TY - JOUR AU - Riesenfeld, C. S. AU - Schloss, P. D. AU - Handelsman, J. PY - 2004 DA - 2004// TI - Metagenomics: genomic analysis of microbial communities JO - Annu Rev Genet VL - 38 UR - https://doi.org/10.1146/annurev.genet.38.072902.091216 DO - 10.1146/annurev.genet.38.072902.091216 ID - Riesenfeld2004 ER - TY - JOUR AU - Gilbert, J. A. AU - Jansson, J. K. AU - Knight, R. PY - 2014 DA - 2014// TI - The Earth Microbiome project: successes and aspirations JO - BMC Biol VL - 12 UR - https://doi.org/10.1186/s12915-014-0069-1 DO - 10.1186/s12915-014-0069-1 ID - Gilbert2014 ER - TY - JOUR AU - Gevers, D. AU - Knight, R. AU - Petrosino, J. F. AU - Huang, K. AU - McGuire, A. L. AU - Birren, B. W. PY - 2012 DA - 2012// TI - The Human Microbiome Project: a community resource for the healthy human microbiome JO - Plos Biol VL - 10 UR - https://doi.org/10.1371/journal.pbio.1001377 DO - 10.1371/journal.pbio.1001377 ID - Gevers2012 ER - TY - JOUR AU - Shade, A. AU - Caporaso, J. G. AU - Handelsman, J. AU - Knight, R. AU - Fierer, N. PY - 2013 DA - 2013// TI - A meta-analysis of changes in bacterial and archaeal communities with time JO - ISME J VL - 7 UR - https://doi.org/10.1038/ismej.2013.54 DO - 10.1038/ismej.2013.54 ID - Shade2013 ER - TY - JOUR AU - Kittelmann, S. AU - Seedorf, H. AU - Walters, W. A. AU - Clemente, J. C. AU - Knight, R. AU - Gordon, J. I. PY - 2013 DA - 2013// TI - Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0047879 DO - 10.1371/journal.pone.0047879 ID - Kittelmann2013 ER - TY - JOUR AU - Pei, A. Y. AU - Oberdorf, W. E. AU - Nossa, C. W. AU - Agarwal, A. AU - Chokshi, P. AU - Gerz, E. A. PY - 2010 DA - 2010// TI - Diversity of 16s rRNA genes within individual prokaryotic genomes JO - Appl Environ Microbiol VL - 76 UR - https://doi.org/10.1128/AEM.02953-09 DO - 10.1128/AEM.02953-09 ID - Pei2010 ER - TY - STD TI - Tian RM, Cai L, Zhang WP, Cao HL, Qian PY. Rare events of intra-genus and intra-species horizontal transfer of the 16s rRNA gene. Genome biology and Evolution. 2015. doi:10.1093/gbe/evv143. ID - ref7 ER - TY - JOUR AU - Janda, J. M. AU - Abbott, S. L. PY - 2007 DA - 2007// TI - 16s rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls JO - J Clin Microbiol VL - 45 UR - https://doi.org/10.1128/JCM.01228-07 DO - 10.1128/JCM.01228-07 ID - Janda2007 ER - TY - JOUR AU - Cole, J. R. AU - Wang, Q. AU - Cardenas, E. AU - Fish, J. AU - Chai, B. AU - Farris, R. J. PY - 2009 DA - 2009// TI - The Ribosomal Database Project: improved alignments and new tools for rRNA analysis JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn879 DO - 10.1093/nar/gkn879 ID - Cole2009 ER - TY - JOUR AU - DeSantis, T. Z. AU - Hugenholtz, P. AU - Larsen, N. AU - Rojas, M. AU - Brodie, E. L. AU - Keller, K. PY - 2006 DA - 2006// TI - Greengenes, a chimera-checked 16s rRNA gene database and workbench compatible with ARB JO - Appl Environ Microbiol VL - 72 UR - https://doi.org/10.1128/AEM.03006-05 DO - 10.1128/AEM.03006-05 ID - DeSantis2006 ER - TY - JOUR AU - Quast, C. AU - Pruesse, E. AU - Yilmaz, P. AU - Gerken, J. AU - Schweer, T. AU - Yarza, P. PY - 2013 DA - 2013// TI - The SILVA ribosomal RNA gene database project: improved data processing and web-based tools JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1219 DO - 10.1093/nar/gks1219 ID - Quast2013 ER - TY - JOUR AU - Vos, M. AU - Quince, C. AU - Pijl, A. S. AU - Hollander, M. AU - Kowalchuk, G. A. PY - 2012 DA - 2012// TI - A comparison of rpoB and 16s rRNA as markers in pyrosequencing studies