Newly Renamed Prokaryote Phyla Cause Uproar

Last month, many microbiologists were surprised to find that the familiar names and nomenclature for the bacteria and archaea they study had been rewritten, seemingly overnight. On December 10, the National Center for Biotechnology Information (NCBI), a collection of biological databases that serves as a reference for researchers, announced that it would be updating how it classifies and names 42 phyla of bacteria and archaea. The names that microbiologists had been using to that point were rendered out of date, creating a disconnect between all previous research and upcoming discoveries.

The actual decision was made earlier—and more gradually than it seemed to some shocked researchers—by the International Committee on Systematics of Prokaryotes (ICSP). The ICSP is an organization of microbiologists and taxonomy experts who maintain the International Code of Nomenclature for Prokaryotes (ICNP), a set of rules dictating how prokaryotic organisms can be named. Until this recent change, the ICNP did not pertain to the rank of phylum, the level of taxonomic organization immediately below kingdom. That left the microbiologists to their own devices, and colloquial names suggested by a given organism’s discoverer took hold.

ICSP chair and Northumbria University microbiologist Iain Sutcliffe tells The Scientist that the exclusion of phyla from the ICNP was a “historical oversight” stemming from a lack of knowledge. Scientists didn’t have the technology to identify or appreciate the immense diversity of prokaryotic life back when the code was first drafted in 1936, Sutcliffe explains. There were so few known prokaryotes at the time that researchers couldn’t justify assigning phyla to microbes at all—the experts organizing taxonomy at the time didn’t know they’d “eventually be able to classify the bacterial world into such huge levels of diversity,” says Sutcliffe. 

“It took us a long time, and it was only with the advent of molecular biology that we got to understand the true scale of the microbial world,” Sutcliffe says.

The change is an attempt to impose order on a vast collection of scientific research fields that, in the absence of official conventions, created a hodgepodge of unofficial phylum names. However, the potential disruption to research has some scientists who felt blindsided by the news up in arms. Shortly after the NCBI announcement, researchers took to Twitter to pick apart the decision, crack jokes, and collectively mourn through memes.

“I’m very attached to not breaking interfaces, which is the effect here,” Newcastle University microbial ecologist Joe Weaver tweeted on December 13, referring to the renaming of the phylum Firmicutes. “Regular naming conventions are great, when used ahead of time. Post-hoc breakages for the sake of ‘regularizing’ ignore human cognitive pitfalls and provide limited benefit.”

Suffix shuffle

With analyses of entire microbial genomes now commonplace, the ICSP decided it was time for its nomenclature to better reflect new genomic discoveries. Some names have remained more accurate than others, but other phylum names are simply outdated, Sutcliffe explains. For example, the phylum previously known as Firmicutes includes organisms that may not be as closely related to one another as initially thought, and will potentially be split up into multiple phyla. These new clades would need new, precise, accurate names, making its renaming particularly “tidy,” Sutcliffe adds. But other phyla have been given drastically different names even without their contents being rearranged or split up; for example, the phylum Tenericutes is now Mycoplasmatota.

The process of updating the code began in 2015, when ICSP scientists published a paper in the International Journal of Systematic and Evolutionary Microbiology, the organization’s official journal, that proposed including phyla in its nomenclature and a system for doing so. Three years later, an expanded team of coauthors made a few slight modifications to the proposed approach. Finally, in February 2021, after what Sutcliffe calls “some huffing and puffing,” the issue was brought to a committee vote and passed 19 to 2. The new phyla nomenclature rules were announced in a June 23 paper. They not only brought phyla under the jurisdiction of the code, but also specified how they can be named. All phyla must now have a Latin name that ends with the suffix “-ota,” and the name of the phylum ought to be adopted from one of the genera within that phylum. For example, the phylum formerly known as Firmicutes was renamed to Bacillota because it contains the genus Bacillus.

At that point, researchers were permitted to submit new names for organisms or taxonomic groups in accordance with the code, Sutcliffe explains. On October 25, microbiologists Aharon Oren and George Garrity published a paper with new names for 42 prokaryotic phyla, which represented the first major attempt to reconcile the names of prokaryotic organisms with the code. Because those names adhere to the new rules, they are now considered the official names for the phyla, which is what prompted NCBI to issue its December announcement that it would be updating its own terminology.

If you ask Sutcliffe, Garrity and Oren are among the best-poised researchers to take on the task of renaming life forms. But University of Nevada, Las Vegas, microbiologist Brian Hedlund tells The Scientist that the two researchers taking it upon themselves to rename such vast swathes of the prokaryotic empire justifiably rubbed some scientists the wrong way—even if he agrees with the ICSP’s decisions.

Garrity, a microbiologist at Michigan State University who’s deeply involved in the process of assigning code-compliant names to prokaryotes, says that the ICSP’s changes are less than alarming. “It’s like dictionary entries,” he tells The Scientist. “How many people get upset about dictionary entries?”

Garrity adds that if scientists “want their names to have value, they have to play by the rules. Don’t complain; learn the rules, and play the game.”

