Genomics throws species definition in question for microbes

phenotypically characterized) were revealed.

"Much of this new knowledge was incorporated into species descriptions, but difficulties in classification persisted and novel issues arose," says Roberts. "Conflicts exist between phenotypic and phylogenetic information, the means for classifying non-cultured microbes are limited under the current paradigm, and microbial species do not always demonstrate the phenotypic or genetic cohesiveness expected of them. For these reasons and others it has become clear that the species classification framework in use today is not capable of fully portraying and organizing microbial diversity."

The report contains an in-depth review of the myriad issues and conflicts involved in the classification of microbes in the post-genomic era, including a discussion on the definition of the term "species." It ends with a set of specific recommendations including, but not limited to:

  • The establishment of a subcommittee within the International Committee on Systematics of Prokaryotes to consider a paradigm shift in the species definition.

  • The need for more thorough study of the mechanisms of speciation before a more meaningful and practical species theory can be developed.

  • The need for more comprehensive and systematic data to uncover whether microorganisms are organized into robust, definable, biologically meaningful clusters that adhere to the concept of species.

  • The acquisition of draft-quality genome sequences for all type strains to help advance the integration of genomic information into our understanding of microbial diversity and enable researchers to map phenotypes to genomes.


Contact: Jim Sliwa
American Society for Microbiology

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