of bacterial diversity JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0030600 DO - 10.1371/journal.pone.0030600 ID - Vos2012 ER - TY - JOUR AU - Vetrovsky, T. AU - Baldrian, P. PY - 2013 DA - 2013// TI - The variability of the 16s rRNA gene in bacterial genomes and its consequences for bacterial community analyses JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0057923 DO - 10.1371/journal.pone.0057923 ID - Vetrovsky2013 ER - TY - JOUR AU - Ong, S. H. AU - Kukkillaya, V. U. AU - Wilm, A. AU - Lay, C. AU - Ho, E. X. P. AU - Low, L. PY - 2013 DA - 2013// TI - Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16s rRNA amplicon sequences JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0060811 DO - 10.1371/journal.pone.0060811 ID - Ong2013 ER - TY - STD TI - Eren AM, Maignien L, Sul WJ, Murphy LG, Grim SL, Morrison HG et al. Oligotyping: differentiating between closely related microbial taxa using 16s rRNA gene data. Methods Ecol Evol. 2013;4(12). doi:10.1111/2041-210X.12114. ID - ref15 ER - TY - JOUR AU - Zaneveld, J. R. AU - Lozupone, C. AU - Gordon, J. I. AU - Knight, R. PY - 2010 DA - 2010// TI - Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives JO - Nucleic Acids Res VL - 38 UR - https://doi.org/10.1093/nar/gkq066 DO - 10.1093/nar/gkq066 ID - Zaneveld2010 ER - TY - JOUR AU - Kitahara, K. AU - Miyazaki, K. PY - 2013 DA - 2013// TI - Revisiting bacterial phylogeny: natural and experimental evidence for horizontal gene transfer of 16s rRNA JO - Mob Genet Elements VL - 3 UR - https://doi.org/10.4161/mge.24210 DO - 10.4161/mge.24210 ID - Kitahara2013 ER - TY - JOUR AU - Achenbach, L. A. AU - Carey, J. AU - Madigan, M. T. PY - 2001 DA - 2001// TI - Photosynthetic and phylogenetic primers for detection of anoxygenic phototrophs in natural environments JO - Appl Environ Microbiol VL - 67 UR - https://doi.org/10.1128/AEM.67.7.2922-2926.2001 DO - 10.1128/AEM.67.7.2922-2926.2001 ID - Achenbach2001 ER - TY - JOUR AU - Walsh, D. A. AU - Bapteste, E. AU - Kamekura, M. AU - Doolittle, W. F. PY - 2004 DA - 2004// TI - Evolution of the RNA polymerase B′ subunit gene (rpoB′) in Halobacteriales: a complementary molecular marker to the SSU rRNA gene JO - Mol Biol Evol VL - 21 UR - https://doi.org/10.1093/molbev/msh248 DO - 10.1093/molbev/msh248 ID - Walsh2004 ER - TY - JOUR AU - Case, R. J. AU - Boucher, Y. AU - Dahllof, I. AU - Holmstrom, C. AU - Doolittle, W. F. AU - Kjelleberg, S. PY - 2007 DA - 2007// TI - Use of 16s rRNA and rpoB genes as molecular markers for microbial ecology studies JO - Appl Environ Microbiol VL - 73 UR - https://doi.org/10.1128/AEM.01177-06 DO - 10.1128/AEM.01177-06 ID - Case2007 ER - TY - JOUR AU - Torriani, S. AU - Felis, G. E. AU - Dellaglio, F. PY - 2001 DA - 2001// TI - Differentiation of Lactobacillus plantarum, L. pentosus, and L. paraplantarum by recA gene sequence analysis and multiplex PCR assay with recA gene-derived primers JO - Appl Environ Microbiol VL - 67 UR - https://doi.org/10.1128/AEM.67.8.3450-3454.2001 DO - 10.1128/AEM.67.8.3450-3454.2001 ID - Torriani2001 ER - TY - JOUR AU - Verbekea, T. J. AU - Sparling, R. AU - Hill, J. E. AU - Links, M. G. AU - Levin, D. AU - Dumonceaux, T. J. PY - 2011 DA - 2011// TI - Predicting relatedness of bacterial genomes using the chaperonin-60 universal target (cpn60 UT): application to Thermoanaerobacter species JO - Syst Appl Microbiol VL - 34 UR - https://doi.org/10.1016/j.syapm.2010.11.019 DO - 10.1016/j.syapm.2010.11.019 ID - Verbekea2011 ER - TY - JOUR AU - Wu, M. AU - Eisen, J. A. PY - 2008 DA - 2008// TI - A simple, fast, and accurate method of phylogenomic inference JO - Genome Biol VL - 9 UR - https://doi.org/10.1186/gb-2008-9-10-r151 DO - 10.1186/gb-2008-9-10-r151 ID - Wu2008 ER - TY - JOUR AU - Liu, B. AU - Gibbons, T. AU - Ghodsi, M. AU - Treangen, T. AU - Pop, M. PY - 2011 DA - 2011// TI - Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences JO - BMC Genomics VL - 12 Suppl 2 UR - https://doi.org/10.1186/1471-2164-12-S2-S4 DO - 10.1186/1471-2164-12-S2-S4 ID - Liu2011 ER - TY - JOUR AU - Segata, N. AU - Huttenhower, C. PY - 2011 DA - 2011// TI - Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0024704 DO - 10.1371/journal.pone.0024704 ID - Segata2011 ER - TY - JOUR AU - Sunagawa, S. AU - Mende, D. R. AU - Zeller, G. AU - Izquierdo-Carrasco, F. AU - Berger, S. A. AU - Kultima, J. R. PY - 2013 DA - 2013// TI - Metagenomic species profiling using universal phylogenetic marker genes JO - Nat Methods VL - 10 UR - https://doi.org/10.1038/nmeth.2693 DO - 10.1038/nmeth.2693 ID - Sunagawa2013 ER - TY - JOUR AU - Schloissnig, S. AU - Arumugam, M. AU - Sunagawa, S. AU - Mitreva, M. AU - Tap, J. AU - Zhu, A. PY - 2013 DA - 2013// TI - Genomic variation landscape of the human gut microbiome JO - Nature VL - 493 UR - https://doi.org/10.1038/nature11711 DO - 10.1038/nature11711 ID - Schloissnig2013 ER - TY - JOUR AU - Ciccarelli, F. D. AU - Doerks, T. AU - Mering, C. AU - Creevey, C. J. AU - Snel, B. AU - Bork, P. PY - 2006 DA - 2006// TI - Toward automatic reconstruction of a highly resolved tree of life JO - Science VL - 311 UR - https://doi.org/10.1126/science.1123061 DO - 10.1126/science.1123061 ID - Ciccarelli2006 ER - TY - JOUR AU - Zeigler, D. R. PY - 2003 DA - 2003// TI - Gene sequences useful for predicting relatedness of whole genomes in bacteria JO - Int J Syst Evol Microbiol VL - 53 UR - https://doi.org/10.1099/ijs.0.02713-0 DO - 10.1099/ijs.0.02713-0 ID - Zeigler2003 ER - TY - JOUR AU - Chen, K. AU - Pachter, L. PY - 2005 DA - 2005// TI - Bioinformatics for whole-genome shotgun sequencing of microbial communities JO - PLoS Comput Biol VL - 1 UR - https://doi.org/10.1371/journal.pcbi.0010024 DO - 10.1371/journal.pcbi.0010024 ID - Chen2005 ER - TY - JOUR AU - Tringe, S. G. AU - Rubin, E. M. PY - 2005 DA - 2005// TI - Metagenomics: DNA sequencing of environmental samples JO - Nat Rev Genet VL - 6 UR - https://doi.org/10.1038/nrg1709 DO - 10.1038/nrg1709 ID - Tringe2005 ER - TY - JOUR AU - Bragg, L. AU - Tyson, G. W. PY - 2014 DA - 2014// TI - Metagenomics using next-generation sequencing JO - Methods Mol Biol VL - 1096 UR - https://doi.org/10.1007/978-1-62703-712-9_15 DO - 10.1007/978-1-62703-712-9_15 ID - Bragg2014 ER - TY - JOUR AU - Koslicki, D. AU - Foucart, S. AU - Rosen, G. PY - 2014 DA - 2014// TI - WGSQuikr: fast whole-genome shotgun metagenomic classification JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0091784 DO - 10.1371/journal.pone.0091784 ID - Koslicki2014 ER - TY - JOUR AU - Segata, N. AU - Waldron, L. AU - Ballarini, A. AU - Narasimhan, V. AU - Jousson, O. AU - Huttenhower, C. PY - 2012 DA - 2012// TI - Metagenomic microbial community profiling using unique clade-specific marker genes JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.2066 DO - 10.1038/nmeth.2066 ID - Segata2012 ER - TY - JOUR AU - Darling, A. E. AU - Jospin, G. AU - Lowe, E. AU - Matsen, F. A. AU - Bik, H. M. AU - Eisen, J. A. PY - 2014 DA - 2014// TI - PhyloSift: phylogenetic analysis of genomes and metagenomes JO - PeerJ VL - 2 UR - https://doi.org/10.7717/peerj.243 DO - 10.7717/peerj.243 ID - Darling2014 ER - TY - JOUR AU - Wu, M. AU - Scott, A. J. PY - 2012 DA - 2012// TI - Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2 JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts079 DO - 10.1093/bioinformatics/bts079 ID - Wu2012 ER - TY - JOUR AU - Miller, C. S. AU - Baker, B. J. AU - Thomas, B. C. AU - Singer, S. W. AU - Banfield, J. F. PY - 2011 DA - 2011// TI - EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data JO - Genome Biol VL - 12 UR - https://doi.org/10.1186/gb-2011-12-5-r44 DO - 10.1186/gb-2011-12-5-r44 ID - Miller2011 ER - TY - JOUR AU - Sharpton, T. J. AU - Riesenfeld, S. J. AU - Kembel, S. W. AU - Ladau, J. AU - O’Dwyer, J. P. AU - Green, J. L. PY - 2011 DA - 2011// TI - PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data JO - PLoS Comput Biol VL - 7 UR - https://doi.org/10.1371/journal.pcbi.1001061 DO - 10.1371/journal.pcbi.1001061 ID - Sharpton2011 ER - TY - JOUR AU - Konstantinidis, K. T. AU - Ramette, A. AU - Tiedje, J. M. PY - 2006 DA - 2006// TI - Toward a more robust assessment of intraspecies diversity, using fewer genetic markers JO - Appl Environ Microbiol VL - 72 UR - https://doi.org/10.1128/AEM.01398-06 DO - 10.1128/AEM.01398-06 ID - Konstantinidis2006 ER - TY - JOUR AU - Tatusov, R. L. AU - Fedorova, N. D. AU - Jackson, J. D. AU - Jacobs, A. R. AU - Kiryutin, B. AU - Koonin, E. V. PY - 2003 DA - 2003// TI - The COG database: an updated version includes eukaryotes JO - BMC Bioinformatics VL - 4 UR - https://doi.org/10.1186/1471-2105-4-41 DO - 10.1186/1471-2105-4-41 ID - Tatusov2003 ER - TY - JOUR AU - Needleman, S. B. AU - Wunsch, C. D. PY - 1970 DA - 1970// TI - A general method applicable to the search for similarities in the amino acid sequence of two proteins JO - J Mol Biol VL - 48 UR - https://doi.org/10.1016/0022-2836(70)90057-4 DO - 10.1016/0022-2836(70)90057-4 ID - Needleman1970 ER - TY - JOUR AU - Benson, D. A. AU - Karsch-Mizrachi, I. AU - Lipman, D. J. AU - Ostell, J. AU - Wheeler, D. L. PY - 2005 DA - 2005// TI - GenBank JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki063 DO - 10.1093/nar/gki063 ID - Benson2005 ER - TY - JOUR AU - Mount, D. W. PY - 2007 DA - 2007// TI - Using the Basic Local Alignment Search Tool (BLAST) JO - CSH Protoc VL - 2007 ID - Mount2007 ER - TY - JOUR AU - Smith, T. F. AU - Waterman, M. S. PY - 1981 DA - 1981// TI - Identification of common molecular subsequences JO - J Mol Biol VL - 147 UR - https://doi.org/10.1016/0022-2836(81)90087-5 DO - 10.1016/0022-2836(81)90087-5 ID - Smith1981 ER - TY - JOUR AU - Konstantinidis, K. T. AU - Tiedje, J. M. PY - 2005 DA - 2005// TI - Towards a genome-based taxonomy for prokaryotes JO - J Bacteriol VL - 187 UR - https://doi.org/10.1128/JB.187.18.6258-6264.2005 DO - 10.1128/JB.187.18.6258-6264.2005 ID - Konstantinidis2005 ER - TY - JOUR AU - Puigbo, P. AU - Garcia-Vallve, S. AU - McInerney, J. O. PY - 2007 DA - 2007// TI - TOPD/FMTS: a new software to compare phylogenetic trees JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm135 DO - 10.1093/bioinformatics/btm135 ID - Puigbo2007 ER - TY - JOUR AU - Kuczynski, J. AU - Stombaugh, J. AU - Walters, W. A. AU - Gonzalez, A. AU - Caporaso, J. G. AU - Knight, R. PY - 2012 DA - 2012// TI - Using QIIME to analyze 16s rRNA gene sequences from microbial communities JO - Curr Protoc Microbiol VL - Chapter 1 ID - Kuczynski2012 ER - TY - JOUR AU - Hill, J. E. AU - Penny, S. L. AU - Crowell, K. G. AU - Goh, S. H. AU - Hemmingsen, S. M. PY - 2004 DA - 2004// TI - cpnDB: a chaperonin sequence database JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.2649204 DO - 10.1101/gr.2649204 ID - Hill2004 ER - TY - JOUR AU - Links, M. G. AU - Dumonceaux, T. J. AU - Hemmingsen, S. M. AU - Hill, J. E. PY - 2012 DA - 2012// TI - The chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0049755 DO - 10.1371/journal.pone.0049755 ID - Links2012 ER - TY - JOUR AU - Hershberg, R. AU - Tang, H. AU - Petrov, D. A. PY - 2007 DA - 2007// TI - Reduced selection leads to accelerated gene loss in Shigella JO - Genome Biol VL - 8 UR - https://doi.org/10.1186/gb-2007-8-8-r164 DO - 10.1186/gb-2007-8-8-r164 ID - Hershberg2007 ER - TY - JOUR AU - Helgason, E. AU - Okstad, O. A. AU - Caugant, D. A. AU - Johansen, H. A. AU - Fouet, A. AU - Mock, M. PY - 2000 DA - 2000// TI - Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis—one species on the basis of genetic evidence JO - Appl Environ Microbiol VL - 66 UR - https://doi.org/10.1128/AEM.66.6.2627-2630.2000 DO - 10.1128/AEM.66.6.2627-2630.2000 ID - Helgason2000 ER - TY - JOUR AU - Ley, R. E. AU - Turnbaugh, P. J. AU - Klein, S. AU - Gordon, J. I. PY - 2006 DA - 2006// TI - Microbial ecology—human gut microbes associated with obesity JO - Nature VL - 444 UR - https://doi.org/10.1038/4441022a DO - 10.1038/4441022a ID - Ley2006 ER - TY - JOUR AU - Turnbaugh, P. J. AU - Hamady, M. AU - Yatsunenko, T. AU - Cantarel, B. L. AU - Duncan, A. AU - Ley, R. E. PY - 2009 DA - 2009// TI - A core gut microbiome in obese and lean twins JO - Nature VL - 457 UR - https://doi.org/10.1038/nature07540 DO - 10.1038/nature07540 ID - Turnbaugh2009 ER - TY - JOUR AU - Yang, F. AU - Zeng, X. W. AU - Ning, K. AU - Liu, K. L. AU - Lo, C. C. AU - Wang, W. PY - 2012 DA - 2012// TI - Saliva microbiomes distinguish caries-active from healthy human populations JO - ISME J VL - 6 UR - https://doi.org/10.1038/ismej.2011.71 DO - 10.1038/ismej.2011.71 ID - Yang2012 ER - TY - JOUR AU - Liu, B. AU - Faller, L. L. AU - Klitgord, N. AU - Mazumdar, V. AU - Ghodsi, M. AU - Sommer, D. D. PY - 2012 DA - 2012// TI - Deep sequencing of the oral microbiome reveals signatures of periodontal disease JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0037919 DO - 10.1371/journal.pone.0037919 ID - Liu2012 ER - TY - JOUR AU - Qin, J. AU - Li, R. AU - Raes, J. AU - Arumugam, M. AU - Burgdorf, K. S. AU - Manichanh, C. PY - 2010 DA - 2010// TI - A human gut microbial gene catalogue established by metagenomic sequencing JO - Nature VL - 464 UR - https://doi.org/10.1038/nature08821 DO - 10.1038/nature08821 ID - Qin2010 ER - TY - JOUR AU - Arumugam, M. AU - Raes, J. AU - Pelletier, E. AU - Paslier, D. AU - Yamada, T. AU - Mende, D. R. PY - 2011 DA - 2011// TI - Enterotypes of the human gut microbiome JO - Nature VL - 473 UR - https://doi.org/10.1038/nature09944 DO - 10.1038/nature09944 ID - Arumugam2011 ER - TY - JOUR AU - Siddiqui, H. AU - Nederbragt, A. J. AU - Lagesen, K. AU - Jeansson, S. L. AU - Jakobsen, K. S. PY - 2011 DA - 2011// TI - Assessing diversity of the female urine microbiota by high throughput sequencing of 16s rDNA amplicons JO - BMC Microbiol VL - 11 UR - https://doi.org/10.1186/1471-2180-11-244 DO - 10.1186/1471-2180-11-244 ID - Siddiqui2011 ER - TY - STD TI - Lan YM, Morrison JC, Hershberg R, Rosen GL. POGO-DB-a database of pairwise-comparisons of genomes and conserved orthologous genes. Nucleic Acids Res. 2014;42(D1):D625–32. doi:10.1093/Nar/Gkt1094. ID - ref59 ER -