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A bacterial culture. Photo: Michael Schiffer/Unsplash
On December 10, the National Centre for Biotechnology Information adopted a new system to name the phylum of some prokaryotes.
Some changes don’t follow logic and can be “misleading”, one scientist said. Another called the new system a “monstrosity”.
Microbiology Twitter has been filled with funny memes in response – but nothing about it actually seems to be fun.
Kochi: Some bacteria are getting new names in the system scientists use to classify all living things. And many scientists who study these life-forms are not pleased because it’s a lot of life-forms, a lot of names and, sometimes, more than one way to name them. All in all, it’s a lot of confusion.
On December 10, an online database of the US National Centre for Biotechnology Information (NCBI), which specifies the standard names of all organisms in other public databases, adopted a new system to name the phylum of some prokaryotes.
Phylum? And prokaryotes?
‘Phylum’ is the rank above ‘class’ but below ‘kingdom’ in the biological classification system. For example, the coconut palm belongs to the kingdom Plantae (plants), the phylum Spermatophyta (seed-producing plants) and the class Monocotyledonae (plants that have monocotyledonous seeds). This way, each rank of the classification describes specific characteristics of an organism.
Prokaryotes are organisms whose cells don’t have a nucleus – including bacteria.
The biological classification system. Image: Peter Halasz/Wikimedia Commons, public domain
According to the new system, all phylum names are to be formed by adding the suffix “-ota” to the stem of the prokaryote’s genus, which is the second-from-bottom taxonomic rank. This will change the names of prokaryotes belonging to 42 phyla. And 42 phyla is a large number of prokaryotes.
A blog post by a biotech company explained that changing the names of ‘mainstream’ microbes would mean both the scientific and consumer literatures will have to be updated. Plus microbiology laboratories will have to update their reports and, if some bacteria have medical implications, clinicians will need to educate their staff and update their patients.
In February this year, the two dozen or so members of the International Committee on Systematics of Prokaryotes (ICSP), representing microbiological societies worldwide, voted to bring in this new system. The ICSP oversees the standard names of cultured archaea (primitive prokaryotes that are similar to bacteria) and bacteria.
The new system also states that an organism’s phylum rank will be included with its scientific name in the NCBI database, and that the phylum will be given priority in the scientific literature. Scientific names are currently based on the Linnaean nomenclature system, named for the Swedish taxonomist Carl Linnaeus (1707-1778). This system recognises species as the basic unit – with different species classified according to their genus, family, order, class and phylum.
The ICSP’s decision applies to names that fall under the International Code of Nomenclature of Prokaryotes.
Phylum names changed. So what?
The process of updating names is expected to be a tedious process, but it also has to be thorough or it could cause a lot of confusion later. Then again, the confusion may have already begun.
The names of 42 phyla of prokaryotes will change (for instance, Acidobacteria will become Acidobacteriota) – but some phyla will be more affected than others:
Firmicutes → Bacillota (bacteria that live in the human gut)
Proteobacteria → Pseudomonadota (bacteria such as Escherichia coli known to cause food-poisoning in humans)
Actinobacteria → Actinomycetota (soil-dwelling bacteria crucial for vegetation because they help decompose organic matter)
Bacteroidetes → Bacteroidota (rod-shaped bacteria that live in a variety of environments, including the human gut)
Microbiology Twitter has been filled with funny memes in response – but nothing about it actually seems to be fun. For example, the phylum Actinobacteria includes organisms that were thought to be fungi, German microbial ecologist Bonilla Rosso tweeted on December 13. But they’re not fungi, so inserting the ‘mykes’ in the new phylum name, Actinomycetota, is “a terrible, misleading mistake”.
These phyla – including Firmicutes and Proteobacteria – are some of the oldest, most-studied and abundant organisms on the planet, he noted – implying a great deal of confusion.
One of the more confounding fallouts of the NCBI’s new system is that scientists and microbiologists working with these organisms will have to look up multiple names for the same bacteria in the existing literature for their work.
