Taxonomic Approaches for Uncultivated Prokaryotes

Abstract

The International Code of Nomenclature of Prokaryotes (ICNP) has identified nearly 99% of bacteria and archaea as uncultivated taxa, which lack taxonomically stable names. ICNP has determined and reframed or refined microbial taxonomy rules based on recommendations from the International Committee on Systematics of Prokaryotes (ICSP). With advances in sequencing technology and bioinformatics tools, the 16S rRNA gene was established as an evolutionary marker for distinguishing bacteria and archaea, with genomes emerging as a superior option. If an argument is correct, such as viruses being named correctly, why can’t bacteria and archaea? “The uncultivated are uncultivated simply because they have never been sustained as an axenic culture, but that does not mean they will not be in the future.” Unidentified fossils were also given authentic names and taxonomic descriptions despite the lack of a life form. Revised rules have helped Candidatus taxa get a provisional category, but their notion of uncultured taxa has continued. Unlike fossils, retrieving the entire genome of an uncultivated environment suggests that these bizarre creatures are still alive there. This book chapter discusses various debates and opinions of taxonomists on naming uncultivated species based on genome sequences obtained through SAGs and MAGs. The use of new tools and development rules for the taxonomy of uncultivated species has been discussed. Moreover, the discussion will highlight how the SeqCode provides a stable and unifying taxonomic framework for naming taxa with the backup of genomic information.