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

By on September 19, 2022 0

A new system for naming certain microbes promises to streamline the process and reduce the backlog created by the thousands of species discovered through DNA analysis in recent years. In an article published today in Natural microbiologythe researchers describe SeqCode, a protocol that allows, for the first time, to name newly discovered bacteria and other prokaryotes based solely on their DNA sequence.

“I think SeqCode, or something like that, is needed for microbiology today, because of the overwhelming reliance on genomic data for microorganism analysis,” says Edward Moore, a microbiologist at the University of Gothenburg, but he’s still not ready to embrace this particular identification system. Until now, microbiologists seeking acceptance that an apparently novel single-celled microbe was real had to follow the protocol outlined in the International Code of Nomenclature of Prokaryotes (ICNP). As part of the process, researchers must successfully grow the species of bacteria, or other prokaryotes called archaea, in the lab and submit a “type” culture, a live or frozen sample of the microbe that would serve as a reference of its identity. . , to at least two global benchmarks. A description published in a scientific journal is also required and must be accepted by the International Committee for Systematics of Prokaryotes (ICSP), which administers the ICNP.

However, with the rise of environmental sequencing and metagenomics, in which all DNA in a sample from air, water, an animal’s gut, or other environment is sequenced and compared to DNA in existing databases to provide information on the organisms present, there was an exponential increase in microbial DNA sequences not belonging to any known prokaryotes; Sometimes researchers can piece together an entire genome, but often a few pieces are missing. About 5,000 microbes identifiable only by their DNA now await attempts at culture and further characterization. The problem of what to call these new additions “is getting harder and harder,” says Gemma Reguera, a microbiologist at Michigan State University and editor of the American Society for Microbiology (ASM). Applied and environmental microbiology log.

The team behind SeqCode developed it in response to some of these issues. “We needed something simpler” than the ICNP protocol, says William Whitman, a microbiologist at the University of Georgia who led the development of SeqCode. Researchers who have deposited and published the DNA sequence of a possible new prokaryote apply via the SeqCode website, no culture required. The system will automatically verify that the sequence is unique by browsing existing databases. SeqCode will also require the proposed name to follow certain guidelines, such as being reported in a scientific publication (nominators must include a citation) and following standardized naming procedures that use Latin appropriately.

Whitman’s first proposal was to have DNA sequences accepted under the ICSP naming protocol in 2015. In 2020, the idea was put to a vote and voted down three to one by the microbiology community. The development of SeqCode as a separate protocol was a response to this vote.

Already, a few microbiologists have started using SeqCode. Jeremy Dodsworth, a geomicrobiologist at California State University, San Bernardino, tentatively gave the name Wolframiiraptor gerlachensis on a hot springs archaeon that depends on tungsten to survive and has several other species from his group’s research, he plans to enter. He and his colleagues were able to grow W. gerlachensis in the laboratory but not by itself, preventing the pure sample needed for culture collection before it can gain a traditional name.

But it’s still unclear if SeqCode will take root, says Iain Sutcliffe, bacteriologist at Northumbria University which also helped develop the alternative. Some microbiologists refuse to accept a genome as sufficient proof of the existence of a species because the organism is not physically identified and cultured in the laboratory. “Newly discovered but uncultured microbes are just hypothetical microbes,” Moore says.

Although Moore recognizes the need to incorporate the DNA-based bacterial species discovery boom into the field, he don’t think it’s necessary – or practical – to assign full Latin-derived names to the thousands of microbes because of the work involved. Instead, he favors a numerical classification system.

For now, the old and new naming system will work in parallel so microbiologists can use one or the other, but Whitman hopes they will eventually merge into one. Moore doesn’t see that happens, because “the ICNP rules and the SeqCode rules conflict with each other,” he says.

Reguera says she and other ASM journal editors will need to evaluate SeqCode further to decide if and how to use it. Personally, she is sold. “I can’t wait to try it,” and she expects many microbial ecologists to do so. Sutcliffe, though hopeful, isn’t sure what will happen next. “Only time will tell if the wider community will use SeqCode.”