Microbiologists propose new DNA-based naming system for microbes

2022-09-19

A new system for naming certain microbes promises to streamline the process and relieve a backlog created by the thousands of species uncovered through DNA analyses in recent years. In a paper published today in Nature Microbiology, researchers describe SeqCode, a protocol that allows, for the first time, the naming of newly discovered bacteria and other prokaryotes based only on their DNA sequence.

“I do think the SeqCode, or something like it, is necessary for microbiology today, due to the overwhelming dependence now on genomic data for analyzing microorganisms,” 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 a seemingly novel single-cell microbe was real have had to follow the protocol outlined in the International Code of Nomenclature of Prokaryotes (ICNP). As part of the process, researchers must succeed in growing the species of bacteria, or other prokaryotes called archaea, in the lab and submit a “type” culture, a living or frozen sample of the microbe that would serve as a reference of its identity, to at least two world’s repositories. A published description in a scientific journal is also required and must be accepted by the International Committee on Systematics of Prokaryotes (ICSP), which administers the ICNP.

However, with the rise of environmental sequencing and metagenomics, in which all the DNA in a sample from the air, water, an animal’s gut, or other environment is sequenced and compared with DNA in existing databases to provide insights into what organisms are present, there’s been an exponential increase in microbial DNA sequences belonging to no known prokaryote; sometimes researchers can piece together an entire genome but often there are a few pieces possibly missing. An estimated 5000 microbes identifiable only by their DNA are now awaiting attempts to culture them and further characterization. The problem of what to call these new additions “is becoming increasingly difficult,” says Gemma Reguera, a microbiologist at Michigan State University who is the editor-in-chief for the American Society for Microbiology’s (ASM’s) Applied and Environmental Microbiology journal.

The team behind SeqCode developed it as a response to some of these issues. “We needed something easier” than the ICNP protocol, explains William Whitman, a microbiologist at the University of Georgia who spearheaded the development of SeqCode. Researchers who have deposited and published the DNA sequence of a possible new prokaryote file an application through the SeqCode website, no cultures required. The system will automatically check to make sure the sequence is unique by going through existing databases. SeqCode will also require that the proposed name follows certain guidelines—such as being reported in a scientific publication (proposers must include a citation) and following standardized naming procedures that use Latin appropriately.

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

Already, a few microbiologists have begun to use SeqCode. Jeremy Dodsworth, a geomicrobiologist at California State University, San Bernardino, has tentatively bestowed the name Wolframiiraptor gerlachensis on an archaeon from hot springs that relies on tungsten to survive and has several more species from his group’s research he plans to enter. He and his colleagues have been able to grow W. gerlachensis in the lab but not by itself, preventing the pure sample needed for the culture collection before it could get a traditional name.

But it’s still unclear whether SeqCode will take hold, says Iain Sutcliffe, a bacteriologist at Northumbria University who also helped develop the alternative. Some microbiologists refuse to accept a genome as sufficient evidence of a species’ existence because the organism is not physically identified and grown in a lab. “Newly discovered but not cultured microbes are simply hypothetical microbes,” Moore says.

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

For now, the old and new naming systems will run in parallel so microbiologists can use either one, but Whitman hopes eventually they will merge into one. Moore doesn’t see that happening, as “the rules of the ICNP and the rules of the SeqCode conflict with each other,” he says.

Reguera says she and other journal editors at ASM will have to evaluate SeqCode further to decide whether and how to use it. Personally, she’s sold. “I am eager to give it a try,” and she expects so will many microbial ecologists. Sutcliffe, though hopeful, is not sure what will happen. “Only time will tell as to whether the wider community will make use of SeqCode.”

Science, 19 September 2022
; https://science.org