Amann RI, Ludwig W, Schleifer KH. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 1995;59(1):143–69.
CAS
PubMed
PubMed Central
Google Scholar
Head I, Saunders J, Pickup R. Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms. Microb Ecol. 1998;35(1):1–21.
Article
CAS
PubMed
Google Scholar
Rappe MS, Giovannoni SJ. The uncultured microbial majority. Annu Rev Microbiol. 2003;57:369–94. https://doi.org/10.1146/annurev.micro.57.030502.090759.
Article
CAS
PubMed
Google Scholar
Stewart EJ. Growing unculturable bacteria. J Bacteriol. 2012;194(16):4151–60. https://doi.org/10.1128/JB.00345-12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci U S A. 1977;74(11):5088–90. https://doi.org/10.1073/pnas.74.11.5088.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schmidt TM, Delong EF, Pace NR. Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. J Bacteriol. 1991;173(14):4371–8. https://doi.org/10.1128/jb.173.14.4371-4378.1991.
Article
CAS
PubMed
PubMed Central
Google Scholar
Simon C, Daniel R. Metagenomic analyses: past and future trends. Appl Environ Microbiol. 2011;77(4):1153–61. https://doi.org/10.1128/AEM.02345-10.
Article
CAS
PubMed
Google Scholar
Goodwin S, Mcpherson JD, Mccombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 2016;17:333–51. https://doi.org/10.1038/nrg.2016.49.
Article
CAS
PubMed
Google Scholar
Bru D, Martin-Laurent F, Philippot L. Quantification of the detrimental effect of a single primer-template mismatch by real-time PCR using the 16S rRNA gene as an example. Appl Environ Microbiol. 2008;74(5):1660–3. https://doi.org/10.1128/AEM.02403-07.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mao D-P, Zhou Q, Chen C-Y, Quan Z-X. Coverage evaluation of universal bacterial primers using the metagenomic datasets. BMC Microbiol. 2012;12:66. https://doi.org/10.1186/1471-2180-12-66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Eloe-Fadrosh EA, Ivanova NN, Woyke T, Kyrpides NC. Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. Nat Microbiol. 2016;1:15032. https://doi.org/10.1038/nmicrobiol.2015.32.
Article
CAS
PubMed
Google Scholar
Marcy Y, Ouverney C, Bik EM, Losekann T, Ivanova N, Martin HG, et al. Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci U S A. 2007;104(29):11889–94. https://doi.org/10.1073/pnas.0704662104.
Article
CAS
PubMed
PubMed Central
Google Scholar
Brown CT, Hug LA, Thomas BC, Sharon I, Castelle CJ, Singh A, et al. Unusual biology across a group comprising more than 15% of domain Bacteria. Nature. 2015;523(7559):208–11. https://doi.org/10.1038/nature14486.
Article
CAS
PubMed
Google Scholar
Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun. 2016;7:13219. https://doi.org/10.1038/ncomms13219.
Article
CAS
PubMed
PubMed Central
Google Scholar
Spang A, Caceres EF, Ettema TJG. Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life. Science. 2017;357:eaaf3883. https://doi.org/10.1126/science.aaf3883.
Article
CAS
PubMed
Google Scholar
Spang A, Saw JH, Jorgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJ. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature. 2015;521(7551):173–9. https://doi.org/10.1038/nature14447.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Backstrom D, Juzokaite L, Vancaester E, et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature. 2017;541(7637):353–8. https://doi.org/10.1038/nature21031.
Article
CAS
PubMed
Google Scholar
Cai M, Liu Y, Yin X, Zhou Z, Friedrich MW, Richter-Heitmann T, et al. Highly diverse Asgard archaea participate in organic matter degradation in coastal sediments. BioRxiv. 2019:858530. https://doi.org/10.1101/858530.
Seitz KW, Dombrowski N, Eme L, Spang A, Lombard J, Sieber JR, et al. Asgard archaea capable of anaerobic hydrocarbon cycling. Nat Commun. 2019;10(1):1822. https://doi.org/10.1038/s41467-019-09364-x.
Article
CAS
PubMed
PubMed Central
Google Scholar
Da Cunha V, Gaia M, Gadelle D, Nasir A, Forterre P. Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes. PLoS Genet. 2017;13(6):e1006810. https://doi.org/10.1371/journal.pgen.1006810.
