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Volumn 136, Issue 5, 2016, Pages 947-956

Skin Microbiome Surveys Are Strongly Influenced by Experimental Design

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; RNA 16S; MESSENGER RNA;

EID: 84978148883     PISSN: 0022202X     EISSN: 15231747     Source Type: Journal    
DOI: 10.1016/j.jid.2016.01.016     Document Type: Article
Times cited : (234)

References (36)
  • 1
    • 84874612821 scopus 로고    scopus 로고
    • The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters
    • Aagaard, K., Petrosino, J., Keitel, W., Watson, M., Katancik, J., Garcia, N., et al. The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters. FASEB J 27 (2013), 1012–1022.
    • (2013) FASEB J , vol.27 , pp. 1012-1022
    • Aagaard, K.1    Petrosino, J.2    Keitel, W.3    Watson, M.4    Katancik, J.5    Garcia, N.6
  • 2
    • 84864037467 scopus 로고    scopus 로고
    • Metabolic reconstruction for metagenomic data and its application to the human microbiome
    • Abubucker, S., Segata, N., Goll, J., Schubert, A.M., Izard, J., Cantarel, B.L., et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol, 8, 2012, e1002358.
    • (2012) PLoS Comput Biol , vol.8 , pp. e1002358
    • Abubucker, S.1    Segata, N.2    Goll, J.3    Schubert, A.M.4    Izard, J.5    Cantarel, B.L.6
  • 3
    • 84941331779 scopus 로고    scopus 로고
    • Back to basics: the influence of DNA extraction and primer choice on phylogenetic analysis of activated sludge communities
    • e0132783–15
    • Albertsen, M., Karst, S.M., Ziegler, A.S., Kirkegaard, R.H., Nielsen, P.H., Back to basics: the influence of DNA extraction and primer choice on phylogenetic analysis of activated sludge communities. PloS One, 10, 2015 e0132783–15.
    • (2015) PloS One , vol.10
    • Albertsen, M.1    Karst, S.M.2    Ziegler, A.S.3    Kirkegaard, R.H.4    Nielsen, P.H.5
  • 6
    • 34147182303 scopus 로고    scopus 로고
    • A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria
    • Chakravorty, S., Helb, D., Burday, M., Connell, N., Alland, D., A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Bicrobiol Methods 69 (2007), 330–339.
    • (2007) J Bicrobiol Methods , vol.69 , pp. 330-339
    • Chakravorty, S.1    Helb, D.2    Burday, M.3    Connell, N.4    Alland, D.5
  • 7
    • 84867391206 scopus 로고    scopus 로고
    • Species-level analysis of DNA sequence data from the NIH Human Microbiome Project
    • Conlan, S., Kong, H.H., Segre, J.A., Species-level analysis of DNA sequence data from the NIH Human Microbiome Project. PloS One 7 (2012), e47075–e47077.
    • (2012) PloS One , vol.7 , pp. e47075-e47077
    • Conlan, S.1    Kong, H.H.2    Segre, J.A.3
  • 9
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar, R.C., Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26 (2010), 2460–2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 10
    • 84879414990 scopus 로고    scopus 로고
    • Topographic diversity of fungal and bacterial communities in human skin
    • Findley, K., Oh, J., Yang, J., Conlan, S., Deming, C., Meyer, J.A., et al. Topographic diversity of fungal and bacterial communities in human skin. Nature. 498 (2013), 367–370.
    • (2013) Nature. , vol.498 , pp. 367-370
    • Findley, K.1    Oh, J.2    Yang, J.3    Conlan, S.4    Deming, C.5    Meyer, J.A.6
  • 11
    • 84884413581 scopus 로고    scopus 로고
    • Propionibacterium acnes strain populations in the human skin microbiome associated with acne
    • Fitz-Gibbon, S., Tomida, S., Chiu, B.-H., Nguyen, L., Du, C., Liu, M., et al. Propionibacterium acnes strain populations in the human skin microbiome associated with acne. J Invest Dermatol 133 (2013), 2152–2160.
    • (2013) J Invest Dermatol , vol.133 , pp. 2152-2160
    • Fitz-Gibbon, S.1    Tomida, S.2    Chiu, B.-H.3    Nguyen, L.4    Du, C.5    Liu, M.6
  • 12
    • 84874444175 scopus 로고    scopus 로고
    • The neuropathic diabetic foot ulcer microbiome is associated with clinical factors
    • Gardner, S.E., Hillis, S.L., Heilmann, K., Segre, J.A., Grice, E.A., The neuropathic diabetic foot ulcer microbiome is associated with clinical factors. Diabetes 62 (2013), 923–930.
