Jumpstart Consortium Human Microbiome Project Data Generation Working Group. Evaluation of 16S rDNA-based community profiling for human microbiome research. PLoS One. 2012;7(6):e39315.
Article
PubMed Central
Google Scholar
Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol. 2013;79(17):5112–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27(16):2194–200.
Article
CAS
PubMed
PubMed Central
Google Scholar
Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 2011;21(3):494–504.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One. 2011;6(12):e27310.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schloss PD, Westcott SL. Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis. Appl Environ Microbiol. 2011;77(10):3219–26.
Article
CAS
PubMed
PubMed Central
Google Scholar
May A, Abeln S, Crielaard W, Heringa J, Brandt BW. Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations. Bioinformatics. 2014;30(11):1530–8.
Article
CAS
PubMed
Google Scholar
Shade A, Caporaso JG, Handelsman J, Knight R, Fierer N. A meta-analysis of changes in bacterial and archaeal communities with time. ISME J. 2013;7(8):1493–506.
Article
PubMed
PubMed Central
Google Scholar
Conlan S, Kong HH, Segre JA. Species-level analysis of DNA sequence data from the NIH human microbiome project. PLoS One. 2012;7(10):e47075.
Article
CAS
PubMed
PubMed Central
Google Scholar
Looft T, Allen HK, Casey TA, Alt DP, Stanton TB. Carbadox has both temporary and lasting effects on the swine gut microbiota. Front Microbiol. 2014;5:276.
Article
PubMed
PubMed Central
Google Scholar
Muyzer G, De Waal EC, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol. 1993;59(3):695–700.
CAS
PubMed
PubMed Central
Google Scholar
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537–41.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.
Article
CAS
PubMed
Google Scholar
Bunge J, Woodard L, Böhning D, Foster JA, Connolly S, Allen HK. Estimating population diversity with CatchAll. Bioinformatics. 2012;28(7):1045–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kennedy K, Hall MW, Lynch MD, Moreno-Hagelsieb G, Neufeld JD. Evaluating bias of Illumina-based bacterial 16S rRNA gene profiles. Appl Environ Microbiol. 2014;80(18):5717–22.
Article
PubMed
PubMed Central
Google Scholar
Brooks JP, Edwards DJ, Harwich MD, Rivera MC, Fettweis JM, Serrano MG, Reris RA, Sheth NU, Huang B, Girerd P. The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies. BMC Microbiol. 2015;15(1):66.
Article
PubMed
PubMed Central
Google Scholar
Nelson MC, Morrison HG, Benjamino J, Grim SL, Graf J. Analysis, optimization and verification of Illumina-generated 16S rRNA gene amplicon surveys. PLoS One. 2014;9(4):e94249.
Article
PubMed
PubMed Central
Google Scholar
Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, Fierer N, Gilbert JA. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. MBio. 2014;5(4):e1371.
Article
Google Scholar
Kunin V, Engelbrektson A, Ochman H, Hugenholtz P. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol. 2010;12(1):118–23.
Article
CAS
PubMed
Google Scholar
Huse SM, Welch DM, Morrison HG, Sogin ML. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol. 2010;12(7):1889–98.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10(10):996–8.
Article
CAS
PubMed
Google Scholar
Flynn JM, Brown EA, Chain FJ, MacIsaac HJ, Cristescu ME. Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods. Ecol Evol. 2015;5:2252–66.
Article
PubMed
PubMed Central
Google Scholar
Parkhill J, Wren BW, Mungall K, Ketley JM, Churcher C, Basham D, Chillingworth T, Davies RM, Feltwell T, Holroyd S, et al. The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences. Nature. 2000;403(6770):665–8.
Article
CAS
PubMed
Google Scholar
Gulig PA, Curtiss R. Plasmid-associated virulence of Salmonella typhimurium. Infect Immun. 1987;55(12):2891–901.
CAS
PubMed
PubMed Central
Google Scholar
Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF. The complete genome sequence of Escherichia coli K-12. Science. 1997;277(5331):1453–62.
Article
CAS
PubMed
Google Scholar
Looft T, Levine UY, Stanton TB. Cloacibacillus porcorum sp. nov., a mucin-degrading bacterium from the swine intestinal tract and emended description of the genus Cloacibacillus. Int J Syst Evol Microbiol. 2013;63(Pt 6):1960–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Harris D, Kinyon JM, Mullin M, Glock R. Isolation and propagation of spirochetes from the colon of swine dysentery affected pigs. Can J Comp Med. 1972;36(1):74.
CAS
PubMed
PubMed Central
Google Scholar
Mullins MA, Register KB, Bayles DO, Dyer DW, Kuehn JS, Phillips GJ. Genome sequence of Haemophilus parasuis strain 29755. Stand Genom Sci. 2011;5(1):61.
Article
CAS
Google Scholar
Park J, Zhang Y, Buboltz AM, Zhang X, Schuster SC, Ahuja U, Liu M, Miller JF, Sebaihia M, Bentley SD. Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens. BMC Genom. 2012;13(1):545.
Article
CAS
Google Scholar
Highlander SK, Hultén KG, Qin X, Jiang H, Yerrapragada S, Mason EO, Shang Y, Williams TM, Fortunov RM, Liu Y. Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus. BMC Microbiol. 2007;7(1):99.
Article
PubMed
PubMed Central
Google Scholar