-
1
-
-
0025199396
-
Model of carbon fixation in microbial mats from 3, 500 Myr ago to the present
-
Rothschild, L. J. & Mancinelli, R. L. Model of carbon fixation in microbial mats from 3, 500 Myr ago to the present. Nature 345, 710-712 (1990).
-
(1990)
Nature
, vol.345
, pp. 710-712
-
-
Rothschild, L.J.1
Mancinelli, R.L.2
-
2
-
-
84860472372
-
Gut matters: Microbe-host interactions in allergic diseases
-
Hormannsperger, G., Clavel, T. & Haller, D. Gut matters: microbe-host interactions in allergic diseases. J Allergy Clin Immunol 129, 1452-1459 (2012).
-
(2012)
J Allergy Clin Immunol
, vol.129
, pp. 1452-1459
-
-
Hormannsperger, G.1
Clavel, T.2
Haller, D.3
-
3
-
-
84927692256
-
The first 1000 cultured species of the human gastrointestinal microbiota
-
Rajilic-Stojanovic, M. & de Vos, W. M. The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol Rev 38, 996-1047 (2014).
-
(2014)
FEMS Microbiol Rev
, vol.38
, pp. 996-1047
-
-
Rajilic-Stojanovic, M.1
De Vos, W.M.2
-
4
-
-
0018936473
-
Secondary structure model for bacterial 16S ribosomal RNA: Phylogenetic, enzymatic and chemical evidence
-
Woese, C. R., et al. Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence. Nucleic Acids Res 8, 2275-2293 (1980).
-
(1980)
Nucleic Acids Res
, vol.8
, pp. 2275-2293
-
-
Woese, C.R.1
-
5
-
-
52949115612
-
Microbiology: Metagenomics
-
Hugenholtz, P. & Tyson, G. W. Microbiology: metagenomics. Nature 455, 481-483 (2008).
-
(2008)
Nature
, vol.455
, pp. 481-483
-
-
Hugenholtz, P.1
Tyson, G.W.2
-
6
-
-
77950251400
-
A human gut microbial gene catalogue established by metagenomic sequencing
-
Qin, J., et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65 (2010).
-
(2010)
Nature
, vol.464
, pp. 59-65
-
-
Qin, J.1
-
7
-
-
84916884469
-
Bacteria from diverse habitats colonize and compete in the mouse gut
-
Seedorf, H., et al. Bacteria from diverse habitats colonize and compete in the mouse gut. Cell 159, 253-266 (2014).
-
(2014)
Cell
, vol.159
, pp. 253-266
-
-
Seedorf, H.1
-
8
-
-
84968918909
-
Population-level analysis of gut microbiome variation
-
Falony, G., et al. Population-level analysis of gut microbiome variation. Science 352, 560-564 (2016).
-
(2016)
Science
, vol.352
, pp. 560-564
-
-
Falony, G.1
-
9
-
-
84896092821
-
The treatment-naive microbiome in new-onset Crohns disease
-
Gevers, D., et al. The treatment-naive microbiome in new-onset Crohns disease. Cell Host Microbe 15, 382-392 (2014).
-
(2014)
Cell Host Microbe
, vol.15
, pp. 382-392
-
-
Gevers, D.1
-
10
-
-
84988930827
-
Do you kiss your mother with that mouth? An authentic large-scale undergraduate research experience in mapping the human oral microbiome
-
Wang, J. T., et al. Do you kiss your mother with that mouth? An authentic large-scale undergraduate research experience in mapping the human oral microbiome. J Microbiol Biol Educ 16, 50-60 (2015).
-
(2015)
J Microbiol Biol Educ
, vol.16
, pp. 50-60
-
-
Wang, J.T.1
-
11
-
-
84968901892
-
Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity
-
Zhernakova, A., et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 352, 565-569 (2016).
-
(2016)
Science
, vol.352
, pp. 565-569
-
-
Zhernakova, A.1
-
12
-
-
78651301328
-
The sequence read archive
-
Leinonen, R., Sugawara, H. & Shumway, M. The sequence read archive. Nucleic Acids Res 39, D19-21 (2011).
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D19-D21
-
-
Leinonen, R.1
Sugawara, H.2
Shumway, M.3
-
13
-
-
84900317657
-
MetaMetaDB: A database and analytic system for investigating microbial habitability
-
Yang, C. C. & Iwasaki, W. MetaMetaDB: a database and analytic system for investigating microbial habitability. PLoS One 9, e87126 (2014).
