Srivastava AK, Schlessinger D. Mechanism and regulation of bacterial ribosomal RNA processing. Annu Rev Microbiol. 1990;44:105–29.
Google Scholar
Brewer TE, Albertsen M, Edwards A, Kirkegaard RH, Rocha EPC, Fierer N. Unlinked rRNA genes are widespread among bacteria and archaea. ISME J. 2020;14:597–608.
Google Scholar
Apirion D, Miczak A. RNA processing in prokaryotic cells. Bioessays. 1993;15:113–20.
Google Scholar
Espejo RT, Plaza N. Multiple ribosomal RNA operons in bacteria; their concerted evolution and potential consequences on the rate of evolution of their 16S rRNA. Front Microbiol. 2018;9:1232.
Google Scholar
Roller BRK, Stoddard SF, Schmidt TM. Exploiting rRNA operon copy number to investigate bacterial reproductive strategies. Nat Microbiol. 2016;1:16160.
Google Scholar
Lim K, Furuta Y, Kobayashi I. Large variations in bacterial ribosomal RNA Genes. Mol Biol Evol. 2012;29:2937–48.
Google Scholar
Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M, Neumaier J, et al. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis. 1998;19:554–68.
Google Scholar
Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci. 1977;74:5088 LP–5090.
Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci. 1985;82:6955 LP–6959.
Park YH, Hori H, Suzuki K, Osawa S, Komagata K. Phylogenetic analysis of the coryneform bacteria by 5S rRNA sequences. J Bacteriol. 1987;169:1801–6.
Google Scholar
Szymanski M, Barciszewska MZ, Erdmann VA, Barciszewski J. 5S Ribosomal RNA Database. Nucleic Acids Res. 2002;30:176–8.
Google Scholar
Pace NR. The small things can matter. PLoS Biol. 2018;16:e3000009.
Google Scholar
Gürtler V. The role of recombination and mutation in 16S–23S rDNA spacer rearrangements. Gene. 1999;238:241–52.
Google Scholar
Snyder AK, Adkins KZ, Rio RVM. Use of the internal transcribed spacer (ITS) regions to examine symbiont divergence and as a diagnostic tool for sodalis-related bacteria. Insects. 2011;2:515–31.
Google Scholar
Man SM, Kaakoush NO, Octavia S, Mitchell H. The internal transcribed spacer region, a new tool for use in species differentiation and delineation of systematic relationships within the Campylobacter genus. Appl Environ Microbiol. 2010;76:3071–81.
Google Scholar
Liguori AP, Warrington SD, Ginther JL, Pearson T, Bowers J, Glass MB, et al. Diversity of 16S-23S rDNA Internal Transcribed Spacer (ITS) reveals phylogenetic relationships in Burkholderia pseudomallei and its near-neighbors. PLoS One. 2011;6:e29323.
Google Scholar
Boyer SL, Flechtner VR, Johansen JR. Is the 16S–23S rRNA internal transcribed spacer region a good tool for use in molecular systematics and population genetics? A case study in cyanobacteria. Mol Biol Evol. 2001;18:1057–69.
Google Scholar
Fisher MM, Triplett EW. Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol. 1999;65:4630–6.
Google Scholar
Brown BL, Watson M, Minot SS, Rivera MC, Franklin RB. MinIONTM nanopore sequencing of environmental metagenomes: a synthetic approach. Gigascience. 2017;6:1–10.
Google Scholar
Hernando-Morales V, Varela MM, Needham DM, Cram J, Fuhrman JA, Teira E. Vertical and seasonal patterns control bacterioplankton communities at two horizontally coherent coastal upwelling sites off Galicia (NW Spain). Microb Ecol. 2018;76:866–84.
Google Scholar
Johnson JS, Spakowicz DJ, Hong B-Y, Petersen LM, Demkowicz P, Chen L, et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun. 2019;10:5029.
Google Scholar
Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, et al. Microbial diversity in the deep sea and the underexplored ‘rare biosphere’. Proc Natl Acad Sci USA. 2006;103:12115–20.
Google Scholar
Nossa CW, Oberdorf WE, Yang L, Aas JA, Paster BJ, Desantis TZ, et al. Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome. World J Gastroenterol. 2010;16:4135–44.
Google Scholar
Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456:53–9.
Google Scholar
Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 2017;551:457–63.
Google Scholar
Kapustina Ž, Medžiūnė J, Alzbutas G, Rokaitis I, Matjošaitis K, Mackevičius G, et al. High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts. Microb Genom. 2021;7:1–16.
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature. 2004;428:37–43.
Google Scholar
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004;304:66–74.
Google Scholar
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 2007;5:e77.
Google Scholar
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, et al. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol. 2019;37:852–7.
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.
Google Scholar
Karst SM, Ziels RM, Kirkegaard RH, Sørensen EA, McDonald D, Zhu Q, et al. High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing. Nat Methods. 2021;18:165–9.