Article
CAS
PubMed
PubMed Central
Google Scholar
Spang A, Eme L, Saw JH, Caceres EF, Zaremba-Niedzwiedzka K, Guy L, et al. Asgard archaea are the closest prokaryotic relatives of eukaryotes. PLoS Genet. 2018;14(3):e1007080. https://doi.org/10.1371/journal.pgen.1007080.
Article
CAS
PubMed
PubMed Central
Google Scholar
Spang A, Stairs CW, Dombrowski N, Eme L, Lombard J, Caceres EF, et al. Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism. Nat Microbiol. 2019;4:1138–48. https://doi.org/10.1038/s41564-019-0406-9.
Article
CAS
PubMed
Google Scholar
Da Cunha V, Gaia M, Nasir A, Forterre P. Asgard archaea do not close the debate about the universal tree of life topology. PLoS Genet. 2018;14(3):e1007215. https://doi.org/10.1371/journal.pgen.1007215.
Article
CAS
PubMed
PubMed Central
Google Scholar
Burns JA, Pittis AA, Kim E. Gene-based predictive models of trophic modes suggest Asgard archaea are not phagocytotic. Nat Ecol Evol. 2018;2(4):697–704. https://doi.org/10.1038/s41559-018-0477-7.
Article
PubMed
Google Scholar
Imachi H, Nobu MK, Nakahara N, Morono Y, Ogawara M, Takaki Y, et al. Isolation of an archaeon at the prokaryote-eukaryote interface. Nature. 2020. https://doi.org/10.1038/s41586-019-1916-6.
Yan YW, Jiang QY, Wang JG, Zhu T, Zou B, Qiu QF, et al. Microbial communities and diversities in mudflat sediments analyzed using a modified metatranscriptomic method. Front Microbiol. 2018;9:93. https://doi.org/10.3389/fmicb.2018.00093.
Article
PubMed
PubMed Central
Google Scholar
Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet GA, et al. Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets. Antonie Van Leeuwenhoek. 2011;100(3):471–5. https://doi.org/10.1007/s10482-011-9598-6.
Article
PubMed
Google Scholar
Karst SM, Dueholm MS, Mcilroy SJ, Kirkegaard RH, Nielsen PH, Albertsen M. Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias. Nat Biotechnol. 2018;36(2):190–5. https://doi.org/10.1038/nbt.4045.
Article
CAS
PubMed
Google Scholar
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41(1):e1. https://doi.org/10.1093/nar/gks808.
Article
CAS
PubMed
Google Scholar
Yarza P, Yilmaz P, Pruesse E, Glockner FO, Ludwig W, Schleifer KH, et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol. 2014;12(9):635–45. https://doi.org/10.1038/nrmicro3330.
Article
CAS
PubMed
Google Scholar
Peplies J, Kottmann R, Ludwig W, Glockner FO. A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes. Syst Appl Microbiol. 2008;31(4):251–7. https://doi.org/10.1016/j.syapm.2008.08.003.
Article
CAS
PubMed
Google Scholar
Youssef N, Sheik CS, Krumholz LR, Najar FZ, Roe BA, Elshahed MS. Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys. Appl Environ Microbiol. 2009;75(16):5227–36. https://doi.org/10.1128/AEM.00592-09.
Article
CAS
PubMed
PubMed Central
Google Scholar
Youssef N, Steidley BL, Elshahed MS. Novel high-rank phylogenetic lineages within a sulfur spring (Zodletone spring, Oklahoma), revealed using a combined pyrosequencing-sanger approach. Appl Environ Microbiol. 2012;78(8):2677–88. https://doi.org/10.1128/AEM.00002-12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wear EK, Wilbanks EG, Nelson CE, Carlson CA. Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton. Environ Microbiol. 2018;20(8):2709–26. https://doi.org/10.1111/1462-2920.14091.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zou B, Li J, Zhou Q, Quan ZX. MIPE: a metagenome-based community structure explorer and SSU primer evaluation tool. PLoS One. 2017;12(3):e0174609. https://doi.org/10.1371/journal.pone.0174609.
Article
CAS
PubMed
PubMed Central
Google Scholar
Galand PE, Casamayor EO, Kirchman DL, Lovejoy C. Ecology of the rare microbial biosphere of the Arctic Ocean. Proc Natl Acad Sci U S A. 2009;106(52):22427–32. https://doi.org/10.1073/pnas.0908284106.
