A team of researchers from the Institute of Microbiology at ETH Zurich analysed DNA samples from aquatic bacteria to create a database with over 30,000 genomes, according to a study published in Nature. The authors believe this is the best way to find natural products in previously underexplored microbial groups and environments.
The oceans are full of different life forms, from blue whales to microorganisms. These microorganisms may be tiny, but they are responsible for ensuring that the entire ecosystem works appropriately. This includes producing about 50% of the oxygen in the atmosphere and removing substantial amounts of CO2 to help fight climate change.
Despite this vital role, research into these microorganisms is minimal. To cover this gap, a group of researchers from the Institute of Microbiology at ETH Zurich analysed publicly available DNA from over 1000 water samples collected at different depths from various locations around the world. The aim was to find new natural products made by these bacteria.
Thanks to new technologies — including environmental DNA analysis (eDNA) — it’s now easier to search for new species in the water. What is still harder to achieve is to analyse what chemical compounds these microorganisms produce that may be beneficial for the environment and potentially for us. The authors believe that the ocean microbiome harbours significant potential for natural products that can be valuable for humans, such as new antibiotics, for example.
Using data sequences from the original projects, the team managed to reconstruct entire bacterial genomes to create a database with 35,000 genomes. This database was then used to search for new microbial species and any promising bio-synthetic gene clusters (BGCs). A BGC is a group of genes that are involved in a particular pathway for a natural product.
From this analysis, the researchers found over 40,000 potentially useful BGCs, as well as previously undiscovered bacterial species and species that were only known to exist in terrestrial environments. In fact, the team found and named a new family of bacteria — Eudoremicrobiaceae — and demonstrated how these are widespread in certain areas and can represent up to 6% of all bacteria present in some areas.
“The relatives in the ocean possess what for bacteria is a giant genome. Fully decrypting it was technically challenging because the organisms had not been cultivated before,” said Shinichi Sunagawa, Professor of Microbiome Research. As it turned out, the newly identified bacteria belong to the group of microorganisms with the highest BGC diversity of all the samples examined. “As things stand, they are the most biosynthetically diverse family in the oceanic water column.”
The team analysed two Eudoremicrobiaceae BGCs in detail. One referred to a gene cluster with enzymes that have never been found in a bacterial BGC before, and the other was for a bioactive natural product that blocks a proteolytic enzyme. Ideally, the team would like to analyse all of the BGCs they found, but this is simply not viable for a database of 40,000 potential natural products. “However, our database has plenty to offer, and it’s accessible to all researchers who wish to use it,” Sunagawa says.
In the future, Sunagawa wants to continue investigating unresolved questions regarding the evolution and ecology of aquatic microorganisms, including how these organisms spread in the ocean. He also wants to determine how these microbes can benefit from their specific genes. Sunagawa believes some of the BGCs they found will play critical roles.
Paoli L, Ruscheweyh HJ, Forneris CC, Hubrich F et al (2022) Biosynthetic potential of the global ocean microbiome. Nature. 2022 Jun 22. doi: 10.1038/s41586-022-04862-3.