
-
-
Frith, M.C.1
Hamada, M.2
Horton, P.3
-
28
-
-
84907952658
-
A frst look at the Oxford Nanopore MinION sequencer
-
Mikheyev, A. S. & Tin, M. M. Y. A frst look at the Oxford Nanopore MinION sequencer. Mol Ecol Resour 14, 1097-1102 (2014).
-
(2014)
Mol Ecol Resour
, vol.14
, pp. 1097-1102
-
-
Mikheyev, A.S.1
Tin, M.M.Y.2
-
29
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis, T. Z. et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72, 5069-5072 (2006).
-
(2006)
Appl Environ Microbiol
, vol.72
, pp. 5069-5072
-
-
DeSantis, T.Z.1
-
30
-
-
79958196766
-
Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis
-
Schloss, P. D. & Westcott, S. L. Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis. Appl Environ Microbiol 77, 3219-3226 (2011).
-
(2011)
Appl Environ Microbiol
, vol.77
, pp. 3219-3226
-
-
Schloss, P.D.1
Westcott, S.L.2
-
31
-
-
80052300610
-
Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering
-
Sul, W. J. et al. Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering. Proc Natl Acad Sci USA 108, 14637-14642 (2011).
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 14637-14642
-
-
Sul, W.J.1
-
32
-
-
84872687670
-
Infammation-associated enterotypes, host genotype, cage and inter-individual efects drive gut microbiota variation in common laboratory mice
-
Hildebrand, F. et al. Infammation-associated enterotypes, host genotype, cage and inter-individual efects drive gut microbiota variation in common laboratory mice. Genome Biol 14, R4 (2013).
-
(2013)
Genome Biol
, vol.14
, pp. R4
-
-
Hildebrand, F.1
-
33
-
-
84938483928
-
Microbial shifs in the aging mouse gut
-
Langille, M. G. et al. Microbial shifs in the aging mouse gut. Microbiome 2, 50 (2014).
-
(2014)
Microbiome
, vol.2
, pp. 50
-
-
Langille, M.G.1
-
34
-
-
84859213056
-
Responses of gut microbiota to diet composition and weight loss in lean and obese mice
-
Ravussin, Y. et al. Responses of gut microbiota to diet composition and weight loss in lean and obese mice. Obesity 20, 738-747 (2012).
-
(2012)
Obesity
, vol.20
, pp. 738-747
-
-
Ravussin, Y.1
-
35
-
-
84903954202
-
Recovery of the gut microbiome following fecal microbiota transplantation
-
Seekatz, A. M. et al. Recovery of the gut microbiome following fecal microbiota transplantation. mBio 5, e00893-00814 (2014).
-
(2014)
MBio 5
, pp. e00893-e00814
-
-
Seekatz, A.M.1
-
36
-
-
84960253261
-
Akkermansia muciniphilaand improved metabolic health during a dietary intervention in obesity: Relationship with gut microbiome richness and ecology
-
Dao, M. C. et al. Akkermansia muciniphilaand improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology. Gut 65, 426-436 (2016).
-
(2016)
Gut
, vol.65
, pp. 426-436
-
-
Dao, M.C.1
-
37
-
-
84863871551
-
Microbial degradation of complex carbohydrates in the gut
-
Flint, H. J., Scott, K. P. , Duncan, S. H., Louis, P. & Forano, E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes 3, 289-306 (2012).
-
(2012)
Gut Microbes
, vol.3
, pp. 289-306
-
-
Flint, H.J.1
Scott, K.P.2
Duncan, S.H.3
Louis, P.4
Forano, E.5
-
38
-
-
84896734943
-
A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes
-
Larsbrink, J. et al. A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes. Nature 506, 498-502 (2014).
-
(2014)
Nature
, vol.506
, pp. 498-502
-
-
Larsbrink, J.1
-
39
-
-
77149149718
-
Diversifcation of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution
-
Oh, P. L. et al. Diversifcation of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution. ISME J 4, 377-387 (2010).
-
(2010)
ISME J
, vol.4
, pp. 377-387
-
-
Oh, P.L.1
-
40
-
-
84887323708
-
Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis
-
Scher, J. U. et al. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. eLife 2, e01202 (2013).
-
(2013)
ELife
, vol.2
, pp. e01202
-
-
Scher, J.U.1
-
41
-
-
0033986423
-
Quantifcation of Diferent Eubacteriumspp. in Human Fecal Samples with Species-Specifc 16S rRNA-Targeted Oligonucleotide Probes
-
Schwiertz, A., Le Blay, G. & Blaut, M. Quantifcation of Diferent Eubacteriumspp. in Human Fecal Samples with Species-Specifc 16S rRNA-Targeted Oligonucleotide Probes. Appl Environ Microbiol 66, 375-382 (2000).
