Divorcing Strain Classification from Species Names

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• 作者：David A. Baltrus¹ ; ^{baltrus@email.arizona.edu" class="auth_mail" title="E-mail the corresponding author}
• 关键词：bacterial taxonomy ; bacterial classification ; high-throughput genomics ; whole-genome sequencing ; LINS ; Pseudomonas syringae
• 刊名：Trends in Microbiology
• 出版年：2016
• 出版时间：June 2016
• 年：2016
• 卷：24
• 期：6
• 页码：431-439
• 全文大小：1461 K

文摘

Confusion about strain classification and nomenclature permeates modern microbiology. Although taxonomists have traditionally acted as gatekeepers of order, the numbers of, and speed at which, new strains are identified has outpaced the opportunity for professional classification for many lineages. Furthermore, the growth of bioinformatics and database-fueled investigations have placed metadata curation in the hands of researchers with little taxonomic experience. Here I describe practical challenges facing modern microbial taxonomy, provide an overview of complexities of classification for environmentally ubiquitous taxa like Pseudomonas syringae, and emphasize that classification can be independent of nomenclature. A move toward implementation of relational classification schemes based on inherent properties of whole genomes could provide sorely needed continuity in how strains are referenced across manuscripts and data sets.