New method for bacteria classification includes all of the strains

Bacteria are one of the most abundant life forms on Earth, comprising roughly 75% of all species. Despite being so common, all the bacteria types are not adequately classified. As a result, Dr Kostas Konstantinidis from the School of Civil and Environmental Engineering at the Georgia Institute of Technology has tackled the longstanding issue by introducing a reliable method for classification of bacteria. This method provides a fresh perspective on bacterial diversity by considering all the bacterial species and strains.

Why the classification of bacteria matters

According to the researchers, existing classification systems often do not reflect how bacteria actually behave. “While there is a working definition for species and strains, this is far from widely accepted in the scientific community,” explained Dr. Konstantinidis. “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.”

Creating a good system for organizing bacteria involves several challenges. In the past, scientists have mostly focused on bacteria that cause diseases. This has led to a classification system that is biased towards certain features of bacteria. Hence, the traditional way of classifying bacteria is not very reliable anymore..

“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,” noted Dr. Konstantinidis.

Classifying Salinibacter ruber species

To address the current challenges, the researchers developed a new way that can handle the vast bacterial diversity. Initially, they collected samples from special salty pools in Spain, called salterns, where seawater undergoes evaporation to produce salt. These unique environments harbor diverse communities of microorganisms, making them ideal for studying bacterial diversity.

Central to their methodology was the utilization of average nucleotide identity (ANI), a concept pioneered by Dr. Konstantinidis. ANI serves as a powerful tool for measuring genetic similarity between bacterial genomes. By applying ANI analysis to the collected isolates, the researchers could discern subtle genetic variations within bacterial populations.

The researchers successfully identified distinct genetic diversity gaps among individual bacteria belonging to the Salinibacter ruber species. These gaps served as natural boundaries, enabling the precise classification of bacteria into distinct species and strains.

Genetic similarity and variation

The experts discovered that bacteria within the same species are very similar genetically, with a score of 96 to 100% on the ANI scale. This means they share almost all their genes. On the other hand, bacteria from different species are much less similar, with less than 85% shared genes. This confirms that different species are truly distinct.

The researchers also looked at about 300 other species of bacteria by examining the genes of 18,000 bacteria. They found similar patterns of variation across all the diverse species. Over 95% of the bacteria studied had similar amounts of genetic variation. This finding confirms that the results likely apply to many different types of bacteria.

Significance of bacteria classification

The result of the study isn’t just a new classification method – it’s an expansion of the tools scientists can employ to study bacteria. The impact is broad, reaching evolutionary biologists, taxonomists, ecologists, and even engineers who work on the environment.

Clinicians treating patients, people who analyze biological data (bioinformaticians), and agencies that set rules (regulatory agencies) will all benefit as well.

Ultimately, this kind of collaboration will drive success in microbiology and other related fields. Furthermore, this can lead to advancements in research, healthcare, and taking better care of the environment.

The study is published in the journal Nature Communications.

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