Egerton S, Culloty S, Whooley J, Stanton C, Ross RP. The gut microbiota of marine fish. Front Microbiol. 2018;9:873.
Article
PubMed
PubMed Central
Google Scholar
Berendsen RL, van Verk MC, Stringlis IA, Zamioudis C, Tommassen J, Pieterse CM, Bakker PA. Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417. BMC Genomics. 2015;16:539.
Article
PubMed
CAS
PubMed Central
Google Scholar
Brito IL, Alm EJ. Tracking strains in the microbiome: insights from metagenomics and models. Front Microbiol. 2016;7:712.
PubMed
PubMed Central
Google Scholar
Mark Welch JL, Dewhirst FE, Borisy GG. Biogeography of the oral microbiome: the site-specialist hypothesis. Annu Rev Microbiol. 2019;73:335–58.
Article
CAS
PubMed
PubMed Central
Google Scholar
D'Amore R, Ijaz UZ, Schirmer M, Kenny JG, Gregory R, Darby AC, Shakya M, Podar M, Quince C, Hall N. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. BMC Genomics. 2016;17:55.
Article
PubMed
CAS
PubMed Central
Google Scholar
Pollock J, Glendinning L, Wisedchanwet T, Watson M. The madness of microbiome: attempting to find consensus “Best Practice” for 16S microbiome studies. Appl Environ Microbiol. 2018;84.
Almeida A, Mitchell AL, Tarkowska A, Finn RD. Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments. Gigascience. 2018;7.
Eren AM, Maignien L, Sul WJ, Murphy LG, Grim SL, Morrison HG, Sogin ML. Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods in ecology and evolution. 2013;4:1111–9.
Article
PubMed Central
Google Scholar
Eren AM, Morrison HG, Lescault PJ, Reveillaud J, Vineis JH, Sogin ML. Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences. The ISME journal. 2015;9:968–79.
Article
CAS
PubMed
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13:581–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Callahan BJ, McMurdie PJ, Holmes SP. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 2017;11:2639–43.
Article
PubMed
PubMed Central
Google Scholar
Edgar RC: UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. bioRxiv 2016:081257.
Edgar RC. Updating the 97% identity threshold for 16S ribosomal RNA OTUs. Bioinformatics. 2018;34:2371–5.
Article
CAS
PubMed
Google Scholar
Tikhonov M, Leach RW, Wingreen NS. Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution. ISME J. 2015;9:68–80.
Article
PubMed
CAS
Google Scholar
Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Zech Xu Z, Kightley EP, Thompson LR, Hyde ER, Gonzalez A, Knight R: Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems 2017, 2.
Kumar PS, Brooker MR, Dowd SE, Camerlengo T. Target region selection is a critical determinant of community fingerprints generated by 16S pyrosequencing. PLoS One. 2011;6:e20956.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yang B, Wang Y, Qian P-Y. Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis. BMC bioinformatics. 2016;17:135.
Article
PubMed
CAS
PubMed Central
Google Scholar
Zhang J, Ding X, Guan R, Zhu C, Xu C, Zhu B, Zhang H, Xiong Z, Xue Y, Tu J, Lu Z. Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake. Sci Total Environ. 2018;618:1254–67.
Article
CAS
PubMed
Google Scholar
Bukin YS, Galachyants YP, Morozov IV, Bukin SV, Zakharenko AS, Zemskaya TI. The effect of 16S rRNA region choice on bacterial community metabarcoding results. Scientific Data. 2019;6:190007.
Article
CAS
PubMed
PubMed Central
Google Scholar
Escapa IF, Chen T, Huang Y, Gajare P, Dewhirst FE, Lemon KP: New insights into human nostril microbiome from the expanded human oral microbiome database (eHOMD): a resource for the microbiome of the human aerodigestive tract. mSystems 2018, 3.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glockner 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
Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glockner FO. The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res. 2014;42:D643–8.
Article
CAS
PubMed
Google Scholar
Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM. Ribosomal database project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42:D633–42.
Article
CAS
PubMed
Google Scholar
McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P. An improved greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6:610–8.
Article
CAS
PubMed
Google Scholar
Edgar R. Taxonomy annotation and guide tree errors in 16S rRNA databases. PeerJ. 2018;6:e5030.
Article
PubMed
CAS
PubMed Central
Google Scholar
Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, Lakshmanan A, Wade WG. The human oral microbiome. J Bacteriol. 2010;192:5002–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Newton IL, Roeselers G. The effect of training set on the classification of honey bee gut microbiota using the Naive Bayesian Classifier. BMC Microbiol. 2012;12:221.