Google Scholar
Jamy M, Foster R, Barbera P, Czech L, Kozlov A, Stamatakis A, et al. Long-read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity. Mol Ecol Resour. 2020;20:429–43.
Google Scholar
Leggett RM, Clark MD. A world of opportunities with nanopore sequencing. J Exp Bot. 2017;68:5419–29.
Google Scholar
Jain M, Olsen HE, Paten B, Akeson M. The Oxford nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol. 2016;17:239.
Google Scholar
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009;323:133–8.
Google Scholar
Graf J, Ledala N, Caimano MJ, Jackson E, Gratalo D, Fasulo D, et al. High-resolution differentiation of enteric bacteria in premature infant fecal microbiomes using a novel rRNA amplicon. mBio. 2021;12:e03656–20.
Google Scholar
Martijn J, Lind AE, Schön ME, Spiertz I, Juzokaite L, Bunikis I, et al. Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon. Environ Microbiol. 2019;21:2485–98.
Google Scholar
Okazaki Y, Fujinaga S, Salcher MM, Callieri C, Tanaka A, Kohzu A, et al. Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing. Microbiome. 2021;9:24.
Google Scholar
Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, et al. Telomere-to-telomere assembly of a complete human X chromosome. Nature. 2020;585:79–84.
Google Scholar
Wenger AM, Peluso P, Rowell WJ, Chang P-C, Hall RJ, Concepcion GT, et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol. 2019;37:1155–62.
Google Scholar
Matsuo Y, Komiya S, Yasumizu Y, Yasuoka Y, Mizushima K, Takagi T, et al. Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinIONTM nanopore sequencing confers species-level resolution. BMC Microbiol. 2021;21:35.
Google Scholar
Calus ST, Ijaz UZ, Pinto AJ. NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform. Gigascience. 2018;7:1–16.
Callahan BJ, Wong J, Heiner C, Oh S, Theriot CM, Gulati AS, et al. High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Res. 2019;47:e103–e103.
Google Scholar
Benítez-Páez A, Portune KJ, Sanz Y. Species-level resolution of 16S rRNA gene amplicons sequenced through the MinIONTM portable nanopore sequencer. Gigascience. 2016;5:4.
Google Scholar
Kumar V, Vollbrecht T, Chernyshev M, Mohan S, Hanst B, Bavafa N, et al. Long-read amplicon denoising. Nucleic Acids Res. 2019;47:e104–e104.
Google Scholar
Wick RR, Judd LM, Holt KE. Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome Biol. 2019;20:129.
Google Scholar
Lane D. 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds). Nucleic acid techniques in bacterial systematics. 1991. Wiley, New York, pp 115–75.
Miller CS, Handley KM, Wrighton KC, Frischkorn KR, Thomas BC, Banfield JF. Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments. PLoS One. 2013;8:e56018–e56018.
Google Scholar
Hunt DE, Klepac-Ceraj V, Acinas SG, Gautier C, Bertilsson S, Polz MF. Evaluation of 23S rRNA PCR primers for use in phylogenetic studies of bacterial diversity. Appl Environ Microbiol. 2006;72:2221–5.
Google Scholar
Volden R, Palmer T, Byrne A, Cole C, Schmitz RJ, Green RE, et al. Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA. Proc Natl Acad Sci. 2018;115:9726 LP–9731.
Gibson DG, Young L, Chuang R-Y, Venter JC, Hutchison CA, Smith HO. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods. 2009;6:343–5.
Google Scholar
Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584.
Google Scholar
Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform. 2009;23:205–11.
Google Scholar
Morisse P, Marchet C, Limasset A, Lecroq T, Lefebvre A. Scalable long read self-correction and assembly polishing with multiple sequence alignment. Sci Rep. 2021;11:761.
Google Scholar
Do CB, Mahabhashyam MSP, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res. 2005;15:330–40.
Google Scholar
dos Santos HRM, Argolo CS, Argôlo-Filho RC, Loguercio LL. A 16S rDNA PCR-based theoretical to actual delta approach on culturable mock communities revealed severe losses of diversity information. BMC Microbiol. 2019;19:74.
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Google Scholar
Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28:3150–2.
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Google Scholar
Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–3.
Google Scholar
Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47:W256–W259.
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 LP–5120.
Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res. 2014;42:D633–42.
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–D596.
Google Scholar
de Oliveira Martins L, Page AJ, Mather AE, Charles IG. Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing. NAR Genom Bioinform. 2019;2:lqz016–lqz016.
Google Scholar
Olesen SW, Duvallet C, Alm EJ. dbOTU3: a new implementation of distribution-based OTU calling. PLoS One. 2017;12:e0176335–e0176335.
Google Scholar
Fichot EB, Norman RS. Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform. Microbiome. 2013;1:10.
Google Scholar
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