Microbiome Analysis of Narragansett Bay Fishes

All Narragansett Bay fish samples, butterfish (n = 22), scup (n = 31), summer flounder (n = 20), smooth dogfish spiral valve (n = 5), smooth dogfish distal intestine (n = 6), were collected in the months of May, June, July, August, and September during 2017—2021 from the fish trawl surveys conducted by the University of Rhode Island Graduate School of Oceanography. Specimens were collected according to the IACUC protocols covering both this study as well as the work of the collection vessel. Fish trawl for samples was approved and permits were obtained from the Rhode Island Department of Environmental Management. The trawl was conducted by the R/V Cap’n Bert which utilized an otter trawl net with an effective opening of 6.5 m and towed at 2 knots for 30 min. Trawling was performed at two sites in Narragansett Bay, Rhode Island: Fox Island and Whale Rock (Fig. 1). After the trawl was emptied on the deck, living target fish were humanely euthanized via a blunt force blow to the head followed by pithing (as recommended by the 2020 AVMA guidelines for euthanasia). Following euthanasia, fish were dissected and the intestinal contents were emptied into Zymo Research bashing bead lysis tubes (Irvine, CA, USA) containing 750uL of ZymoBIOMICS Lysis Solution (Irvine, CA, USA), shaken, and stored on ice until extraction. Water samples were collected ~ 1 m above the seafloor using a Niskin flask. For each individual seawater sample (n = 12), one liter of seawater was filtered through a 0.22 μm membrane from which a 3 × 3 cm section was added to a Zymo Research bashing bead lysis tubes (Irvine, CA, USA) containing 750uL of ZymoBIOMICS Lysis Solution (Irvine, CA, USA), shaken, and stored on ice until extraction. The three large offshore shark species, thresher (n = 4), mako (n = 4), and porbeagle shark (n = 5), were collected from specimens caught as part of recreational shark tournaments in Massachusetts and Rhode Island. The samples were caught in the offshore waters from Rhode Island to Maine. All shark samples were collected postmortem from sharks collected by licensed recreational fishermen. The sharks were dissected and contents from the spiral valve were transferred into Zymo Research bashing bead lysis tubes (Irvine, CA, USA) containing 750uL of ZymoBIOMICS Lysis Solution (Irvine, CA, USA), shaken, and stored on ice until they could be frozen and subsequently extracted.