MicroBinfie Podcast, 69 Background to bacterial taxonomy - MicroBinfie Podcast
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MicroBinfie Podcast, 69 Background to bacterial taxonomy

  • Dec 16, 2021

There has been a lot of discussion about bacterial taxonomy recently announced regarding phyla, and this revealed a lot of misconceptions around taxonomy in general. Today we discuss the background to bacterial taxonomy with: Professor Phil Hugenholtz, Professor Iain Sutcliffe and Professor Mark Pallen.

Selective bibliography as pdf: https:// github.com/MicroBinfie/MicroBinfie.github.io/raw/45db8eb57d73217644907 3065dbdacc88a288fe9/assets/Taxonomy_Selective_bibliography.pdf

Selective bibliography

Linnaeus and classification

  • https://en.wikipedia.org/wiki/10th_edition_of_Systema_Naturae
  • W. T. Stearn The Background of Linnaeus’s Contributions to the Nomenclature and Methods of Systematic Biology Systematic Zoology, 8 (1), Mar., 1959), pp. 4-22 http://www.jstor.org/stable/2411603
  • Daniel F. Austin. The Nuance and Wit of Carolus Linnaeus The Palmetto 13(4), 1993 https://www.fnps.org/assets/pdf/palmetto/v13i4p8austin.pdf

Darwin and evolution

  • http://darwin-online.org.uk/Variorum/Introduction.html
  • Kevin Padian Charles Darwin’s Views of Classification in Theory and Practice Syst. Biol. 48(2):352–364, 1999 https://doi.org/10.1080/106351599260337

Hennig and cladistics

  • http://aracnologia.macn.gov.ar/st/biblio/Hennig%201966%20Phylogenetic%20Systematics.pdf
  • Hennig, Willi (1975), “‘Cladistic analysis or cladistic classification?’: a reply to Ernst Mayr” (PDF), Systematic Zoology, 24 (2): 244–256, https://doi.org/10.2307/2412765
  • Chi-Chun Ho, Susanna K. P. Lau, Patrick C. Y. Woo. Romance of the three domains: how cladistics transformed the classification of cellular organisms Protein Cell 2013, 4(9): 664–676 https://doi.org/10.1007/s13238-013-3050-9

Woese, sequences and domains

  • Woese CR. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221-71. https://doi.org/10.1128/mr.51.2.221-271.1987
  • Problems with “procaryote”. Pace NR. J Bacteriol. 2009 Apr;191(7):2008-10; discussion 2011. https://doi.org/10.1128/JB.01224-08

Hugenholtz and GTDB

  • Novel division level bacterial diversity in a Yellowstone hot spring. Hugenholtz P, Pitulle C, Hershberger KL, Pace NR. J Bacteriol. 1998 Jan;180(2):366-76. https://doi.org/10.1128/JB.180.2.366-376.1998
  • A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, Hugenholtz P.Nat Biotechnol. 2018 Nov;36(10):996-1004. https://doi.org/10.1038/nbt.4229
  • Genome Taxonomy Database: https://gtdb.ecogenomic.org/
  • GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH.Bioinformatics. 2019 Nov 15;36(6):1925-7. https://doi.org/10.1093/bioinformatics/btz848
  • A complete domain-to-species taxonomy for Bacteria and Archaea. Parks DH, Chuvochina M, Chaumeil PA, Rinke C, Mussig AJ, Hugenholtz P.Nat Biotechnol. 2020 Sep;38(9):1079-1086. https://doi.org/10.1038/s41587-020-0501-8
  • GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil PA, Hugenholtz P.Nucleic Acids Res. 2021 Sep 14:gkab776. https://doi.org/10.1093/nar/gkab776
  • Reclassification of Shigella species as later heterotypic synonyms of Escherichia coli in the Genome Taxonomy DatabaseDonovan H. Parks, Maria Chuvochina, Peter R. Reeves, Scott A. Beatson, Philip Hugenholtz https://doi.org/10.1101/2021.09.22.461432

Sutcliffe and modernizing bacterial taxonomy

  • Challenging the anthropocentric emphasis on phenotypic testing in prokaryotic species descriptions: rip it up and start again. Sutcliffe IC. Front Genet. 2015 Jun 17;6:218. https://doi.org/10.3389/fgene.2015.00218
  • Roadmap for naming uncultivated Archaea and Bacteria. Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL.Nat Microbiol. 2020 Aug;5(8):987-994. https://doi.org/10.1038/s41564-020-0733-x
  • Addressing the sublime scale of the microbial world: reconciling an appreciation of microbial diversity with the need to describe species. Sutcliffe IC, Rosselló-Móra R, Trujillo ME.New Microbes New Infect. 2021 Aug 13;43:100931. https://doi.org/10.1016/j.nmni.2021.100931
  • Out with the old and in with the new: time to rethink twentieth century chemotaxonomic practices in bacterial taxonomy. Vandamme P, Sutcliffe I.Int J Syst Evol Microbiol. 2021 Nov;71(11).https://doi.org/10.1099/ijsem.0.005127

Pallen and modernizing bacterial nomenclature

  • Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture.Gilroy R, Ravi A, Getino M, Pursley I, Horton DL, Alikhan NF, Baker D, Gharbi K, Hall N, Watson M, Adriaenssens EM, Foster-Nyarko E, Jarju S, Secka A, Antonio M, Oren A, Chaudhuri RR, La Ragione R, Hildebrand F, Pallen MJ. PeerJ. 2021 Apr 6;9:e10941. https://10.7717/peerj.10941
  • Bacterial nomenclature in the era of genomics M. J. Pallen New Microbe and New Infect 2021; 44: 100942 https://doi.org/10.1016/j.nmni.2021.100942
  • The Next Million Names for Archaea and Bacteria. Pallen MJ, Telatin A, Oren A. Trends Microbiol. 2021 Apr;29(4):289-298. https://doi.org/10.1016/j.tim.2020.10.009
  • Naming the Unnamed: Over 45,000 Candidatus Names for Unnamed Archaea and Bacteria in the Genome Taxonomy Database M Pallen, NF Alikhan. Preprints. https://doi.org/10.20944/preprints202111.0557.v1