-
(2014)
PLoS One
, vol.9
, pp. e87126
-
-
Yang, C.C.1
Iwasaki, W.2
-
14
-
-
84891160133
-
Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae
-
Lagkouvardos, I., Weinmaier, T., Lauro, F. M., Cavicchioli, R., Rattei, T. & Horn, M. Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae. ISME J 8, 115-125 (2014).
-
(2014)
ISME J
, vol.8
, pp. 115-125
-
-
Lagkouvardos, I.1
Weinmaier, T.2
Lauro, F.M.3
Cavicchioli, R.4
Rattei, T.5
Horn, M.6
-
15
-
-
84884904719
-
UPARSE: Highly accurate OTU sequences from microbial amplicon reads
-
Edgar, R. C. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10, 996-998 (2013).
-
(2013)
Nat Methods
, vol.10
, pp. 996-998
-
-
Edgar, R.C.1
-
16
-
-
8144226856
-
The gut microbiota as an environmental factor that regulates fat storage
-
Backhed, F., et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci USA 101, 15718-15723 (2004).
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 15718-15723
-
-
Backhed, F.1
-
17
-
-
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
-
18
-
-
84878465280
-
Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity
-
Everard, A., et al. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci USA 110, 9066-9071 (2013).
-
(2013)
Proc Natl Acad Sci USA
, vol.110
, pp. 9066-9071
-
-
Everard, A.1
-
19
-
-
84875369840
-
An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice
-
Fei, N. & Zhao, L. An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice. ISME J 7, 880-884 (2013).
-
(2013)
ISME J
, vol.7
, pp. 880-884
-
-
Fei, N.1
Zhao, L.2
-
20
-
-
84908406670
-
Clostridium ramosum promotes high-fat diet-induced obesity in gnotobiotic mouse models
-
e01530-01514
-
Woting, A., Pfeiffer, N., Loh, G., Klaus, S. & Blaut, M. Clostridium ramosum promotes high-fat diet-induced obesity in gnotobiotic mouse models. MBio 5, e01530-01514 (2014).
-
(2014)
MBio
, vol.5
-
-
Woting, A.1
Pfeiffer, N.2
Loh, G.3
Klaus, S.4
Blaut, M.5
-
21
-
-
84871228591
-
Acetatifactor muris gen. nov., sp. nov., a novel bacterium isolated from the intestine of an obese mouse
-
Pfeiffer, N., Desmarchelier, C., Blaut, M., Daniel, H., Haller, D. & Clavel, T. Acetatifactor muris gen. nov., sp. nov., a novel bacterium isolated from the intestine of an obese mouse. Arch Microbiol 194, 901-907 (2012).
-
(2012)
Arch Microbiol
, vol.194
, pp. 901-907
-
-
Pfeiffer, N.1
Desmarchelier, C.2
Blaut, M.3
Daniel, H.4
Haller, D.5
Clavel, T.6
-
22
-
-
84988923560
-
Gut barrier impairment by high-fat diet in mice depends on housing conditions
-
Muller, V. M., et al. Gut barrier impairment by high-fat diet in mice depends on housing conditions. Mol Nutr Food Res (2015).
-
(2015)
Mol Nutr Food Res
-
-
Muller, V.M.1
-
23
-
-
84919643021
-
High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity
-
Schulz, M. D., et al. High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity. Nature 514, 508-512 (2014).
-
(2014)
Nature
, vol.514
, pp. 508-512
-
-
Schulz, M.D.1
-
24
-
-
84905495117
-
Incorporation of therapeutically modified bacteria into gut microbiota inhibits obesity
-
Chen, Z., et al. Incorporation of therapeutically modified bacteria into gut microbiota inhibits obesity. J Clin Invest 124, 3391-3406 (2014).
-
(2014)
J Clin Invest
, vol.124
, pp. 3391-3406
-
-
Chen, Z.1
-
25
-
-
2942620063
-
Discovery of the novel candidate phylum Poribacteria marine sponges
-
Fieseler, L., Horn, M., Wagner, M. & Hentschel, U. Discovery of the novel candidate phylum "Poribacteria" in marine sponges. Appl Environ Microbiol 70, 3724-3732 (2004).
-
(2004)
Appl Environ Microbiol
, vol.70
, pp. 3724-3732
-
-
Fieseler, L.1
Horn, M.2
Wagner, M.3
Hentschel, U.4
-
26
-
-
84900313954
-
The candidate phylum Poribacteria by single-cell genomics: New insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features
-
Kamke, J., et al. The candidate phylum Poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features. PLoS One 9, e87353 (2014).
-
(2014)
PLoS One
, vol.9
, pp. e87353
-
-
Kamke, J.1
-
27
-
-
84888200073
-
Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges
-
Kamke, J., et al. Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. ISME J 7, 2287-2300 (2013).
