A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?

Abstract

Taxonomy is often criticized for being too conservative and too slow and having limited relevance because it has not taken into consideration the latest methods and findings. Yet the cumulative work product of its practitioners underpins contemporary microbiology and serves as a principal means of shaping and referencing knowledge. Using methods drawn from the field of exploratory data analysis, this minireview examines the current state of the field as it transitions from a taxonomy based on 16S rRNA gene sequences to one based on whole-genome sequences and tests the validity of some commonly held beliefs.

1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

“…Typically, a type strain has well-characterized taxonomic and phenotypic data, isolation source metadata, and other criteria, as defined by the International Code of Nomenclature of Prokaryotes (ICNP) 10 . As of December 5, 2015, there were 12,981 bacterial and archaeal species with valid, published names, with 650 new type strains added (on average) every year 11,12 . However, despite their importance, the genomes of only 826 type strains were publicly available at the start of this study.…”

Selection of representative genomes for 24,706 bacterial and archaeal species clusters provide a complete genome-based taxonomy

“…This has resulted in large-scale initiatives such as the Genomic Encyclopedia of Bacteria and Archaea (GEBA) producing thousands of isolate genomes assembled from type strains (Kyrpides et al, 2014;Mukherjee et al, 2017) and numerous studies reporting thousands of metagenome-assembled genomes (MAGs) recovered from a diverse range of environments (Parks et al, 2017;Chen et al, 2019;Pasolli et al, 2019). The availability of a large number of genome assemblies provides a wealth of genomic information for taxonomic classification (Konstantinidis and Tiedje, 2005a; Thompson et al, 2015;Garrity, 2016;Hugenholtz et al, 2016) which has been leveraged to reclassify specific bacterial lineages including the Epsilonproteobacteria (Waite et al, 2017), Actinobacteria (Nouioui et al, 2018), and Lactobacillus (Wittouck et al, 2019). We recently made use of this expansion in public genomes to produce the Genome Taxonomy Database (GTDB), a comprehensive genome-based taxonomy with bacterial and archaeal taxa circumscribed on the basis of monophyly and relative evolutionary divergence (Parks et al, 2018).…”

Taxonomy and nomenclature of bacteria with clinical and scientific importance: current concepts for pharmacists and pharmaceutical scientists

“…One of the most important milestones was the launch of the Human Microbiome Project (HMB; the first phase of which was launched in 2007), with the aim of characterize the human gut microbial flora in healthy (physiological) and disease states; the long-term aim of this project was to find causation between human pathologies (e.g., autoimmune disorders, obesity, diabetes, neuropsychiatric disorders, diseases affecting the cardiovascular system) and qualitative/quantitative changes in the microbiome [14][15][16]. Microbial culturomics (a technique allowing for the culturing of previously unculturable bacterial species by reproducing their natural habitats using complex methods, with the aid of matrix-assisted laser desorption-ionization time-of-flight mass spectrometry [MALDI-TOF MS] and whole-genome sequencing [WGS]) has also resulted in the description of a staggering number of novel taxa [17][18][19]. Sequencing technologies also had a significant role in the description of the prokaryotic genetic diversity.…”