Episode 70: Bacterial Taxonomy: the grand vista is ahead of us

The microbinfie podcast explores the transformative impact of genomics on bacterial taxonomy, featuring expert insights into how modern molecular techniques are revolutionizing our understanding of bacterial classification and evolutionary relationships.

Discussion Highlights

Genomics has significantly altered the framework of bacterial taxonomy by:

1. Refining Phylogenetic Relationships: Genomics allows for more precise phylogenetic trees based on DNA sequences rather than solely on phenotypic characteristics.

2. Discovering New Lineages: The ability to sequence genomes quickly and affordably has led to the discovery of previously unknown bacterial lineages.

3. Clarifying Species Concepts: Genomic data has helped clarify what constitutes a bacterial species, challenging many traditional concepts.

Key Points

1. Genomic Taxonomy Approaches

• Genome Taxonomy Database (GTTB) represents a comprehensive genomic approach to bacterial classification
• Uses 120 single-copy conserved genes for phylogenetic tree construction
• Employs relative evolutionary divergence to assign taxonomic ranks

2. Taxonomic Challenges and Discoveries

• Traditional classification methods are being challenged by molecular techniques
• Examples like Mycoplasma and Candidate Phyla Radiation (CPR) demonstrate complexity of bacterial evolution
• Molecular methods reveal surprising evolutionary relationships

3. Nomenclature and Scientific Adaptation

• Taxonomic frameworks must remain flexible to accommodate new scientific knowledge
• Renaming organisms can be controversial but scientifically necessary
• Rapid technological advances drive continuous taxonomic refinement

Take-Home Messages

• Genomic methods are fundamentally transforming bacterial taxonomy
• Scientific classification must prioritize accurate evolutionary understanding
• Flexibility and openness to change are crucial in taxonomic research

Selective Bibliography

For those interested in exploring the topics discussed in this episode further, here is a curated list of references (care of Mark Pallen) categorized by key figures and themes in bacterial taxonomy:

Linnaeus and classification

• 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. PDF

Darwin and evolution

• Darwin Variorum Introduction
• 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

• Hennig 1966 - Phylogenetic Systematics (PDF)
• Hennig, Willi (1975). 'Cladistic analysis or cladistic classification?': a reply to Ernst Mayr. 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
• Pace NR. Problems with "procaryote". J Bacteriol. 2009 Apr;191(7): 2008-10; discussion 2011. https://doi.org/10.1128/JB.01224-08

Hugenholtz and GTDB

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

Sutcliffe and modernizing bacterial taxonomy

• Sutcliffe IC. Challenging the anthropocentric emphasis on phenotypic testing in prokaryotic species descriptions: rip it up and start again. Front Genet. 2015 Jun 17;6: 218. https://doi.org/10.3389/fgene.2015.00218
• Renner SS. A Return to Linnaeus's Focus on Diagnosis, Not Description: The Use of DNA Characters in the Formal Naming of Species. Syst Biol. 2016 Nov;65(6): 1085-1095. https://doi.org/10.1093/sysbio/syw032
• 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, et al. Roadmap for naming uncultivated Archaea and Bacteria. Nat Microbiol. 2020 Aug;5(8): 987-994. https://doi.org/10.1038/s41564-020-0733-x
• Sutcliffe IC, Rosselló-Móra R, Trujillo ME. Addressing the sublime scale of the microbial world: reconciling an appreciation of microbial diversity with the need to describe species. New Microbes New Infect. 2021 Aug 13;43: 100931. https://doi.org/10.1016/j.nmni.2021.100931
• Vandamme P, Sutcliffe I. Out with the old and in with the new: time to rethink twentieth century chemotaxonomic practices in bacterial taxonomy. Int J Syst Evol Microbiol. 2021 Nov;71(11). https://doi.org/10.1099/ijsem.0.005127

Pallen and modernizing bacterial nomenclature

• 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. Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture. PeerJ. 2021 Apr 6;9: e10941. https://10.7717/peerj.10941
• Pallen MJ. Bacterial nomenclature in the era of genomics. New Microbe and New Infect 2021; 44: 100942. https://doi.org/10.1016/j.nmni.2021.100942
• Pallen MJ, Telatin A, Oren A. The Next Million Names for Archaea and Bacteria. Trends Microbiol. 2021 Apr;29(4): 289-298. https://doi.org/10.1016/j.tim.2020.10.009
• Pallen M, Alikhan NF. Naming the Unnamed: Over 45,000 Candidatus Names for Unnamed Archaea and Bacteria in the Genome Taxonomy Database. Preprints. https://doi.org/10.20944/preprints202111.0557.v1