-
(2013)
ISME J
, vol.7
, pp. 2287-2300
-
-
Kamke, J.1
-
28
-
-
78650591665
-
Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges
-
Siegl, A., et al. Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J 5, 61-70 (2011).
-
(2011)
ISME J
, vol.5
, pp. 61-70
-
-
Siegl, A.1
-
29
-
-
84857121586
-
Assessing the complex sponge microbiota: Core, variable and species-specific bacterial communities in marine sponges
-
Schmitt, S., et al. Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges. ISME J 6, 564-576 (2012).
-
(2012)
ISME J
, vol.6
, pp. 564-576
-
-
Schmitt, S.1
-
30
-
-
84872914192
-
'Sponge-specific' bacteria are widespread (but rare) in diverse marine environments
-
Taylor, M. W., et al. Sponge-specific bacteria are widespread (but rare) in diverse marine environments. ISME J 7, 438-443 (2013).
-
(2013)
ISME J
, vol.7
, pp. 438-443
-
-
Taylor, M.W.1
-
31
-
-
77955263252
-
Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts
-
Webster, N. S., et al. Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts. Environ Microbiol 12, 2070-2082 (2010).
-
(2010)
Environ Microbiol
, vol.12
, pp. 2070-2082
-
-
Webster, N.S.1
-
32
-
-
84940984953
-
Primer and platform effects on 16S rRNA tag sequencing
-
Tremblay, J., et al. Primer and platform effects on 16S rRNA tag sequencing. Front Microbiol 6, 771 (2015).
-
(2015)
Front Microbiol
, vol.6
, pp. 771
-
-
Tremblay, J.1
-
33
-
-
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
-
34
-
-
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
-
35
-
-
84870814915
-
SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data
-
Kopylova, E., Noe, L. & Touzet, H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics 28, 3211-3217 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 3211-3217
-
-
Kopylova, E.1
Noe, L.2
Touzet, H.3
-
36
-
-
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
-
37
-
-
84891787231
-
Ribosomal Database Project: Data and tools for high throughput rRNA analysis
-
Cole, J. R., et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42, D633-642 (2014).
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D633-D642
-
-
Cole, J.R.1
-
38
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200 (2011).
-
(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
-
39
-
-
34548293679
-
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang, Q., Garrity, G. M., Tiedje, J. M. & Cole, J. R. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73, 5261-5267 (2007).
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
40
-
-
84864134721
-
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
-
Pruesse, E., Peplies, J. & Glockner, F. O. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823-1829 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 1823-1829
-
-
Pruesse, E.1
Peplies, J.2
Glockner, F.O.3
-
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, D590-596 (2013).
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D590-D596
-
-
Quast, C.1
-
42
-
-
79952001955
-
Clustering 16S rRNA for OTU prediction: A method of unsupervised Bayesian clustering
-
Hao, X., Jiang, R. & Chen, T. Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering. Bioinformatics 27, 611-618 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 611-618
-
-
Hao, X.1
Jiang, R.2
Chen, T.3
-
43
-
-
84937442075
-
Compact graphical representation of phylogenetic data and metadata with GraPhlAn
-
Asnicar, F., Weingart, G., Tickle, T. L., Huttenhower, C. & Segata, N. Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PeerJ 3, e1029 (2015).
-
(2015)
PeerJ
, vol.3
, pp. e1029
-
-
Asnicar, F.1
Weingart, G.2
Tickle, T.L.3
Huttenhower, C.4
Segata, N.5
-
44
-
-
67249096511
-
ESPRIT: Estimating species richness using large collections of 16S rRNA pyrosequences
-
Sun, Y., et al. ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res 37, e76 (2009).
-
(2009)
Nucleic Acids Res
, vol.37
, pp. e76
-
-
Sun, Y.1
-
45
-
-
84938548589
-
Gut metabolites and bacterial community networks during a pilot intervention study with flaxseeds in healthy adult men
-
Lagkouvardos, I., et al. Gut metabolites and bacterial community networks during a pilot intervention study with flaxseeds in healthy adult men. Mol Nutr Food Res 59, 1614-1628 (2015).
-
(2015)
Mol Nutr Food Res
, vol.59
, pp. 1614-1628
-
-
Lagkouvardos, I.1
-
46
-
-
84958896052
-
Dysbiotic gut microbiota causes transmissible Crohns disease-like ileitis independent of failure in antimicrobial defence
-
Schaubeck, M., et al. Dysbiotic gut microbiota causes transmissible Crohns disease-like ileitis independent of failure in antimicrobial defence. Gut (2015).
-
(2015)
Gut
-
-
Schaubeck, M.1
-
47
-
-
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
|