Research upheaval

The names that drew the most ire from researchers who spoke with The Scientist or vented on Twitter were the changes from Firmicutes to Bacillota and from Proteobacteria to Pseudomonadota. These dramatic phyla renamings will “make research a little harder,” University of Tennessee, Knoxville, microbiologist Karen Lloyd tells The Scientist. Other phylum names represent subtler shifts—scientists say they’re less upset about Bacteroidetes becoming Bacteroidota, for example.

In Lloyd’s view, shared by some others in the field, the updates to the code represent a disconnect between the ICSP and countless microbiologists who will now face a period of disruption and discontinuity in their research.

“What we call things doesn’t matter to me,” Lloyd says. “I appreciate that people put thought into this, and I appreciate it’s helpful to have a code when you’re naming things. But all I care about is that things are practical and useful and that we can go forward and study the natural world.”

Lloyd tweeted her frustration that the decision means scientists will have to preserve continuity themselves by doing  “a deep dive on what everything used to be called.”

“I would prefer that whoever the next person is to declares themself the nomenclature god would defer to the names in current use even if they don’t meet the strict linguistic standards of the Code,” Lloyd wrote in another tweet.

The phyla renaming, Lloyd argues, threatens scientists’ ability to do their work by potentially shattering continuity among papers published before, during, and after the transition period microbiologists now find themselves in. “So why are we doing it?” Lloyd asks. “How does it help science?” To her, continuity outweighs standardization.

Other researchers, such as Georgia Tech environmental engineer Ameet Pinto, were also frustrated and confused by the news. Yet Pinto—whose tweet about the update alerted many researchers, Lloyd included, to the changes—was more understanding of the ICSP’s decision.

“My tweet was primarily driven by the inconvenience it is going to cause my own research in terms of getting used to new taxonomies—but this is not new, and if the experts agree that it is essential, then it is a good thing,” Pinto tells The Scientist via Twitter message.

But Lloyd argues that the risks of a massive nomenclature update extend beyond annoyance over increasingly “obscured names.” Microbes that are important to disease research, infrastructure maintenance, food safety, and other real-world applications now have different names than what’s written in the vast bodies of work describing them, potentially causing safety hazards, she says.

“As far as I’m aware, there’s not a lot of controversy about [the now-outdated] names,” Lloyd says. She suggests that it would have been better to leave them alone, given how the change will impact “vast, vast amounts of literature in really disparate fields that don’t talk to each other.”

Despite the differences among these fields, “we all use the same phyla names,” she adds. “I would argue that it is a quite good, organic, grassroots code that’s developed.”

Of course, the ICSP isn’t tinkering around to disrupt research and make life difficult. Several microbiology researchers involved in nomenclature tell The Scientist that they believe the near-term headaches occasioned by the change are worth the long-term benefits of a more unified code.

Standardizing Prokaryota

As biotechnology has improved, so too has scientists’ understanding of the natural world and its microorganisms. That calls for changes in how we classify and refer to those organisms, Hedlund says.

“My biggest reaction is that this is a good thing,” Hedlund said. “We shouldn’t expect taxonomy and names to be stable. If they were stable, it means that we understand everything—and we just don’t.”

Similarly, Sutcliffe says that the code is—and always was—a living document.

See “Researchers Propose Automating the Naming of Novel Microbes

Standardizing the code will make education and research communications simpler in the long run, Hedlund says, even though he is facing the same issues as other scientists grappling with the new names. However, he does have reservations on some of the specifics. He argues that the “-ota” suffix of a new phylum is more important for standardization than whatever comes before it, so he suggests that a name along the lines of Proteobacterota may have been a viable compromise—at least enough so to be considered and debated—to provide continuity with the name Proteobacteria.

On the other hand, Hedlund suggests that there’s no technical reason to keep the name Proteobacteria around; it’s simply what the experts decided to use in the past.

“The future is much longer than the past in microbiology,” Hedlund says. The question the research community needs to ask itself, he adds, is “in 100 years, in 1,000 years, do we want to be using these names for groups that would no longer make any sense in a future student or researcher’s eyes?” Hedlund adds that the criticism circulating on Twitter indicates “that people are either stuck in the present or in the recent past.”

History rhymes

History may offer some clues about what the future of this nomenclature will look like. The ICNP has been overhauled before—many of the names currently being replaced first emerged in the 1980s when the code went through a similar shift, spurred by a similar leap forward in technology.

In the 1980s, scientists learned that 16S rDNA sequences could be used to identify and differentiate bacteria at the level of individual species. The subsequent switch from chemotaxic analysis—that is, grouping organisms based on physical structures or metabolic capabilities—to genetics represented a technological and scientific advance beyond existing classification techniques and taxonomic concepts. It revealed that prior names and classifications were inaccurate, leading to a revision of the nomenclature code, Hedlund explains.

“Once the 16S stuff came in, scientists asked, ‘Should we just keep these names for groups that don’t exist, or should we overhaul it?’ And they overhauled it,” Hedlund says. “To me, that was clearly appropriate. And all the names that people are using now, that people are complaining about [losing], that’s where those names came from.”