    • (2013) Diabetes , vol.62 , pp. 923-930
    • Gardner, S.E.1    Hillis, S.L.2    Heilmann, K.3    Segre, J.A.4    Grice, E.A.5
  • 13
    • 84906829581 scopus 로고    scopus 로고
    • The Earth Microbiome project: successes and aspirations
    • Gilbert, J.A., Jansson, J.K., Knight, R., The Earth Microbiome project: successes and aspirations. BMC Biol, 12, 2014, 69.
    • (2014) BMC Biol , vol.12 , pp. 69
    • Gilbert, J.A.1    Jansson, J.K.2    Knight, R.3
  • 14
    • 84978047241 scopus 로고    scopus 로고
    • Pgirmess: data analysis in ecology. R package version 1.6.4
    • Giraudoux P. Pgirmess: data analysis in ecology. R package version 1.6.4, http://CRAN.R-project.org/package=pgirmess; 2015.
    • (2015)
    • Giraudoux, P.1
  • 15
    • 66349083859 scopus 로고    scopus 로고
    • Topographical and temporal diversity of the human skin microbiome
    • Grice, E.A., Kong, H.H., Conlan, S., Deming, C.B., Davis, J., Young, A.C., et al. Topographical and temporal diversity of the human skin microbiome. Science 324 (2009), 1190–1192.
    • (2009) Science , vol.324 , pp. 1190-1192
    • Grice, E.A.1    Kong, H.H.2    Conlan, S.3    Deming, C.B.4    Davis, J.5    Young, A.C.6
  • 16
    • 84885796893 scopus 로고    scopus 로고
    • Taxonomic precision of different hypervariable regions of 16S rRNA gene and annotation methods for functional bacterial groups in biological wastewater treatment
    • Guo, F., Ju, F., Cai, L., Zhang, T., Taxonomic precision of different hypervariable regions of 16S rRNA gene and annotation methods for functional bacterial groups in biological wastewater treatment. PloS One, 8, 2013, e76185.
    • (2013) PloS One , vol.8 , pp. e76185
    • Guo, F.1    Ju, F.2    Cai, L.3    Zhang, T.4
  • 17
    • 79952006773 scopus 로고    scopus 로고
    • Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
    • Haas, B.J., Gevers, D., Earl, A.M., Feldgarden, M., Ward, D.V., Giannoukos, G., et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21 (2011), 494–504.
    • (2011) Genome Res , vol.21 , pp. 494-504
    • Haas, B.J.1    Gevers, D.2    Earl, A.M.3    Feldgarden, M.4    Ward, D.V.5    Giannoukos, G.6
  • 18
    • 84889010432 scopus 로고    scopus 로고
    • Microbial ecology of the skin in the era of metagenomics and molecular microbiology
    • a015362–2
    • Hannigan, G.D., Grice, E.A., Microbial ecology of the skin in the era of metagenomics and molecular microbiology. Cold Spring Harbor Perspect Med, 3, 2013 a015362–2.
    • (2013) Cold Spring Harbor Perspect Med , vol.3
    • Hannigan, G.D.1    Grice, E.A.2
  • 19
    • 84946600312 scopus 로고    scopus 로고
    • The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome
    • e01578–15
    • Hannigan, G.D., Meisel, J.S., Tyldsley, A.S., Zheng, Q., Hodkinson, B.P., SanMiguel, A.J., et al. The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. MBio, 6, 2015 e01578–15.
    • (2015) MBio , vol.6
    • Hannigan, G.D.1    Meisel, J.S.2    Tyldsley, A.S.3    Zheng, Q.4    Hodkinson, B.P.5    SanMiguel, A.J.6
  • 20
    • 84862286169 scopus 로고    scopus 로고
    • A framework for human microbiome research
    • Human Microbiome Project Consortium. A framework for human microbiome research. Nature 486 (2012), 215–221.
    • (2012) Nature , vol.486 , pp. 215-221
  • 21
    • 84862276328 scopus 로고    scopus 로고
    • Structure, function and diversity of the healthy human microbiome
    • Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486 (2012), 207–214.
    • (2012) Nature , vol.486 , pp. 207-214
  • 22
    • 84862192626 scopus 로고    scopus 로고
    • Evaluation of 16S rDNA-based community profiling for human microbiome research
    • Jumpstart Consortium Human Microbiome Project Data Generation Working Group. Evaluation of 16S rDNA-based community profiling for human microbiome research. PloS One, 7, 2012, e39315.
