A new way to name bacteria: 300-year-old system modified for scientific advances

About 300 years ago the Swedish botanist Carl Linnaeus secured his place in scientific history when he developed what is known as the binomial system.

The year was 1737 and, due to the huge variety of plants and animals collected by naturalist explorers in different parts of the world, Linnaeus saw the need to develop a logical system to classify and group this material in a systematic way.

It is a system that has stood the test of time – its original formula is still in use.

The naming convention applies to all biological organisms: plants, animals, and bacteria. Each species gets a name consisting of two parts. The genus name is similar to a surname; All species sharing this name are closely related.

The second name is unique to each species within the genus. This combination creates a unique name for any described organism. Well-known examples include Homo sapiens (modern humans) and Escherichia coli (bacteria).

One of the main advantages of assigning universally accepted specific names is that it helps people, and especially scientists, to communicate clearly about a specific organism, regardless of language or geographic barriers.

Another boon is that unique names tie together all available information on a species. It also helps scientists understand the shared characteristics and relationships between organisms.

Naming decisions are not made in a vacuum. Although ideas about what species are and how to identify them have evolved over the past 300 years, the naming system proposed by Linnaeus remained unchanged.

There are “rule books” for naming organisms, commonly referred to as “codes”. There are different codes for naming animals, plants, algae and fungi, viruses and bacteria.

The Botanical Code, which initially also dealt with bacteria, was first developed in 1867 and is revised every six years during the International Botanical Congress. The bacterial code was first published as a separate document in 1947 and was updated this year by the International Committee on Systematics of Prokaryotes.

But the existing code was not enough to deal with advances in technology that have changed the way prokaryotes are studied. Therefore, a new, supplementary code is introduced.

a stable system

If the description of a new species meets all the requirements set out in the regulations in the relevant code, the name will be valid – made permanent.

Each new species is also associated with type material: something concrete to compare to other individuals. This type can also be represented by museum or herbarium examples, living cultures or drawings.

One of the main advantages of assigning universally accepted specific names is that it helps people, and especially scientists, to communicate clearly about a specific organism regardless of language or geographic barrier. (Photo: Pixabay)

But this system does not work well for prokaryotes. These single-celled organisms, which do not have a nucleus, are commonly known as bacteria (although they also include archaea, a group of microscopic organisms similar to but distinct from bacteria).

Prokaryotes are named under the International Code of Nomenclature for Prokaryotes.

Unlike the naming rule books of other disciplines, this code is strict about type material: only pure cultures of bacteria, available from collections in two different countries, count as type material. But there is a problem: Most bacteria still cannot be grown in pure culture, let alone in Petri dishes in the laboratory.

This meant that he could not be named under the code.

A new initiative, SeqCode, will change the game by allowing DNA sequencing data to serve as type. I was one of many biologists from around the world involved in creating SeqCode and I believe this to be a great achievement.

A formal and stable naming system for all bacteria will help science unlock the hidden potential of the planet’s biodiversity and understand their role in ecosystem functioning.

It will also help scientists communicate their findings to one another – perhaps a major step toward identifying the next generation of antibiotics or cancer treatments.

genome sequencing

It is not known how many prokaryotic species there are – there could be millions or even trillions. But so far only about 18,000 have been given permanent (valid) names.

The growing ubiquity of genome sequencing is an opportunity to change that. Instead of developing a prokaryotic species in a laboratory and describing its characteristics, biologists can now directly sequence the organisms’ DNA from an environmental sample to obtain a complete or near complete genome.

The genome is the bacterium’s DNA blueprint that encodes all the functions that the organism will be able to perform.

The sequence data is stable enough and can be used to identify other members belonging to the same species.

In 2018 an international group of bacterial taxonomists and ecologists participated in a workshop in the US, funded by the US National Science Foundation, to discuss the future of bacterial taxonomy.

Attendees recognized that genome sequencing was a good, scientifically sound way to give permanent names to many prokaryotes. This idea was supported by many other microbiologists around the world.

However, the proposal to change the existing code to allow genome sequences as types was not accepted by the International Committee on Systematics of Prokaryotes. With support from the International Society for Microbial Ecology, some of the meeting attendees began discussing other possibilities.

The idea of ​​an entirely different code emerged for naming genomically described prokaryotes. Extensive consultations followed and, in September 2022, the SeqCode – or, to give it its full name, the code of naming prokaryotes described from sequence data – was launched.

It does not replace existing code. Bacteria can be named under the bacterial code even when pure cultures are available.

It is possible that, in the coming years, similar adjustments – or new codes may be made – to the nomenclature of other genomically described microbes, such as yeasts and other fungi.

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