Scientific literature on turkey gut microbiota is scarce, and there is a lack of knowledge regarding associations between the microbiota and relevant health challenges of turkeys raised for meat. Monensin is an ionophore used for prevention of coccidiosis in turkey. Ionophores have an inhibiting effect on gram-positive bacteria, and thus also have a controlling effect on pathogens such as Clostridium perfringens, preventing diseases such as necrotic enteritis (NE) and gizzard erosion and ulceration syndrome (GEU). Monensin was phased out of the Norwegian turkey production during 2022. As a result, there has been a substantial increase of GEU and NE outbreaks, and today approximately 20 % of all turkey flocks are treated with antibiotics. Antibiotics have an obvious effect on the bacterial fraction of the gut microbiota, depending on the type used. It is therefore interesting to compare treatment effects on the gut microbiota for both monensin and antibiotics, and study how the changes in the gut microbiota composition might affect the health of the animal. Knowledge of the turkey gut microbiota composition in the absence of ionophores is of interest for both ongoing and planned research projects at NVI. ICONIC investigates the impact of ionophores, including development of resistance to ionophores and co-resistance to other antibiotics in both enterococci and staphylococci. TEiCON aims to identify and quantify specific coccidia (Eimeria species) and C. perfringens in fecal samples from poultry including turkey, and connect these results to coccidiosis and NE. GizMo, a proposal to FFL/JA, aims to generate more knowledge on the etiology and pathophysiology of GEU in turkeys, by means of shotgun metagenomics in unbiased screening for potential infectious agents associated with the syndrome. The present pilot study will provide knowledge of importance for all these projects. During 2022, caecal samples from 110 turkey flocks were collected and stored within the framework of NORM-VET. Both flocks raised with and without monensin were sampled, as well as flocks treated with antibiotics. In this project, DNA from the samples are to be extracted and sent to the Norwegian Sequencing Center for metagenomic shotgun sequencing. After sequencing, the reads will be quality controlled and taxonomically classified. Treated and non-treated groups will be compared with different bioinformatic methods. Additionally, the presence of individual species and genes of interest will be investigated, and compared to previous culturing results. Metadata is available from NORM-VET, and data about the flocks may be retrieved from HelseFjørfe and/or Nortura (contact established). A previous dataset with 44 shotgun-sequenced samples from turkeys sampled in 2020 is available for comparison, if additional data is needed for the monensin-treated fraction of the samples.
