-
1
-
-
84934989481
-
Bioinformatic amplicon read processing strategies strongly affect eukaryotic diversity and the taxonomic composition of communities
-
Majaneva, M., Hyytiäinen, K., Varvio, S. L., Nagai, S. & Blomster, J. Bioinformatic amplicon read processing strategies strongly affect eukaryotic diversity and the taxonomic composition of communities. PLoS One 10, e0130035 (2015).
-
(2015)
PLoS One
, vol.10
, pp. e0130035
-
-
Majaneva, M.1
Hyytiäinen, K.2
Varvio, S.L.3
Nagai, S.4
Blomster, J.5
-
2
-
-
84953911745
-
Microbial community analysis with ribosomal gene fragments from shotgun metagenomes
-
Guo, J., Cole, J. R., Zhang, Q., Brown, C. T. & Tiedje, J. M. Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes. Appl. Environ. Microbiol. 82, 157-166 (2015).
-
(2015)
Appl. Environ. Microbiol
, vol.82
, pp. 157-166
-
-
Guo, J.1
Cole, J.R.2
Zhang, Q.3
Brown, C.T.4
Tiedje, J.M.5
-
3
-
-
84904575496
-
Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing
-
Mitra, S. et al. Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing. BMC Genomics 14, S16 (2013).
-
(2013)
BMC Genomics
, vol.14
, pp. S16
-
-
Mitra, S.1
-
4
-
-
84915817893
-
Comparison of bacterial culture and 16S rRNA community profiling by clonal analysis and pyrosequencing for the characterization of the dentine caries-associated microbiome
-
Schulze-Schweifing, K., Banerjee, A. & Wade, W. G. Comparison of bacterial culture and 16S rRNA community profiling by clonal analysis and pyrosequencing for the characterization of the dentine caries-associated microbiome. Front. Cell. Infect. Microbiol. 4, 164 (2014).
-
(2014)
Front. Cell. Infect. Microbiol
, vol.4
, pp. 164
-
-
Schulze-Schweifing, K.1
Banerjee, A.2
Wade, W.G.3
-
5
-
-
84928526705
-
Comparing high-throughput platforms for sequencing the V4 region of SSU-rDNA in environmental microbial eukaryotic diversity surveys
-
Mahé, F. et al. Comparing high-throughput platforms for sequencing the V4 region of SSU-rDNA in environmental microbial eukaryotic diversity surveys. J. Eukaryot. Microbiol. 62, 338-345 (2015).
-
(2015)
J. Eukaryot. Microbiol
, vol.62
, pp. 338-345
-
-
Mahé, F.1
-
6
-
-
84856770811
-
Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample
-
Luo, C., Tsementzi, D., Kyrpides, N., Read, T. & Konstantinidis, K. T. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS One 7, e30087 (2012).
-
(2012)
PLoS One
, vol.7
, pp. e30087
-
-
Luo, C.1
Tsementzi, D.2
Kyrpides, N.3
Read, T.4
Konstantinidis, K.T.5
-
7
-
-
84899531657
-
Analysis optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys
-
Nelson, M. C., Morrison, H. G., Benjamino, J., Grim, S. L. & Graf, J. Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys. PLoS One 9, e94249 (2014).
-
(2014)
PLoS One
, vol.9
, pp. e94249
-
-
Nelson, M.C.1
Morrison, H.G.2
Benjamino, J.3
Grim, S.L.4
Graf, J.5
-
8
-
-
84917709088
-
Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling
-
Salipante, S. J. et al. Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling. Appl. Environ. Microbiol. 80, 7583-7591 (2014).
-
(2014)
Appl. Environ. Microbiol
, vol.80
, pp. 7583-7591
-
-
Salipante, S.J.1
-
9
-
-
84907525758
-
Data analysis for 16S microbial profiling from different benchtop sequencing platforms
-
Pylro, V. S. et al. Data analysis for 16S microbial profiling from different benchtop sequencing platforms. J. Microbiol. Methods 107, 30-37 (2014).
-
(2014)
J. Microbiol. Methods
, vol.107
, pp. 30-37
-
-
Pylro, V.S.1
-
10
-
-
84899535363
-
Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics
-
Poretsky, R., Rodriguez-R, L. M., Luo, C., Tsementzi, D. & Konstantinidis, K. T. Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics. PLoS One 9, e93827 (2014).
