What's in the name? A lot, actually. For the scientific community, names and labels help organize the world's living beings so that they can be identified, studied, and regulated. But for bacteria, there has never been a reliable way to organize them tightly into species and strains. This is a problem because bacteria are one of the most prevalent life forms, accounting for about 75% of all living species on Earth.
An international team of researchers is trying to overcome this challenge, which has long puzzled scientists studying bacteria. Richard C., School of Civil and Environmental Engineering, Georgia Institute of TechnologyProfessor Kostas Konstantinidis Tucker co-led a study to investigate the nature of bacteria, with the aim of identifying a scientifically feasible way to organize them into species and strains. To do this, the researchers let the data point them in the right direction.
Their study was published in the journal Nature Communications.
While there is a valid definition of species and strains, this is far from being widely accepted in the scientific community," Konstantinidis said. "This is because these classifications are based on human criteria that don't necessarily translate well to the patterns we see in our natural environment.
For example, he said, "If we classify primates using the same criteria as the E. coli classification, then all primates — from lemurs to humans to chimpanzees — belong to one species."
There are many reasons why a comprehensive organizational system is difficult to design, but it often comes down to who gets the most attention and why. More scientific attention often leads to these bacteria becoming more narrow-minded. For example, bacterial species containing toxic strains have been extensively studied for their links to disease and health.
This is due to the need to distinguish harmful strains from harmless strains. However, recent findings have shown that even defining the type of bacteria by toxicity is unreliable.
Despite the obvious cornerstone importance of the concepts of species and strains for microbiology, these concepts remain ill-defined and confusing," says Constantinidas.
The team collected the bacteria from two salterns in Spain. A salt cage is a building structure in which seawater evaporates to form salt for consumption. They have a diverse microbial community and are ideal places to study bacteria in their natural environment. This is important for understanding the diversity of populations, as bacteria often undergo genetic changes when exposed to a laboratory environment.
The team sequenced 138 randomly isolated Salinibacter Ruber bacteria from these salterns. To determine natural gaps in genetic diversity, the researchers then compared the isolates to themselves using a measurement called mean nucleotide identity (ANI) – a concept proposed by Konstantinidis early in his career. ANI is a reliable measure of the correlation between any two genomes and is used to study the correlation between microorganisms and viruses, as well as between animals. For example, the ani between humans and chimpanzees is about 987%。
The analysis confirms the team's previous observation that microbial species do exist and can be reliably described using ANI. They found that members of the same species of bacteria showed a genetic correlation of typically 96% to 100% on the ANI scale, while correlations with members of other species were typically less than 85%.
The data show that in the Salinibacter Ruber species, the ANI value is about 99A natural difference of 5% that can be used to distinguish the species into various strains. In a sister article published in MBIO, the team examined about 300 bacterial species based on 18,000 genomes that were recently sequenced and available in public databases. They observed a similar pattern of diversity in more than 95% of the species.
We believe this work expands the molecular toolbox for accurately characterizing important units of diversity at the species level and within species, which we believe will benefit future microdiversity studies in clinical and environmental settings," Konstantinidis said.
The team hopes that their research will be of interest to any professional working with bacteria, including evolutionary biologists, taxonomists, ecologists, environmental engineers, clinicians, bioinformaticians, regulators, and more. It is available via Konstantinidis and GitHub for easy access and use by the scientific and regulatory community.
We hope that these communities will be receptive to the new results and methods for a more robust and reliable identification of the species and strains they offer compared to the current practice," said Konstantinidice.