    • (2012) PloS One , vol.7 , pp. e39315
  • 23
    • 84884127512 scopus 로고    scopus 로고
    • Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
    • Langille, M.G.I., Zaneveld, J., Caporaso, J.G., McDonald, D., Knights, D., Reyes, J.A., et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 31 (2013), 814–821.
    • (2013) Nat Biotechnol. , vol.31 , pp. 814-821
    • Langille, M.G.I.1    Zaneveld, J.2    Caporaso, J.G.3    McDonald, D.4    Knights, D.5    Reyes, J.A.6
  • 24
    • 77958610660 scopus 로고    scopus 로고
    • pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
    • Matsen, F.A., Kodner, R.B., Armbrust, E.V., pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformat, 11, 2010, 538.
    • (2010) BMC Bioinformat , vol.11 , pp. 538
    • Matsen, F.A.1    Kodner, R.B.2    Armbrust, E.V.3
  • 26
    • 84899531657 scopus 로고    scopus 로고
    • Analysis, optimization and verification of illumina-generated 16S rRNA gene amplicon surveys
    • e94249–14
    • 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, 2014 e94249–14.
    • (2014) PloS One , vol.9
    • Nelson, M.C.1    Morrison, H.G.2    Benjamino, J.3    Grim, S.L.4    Graf, J.5
  • 27
    • 84908074440 scopus 로고    scopus 로고
    • Biogeography and individuality shape function in the human skin metagenome
    • Oh, J., Byrd, A.L., Deming, C., Conlan, S., NISC, Comparative Sequencing Program, Kong, H.H., et al. Biogeography and individuality shape function in the human skin metagenome. Nature. 514 (2014), 59–64.
    • (2014) Nature. , vol.514 , pp. 59-64
    • Oh, J.1    Byrd, A.L.2    Deming, C.3    Conlan, S.4    NISC, C.S.P.5    Kong, H.H.6
  • 29
    • 84907095419 scopus 로고    scopus 로고
    • R: a language and environment for statistical computing
    • Austria Vienna
    • R Core Team. R: a language and environment for statistical computing. R Foundation for Statistical Computing, 2015, Austria, Vienna.
    • (2015) R Foundation for Statistical Computing
  • 30
    • 84920644670 scopus 로고    scopus 로고
    • Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
    • Salter, S.J., Cox, M.J., Turek, E.M., Calus, S.T., Cookson, W.O., Moffatt, M.F., et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol, 12, 2014, 87.
    • (2014) BMC Biol , vol.12 , pp. 87
    • Salter, S.J.1    Cox, M.J.2    Turek, E.M.3    Calus, S.T.4    Cookson, W.O.5    Moffatt, M.F.6
  • 31
    • 79952390994 scopus 로고    scopus 로고
    • Fast identification and removal of sequence contamination from genomic and metagenomic datasets
    • Schmieder, R., Edwards, R., Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PloS One, 6, 2011, e17288.
    • (2011) PloS One , vol.6 , pp. e17288
    • Schmieder, R.1    Edwards, R.2
  • 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 (2007), 5261–5267.
    • (2007) Appl Environ Microbiol , vol.73 , pp. 5261-5267
    • Wang, Q.1    Garrity, G.M.2    Tiedje, J.M.3    Cole, J.R.4
  • 35
    • 77955067191 scopus 로고    scopus 로고
    • Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags
    • Wu, G.D., Lewis, J.D., Hoffmann, C., Chen, Y.-Y., Knight, R., Bittinger, K., et al. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol 10 (2010), 206–214.
    • (2010) BMC Microbiol , vol.10 , pp. 206-214
    • Wu, G.D.1    Lewis, J.D.2    Hoffmann, C.3    Chen, Y.-Y.4    Knight, R.5    Bittinger, K.6
  • 36
    • 84961291157 scopus 로고    scopus 로고
    • Which is more important for classifying microbial communities: who's there or what they can do?
    • Xu, Z., Malmer, D., Langille, M.G.I., Way, S.F., Knight, R., Which is more important for classifying microbial communities: who's there or what they can do?. ISME J 8 (2014), 2357–2359.
    • (2014) ISME J , vol.8 , pp. 2357-2359
    • Xu, Z.1    Malmer, D.2    Langille, M.G.I.3    Way, S.F.4    Knight, R.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.