-
(2014)
PLoS One
, vol.9
, pp. e93827
-
-
Poretsky, R.1
Rodriguez-R, L.M.2
Luo, C.3
Tsementzi, D.4
Konstantinidis, K.T.5
-
11
-
-
84957431829
-
Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing
-
Ranjan, R., Rani, A., Metwally, A., McGee, H. S. & Perkins, D. L. Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing. Biochem. Biophys. Res. Commun. 469, 967-977 (2016).
-
(2016)
Biochem. Biophys. Res. Commun
, vol.469
, pp. 967-977
-
-
Ranjan, R.1
Rani, A.2
Metwally, A.3
McGee, H.S.4
Perkins, D.L.5
-
12
-
-
84940567255
-
Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi
-
Tedersoo, L. et al. Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi. MycoKeys 10, 1-43 (2015).
-
(2015)
MycoKeys
, vol.10
, pp. 1-43
-
-
Tedersoo, L.1
-
13
-
-
84927129625
-
Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing. Front
-
Chan, C. S., Chan, K.-G., Tay, Y.-L., Chua, Y.-H. & Goh, K. M. Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing. Front. Microbiol. 6, 177 (2015).
-
(2015)
Microbiol
, vol.6
, pp. 177
-
-
Chan, C.S.1
Chan, K.-G.2
Tay, Y.-L.3
Chua, Y.-H.4
Goh, K.M.5
-
14
-
-
84959450570
-
Comparing apples and oranges?: Next generation sequencing and its impact on microbiome analysis
-
Clooney, A. G. et al. Comparing apples and oranges?: Next generation sequencing and its impact on microbiome analysis. PLoS One 11, e0148028 (2016).
-
(2016)
PLoS One
, vol.11
, pp. e0148028
-
-
Clooney, A.G.1
-
15
-
-
84966430254
-
Characterization of the gut microbiome using 16S or shotgun metagenomics
-
Jovel, J. et al. Characterization of the gut microbiome using 16S or shotgun metagenomics. Front. Microbiol. 7, 459 (2016).
-
(2016)
Front. Microbiol
, vol.7
, Issue.459
-
-
Jovel, J.1
-
16
-
-
84986252840
-
A global eDNA comparison of freshwater bacterioplankton assemblages focusing on large-river floodplain lakes of Brazil
-
Tessler, M. & Brugler, M. R. et al. A global eDNA comparison of freshwater bacterioplankton assemblages focusing on large-river floodplain lakes of Brazil. Microb. Ecol., 73, 61-74 (2017).
-
(2017)
Microb. Ecol
, vol.73
, pp. 61-74
-
-
Tessler, M.1
Brugler, M.R.2
-
17
-
-
79952369878
-
A guide to the natural history of freshwater lake bacteria
-
Newton, R. J., Jones, S. E., Eiler, A., McMahon, K. D. & Bertilsson, S. A guide to the natural history of freshwater lake bacteria. Microbiol. Mol. Biol. Rev. 75, 14-49 (2011).
-
(2011)
Microbiol. Mol. Biol. Rev
, vol.75
, pp. 14-49
-
-
Newton, R.J.1
Jones, S.E.2
Eiler, A.3
McMahon, K.D.4
Bertilsson, S.5
-
18
-
-
84997142688
-
The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report
-
MetaSUB International Consortium. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome 4, 24 (2016).
-
(2016)
Microbiome
, vol.4
, pp. 24
-
-
-
19
-
-
84863981120
-
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
-
Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 6, 1621-1624 (2012).
-
(2012)
ISME J
, vol.6
, pp. 1621-1624
-
-
Caporaso, J.G.1
-
20
-
-
84871826193
-
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
-
Fierer, N. et al. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Natl. Acad. Sci. USA 109, 21390-21395 (2012).
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 21390-21395
-
-
Fierer, N.1
-
21
-
-
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, D633-42 (2014).
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D633-D642
-
-
Cole, J.R.1
-
22
-
-
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, D590-6 (2013).
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D590-D596
-
-
Quast, C.1
-
23
-
-
84857122937
-
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
-
McDonald, D. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 6, 610-618 (2012).
-
(2012)
ISME J
, vol.6
, pp. 610-618
-
-
McDonald, D.1
-
24
-
-
84906944378
-
Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities
-
Logares, R. et al. Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities. Environ. Microbiol. 16, 2659-2671 (2014).
