Page path:

The Who's Who of Bacteria: A Reliable Way to Define Species and Strains

Mar 11, 2024

Scientists take a leap towards estimating the number of strains that make up a natural bacterial population

What’s in a name? A lot, actually.

For the scientific community, names and labels help organize the world’s organisms so they can be identified and studied. But for bacteria, there has never been a reliable method to cohesively organize them into species and strains. It’s a problem, because bacteria are one of the most prevalent life forms, making up roughly 75% of all living species on Earth.

An international research team sought to overcome this challenge, which has long plagued scientists who study bacteria. The study represents a collaborative effort involving Rudolf Amann from the Max Planck Institute for Marine Microbiology (Bremen, Germany), Ramon Rosselló-Móra from IMEDEA (Mallorca, Spain), and Kostas Konstantinidis from the Georgia Tech Institute (Atlanta, US). The results of this research, now published in the journal Nature Communications and first-authored by Tomeu Viver, who was a member of the Max Planck Institute for Marine Microbiology during the last two years, investigates natural divisions in bacteria with a goal of determining a scientifically viable method for organizing them into species and strains. To do this, the researchers let the data show them the way.

A photo of the saltern site in Spain where a significant portion of the research was done. A saltern is used to produce salt for human consumption and is a natural environment for Salinibacter ruber bacterium. (© Mercedes Urdiain/Marine Microbiology Group (MMG) of the IMEDEA)

“While there is a working definition for species and strains, this is far from widely accepted in the scientific community,” Konstantinidis said. “This is because those classifications are based on humans’ standards that do not necessarily translate well to the patterns we see in the natural environment. If we were to classify primates using the same standards that are used to classify E. coli, then all primates — from lemurs to humans to chimpanzees — would belong to a single species.”

The research team collected bacteria from two salterns in Spain. Salterns are built structures in which seawater evaporates to form salt for consumption. They harbor diverse communities of microorganisms and are ideal locations to study bacteria in their natural environment. This is important for understanding diversity in populations because bacteria often undergo genetic changes when exposed in lab environments.

The team recovered and sequenced 138 random isolates of Salinibacter ruber bacteria from these salterns. To identify natural gaps in genetic diversity, the researchers then compared the isolates against themselves using a measurement known as average nucleotide identity (ANI) — a concept Konstantinidis developed early in his career. ANI is a robust measure of relatedness between any two genomes and is used to study relatedness among microorganisms and viruses, as well as animals. For instance, the ANI between humans and chimpanzees is about 98.7%.

The analysis confirmed the team’s previous observations that microbial species do exist and could be reliably described using ANI. They found that members of the same species of bacteria showed genetic relatedness typically ranging from 96 to 100% on the ANI scale, and generally less than 85% relatedness with members of other species.

The data revealed a natural gap in ANI values around 99.5% ANI within the Salinibacter ruber species that could be used to differentiate the species into its various strains. In a companion paper published in mBio, the flagship journal of the American Society for Microbiology, the team examined about 300 additional bacterial species based on 18,000 genomes that had been recently sequenced and become available in public databases. They observed similar diversity patterns in more than 95% of the species.

“We think this work expands the molecular toolbox for accurately describing important units of diversity at the species level and within species, and we believe it will benefit future microdiversity studies across clinical and environmental settings,” Konstantinidis said.

Ori­ginal pub­lic­a­tion

Viver, T., Conrad, R.E., Rodriguez-R, L.M. et al. Towards estimating the number of strains that make up a natural bacterial population. Nat Commun 15, 544 (2024).


Par­ti­cip­at­ing in­sti­tu­tions

  • Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
  • Max Planck Institute for Marine Microbiology, Bremen, Germany
  • Georgia Institute of Technology, Atlanta, GA, USA
  • Universität of Innsbruck, Innsbruck, Austria
  • Universidad de Las Palmas de Gran Canaria, Canary Islands, Spain
  • University of Pretoria, Pretoria, South Africa
  • University of the Balearic Islands, Palma, Spain

Please dir­ect your quer­ies to:

Head of Press & Communications

Press Office

Dr. Fanni Aspetsberger

MPI for Marine Microbiology
Celsiusstr. 1
D-28359 Bremen




+49 421 2028-9470

Dr. Fanni Aspetsberger
Back to Top