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Volumn 7, Issue 1, 2017, Pages

Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing

(12)  Tessler, Michael a   Neumann, Johannes S b   Afshinnekoo, Ebrahim c,d,e   Pineda, Michael c,d   Hersch, Rebecca a   Velho, Luiz Felipe M f,g   Segovia, Bianca T f   Lansac Toha, Fabio A f   Lemke, Michael h   Desalle, Rob a   Mason, Christopher E c,d,i   Brugler, Mercer R a,j  


Author keywords

[No Author keywords available]

Indexed keywords

AMPLICON; BIODIVERSITY; CLADISTICS; COMMUNITY ECOLOGY; FAMILY STUDY; NUTRIENT; PIPELINE; QUANTITATIVE STUDY; SAMPLING; BACTERIUM; BIOLOGY; BIOTA; CLASSIFICATION; DNA SEQUENCE; GENETICS; GROWTH, DEVELOPMENT AND AGING; HIGH THROUGHPUT SEQUENCING; METAGENOMICS; MICROBIOLOGY; PROCEDURES;

EID: 85026644382     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/s41598-017-06665-3     Document Type: Article
Times cited : (155)

References (39)
  • 1
    • 84934989481 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 18
    • 84997142688 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 30
    • 84864440400 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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


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