Seasonal variations in the intestinal microbiota of farmed Atlantic salmon (Salmo salar L.)

Seasonal variations in seawater conditions, including temperature and bacterial £ora populations could be expected to in£uence the intestinal microbiota of ¢sh. In order to improve the understanding of the in£uence of environment and diet on the bacterial composition, further studies of farmed Atlantic salmon (Salmo salar L.) intestinal microbiota are required. It has been reported that through manipulation of dietary composition, the microbiota can potentially be changed and controlled (Ring , Sperstad, Myklebust, Refstie & Krogdahl 2006; Bakke-McKellep, Penn, Salas, Refstie, Sperstad, Landsverk, Ring & Krogdahl 2007; Ring , Sperstad, Kraugerud & Krogdahl 2008). As diet, also geographic location may in£uence the intestinal microbiota (Holben,Williams, Gilbert, Saarinen, Sarkilahti & Apajalahti 2002), and seasonal variations could exert a similar eiect. Recently, the bacterial £ora of Atlantic salmon have been widely studied (e.g. Holben et al.2002; Bakke-McKellep et al.2007; Hovda, Lunestad, Fontanillas & Rosnes 2007; Liu, Zhou, Yao, Shi, He, H lvold & Ring 2008; Ring et al. 2008). The intestinal microbiota of ¢sh has been shown to be more variable than ¢rst suggested, particularly in data generated from studies since the introduction of molecular-based methods. The use of molecular biological methods decreases possible biases commensurate with approaches reliant on bacterial cultivation. The use of such methods are based on analyses of the bacterial DNA using polymerase chain reaction (PCR) and 16S rDNA sequencing, and further bacterial identi¢cation. This approach is well established in the study of microbial ecology, and several authors have used suchmethods in the study of ¢sh intestine (Verner-Jeireys, Shields, Bricknell & Birkbeck 2003; Huber, Spanggaard, Appel, Rossen, Nielsen & Gram2004; Martin, Ross, Quetin & Murray 2006; Pond, Stone & Alderman 2006; Hovda, Lunestad, Fontanillas et al. 2007; Kim, Brunt & Austin 2007; Ring et al. 2008; Bjornsdottir, Johannsdottir, Coe, Smaradottir, Agustsson, Sigurgisladottir & Gudmundsdottir 2009; Merri¢eld, Burnard, Bradley, Davies & Baker 2009). Denaturing gradient gel electrophoresis (DGGE) enables studies of complex bacterial communities, and additional sequencing makes identi¢cation of the species present in the sample possible.The method provides information about the predominant bacterial £ora in the sample, regardless of their ability to grow on agar. Furthermore, the methodology can be used to study population dynamics and for time studies, such as studying seasonal variations in the gut microbiota. Denaturing gradient gel electrophoresis compares samples based on base diierences in the GC content of the DNA sequence of diierent bacteria. By analysing the same 16S rDNA region, bacterial variations can be detected. There are, to our knowledge, only three studies from the last decade examining the gut microbiota during an annual cycle, all using ¢sh from ponds, in Saudi Arabia, Japan and France (Al-Harbi & NaimUddin 2004; Hagi, Tanaka, Iwamura & Hoshino 2004; Naviner, Giraud, Le Bris, Armand, Mangion & Ganiere 2006). Whereas, some older papers also discuss the bacterial £ora of gut, using bacterial cultivation (Liston1956; Okuzumi & Awano1983). This is the ¢rst