Previously Unknown Ocean Virus Family May Also Populate the Human Gut

"Bacteria are key components at the bottom of the ocean's food chain, meaning that viruses—which can infect and kill bacteria—are also vital for understanding the ocean's health and function," says study co-leader Libusha Kelly, Ph.D., assistant professor of systems & computational biology and of microbiology & immunology at Einstein. She notes that viruses also kill bacteria in the human body. "By expanding what's known about the kinds of viruses that infect bacteria," she says, "this study allows us to look at other ecosystems like the human gut, to detect previously unknown viruses and to learn how they might be influencing bacterial populations that are vital for health or that contribute to disease."

The most abundant viruses in the oceans (and on the entire planet) are so-called double-stranded DNA (dsDNA) viruses. Of these viruses, the "tailed" variety (their tails are used to infect bacteria) have been extensively studied. "Non-tailed" dsDNA viruses appear to be quite common but are less well understood—mainly because they are difficult to culture and analyze. "Our collaborator Martin Polz at MIT developed a model system that overcomes these limitations," says Dr. Kelly, "making it possible to study the role of viruses in complex microbial communities in the lab."

In the new study, lead author Kathryn M. Kauffman, Ph.D., a postdoctoral associate in Dr. Polz's lab at MIT, collected daily samples for three months from waters off the Massachusetts coast. Viruses found in the samples were incubated for two weeks in cultures of Vibrionaceae bacteria (a common family of marine bacteria). More than 200 viruses that successfully infected and multiplied in the Vibrionaceae bacteria were randomly selected for genomic analysis.

Eighteen of the viruses were found to be members of a new family of small, non-tailed dsDNA viruses. The researchers named the new family Autolykiviridae, after Autolykos, a character in Greek mythology notorious for being difficult to catch.

In experiments involving more than 300 strains of Vibrionaceae bacteria, the Autolykiviridae viruses killed many more strains of Vibrionaceae species than the tailed viruses in the water samples. "They caused about 40 percent of the bacterial killing observed, despite comprising just 10 percent of the viruses that we isolated," says Dr. Kelly.

The Kelly lab next asked whether these viruses preyed on bacteria besides the Vibrionacea. Her lab conducted computational analyses showing that viruses related to the Autolykiviridae infect many other types of marine bacteria, suggesting that these viruses are important predators, not only in the area in which they were isolated but potentially the entire ocean. "We showed that viruses related to the Autolykiviridae are infecting many diverse groups of ocean bacteria as well as other bacterial groups that we cannot currently identify," says Dr. Kelly.

The researchers found several reasons why previous ocean studies of viral diversity have almost entirely missed non-tailed dsDNA viruses such as the Autolykiviridae. A key reason: Viral genomes are often bound to proteins. To efficiently extract the DNA of viral genomes, researchers should use proteases (enzymes that break down proteins) but often don't do so.

Dr. Kelly believes that the presence of Autolykiviridae-like viruses is not limited to the oceans. "We've found related viral sequences in the gut microbiome," she says, "but we don't yet know how they influence microbial communities in the gut or how important they are for health."

"Investigating the diversity of non-tailed dsDNA bacterial viruses in other environmental systems is a major next step," says Dr. Kauffman. "We also need to uncover the molecular basis of the distinctive interactions of the Autolykiviridae with their hosts."

The study is titled, "A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria." The other Einstein authors are: Julia M. Brown, Ph.D., and William K. Chang, Ph.D. Additional authors include: Fatima A. Hussain, Joy Yang, Philip Arevalo, David VanInsberghe, Joseph Elsherbini, and Michael B. Cutler, all of MIT; and Radhey S. Sharma, Ph.D., of the University of Delhi, who was a visiting researcher at MIT.

This work was supported by grants from the National Science Foundation and the WHOI Ocean Ventures Fund.

The authors declare no competing financial interests.

About Albert Einstein College of Medicine
Albert Einstein College of Medicine, part of Montefiore, is one of the nation's premier centers for research, medical education and clinical investigation. During the 2017-2018 academic year, Einstein is home to 697 M.D. students, 181 Ph.D. students, 108 students in the combined M.D./Ph.D. program, and 265 postdoctoral research fellows. The College of Medicine has more than 1,900 full-time faculty members located on the main campus and at its clinical affiliates. In 2017, Einstein received more than $174 million in awards from the National Institutes of Health (NIH). This includes the funding of major research centers at Einstein in aging, intellectual development disorders, diabetes, cancer, clinical and translational research, liver disease, and AIDS. Other areas where the College of Medicine is concentrating its efforts include developmental brain research, neuroscience, cardiac disease, and initiatives to reduce and eliminate ethnic and racial health disparities. Its partnership with Montefiore, the University Hospital and academic medical center for Einstein, advances clinical and translational research to accelerate the pace at which new discoveries become the treatments and therapies that benefit patients. Einstein runs one of the largest residency and fellowship training programs in the medical and dental professions in the United States through Montefiore and an affiliation network involving hospitals and medical centers in the Bronx, Brooklyn and on Long Island. For more information, please visit www.einstein.yu.edu, read our blog, follow us on Twitter, like us on Facebook, and view us on YouTube.

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