Article
PubMed
PubMed Central
Google Scholar
Seedorf H, Kittelmann S, Henderson G, Janssen PH. RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments. PeerJ. 2014;2:e494.
Article
PubMed
PubMed Central
Google Scholar
Ritari J, Salojarvi J, Lahti L, de Vos WM. Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database. BMC Genomics. 2015;16:1056.
Article
PubMed
CAS
PubMed Central
Google Scholar
McIlroy SJ, Saunders AM, Albertsen M, Nierychlo M, McIlroy B, Hansen AA, Karst SM, Nielsen JL, Nielsen PH. MiDAS: the field guide to the microbes of activated sludge. Database (Oxford). 2015;2015:bav062.
Article
CAS
Google Scholar
Deshpande V, Wang Q, Greenfield P, Charleston M, Porras-Alfaro A, Kuske CR, Cole JR, Midgley DJ, Tran-Dinh N. Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences. Mycologia. 2016;108:1–5.
Article
PubMed
Google Scholar
McIlroy SJ, Kirkegaard RH, McIlroy B, Nierychlo M, Kristensen JM, Karst SM, Albertsen M, Nielsen PH: MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups. Database (Oxford) 2017, 2017.
Mikaelyan A, Kohler T, Lampert N, Rohland J, Boga H, Meuser K, Brune A. Classifying the bacterial gut microbiota of termites and cockroaches: a curated phylogenetic reference database (DictDb). Syst Appl Microbiol. 2015;38:472–82.
Article
CAS
PubMed
Google Scholar
Rohwer RR, Hamilton JJ, Newton RJ, McMahon KD: TaxAss: leveraging a custom freshwater database achieves fine-scale taxonomic resolution. mSphere 2018, 3.
Henderson G, Yilmaz P, Kumar S, Forster RJ, Kelly WJ, Leahy SC, Guan LL, Janssen PH. Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework. PeerJ. 2019;7:e6496.
Article
PubMed
CAS
PubMed Central
Google Scholar
Chen T, Yu WH, Izard J, Baranova OV, Lakshmanan A, Dewhirst FE: The human oral microbiome database: a web accessible resource for investigating oral microbe taxonomic and genomic information. Database (Oxford) 2010, 2010:baq013.
Conlan S, Kong HH, Segre JA. Species-level analysis of DNA sequence data from the NIH Human Microbiome Project. PLoS One. 2012;7:e47075.
Article
CAS
PubMed
PubMed Central
Google Scholar
Al-Hebshi NN, Nasher AT, Idris AM, Chen T. Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: application to oral carcinoma samples. J Oral Microbiol. 2015;7:28934.
Article
PubMed
CAS
Google Scholar
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73:5261–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lan Y, Wang Q, Cole JR, Rosen GL. Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms. PLoS One. 2012;7:e32491.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vinje H, Liland KH, Almoy T, Snipen L. Comparing K-mer based methods for improved classification of 16S sequences. BMC Bioinformatics. 2015;16:205.
Article
PubMed
PubMed Central
Google Scholar
Murali A, Bhargava A, Wright ES. IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences. Microbiome. 2018;6:140.
Article
PubMed
PubMed Central
Google Scholar
Edgar RC. Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences. PeerJ. 2018;6:e4652.
Article
PubMed
PubMed Central
Google Scholar
Russell S, Norvig P: Artificial Intelligence: A Modern Approach. Prentice Hall Press; 2009.
Werner JJ, Koren O, Hugenholtz P, DeSantis TZ, Walters WA, Caporaso JG, Angenent LT, Knight R, Ley RE. Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME J. 2012;6:94–103.
Article
CAS
PubMed
Google Scholar
Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, Miller S, Nadarajan R, Brodie EL, Lynch SV. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens. PLoS One. 2015;10:e0117617.
Article
PubMed
CAS
PubMed Central
Google Scholar
Earl JP, Adappa ND, Krol J, Bhat AS, Balashov S, Ehrlich RL, Palmer JN, Workman AD, Blasetti M, Sen B, et al. Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes. Microbiome. 2018;6:190.
Article
PubMed
PubMed Central
Google Scholar
Callahan BJ, Wong J, Heiner C, Oh S, Theriot CM, Gulati AS, McGill SK, Dougherty MK. High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Res. 2019.
Beye M, Bakour S, Le Dault E, Rathored J, Michelle C, Cadoret F, Raoult D, Fournier PE. Peptoniphilus lacydonensis sp. nov., a new human-associated species isolated from a patient with chronic refractory sinusitis. New Microbes New Infect. 2018;23:61–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nguyen NP, Mirarab S, Liu B, Pop M, Warnow T. TIPP: taxonomic identification and phylogenetic profiling. Bioinformatics. 2014;30:3548–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Allard G, Ryan FJ, Jeffery IB, Claesson MJ. SPINGO: a rapid species-classifier for microbial amplicon sequences. BMC Bioinformatics. 2015;16:324.
