Whither Extensive Genomic-Based Microbial Taxonomic Revision?

摘要: In the study published by Potter et al. in this issue of Clinical Chemistry (1), 103 genomes under auspices either Gardnerella vaginalis or spp. contributed to National Center for Biotechnology Information database were accessed with goal further elucidating subspecies new species designations (termed genomospecies context silico analysis). This genus is one several that can contribute dynamic disease entity bacterial vaginosis. A Canadian group has recently identified differentiating genetic patterns between vaginosis-, aerobic vaginitis-, and Lactobacillus spp.-dominated vaginal microbiomes (2). Intricate characterization novel taxa within may identify target organisms subsequent studies pathogenesis. In lieu traditional DNA-DNA hybridization standard, used 4 modalities analysis whole genome assemblies. These included 2 average nucleotide identity (ANI)3 platforms (3), tetranucleotide frequency (4), amino acid (AAI) (5). The authors a conservative criterion assignment (i.e., concordant results derived from ≥2 characterization). Classifications supported ancillary core genome, accessory metatranscriptome analyses. Using algorithm, report 9 genomospecies—verifying taxonomic designation piotii sp. nov. but suggesting potential conflicts status leopoldii swidsinskii (6). Past literature espoused prokaryotic species-level ANI cutoffs 94% 96% (3). recent publication, Ciufo (7) evaluated threshold identifying 335 which at least 10 GenBank assemblies available alignments above 10% coverage. compared submitted type taxon assembly labeled as (taxonomic agreement) discordant disagreement). comparisons was 97.1%, …