animals Article Application of Next-Generation Sequencing for the Determination of the Bacterial Community in the Gut Contents of Brackish Copepod Species (Acartia hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus) Yeon-Ji Chae 1, Hye-Ji Oh 1,* , Kwang-Hyeon Chang 1 , Ihn-Sil Kwak 2 and Hyunbin Jo 3,* 1 Department of Environmental Science and Engineering, Kyung Hee University, Yongin 1732, Korea;
[email protected] (Y.-J.C.);
[email protected] (K.-H.C.) 2 Department of Ocean Integrated Science, Chonnam National University, Yeosu 59626, Korea;
[email protected] 3 Institute for Environment and Energy, Pusan National University, Busan 46241, Korea * Correspondence:
[email protected] (H.-J.O.);
[email protected] (H.J.); Tel.: +82-10-9203-2036 (H.-J.O.); +82-10-8807-7290 (H.J.) Simple Summary: Copepods are important components of marine coastal food chains, supporting fishery resources by providing prey items mainly for fish. Copepods interact with small microorgan- isms via feeding on phytoplankton. DNA methods can determine the gut contents of copepods and provide important information regarding how copepods interact with phytoplankton and bacteria. In the present study, we designed a method for extracting the gut content DNA from small-sized Citation: Chae, Y.-J.; Oh, H.-J.; copepods that are important in coastal and brackish areas. Based on DNA analyses, Rhodobacter- Chang, K.-H.; Kwak, I.-S.; Jo, H. aceae, which is common in marine waters and sediments, was most abundant in the gut contents Application of Next-Generation of the three copepod species (Acartia hudsonica, Sinocalanus tenellus, and Pseudodiaptomus inopinus). Sequencing for the Determination of However, the detailed composition of bacteria was different among species and locations.