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Microbiologists suggest new DNA-based naming system for microbes | Science


A brand new system for naming sure microbes guarantees to streamline the method and spotlight a backlog created by the 1000’s of species uncovered by DNA analyzes in recent times. In a paper revealed at this time in Nature Microbiologyresearchers describe SeqCode, a protocol that enables, for the primary time, the naming of newly found micro organism and different prokaryotes primarily based solely on their DNA sequence.

“I do assume the SeqCode, or one thing prefer it, is critical for microbiology at this time, as a result of overwhelming dependence now on genomic knowledge for analyzing microorganisms,” says Edward Moore, a microbiologist on the College of Gothenburg—however he is nonetheless not able to embrace this explicit identification system. Till now, microbiologists looking for acceptance {that a} seemingly novel single-cell microbe was actual had needed to comply with the protocol outlined within the Worldwide Code of Nomenclature of Prokaryotes (ICNP). As a part of the method, researchers should achieve rising the species of micro organism, or different prokaryotes referred to as archaea, within the lab and submit a “sort” tradition, a dwelling or frozen pattern of the microbe that might function a reference of its identification , to no less than two world’s repositories. A printed description in a scientific journal can also be required and have to be accepted by the Worldwide Committee on Systematics of Prokaryotes (ICSP), which administers the ICNP.

Nonetheless, with the rise of environmental sequencing and metagenomics, wherein all of the DNA in a pattern from the air, water, an animal’s intestine, or different setting is sequenced and in contrast with DNA in current databases to supply insights into what organisms are current, there’s been an exponential improve in microbial DNA sequences belonging to no recognized prokaryote; typically researchers can piece collectively a complete genome however usually there are a couple of items presumably lacking. An estimated 5000 microbes identifiable solely by their DNA at the moment are awaiting makes an attempt to tradition them and additional characterization. The issue of what to name these new additions “is changing into more and more tough,” says Gemma Reguera, a microbiologist at Michigan State College who’s the editor-in-chief for the American Society for Microbiology’s (ASM’s) Utilized and Environmental Microbiology journal.

The workforce behind SeqCode developed it as a response to a few of these points. “We wanted one thing simpler” than the ICNP protocol, explains William Whitman, a microbiologist on the College of Georgia who spearheaded the event of SeqCode. Researchers who’ve deposited and revealed the DNA sequence of a attainable new prokaryote file an utility by the SeqCode web site, no cultures required. The system will routinely examine to verify the sequence is exclusive by going by current databases. SeqCode may even require that the proposed identify follows sure tips—reminiscent of being reported in a scientific publication (proposers should embody a quotation) and following standardized naming procedures that use Latin appropriately.

Whitman’s first proposal was to have DNA sequences be accepted as a part of the ICSP naming protocol in 2015. In 2020, the concept was put to a vote and rejected three to at least one by the microbiology neighborhood. SeqCode’s improvement as a separate protocol was a response to that vote.

Already, a couple of microbiologists have begun to make use of SeqCode. Jeremy Dodsworth, a geomicrobiologist at California State College, San Bernardino, has tentatively bestowed the identify Wolframiiraptor gerlachensis on an archaeon from sizzling springs that depends on tungsten to outlive and has a number of extra species from his group’s analysis he plans to enter. He and his colleagues have been in a position to develop W. gerlachensis within the lab however not by itself, stopping the pure pattern wanted for the tradition assortment earlier than it might get a conventional identify.

Nevertheless it’s nonetheless unclear whether or not SeqCode will take maintain, says Iain Sutcliffe, a bacteriologist at Northumbria College who additionally helped develop the choice. Some microbiologists refuse to just accept a genome as ample proof of a species’ existence as a result of the organism isn’t bodily recognized and grown in a laboratory. “Newly found however not cultured microbes are merely hypothetical microbes,” Moore says.

Though Moore acknowledges the necessity to incorporate the increase in DNA-based discovery of bacterial species into the sphere, he would not assume it’s a necessity—or sensible—to assign full Latin-derived names to the 1000’s of microbes due to the work concerned. He favors a numerical classification system as an alternative.

For now, the previous and new naming techniques will run in parallel so microbiologists can use both one, however Whitman hopes finally they’ll merge into one. Moore would not see that taking place, as “the principles of the ICNP and the principles of the SeqCode battle with one another,” he says.

Reguera says she and different journal editors at ASM should consider SeqCode additional to determine whether or not and tips on how to use it. Personally, she’s bought. “I’m keen to present it a attempt,” and he or she expects so will many microbial ecologists. Sutcliffe, although hopeful, isn’t positive what’s going to occur. “Solely time will inform as as to whether the broader neighborhood will make use of SeqCode.”

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