Chousalkar, KapilWoolford, LucyHein, WayneStanley, DanaMoore, RobJoat, Nitish Narendra2022-01-242022-01-242021https://hdl.handle.net/2440/134175In the last two decades, the focus on chicken gut microbiota has increased exponentially due to its critical role in digestion, nutrient absorption, modulation of immunity, and protection against enteric pathogens. Thus, understanding its role in food-producing animals like chickens is essential because it can act as a source of zoonotic diseases. In chickens, the majority of the research in gut microbiota is focused on broilers and there was a need for detailed studies in layer chickens. In chapter 2, the development and composition of gut microbiota of hens housed in a single aged cage farm was studied from hatch to week 75. These hens were reared in cages from day old. The results showed that the richness of gut microbiota increased with the age and stabilized from a mid-lay phase (week 40). The gut microbiota was dominated by Firmicutes at an early age which was replaced by phylum Bacteroidetes at the later stages. The gut microbiota richness reduced significantly at week 18, after shifting the flock from the rear to the production shed. Flock's production performance was optimal till the end of the production cycle. The layer birds are raised in different housing systems such as cage, free-range, and barn housing. Chapter 3 focused on understanding the gut microbiota development in three commercial layer flocks raised in different housing systems from hatch to end of production cycle i. e flock A (Free Range), flock B (Barn), and flock C (multi-age cage system). The taxonomic composition of gut microbiota in all three flocks was significantly different. All three flocks showed significant differences in the development pattern of gut microbiota. The richness of gut microbiota was significantly different between and within all three flocks. In flock A and B, the richness of gut microbiota increased with age. In flock C, the richness of gut microbiota increased up to week 20 after which it remained relatively stable. The gut microbiota in flock A and B was dominated by phylum Firmicutes up to mid lay phase after which it was dominated by phylum Bacteroidetes. In flock C, phylum Bacteroidetes was dominant from an early lay phase. The richness of gut microbiota decreased at week 18 in two flocks (A and C) which could have been due to shifting to production shed, change in feed, transportation stress, the onset of lay. Different enteric pathogens and stressors can disrupt the gut microbiota composition and significantly reduces the richness and diversity of gut microbiota. In chapter 4, the effect of Salmonella Typhimurium on gut microbiota was assessed. Further, this study focused on the effect of different potential stressors on Salmonella Typhimurium shedding and gut microbiota composition in pullets. The study showed persistent shedding of Salmonella Typhimurium in all the infected birds for up to week 8 postinfection. The Salmonella Typhimurium shedding increased significantly due to intramuscular injections and feed withdrawal. The intramuscular injections disrupted the gut microbiota composition leading to a significant reduction in abundance of phylum Firmicutes and increase in phylum Proteobacteria which could lead to dysbiosis in chickens. This study produced robust data regarding gut microbiota development in layer chickens in different housing systems. In all 4 flocks, phylum Firmicutes dominated at an early age which was replaced by phylum Bacteroidetes in mid and late lay phases. The taxonomic composition of gut microbiota varied considerably between all 4 flocks. However, the production performance was high in all four flocks, which shows that different communities can produce similar productivity. Multiple variables were identified which could potentially change gut microbiota such as intramuscular injection, feed withdrawal, transportation, and the onset of lay. Typhimurium infection at an early agecan disrupt the gut microbiota and reduce richness and diversity. Therefore, it is important to formulate interventions to reduce potential pathogen colonisation. This could be done by modifying diet using probiotics and prebiotics.enGut microbiotaSalmonella typhimuriumlayersThesis