In Greek, the word eudora means “she of good gifts”. It was the name given to various mythological sea nymphs, patrons of, among other things, sailing and bountiful catches. Now, Eudora also refers to a group of newly discovered bacteria from the ocean that promise similar rewards. A recent study reveals that Candidatus Eudoremicrobium holds the genetic blueprints for producing an array of natural products with potential applications in medicine and biotechnology. And they’re likely not the only ones. Numerous microbes yet to be characterized across the vast ocean could harbor similar treasures. The key to finding them lies in applying the tools of microbiomics.
Microbiomics refers to the study of microbiomes using tools like DNA sequencing to reconstruct the genomes of microbes directly from the wild. This approach is becoming popular among scientists whose job is to mine the natural world for medically or technologically important compounds, such as antibiotics. One big reason why is access.
Microbiomics allows entry into the inner workings of potentially valuable microbes that for one reason or another have not yet been cultivated in the lab.
That’s how researchers discovered Eudoremicrobium. These microbes belong to a newly described family of bacteria with the potential for synthesizing the most diverse array of natural products in the open ocean today.
To probe for microbes like these, the team gathered more than 1,000 publicly available datasets from samples spanning 215 sites across the ocean and more than 5 kilometers deep. Using advanced bioinformatics and supercomputer systems, they reconstructed over 26,000 genomes belonging to bacteria and archaea. Combining those genomes with another 8,500 gathered from single cells and lab-cultivated microbes yielded the Ocean Microbiomics Database.
The OMD captures 40 to 60% of all tested metagenomic data for the open ocean, expanding the known genomic universe of earth’s largest ecosystem two- to three-fold.
Among these thousands of genomes, the team identified nearly 40,000 biosynthetic gene clusters, groups of two or more genes that code for potentially useful compounds. After grouping these gene clusters into 8,000 families, the researchers found that the majority of them were previously unknown. The compounds they encode serve a variety of functions, including protection against other organisms and nutrient absorption. And some could be useful for drug development or other applications.
Biosynthetic gene clusters detected from Eudoremicrobium were linked to the production of at least two promising chains of amino acids. The shorter one was found to inhibit neutrophil elastase, an enzyme that, if left unchecked, can cause severe tissue damage. The longer one was found to undergo a large number of unusual chemical modifications—some of which are extremely difficult to reproduce in the lab.
And these discoveries could just be the beginning. Microbiomics is likely to continue to reveal new and valuable microorganisms across unexplored regions of the planet. For researchers mining the ocean for prized natural products, Eudoremicrobium, just like their mythological namesake, could be a signal of treasures yet to come.
To access the Ocean Microbiomics Database online, visit microbiomics.io/ocean.