“All previous research is lost to anyone who doesn’t have the time to do a deep dive on what everything used to be called,” Karen Lloyd, a microbiologist at the University of Tennessee, wrote as part of a series of tweets on December 13. She also called the new names a “monstrosity”.
There’s an even deeper problem.
The International Code of Nomenclature of Prokaryotes – a.k.a. the Code – will only name prokaryotes that scientists have grown, stored and studied in the lab. Another way of saying this is that the Code recognises only lab-cultured specimens as the type material, not the prokaryote’s genome or anything else.
Microbiologists realised they had a naming problem in the 2000s because many branches of the tree of life that the prokaryotes occupied hadn’t even been cultured in the lab. And even if they were cultured, many cultures were unlikely to meet the standards set by the Code. For example, no other species should be present in the culture, the subject species should grow quickly and the cultures should be easily storable.
A phylogenetic tree of Firmicutes, showing the various classes under it. Image: Wikimedia Commons, source of data
The result, Lloyd wrote, is that the Code automatically refuses to name species that coexist near each other, grow too slowly or need to be handled carefully.
Instead, according to her, some scientists have been trying to set up a new code that uses the prokaryotes’ genomes as the type material instead of their cultures.
But there are problems here as well. Many databases store different kinds of genetic information. For example, some have sequences of the slow-evolving 16S RNA gene common among prokaryotes, while others provide sequences of whole genomes. This mismatch is hard to bridge.
The scientist groups that maintain these databases also update them rapidly, without inputs from the right stakeholders, leading to “dangerous mistakes”, in Lloyd’s words. She cited the example of Geobacter, a genus of bacteria that can oxidise organic compounds and metals into carbon dioxide. In 2020, scientists renamed Geobacter to Citrifermentans even though, Lloyd wrote, Geobacter does not ferment citrate.
Was the change even necessary?
Thanks to more teams working on microbiology and obtaining sequences for a diverse array of bacteria and archaea worldwide, we have been finding new prokaryotic species, genera and phyla. Rapidly.
“Microbiology has entered a golden era of discovery,” scientists (including Aharon Oren, a coauthor of the paper listing the new names of the 42 phyla) wrote in an April 2021 paper. According to their assessment, there are over a million names for bacteria and archaea, even as advances in biotechnology – including genome-sequencing – are unearthing more and more information on how similar or different each species is from another.
Naming such a diverse group of organisms in a self-consistent way is hard – even if, sometimes, experts try to make sure they don’t change too much too quickly either.
For example, last year, a small group of scientists broke up the genus Lactobacillus into 25 genera1. The names of 10 of them, including the probiotic Lactobacillus species, began with the letter ‘L’ so the change wouldn’t hit science and industry too hard. They also built a web-based tool to explain the name of each species.
According to Lloyd, and in the same spirit, it is better to use the names we are currently using even if they don’t meet the Code’s strict standards.
At the same time, the prokaryotes are a diverse bunch, so there is an unavoidable trade-off between keeping their existing names and updating them. As Rosso, the microbial ecologist, tweeted, it is something we will have to live with.
Philip Hugenholtz, who studies microbial ecology and evolution at the University of Queensland and is a member of the ICSP, defended the new system as a small price to pay. For example, he tweeted that including the phylum in the Code makes its association with the standard name clearer, and gives phylum names more importance in the scientific literature. And both these changes can “remove potential ambiguity and conflict”.
And for most phyla, this new rule means only “small” tweaks to their names, such as Acidobacteria to Acidobacteriota and Bacteroidetes to Bacteroidota. The only “major exceptions”, in his words, are Proteobacteria, Firmicutes and Actinobacteria – because these names weren’t derived from the name of a genus.
“So in summary, names aren’t changing all the time, and this affects only a tiny, albeit important, number of names…,” he finished. “And exceptions can be made, so Proteobacteria and Firmicutes could stand.”
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