-
(2014)
Environ. Microbiol
, vol.16
, pp. 2659-2671
-
-
Logares, R.1
-
25
-
-
84880163034
-
How taxonomic diversity, community structure, and sample size determine the reliability of higher taxon surrogates
-
Neeson, T. M., Van Rijn, I. & Mandelik, Y. How taxonomic diversity, community structure, and sample size determine the reliability of higher taxon surrogates. Ecol. Appl. 23, 1216-1225 (2013).
-
(2013)
Ecol. Appl
, vol.23
, pp. 1216-1225
-
-
Neeson, T.M.1
Van Rijn, I.2
Mandelik, Y.3
-
26
-
-
84865082160
-
Associating microbiome composition with environmental covariates using generalized UniFrac distances
-
Chen, J. et al. Associating microbiome composition with environmental covariates using generalized UniFrac distances. Bioinformatics 28, 2106-2113 (2012).
-
(2012)
Bioinformatics
, vol.28
, pp. 2106-2113
-
-
Chen, J.1
-
27
-
-
84862276328
-
Structure, function and diversity of the healthy human microbiome
-
The Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207-214 (2012).
-
(2012)
Nature
, vol.486
, pp. 207-214
-
-
-
28
-
-
84895751645
-
PhyloSift: Phylogenetic analysis of genomes and metagenomes
-
Darling, A. E. et al. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2, e243 (2014).
-
(2014)
PeerJ
, vol.2
, pp. e243
-
-
Darling, A.E.1
-
29
-
-
84916892245
-
Ten years of pan-genome analyses
-
Vernikos, G., Medini, D., Riley, D. R. & Tettelin, H. Ten years of pan-genome analyses. Curr. Opin. Microbiol. 23, 148-154 (2015).
-
(2015)
Curr. Opin. Microbiol
, vol.23
, pp. 148-154
-
-
Vernikos, G.1
Medini, D.2
Riley, D.R.3
Tettelin, H.4
-
30
-
-
84864440400
-
Metagenomic microbial community profiling using unique clade-specific marker genes
-
Segata, N. et al. Metagenomic microbial community profiling using unique clade-specific marker genes. Nat. Methods 9, 811-814 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 811-814
-
-
Segata, N.1
-
31
-
-
84964994621
-
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
-
Truong, D. T. et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat. Methods 12, 902-903 (2015).
-
(2015)
Nat. Methods
, vol.12
, pp. 902-903
-
-
Truong, D.T.1
-
32
-
-
84925104897
-
Geospatial resolution of human and bacterial diversity with city-scale metagenomics
-
Afshinnekoo, E. et al. Geospatial resolution of human and bacterial diversity with city-scale metagenomics. Cell Syst 1, 72-87 (2015).
-
(2015)
Cell Syst
, vol.1
, pp. 72-87
-
-
Afshinnekoo, E.1
-
33
-
-
85018313637
-
International standards for genomes, transcriptomes, and metagenomes
-
Mason, C. E., Afshinnekoo, E., Tighe, S., Wu, S. & Levy, S. International standards for genomes, transcriptomes, and metagenomes. J Biomol Tech. 28, 8-18 (2017).
-
(2017)
J Biomol Tech
, vol.28
, pp. 8-18
-
-
Mason, C.E.1
Afshinnekoo, E.2
Tighe, S.3
Wu, S.4
Levy, S.5
-
34
-
-
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
-
36
-
-
84872497741
-
Vegan: Community ecology package
-
Oksanen, J. et al. Vegan: Community Ecology Package. R-package version 2 (2013).
-
(2013)
R-package Version
, vol.2
-
-
Oksanen, J.1
-
37
-
-
84868625527
-
Next-generation sequencing of microbial communities in the Athabasca River and its tributaries in relation to oil sands mining activities
-
Yergeau, E. et al. Next-generation sequencing of microbial communities in the Athabasca River and its tributaries in relation to oil sands mining activities. Appl. Environ. Microbiol. 78, 7626-7637 (2012).
-
(2012)
Appl. Environ. Microbiol
, vol.78
, pp. 7626-7637
-
-
Yergeau, E.1
-
38
-
-
84878647680
-
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities
-
Shakya, M. et al. Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities. Environ. Microbiol. 15, 1882-1899 (2013).
-
(2013)
Environ. Microbiol
, vol.15
, pp. 1882-1899
-
-
Shakya, M.1
-
39
-
-
84865591846
-
A tale of three next generation sequencing platforms: Comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
-
Quail, M. A. et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13, 341 (2012).
-
(2012)
BMC Genomics
, vol.13
, pp. 341
-
-
Quail, M.A.1
|