The ocean is teeming with life, from the largest animal ever on earth – the blue whale – to the tiny insects. In addition to their quantity, these bacteria are also important in ensuring that the entire ecosystem and climate work properly. For example, there are varieties that work photo-synthetically such as cyano-bacteria that produce about 50 percent of the oxygen in the atmosphere. In addition, by releasing carbon dioxide into the atmosphere, microorganisms help to combat global warming. Despite this important role, research into the diversity of microbes found in the oceans has so far become complex. Therefore, a team of researchers led by Shinichi Sunagawa, Professor of Microbiome Research, is working closely with JörnPiel’s team to investigate this diversity. Both groups are from the Institute of Microbiology in ETH Zurich.
To discover new biological products, Sunagawa and his team examined publicly available DNA data from 1,000 water samples collected at various depths in all oceans of the world. The data came from sources such as sea voyages and viewing platforms located offshore. Thanks to modern technology such as DNA analysis (DNA), it is now easier to search for new species and to identify any known species that can be found there. But what is not known at all is what special effects sea microbes provide – in other words, what chemical compounds they make are important for biological communication. In the best case scenario, such combinations can benefit people too. Emphasizing research is the idea that the marine microbiome has enormous potential in natural products that may appear to be beneficial, for example because of its antibiotic properties.
The extracted eDNA present in the samples was followed by real researchers of various trips. By rebuilding all the genomes in the computer, scientists have successfully eliminated encryption encoded – protein plans. Finally, they merged this new data with 8,500 existing genome data sets for marine insects on a single site. This has given them 35,000 genomes to use in their search for new microbial species and, in particular, promising biosynthetic gene expression (BGCs). BGC is a collection of genes that provide a synthetic product of a natural product.
New species and new molecules have been discovered
In this genetic data, the researchers found not only the most potent BGCs – about 40,000 in total – but also the previously undiagnosed bacterial species that are part of the phylum Eremio bacterota. This group of bacteria was known to exist only on earth and did not show any specific biosynthetic diversity. Sunagawa and his team named the new family of these viruses Eudore microbiaceae, and they were able to show that these viruses are common and widespread: one species of this family, Eudore microbium malaspinii, makes up 6 percent of all viruses present in a particular area coastal areas.
“Relatives at sea have bacteria that are a large genome. Completely removing the text has been a challenge because living things had never been cultivated before,” Sunagawa said. In addition, new viruses from a group of microorganisms are proud of the high BGC variability of all tested samples. “As things stand, they are a very different family from the ocean column,” he said. The researchers looked at the two Eudore microbiaceae BGCs in detail. One was a genetic component containing the genetic code of enzymes, according to Sunagawa, which had never been found in the galaxy in BGC bacteria before. Another example tested was a natural bioactive product that inhibits proteolytic enzyme.
Verification of the test led to a claim
In collaboration with the team led by JörnPiel, researchers are using experiments to confirm the structure and function of both natural products. As E. malaspinii could not be planted, Piel’s team had to attach the genes to the model bacteria in order to act as a natural product plan. The virus then produces complementary substances. Finally, researchers isolated molecules from living cells, determined their formation and confirmed biological activity.
This was necessary because in some cases, the enzymatic activity predicted by computer programs was inconsistent with research results. “Computer predictions of how the enzyme will trigger chemical reactions,” Sunagawa said. “That’s why such predictions should be confirmed in the lab if there is any doubt.” Doing so is a costly and time-consuming task on an estimated 40,000 natural product sites. “However, our database has a lot to offer, and is accessible to all researchers who wish to use it,” Sunagawa said.In addition to the ongoing collaboration with Piel’s team to discover new natural products, Sunagawa seeks to investigate unresolved questions on the evolution and evolution of marine organisms. This includes the way microorganisms are dispersed in the ocean considering that they can be spread over long distances by inactivity. You also want to find out what biological or evolutionary benefits are caused by germs, Â Sunagawa suspects that BGCs may play a major role.
Source Journal Reference:  Lucas Paoli, Hans-Joachim Ruscheweyh, Clarissa C. Forneris, Florian Hubrich, Satria Kautsar, Agneya Bhushan, Alessandro Lotti, Quentin Clayssen, Guillem Salazar, Alessio Milanese, Charlotte I. Carlström, Chrysa Papadopoulou, Daniel Gehrig, Mikhail Karasikov, Harun Mustafa, Martin Larralde, Laura M. Carroll, Pablo Sánchez, Ahmed A. Zayed, Dylan R. Cronin, Silvia G. Acinas, Peer Bork, Chris Bowler, Tom O. Delmont, Josep M. Gasol, Alvar D. Gossert, André Kahles, Matthew B. Sullivan, Patrick Wincker, Georg Zeller, Serina L. Robinson, Jörn Piel, Shinichi Sunagawa. Biosynthetic potential of the global ocean microbiome. Nature, 2022; DOI: 10.1038/s41586-022-04862-3