Article
PubMed
CAS
PubMed Central
Google Scholar
Edgar RC: SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences. bioRxiv 2016:074161.
Gao X, Lin H, Revanna K, Dong Q. A Bayesian taxonomic classification method for 16S rRNA gene sequences with improved species-level accuracy. BMC Bioinformatics. 2017;18:247.
Article
PubMed
CAS
PubMed Central
Google Scholar
Liland KH, Vinje H. Snipen L: microclass: an R-package for 16S taxonomy classification. BMC Bioinformatics. 2017;18:172.
Article
PubMed
CAS
PubMed Central
Google Scholar
Matias Rodrigues JF, Schmidt TSB, Tackmann J, von Mering C. MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis. Bioinformatics. 2017;33:3808–10.
Article
PubMed
CAS
PubMed Central
Google Scholar
Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, Huttley GA, Gregory Caporaso J. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin. Microbiome. 2018;6:90.
Article
PubMed
PubMed Central
Google Scholar
Zheng Q, Bartow-McKenney C, Meisel JS, Grice EA. HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies. Genome Biol. 2018;19:82.
Article
PubMed
CAS
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;79:5112–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mitra A, Skrzypczak M, Ginalski K, Rowicka M. Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform. PLoS One. 2015;10:e0120520.
Article
PubMed
CAS
PubMed Central
Google Scholar
Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26:1641–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, Bouffard GG, Blakesley RW, Murray PR, Green ED, et al. Topographical and temporal diversity of the human skin microbiome. Science. 2009;324:1190–2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kong HH, Oh J, Deming C, Conlan S, Grice EA, Beatson MA, Nomicos E, Polley EC, Komarow HD, Murray PR, et al. Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome research. 2012;22:850–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oh J, Conlan S, Polley EC, Segre JA, Kong HH. Shifts in human skin and nares microbiota of healthy children and adults. Genome medicine. 2012;4:77.
Article
PubMed
PubMed Central
Google Scholar
Findley K, Oh J, Yang J, Conlan S, Deming C, Meyer JA, Schoenfeld D, Nomicos E, Park M, Kong HH, Segre JA. Topographic diversity of fungal and bacterial communities in human skin. Nature. 2013;498:367–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oh J, Freeman AF, Park M, Sokolic R, Candotti F, Holland SM, Segre JA, Kong HH. The altered landscape of the human skin microbiome in patients with primary immunodeficiencies. Genome research. 2013;23:2103–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oh J, Byrd AL, Deming C, Conlan S, Kong HH, Segre JA. Biogeography and individuality shape function in the human skin metagenome. Nature. 2014;514:59–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pei Z, Bini EJ, Yang L, Zhou M, Francois F, Blaser MJ. Bacterial biota in the human distal esophagus. Proc Natl Acad Sci U S A. 2004;101:4250–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pei Z, Yang L, Peek RM, Jr Levine SM, Pride DT, Blaser MJ. Bacterial biota in reflux esophagitis and Barrett's esophagus. World J Gastroenterol. 2005;11:7277–83.
Article
PubMed
PubMed Central
Google Scholar
Harris JK, De Groote MA, Sagel SD, Zemanick ET, Kapsner R, Penvari C, Kaess H, Deterding RR, Accurso FJ, Pace NR. Molecular identification of bacteria in bronchoalveolar lavage fluid from children with cystic fibrosis. Proc Natl Acad Sci U S A. 2007;104:20529–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
van der Gast CJ, Walker AW, Stressmann FA, Rogers GB, Scott P, Daniels TW, Carroll MP, Parkhill J, Bruce KD. Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities. ISME J. 2011;5:780–91.
Article
PubMed
CAS
Google Scholar
Flanagan JL, Brodie EL, Weng L, Lynch SV, Garcia O, Brown R, Hugenholtz P, DeSantis TZ, Andersen GL, Wiener-Kronish JP, Bristow J. Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. J Clin Microbiol. 2007;45:1954–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
Perkins SD, Woeltje KF, Angenent LT. Endotracheal tube biofilm inoculation of oral flora and subsequent colonization of opportunistic pathogens. Int J Med Microbiol. 2010;300:503–11.
Article
CAS
PubMed
Google Scholar
Shelef KM: Ecology in the dentist’s chair: patterns of biogeography and stability in human subgingival microbial communities. Stanford University, Department of Biology; 2013.
O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016;44:D733–45.
Article
CAS
PubMed
Google Scholar