-
(2000)
Appl Environ Microbiol
, vol.66
, pp. 375-382
-
-
Schwiertz, A.1
Le Blay, G.2
Blaut, M.3
-
42
-
-
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
-
43
-
-
58149389297
-
Diferential Efects of Bifdobacterium pseudolongum Strain Patronus and Metronidazole in the Rat Gut
-
Vasquez, N., Suau, A., Magne, F., Pochart, P. & Pélissier, M.-A. Diferential Efects of Bifdobacterium pseudolongum Strain Patronus and Metronidazole in the Rat Gut. Appl Environ Microbiol 75, 381-386 (2009).
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 381-386
-
-
Vasquez, N.1
Suau, A.2
Magne, F.3
Pochart, P.4
Pélissier, M.-A.5
-
44
-
-
84862230115
-
Obesity-associated gut microbiota is enriched in Lactobacillus reuteri and depleted in Bifdobacterium animalis and Methanobrevibacter smithii
-
Million, M. et al. Obesity-associated gut microbiota is enriched in Lactobacillus reuteri and depleted in Bifdobacterium animalis and Methanobrevibacter smithii. Int J Obes 36, 817-825 (2012).
-
(2012)
Int J Obes
, vol.36
, pp. 817-825
-
-
Million, M.1
-
45
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948 (2007).
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
-
46
-
-
84901847186
-
Relating the metatranscriptome and metagenome of the human gut
-
Franzosa, E. A. et al. Relating the metatranscriptome and metagenome of the human gut. Proc Natl Acad Sci USA 111, E2329-E2338, doi: 10.1073/pnas.1319284111 (2014).
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, pp. E2329-E2338
-
-
Franzosa, E.A.1
-
47
-
-
84935842989
-
Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species
-
Cao, H. X. et al. Metatranscriptome analysis reveals host-microbiome interactions in traps of carnivorous Genlisea species. Front Microbiol 6, 526, doi: 10.3389/fmicb.2015.00526 (2015).
-
(2015)
Front Microbiol
, vol.6
, pp. 526
-
-
Cao, H.X.1
-
48
-
-
84878631963
-
Microbial phylogenetic profling with the Pacifc Biosciences sequencing platform
-
Fichot, E. B. & Norman, R. S. Microbial phylogenetic profling with the Pacifc Biosciences sequencing platform. Microbiome 1, 10, doi: 10.1186/2049-2618-1-10 (2013).
-
(2013)
Microbiome
, vol.1
, pp. 10
-
-
Fichot, E.B.1
Norman, R.S.2
-
49
-
-
84922297921
-
Bifdobacterium bifdum as an example of a specialized human gut commensal
-
Turroni, F. et al. Bifdobacterium bifdum as an example of a specialized human gut commensal. Front Microbiol 5, 437 (2014).
-
(2014)
Front Microbiol
, vol.5
, pp. 437
-
-
Turroni, F.1
-
50
-
-
84858709310
-
Freezing fecal samples prior to DNA extraction afects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis
-
Bahl, M. I., Bergström, A. & Licht, T. R. Freezing fecal samples prior to DNA extraction afects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis. FEMS Microbiol Lett 329, 193-197 (2012).
-
(2012)
FEMS Microbiol Lett
, vol.329
, pp. 193-197
-
-
Bahl, M.I.1
Bergström, A.2
Licht, T.R.3
-
51
-
-
84921858909
-
Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG
-
Goyal, P. et al. Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG. Nature 516, 250-253 (2014).
-
(2014)
Nature
, vol.516
, pp. 250-253
-
-
Goyal, P.1
-
52
-
-
84971280828
-
Tree decades of nanopore sequencing
-
Deamer, D., Akeson, M. & Branton, D. Tree decades of nanopore sequencing. Nat Biotechnol 34, 518-524 (2016).
-
(2016)
Nat Biotechnol
, vol.34
, pp. 518-524
-
-
Deamer, D.1
Akeson, M.2
Branton, D.3
-
53
-
-
84924426384
-
Poretools: A toolkit for analyzing nanopore sequence data
-
Loman, N. J. & Quinlan, A. R. Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics 30, 3399-3401 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 3399-3401
-
-
Loman, N.J.1
Quinlan, A.R.2
-
54
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
55
-
-
84890330527
-
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0
-
Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 30, 2725-2729 (2013).
-
(2013)
Mol Biol Evol
, vol.30
, pp. 2725-2729
-
-
Tamura, K.1
Stecher, G.2
Peterson, D.3
Filipski, A.4
Kumar, S.5
|