Main menu

Pages

Microbiologists propose a new DNA-based naming system for microorganisms.chemistry

featured image

A new system for naming specific microorganisms promises to streamline the process and alleviate the backlog created by the thousands of species discovered by DNA analysis in recent years.In a paper published today at natural microbiologyresearchers describe SeqCode, a protocol that allows for the first time to name newly discovered bacteria and other prokaryotes based solely on their DNA sequences.

“I think we need SeqCode or something similar in microbiology today because we rely so overwhelmingly on genomic data to analyze microbes.” Microbiologist Edward Moore of the University of Gothenburg says he is not yet ready to accept this particular identification system. The protocol outlined in the Prokaryotic Nomenclature Convention (ICNP) had to be followed. As part of the process, researchers must successfully grow bacterial species, or other prokaryotic organisms called archaea, in the laboratory and submit “type” cultures, live or frozen samples of the microbes. I have. , in at least two world repositories. Descriptions published in scientific journals are also required and must be approved by the International Committee on Prokaryotic Phylogenetics (ICSP), which governs ICNP.

However, with the rise of environmental sequencing and metagenomics, all DNA in air, water, animal gut, or other samples from the environment is sequenced and compared to DNA in existing databases to identify which organism. gives insight into whether there is There is an exponential increase in the DNA sequences of microorganisms that do not belong to any known prokaryotes. Sometimes researchers are able to piece together entire genomes, but often there are some fragments that may be missing.An estimated 5000 microorganisms, identifiable only by their DNA, Awaiting culture and further characterization attempts. The question of what to call these new additives is “increasingly difficult,” says her Gemma Reguera, a microbiologist at Michigan State University and editor-in-chief of the American Society for Microbiology (ASM). Applied and Environmental Microbiology journal.

The team behind SeqCode developed SeqCode in response to some of these issues. William Whitman, a microbiologist at the University of Georgia who led the development of SeqCode, explains that “we needed something simpler” than the ICNP protocol. A researcher who has deposited and published his DNA sequence of a possible new prokaryote submits an application through the SeqCode website. No culturing required. The system automatically checks to make sure the sequence is unique by looking at the existing database. SeqCode also requires that proposed names follow certain guidelines. For example, being reported in scientific publications (proponents should include citations) and following standardized naming procedures with proper use of Latin.

Whitman’s first proposal was to accept DNA sequences as part of the ICSP naming protocol in 2015. In 2020, the idea was put to a vote and he was rejected 3-1 by the microbiology community. His development of SeqCode as a separate protocol was a response to that vote.

Several microbiologists have already started using SeqCode.Jeremy Dosworth, a geomicrobiologist at California State University, San Bernardino, tentatively named it Wolframiraptor gerlachensis There are several more species he plans to enter from his group’s research, with archaeons from hot springs that rely on tungsten for survival. W. Gerakensis Laboratories prevent the pure samples required for culture collections before they get their traditional name, rather than per se.

However, it remains to be seen if SeqCode will take hold. Bacteriologist Ian Sutcliffe The University of Northumbria, who also contributed to the development of alternatives. Some microbiologists refuse to accept genomes as sufficient evidence for the existence of species. This is because the organism has not been physically identified and cultivated in a laboratory. “Newly discovered but uncultured microbes are just hypothetical microbes,” says Moore.

Moore acknowledges the need to incorporate the boom in DNA-based bacterial species discovery into the field, Due to the work involved, we do not believe it is necessary to assign full Latin-derived names to thousands of microorganisms. He prefers numerical classification systems instead.

For now, the old and new naming systems run side-by-side, so microbiologists can use either one, but Whitman hopes that eventually they will merge into one. is.Moore didn’t see it Because “the rules of ICNP and the rules of SeqCode contradict each other”.

Reguera says she and other ASM journal editors will need to evaluate SeqCode further to decide whether and how to use it. Personally, she is sold. “I’d love to try it,” she says, hoping many microbial ecologists will. “Time will tell if the wider community will take advantage of her SeqCode.”

Comments