Hedlund adds that microbiology now finds itself in a “second revolution,” in which 16S is rendered outdated by the ability to analyze full genomes to better understand how microbes are related. The names that were adopted—unofficially—as scientists made new discoveries through 16S sequencing were sometimes trivial, Garrity explains, and are “not consistent with other parts of the code of nomenclature.” He gives the example of Proteobacteria, which was a novel name not based on the name of a genus within that phylum. 

The future is much longer than the past in microbiology.

—Brian Hedlund, University of Nevada, Las Vegas

Changes in nomenclature are “what happens,” says Sutcliffe. “The science moves on, and it’s like a picture that’s a bit fuzzy coming into better focus.” He adds that, in his experience, “people do get used to it quite quickly.”

Looking forward, Hedlund says, a big question will be whether current genomic analyses hold on to their position as the gold standard for classification or if some new, yet-undiscovered technology will take their place in the distant future.

For now, “the genome, I think, has to be the unit that we use to compare relatedness of organisms,” Hedlund says. “The details of how we do it will get better, but I think what we’re doing now is pretty good.”

During the transition, researchers will have to take some extra steps to accommodate the changes in the papers they’re writing or reviewing. Lloyd suggests that researchers specify which versions of which databases they use in case some aren’t yet using the updated names, and perhaps include lists of the previous names for any organisms they mention. That way, they can bridge the gap between new research and the decades of important work that preceded it.

“Things like this have happened before,” Desert Research Institute molecular ecologist Alison Murray tells The Scientist. “I think it will be a bit of a bother, but when we’re actually writing, we might put both names, which is how it’s been done in the past.” 

“We need a language in which to communicate the diversity of life on earth,” Murray adds, and just as new knowledge forces change, accommodating those changes is “part of the history of science.”

A Code for the Uncultured

Although it’s considered the official naming convention among microbiologists, the International Code of Nomenclature for Prokaryotes (ICNP) does have flaws and gaps that researchers in the field have had to fill in themselves. The biggest gap in the ICNP, aside from the historical exclusion of phyla, stems from the requirements that scientists have to meet in order to officially name a new prokaryote. Under the rules of the code, researchers are required to cultivate pure reference samples of any new prokaryote they wish to name. They must then store samples in at least two publicly accessible culture collections located in different countries so that the research community can obtain subcultures for further study.

That excludes most of the prokaryotic life on earth, University of Tennessee, Knoxville, microbiologist Karen Lloyd says, much of which grows slowly or under such specific conditions that scientists haven’t successfully cultured the organisms.

Expecting scientists to be able to culture the vast diversity of prokaryotic life using known lab techniques is like expecting a fern, an elephant, and a fungus to thrive under identical conditions, Desert Research Institute molecular ecologist Alison Murray says. “We can culture between a tenth of a percent and one percent of [microorganisms],” she explains. “We can’t give them [all] one culture condition and expect them to grow.” Sometimes, researchers can obtain an organism’s genome years or decades before they manage to cultivate it, making the ICNP’s requirement that an organism be cultured all but irrelevant.

The exclusion of uncultured microbes also means that researchers who conduct environmental research in the field rather than in a lab are unable to officially name their discoveries, resulting in a rapid proliferation of unofficial, inconsistent names that scientists have been grappling with for years, according to a recent literature review.

In 2020, a long list of researchers that includes Lloyd and Murray along with University of Nevada, Las Vegas, microbiologist Brian Hedlund and International Committee on Systematics of Prokaryotes (ICSP) chair Iain Sutcliffe published a consensus statement in Nature Microbiology that laid out a path to formally naming and classifying uncultivated prokaryotes. The two options detailed in the paper were inclusion in the ICNP or the creation of a new, parallel code of nomenclature to pick up where the ICNP leaves off.

Shortly thereafter, the ICSP voted to reject a 2016 proposal from University of Georgia microbiologist William Whitman to include uncultivated prokaryotes in the ICNP—Sutcliffe says he was in the vastly outnumbered minority that wanted to include them—forcing the researchers to choose the latter plan. Thus, the SeqCode initiative was born. Research papers defining the SeqCode guidelines are still undergoing peer review, Hedlund says, but the overarching idea is that genomic data, rather than cultivated samples, will form the basis of inclusion in the code of nomenclature. Any new official names added to the ICNP will also be added to SeqCode so that the two systems don’t conflict.

Having a SeqCode that names uncultivated prokaryotes during the years or decades it takes scientists to learn how to cultivate them, Sutcliffe says, will be “very valuable.” He adds that he feels the ideal solution to this “thorny problem that will outlive me” is to arrive at one integrated code.

Meanwhile, Lloyd points out a third system called the Genome Taxonomy Database (GTDB) that defines taxonomy based on a single equation that calculates relative evolutionary distance, or the number of changes in DNA, from one level to another in taxonomic hierarchy. It’s a nice tool, Lloyd says, and an interesting approach to classification, but she adds that she’s not quite ready to adopt it and “throw away” all of the existing concepts of taxonomy from which it departs, since the reliance on a single calculation makes the approach less nuanced than the more comprehensive analyses that inform SeqCode.

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