Article
PubMed
PubMed Central
Google Scholar
Lynch MDJ, Neufeld JD. Ecology and exploration of the rare biosphere. Nat Rev Microbial. 2015;13(4):217–29. https://doi.org/10.1038/nrmicro3400.
Article
CAS
Google Scholar
Kendall MM, Wardlaw GD, Tang CF, Bonin AS, Liu Y, Valentine DL. Diversity of Archaea in marine sediments from Skan Bay, Alaska, including cultivated methanogens, and description of Methanogenium boonei sp. nov. Appl Environ Microbiol. 2007;73(2):407–14. https://doi.org/10.1128/AEM.01154-06.
Hoshino T, Inagaki F. A comparative study of microbial diversity and community structure in marine sediments using poly(a) tailing and reverse transcription-PCR. Front Microbiol. 2013;4:160. https://doi.org/10.3389/fmicb.2013.00160.
Article
PubMed
PubMed Central
Google Scholar
Garg SG, Kapust N, Lin W, Tria FDK, Nelson-Sathi S, Gould SB. Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled genomes. BioRxiv. 2019;731091. https://doi.org/10.1101/731091.
Liu Y, Zhou Z, Pan J, Baker BJ, Gu JD, Li M. Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota. ISME J. 2018;12(4):1021–31. https://doi.org/10.1038/s41396-018-0060-x.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cai M, Liu Y, Zhou Z, Yang Y, Pan J, Gu J-D, et al. Asgard archaea are diverse, ubiquitous, and transcriptionally active microbes. BioRxiv. 2018;374165. https://doi.org/10.1101/374165.
Seitz KW, Lazar CS, Hinrichs KU, Teske AP, Baker BJ. Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction. ISME J. 2016;10(7):1696–705. https://doi.org/10.1038/ismej.2015.233.
Article
CAS
PubMed
PubMed Central
Google Scholar
Guo J, Cole JR, Zhang Q, Brown CT, Tiedje JM. Microbial community analysis with ribosomal gene fragments from shotgun metagenomes. Appl Environ Microbiol. 2016;82(1):157–66. https://doi.org/10.1128/AEM.02772-15.
Article
CAS
PubMed
Google Scholar
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, 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. https://doi.org/10.1128/AEM.01541-09.
Article
CAS
PubMed
PubMed Central
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:D590–6. https://doi.org/10.1093/nar/gks1219.
Article
CAS
PubMed
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26(19):2460–1. https://doi.org/10.1093/bioinformatics/btq461.
Article
CAS
PubMed
Google Scholar
Juretschko S, Timmermann G, Schmid M, Schleifer KH, Pommerening-Roser A, Koops HP, et al. Combined molecular and conventional analyses of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira-like bacteria as dominant populations. Appl Environ Microbiol. 1998;64(8):3042–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Delong EF. Archaea in coastal marine environments. Proc Natl Acad Sci U S A. 1992;89(12):5685–9. https://doi.org/10.1073/pnas.89.12.5685.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics. 2012;13:134. https://doi.org/10.1186/1471-2105-13-134.
Article
CAS
PubMed
PubMed Central
Google Scholar
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. https://doi.org/10.1093/nar/gkt1244.
Article
CAS
PubMed
Google Scholar
Baker GC, Smith JJ, Cowan DA. Review and re-analysis of domain-specific 16S primers. J Microbiol Methods. 2003;55(3):541–55. https://doi.org/10.1016/j.mimet.2003.08.009.
Article
CAS
PubMed
Google Scholar
Fantini E, Gianese G, Giuliano G, Fiore A. Bacterial metabarcoding by 16S rRNA gene ion torrent amplicon sequencing. Methods Mol Biol. 2015;1231:77–90. https://doi.org/10.1007/978-1-4939-1720-4_5.
Article
CAS
PubMed
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(5):335–6. https://doi.org/10.1038/nmeth.f.303.
Article
CAS
PubMed
PubMed Central
Google Scholar
Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36(10):996–1004. https://doi.org/10.1038/nbt.4229.
Article
CAS
PubMed
Google Scholar
Pruesse E, Peplies J, Glockner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics. 2012;28(14):1823–9. https://doi.org/10.1093/bioinformatics/bts252.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28(10):2731–9. https://doi.org/10.1093/molbev/msr121.
Article
CAS
PubMed
PubMed Central
Google Scholar
Letunic I, Bork P. Interactive tree of life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47(W1):W242–5. https://doi.org/10.1093/nar/gkz239.
Article
Google Scholar