Monensin phase-out in Norwegian turkey production decreases Bifidobacterium spp. abundance while enhancing microbial diversity

Intestinal tissue damage caused by coccidiosis is an important predisposing factor for necrotic enteritis in turkeys, and both diseases are common health issues in turkey production. In Norway, the in-feed ionophore coccidiostat monensin has been used as a preventive measure to combat coccidiosis since the late 1980s. In 2022, however, preventive use of monensin was phased out, which led to an undesired increase in antibiotic treatments among turkey flocks, largely due to necrotic enteritis. The aim of this study was to investigate the overall effects of the preventive monensin use and antibiotic treatment on the turkey caecal microbiota. A total of 102 flock samples from the Norwegian turkey population were included, and metagenomic datasets were generated through shotgun sequencing. All datasets were processed with the Taxprofiler pipeline, followed by diversity, redundancy and differential abundance analyses in R. A significant decrease in alpha and beta diversity was observed for the caecal samples from turkeys exposed to monensin, compared with the non-exposed. An increased abundance of <i>Bifidobacterium</i> spp. was observed in the samples from monensin-exposed turkeys, including <i>Bifidobacterium pullorum</i>, <i>Bifidobacterium longum</i>, <i>Bifidobacterium pseudolongum</i>, <i>Bifidobacterium pseudocatenulatum</i> and <i>Bifidobacterium animalis</i>. Additionally, a decrease in <i>Megamonas</i> and <i>Megasphaera</i> species was detected in these samples. Further, species within the <i>Clostridium</i> genus were higher in abundance among the samples from female turkeys compared with male turkeys. The results indicate that the use of monensin seems to decrease the overall diversity and promote the abundance of <i>Bifidobacterium</i> spp. in the caecum of turkeys, while decreasing the abundance of <i>Megamonas</i> and <i>Megasphaera</i> species. The use of monensin may be beneficial for the gut microbiota due to an increase in favourable <i>Bifidobacterium</i> spp. In contrast, treatment with phenoxymethylpenicillin (penicillin V) early in the turkey life cycle does not seem to cause long-term changes in the caecal microbiota composition. However, further studies are needed to investigate the effects of a decreased abundance of <i>Bifidobacterium</i> spp. and increased gut microbiota diversity in turkeys in the absence of monensin use.