what’s in a name? For microorganisms, it seems a lot.
Prokaryotes are single-celled microorganisms – bacteria is an example – found in abundance throughout the world. They are found in oceans, in soil, in harsh environments such as hot springs, and even alongside and inside other living things including humans.
In short, they are ubiquitous, and scientists around the world are working to classify and communicate them. But here’s the problem: most of them don’t have a name.
Less than 0.2% of known prokaryotes have been officially named because current regulations – outlined in the International Code of Nomenclature for Prokaryotes (ICNP) – require new species to be grown in the laboratory and distributed free of charge as pure, viable cultures in groups. Basically, to name it, you need to have several physical samples to prove it.
in Article published on September 19 in the magazine Nature Microbiologya team of scientists has introduced a new system, SeqCode, and a corresponding scoring gate that can help microbiologists effectively classify and communicate the vast number of identified and uncultivated prokaryotes.
“Our goal is to standardize field and laboratory studies in microbiology and respond to important recent advances in environmental genomics by providing a pathway for naming the majority of identified and not formally named prokaryotes,” said the UNLV microbiologist. Brian Hedlund, lead author of the paper and lead collaborator on the development of SeqCode. “SeqCode must serve the community by promoting high standards of genome quality, good naming practices, and a well-ordered database.”
Nearly 850 scientists representing multiple disciplines from more than 40 countries participated in a series of NSF-funded online workshops in 2021 to develop the new SeqCode, which uses genome sequence data for both cultured and uncultivated prokaryotes as the basis for its naming.
Since the 2000s, scientists studying prokaryotes in environments around the world have used environmental genomics techniques to sample and study them, and hundreds of thousands of genome sequences are available in public databases. The community participating in the workshops, organized by Hedlund and colleague Anna-Louise Reysenbach of Portland State University, overwhelmingly supported the development of an alternative to ICNP that would accept DNA sequencing data and ultimately improve resources for researchers.
“The key pieces were set for the orderly expansion of prokaryotic methodologies to the entire prokaryotic tree of life,” said William B. Whitman, author of SeqCode and a microbiologist at the University of Georgia. “This expansion will serve research and the broader community by providing a common language for all prokaryotes that are systematically organized and supported by data-rich genomic datasets and associated metadata.”
To qualify for inclusion in SeqCode, genomes must meet stringent scientific criteria for quality, stability and open data sharing. Although not yet universally accepted, SeqCode is essentially consistent with well-established international principles for naming other organisms, including plants and animals.
“Any organism with a high-quality genome sequence – from a pure culture or not – can be named under SeqCode,” Hedlund said. “We will also automatically accept all names formed under ICNP. I expect SeqCode will be used over time more frequently than ICNP.”
Creating clarity in the midst of chaos
The authors argue that one of the primary goals of the new system is to reverse the trend in the field where “unstructured” nouns are used in the literature out of necessity. This can lead to errors that increase the likelihood of renaming later, making it difficult for scientists to review and compare data and communicate effectively. On the contrary, the authors argue that SeqCode “includes the principles of findability, accessibility, interoperability, and reuse.”
Hudlund cited chlamydia and related organisms as an example. Since these organisms cannot be cultivated, stored or distributed as pure cultures, they cannot currently be officially named.
“It can be very confusing for clinicians not to have valid names for newly discovered chlamydia,” Hedlund says. “There is a risk that these names will be poorly indexed, which could stifle outbreak tracking and communication between scientists, clinicians and the public.”
Although the intended goal is to create clarity and synergy with accepted criteria for naming, this step is not without controversy.
SeqCode follows an earlier attempt by scientists to modify the ICNP to allow non-cultivated prokaryotes to be named based on the presence of a DNA sequence that would serve as a guide (or ‘type’) for the organism – as opposed to ICNP rules that now require culture into two permanent sets.
In 2020, a team led by Desert Research Institute biologist Alison Murray published a paper, also in English Nature Microbiology, which was co-authored or endorsed by nearly 120 scientists representing 22 countries calling for action on proposed modifications to the ICNP to accept DNA sequences as a species or to take an alternative route. However, the proposed modifications were rejected by the International Committee on Prokaryotic Methodologies, the group responsible for regulating the naming of prokaryotes.
“It is clear that the global community of scientists is ready to change a paradigm in how prokaryotes are named — to include the breadth of prokaryotic life,” Murray said. Modern genomic techniques can decompose the genomes of uncultured organisms with the high degree of accuracy necessary to ensure the safety and stability of the field of microbiology. Naming these taxa is a way to communicate their existence and evolutionary history and to predict their physiological capabilities. “
The setback of 2020 led to a redoubling of efforts among the growing cadre of scientists and, ultimately, the “alternative path” that led to the formation of SeqCode.
“Many people came to the table to share their views, energy and skills to make this happen,” Hedlund said. “The response from our workshops from scientists around the world has been amazing and helped verify why it is time for a formal change in how prokaryotes are named.”
Tension still exists among some scientists, who argue that not much can be known about uncultivated prokaryotes than those that can be grown and manipulated in the lab as pure cultures. In addition, nuances in the processing and interpretation of DNA sequencing data can lead to erroneous conclusions, a point which Hedlund claims is also true in studies of pure cultures.
The authors say that this new system is not intended to discourage conventional prokaryotic farming, but instead is designed by the scientific community to improve communication across microbial sciences.
“We view ‘SeqCode v.1.0’ as a necessary first step towards a standardized system of nomenclature to communicate the full diversity of prokaryotes and will collaborate with the community towards realizing this vision,” the authors wrote.
Reference: Hedlund BP, Chuvochina M, Hugenholtz P, et al. SeqCode: prokaryotes naming code described from sequencing data. nat microbiol. 2022: 1-7. dui: 10.1038 / s41564-022-01214-9
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