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Genomics throws species definition in question for microbes

Until a decade ago, scientists categorized microorganisms almost exclusively by their physical characteristics: how they looked, what they ate, and the by-products they produced. With the advent of genomic sequencing and genetic analysis in the 1990s, our understanding of the relationships between different microorganisms fundamentally changed. In light of this new knowledge, what exactly is the definition of a microbial species, and how should microbiologists be categorizing microorganisms? These questions are the focus of a new report released by the American Academy of Microbiology (AAM) entitled Reconciling Microbial Systematics and Genomics.

"It is clear that the current system for designating microbial species is somewhat functional, but inadequate in many ways. It is unclear whether this system should be replaced or renovated," says Richard Roberts of New England Biolabs, one of the authors of the report.

The report is the result of a colloquium convened by the AAM in September 2006. Participants with expertise in microbial taxonomy, systematics, ecology, physiology and other areas described the history of microbial taxonomy, the state of the field today, and how work in the field should proceed in the future. The report is a record of their comments and recommendations.

In the late 1800s, in order to make sense of the vast diversity of microbiological organisms, microbial taxonomists developed a system of placing microorganisms into categories in which each organism was granted a "genus" and "species" designation. At the time, physical (or phenotypic) properties were the only means of describing microorganisms, so the system was based on measurable and observable characteristics of the organisms, not genetic traits.

In the late 20th century, molecular biology uncovered the genetic relationships between microorganisms, and some of the secrets of microbes that had yet to be cultured in the lab (and hence phenoty
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Source:American Society for Microbiology


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