Search for: All records

As the name of the genusPantoea(“of all sorts and sources”) suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genusPantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified. 

Traditional taxonomy provides a hierarchical organization of bacte- ria and archaea across taxonomic ranks from kingdom to subspecies. More recently, bacterial taxonomy has been more robustly quanti- fied using comparisons of sequenced genomes, as in the Genome Taxonomy Database (GTDB), resolving down to genera and species. Such taxonomies have proven useful in many contexts, yet lack the flexibility and resolution of a more fine-grained approach. We apply our Life Identification Number (LIN) approach as a com- mon, quantitative framework to tie existing (and future) bacterial taxonomies together, increase the resolution of genome-based dis- crimination of taxa, and extend taxonomic identification below the species level in a principled way. We utilize our existing concept of a LINgroup as an organizational concept for microorganisms that are closely related by overall genomic similarity, to help resolve some of the confusions and unforeseen negative effects of nomen- clature changes of microbes due to genome-based reclassification. Our results obtained from experimentation demonstrate the value of LINs and LINgroups in mapping between taxonomies, translat- ing between different nomenclatures, and integrating them into a single taxonomic framework. 

Genomics has put prokaryotic rank-based taxonomy on a solid phylogenetic foundation. However, most taxonomic ranks were set long before the advent of DNA sequencing and genomics. In this concept paper, we thus ask the following question: should prokaryotic classification schemes besides the current phylum-to-species ranks be explored, developed, and incorporated into scientific discourse? Could such alternative schemes provide better solutions to the basic need of science and society for which taxonomy was developed, namely, precise and meaningful identification? A neutral genome-similarity based framework is then described that could allow alternative classification schemes to be explored, compared, and translated into each other without having to choose only one as the gold standard. Classification schemes could thus continue to evolve and be selected according to their benefits and based on how well they fulfill the need for prokaryotic identification.