Gut microbiota variations during the productive lifespan of two high-yielding laying hen breeds

Gut microbiota affects nutrient digestion, pathogen inhibition, gut epithelium nourishment, endocrine activity, and interaction with the gut-associated immune system. In laying hens, previous studies focused their research on using feces, or specific gastrointestinal (GIT) sections and analysed single production stages in the life of laying hens and the animals' response to particular conditions such as a change in the diet. This study aimed to characterise the active intestinal microbial community in two commercially laying hen breeds: Lohmann Brown-Classic (LB) and Lohmann LSL-Classic (LSL), during their complete productive life. All birds were kept under the same diet, housing, and management conditions. Digesta samples of the crop, gizzard, duodenum, ileum, and caeca were collected at 10, 16, 24, 30, and 60 weeks of life to represent the whole production period. RNA was extracted from 500 samples and analysed by target amplicon sequencing. Phylogenetic analysis of the bacterial sequences was assessed using Mothur, followed by multivariate statistical analysis. A statistical significance was observed for the breed, GIT section, the production period and the combination of all factors (p<0.05). Depending on the breed, the detected genera differed in the abundance level within GIT sections or production periods. The most significant shifts in the active microbiota of the laying hens were observed from the early life on (week 10) and with the transition into the laying period between weeks 16 and 24. Furthermore, deep analysis using metagenomic shotgun sequencing of weeks 16 and 24 revealed the functional shifts during this phase. Functional profiling showed differences between the breeds besides up- and downregulated functions with the onset of the laying phase. The taxonomical profile has been compared with the 16S rRNA gene amplicon sequencing results to indicate methodical differences. We conclude that the breed and production period stage impact intestinal microbiota dynamics.