Dolphin Mouth Swabs Lift the Lid on Bacterial “Dark Matter” Present
What is the first thing that comes to your mind when you hear “dolphin”? would you say flipper? Or maybe go with SeaWorld? These are about the closest interactions most of us ever have with these amazing marine mammals. But they are so much more than trick performing, problem-solving beauties. The more we learn about dolphins, the cooler they get.
With over 43 species of dolphins living in all parts of the world, these creatures are full of surprises. Adding to this, researchers at the Stanford University have now found two previously unknown phyla of bacteria inside the mouths of dolphins.
By studying the new bacteria, which were little known to researchers in the past, scientists may develop new insights into bacterial diversity, dolphin health and the unique nature of marine mammals in general, said David Relman, professor of microbiology and immunology at the Stanford School of Medicine.
The U.S. Navy’s Marine Mammal Program reached out to Relman more than 10 years ago for help in keeping its dolphins healthy. The animals are highly trained and perform missions at sea.
Previous research by Relman’s group, in collaboration with the program
, revealed a surprising number of never-before-seen bacteria in dolphin and other marine mammal samples, particularly those swabbed from the dolphins’ mouths, said Relman, who is also chief of infectious diseases at the Veterans Affairs Palo Alto Health Care System. Some of the bacteria found in the current study are affiliated with poorly understood branches of the bacterial tree.“These organisms, about which we have known just a tiny bit, are basically the dark matter of the biological world,” he said. “We knew there was gold in those dolphin mouths, and we decided it was time to go after it with more comprehensive methods.”
In the present study, the researchers identified bacterial lineages by reconstructing their genomes from short bits of DNA. The genome of a given cell serves as its blueprint and contains all its operating instructions, encoded in DNA. The researchers named one of the newly identified lineages Delphibacteria, in honor of the dolphins (Delphinidae is the Latin name for oceanic dolphins).
The researchers differentiated between bacteria and predicted their behavior by looking broadly at their genomes. “What we do first is shear the DNA into a bunch of little bits and pieces, the mix of DNA is sequenced, and we then try to figure out how the genomes were originally assembled,” says lead author Natasha Dudek, a graduate student at the University of California, Santa Cruz.
If a gene is one piece of a puzzle, the researchers put together the whole puzzle.
By looking at the genes encoded in their genomes, the researchers can also predict how the new bacteria might behave. Genetic differences are also likely to correspond to differences in behavior, Relman said. For example, large insertions in one newly discovered phylum’s genome give rise to unusual Cas9 proteins, of CRISPR-Cas9 fame, Relman explained, “Typically, people are interested in small Cas9 proteins that might be easy to manipulate and deliver into cells… These are the opposite — they’re enormously big.’ Different structures in the genes that encode these proteins account for the size difference, and the researchers suggest these large Cas9 proteins have different properties from those known before.”
Exploring these differences may give scientists insight into how marine mammals adapted to life in the ocean, as well as an appreciation for the breadth of bacterial diversity on Earth.
