Quantifying Strain Variability in Natural Bacterial Populations

Researchers led by Kostas Konstantinidis from the Georgia Institute of Technology developed a novel approach to categorize bacteria into distinct species and strains, addressing a long-standing challenge in microbiology. Their findings, published in Nature Communications and mBio, provide a more accurate method for identifying and classifying bacteria, crucial for various fields. 

The scientific community relies on names and labels to effectively categorize and understand the world's various organisms, allowing for their identification, study, and regulation. However, when it comes to bacteria, there has always been a lack of a dependable approach to systematically organize them into distinct species and strains. This poses a significant challenge considering that bacteria constitute approximately 75% of all living species on Earth, making them one of the most abundant life forms.

The researchers embarked on a mission to tackle this obstacle by exploring inherent divisions in bacteria. 

Their ultimate objective was to establish a scientifically sound approach for categorizing bacteria into distinct species and strains. To achieve this, the researchers relied on the data to guide their investigation.

While there is a working definition for species and strains, this is far from widely accepted in the scientific community. This is because those classifications are based on human 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.”

Kostas Konstantinidis, Richard C. Tucker Professor, School of Civil and Environmental Engineering, Georgia Institute of Technology

Developing a comprehensive organizing system has proven challenging due to various factors, with a key aspect being the allocation of attention and the reasons behind it. Typically, bacteria that receive more scientific focus tend to be categorized in a more specific manner. For instance, bacteria housing toxic strains have been extensively researched due to their links to diseases and overall health.

This emphasis on distinguishing harmful strains from benign ones has been crucial. Nevertheless, recent findings have indicated that classifying bacteria based on toxicity alone may not be entirely dependable.

Konstantinidis added, “Despite the obvious, cornerstone importance of the concepts of species and strains for microbiology, these remain, nonetheless, ill-defined and confusing.”

The team of researchers gathered bacteria from two salterns located in Spain. Salterns are constructed facilities where seawater is evaporated to produce salt for human consumption.

These salterns provide a suitable habitat for various microorganisms and serve as excellent sites for studying bacteria in their natural surroundings. This research is crucial for comprehending the diversity within bacterial populations, as these organisms frequently undergo genetic modifications when subjected to laboratory conditions.

The researchers collected and analyzed 138 random isolates of Salinibacter ruber bacteria from the salterns. To pinpoint natural variations in genetic diversity, they conducted a comparison of the isolates using the average nucleotide identity (ANI) metric, a concept that Konstantinidis pioneered in his early career. ANI serves as a reliable indicator of genetic relatedness between different genomes and is commonly employed in the study of relationships among microorganisms, viruses, and even animals. For example, the ANI value between humans and chimpanzees is approximately 98.7%.

The team’s previous observations were substantiated by the analysis, which revealed the existence of microbial species that could be accurately characterized using ANI. It was determined that bacteria belonging to the same species exhibited genetic similarity ranging from 96% to 100% on the ANI scale while displaying less than 85% relatedness with members of different species.

The data unveiled an inherent disparity in ANI values at approximately 99.5% ANI within the Salinibacter rubber species, which could aid in distinguishing the species among its different strains.

In a related study published in mBio, the primary journal of the American Society for Microbiology, the researchers analyzed around 300 more bacterial species using 18,000 genomes that had been newly sequenced and were accessible in public databases. They noted comparable diversity trends in over 95% of the species.

Konstantinidis stated, “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.”

The research conducted by the team is anticipated to capture the attention of various professionals engaged in the field of bacteria, encompassing evolutionary biologists, taxonomists, ecologists, environmental engineers, clinicians, bioinformaticians, regulatory agencies, and more. To ensure easy accessibility and utilization by the scientific and regulatory communities, the research can be accessed online via Konstantinos’ website and GitHub.

Konstantinidis concluded, “We hope that these communities will embrace the new results and methodologies for the more robust and reliable identification of species and strains they offer, compared to the current practice.”