Abstract
Gut microbiota affects health, metabolism and immunity of the host, and in the case of livestock, also food-safety. Here, 16S rRNA gene high-throughput Illumina sequencing was used to describe the microbiome of chicken caeca in two different breeds and management systems throughout their whole productive lifespan. Broilers (Ross-308), as a fast-growing breed reared in an intensive system for 42-days, and a slow-growing breed of chicken (Sasso-T451A) reared in an extensive farming system with outdoor access for 86-days, were compared. The core microbiome and differentially abundant taxa, as well as taxa associated with age were identified. Age was identified as the strongest influencing factor in caecal microbiota composition, and, in general, each age-group showed an age-associated community profile, with a transition period at the middle of their lifespan. However, substantial differences were observed in the composition of caecal microbiota of both chicken breeds, microbiota being richer and more complex in free-range chicken than in broilers. Several taxa positively/negatively correlated with Campylobacter relative abundance were also identified. Especially noteworthy was the identification by microbial community comparison of microbiota profiles suggestive of dysbiosis in several free-range chickens, probably associated to the typhlitis observed in the lumen of their caeca.
Highlights
Gut microbiota is considered as an additional organ due to its vital importance on the physiological, metabolic, immunological, and digestion and nutritional uptake functions of the host[1]
The aim of this study was to thoroughly characterize the caecal microbiota in two breeds of chickens fed with different diets and bred under different production systems throughout their complete lifespan; Ross-308 broilers reared for 42 days, as the fast-growing breed used in intensive chicken meat production, and a slow-growing breed (Sasso-T451A) reared in a free-range system for 84 days
The effect of breed, diet and production system was assessed to obtain a comprehensive knowledge of how microbiota develops as chickens grow in the different phases of their productive life, and the following questions were addressed: (i) How do caecal microbial communities change during the productive life of chickens? (ii) Does supplementation of diet with calcium butyrate and dry whey influence the caecal microbial community patterns in broilers? iii) Do caecal microbiome temporal dynamics vary between fast-growing and slow-growing breeds? iv) Which microbial taxa are representative of each age-group? (v) Is there a core microbiota for all age-groups in each breed, and a core microbiota for both breeds throughout their productive life? (vi) Which taxa tend to coexist with Campylobacter in the chicken caeca?
Summary
Gut microbiota is considered as an additional organ due to its vital importance on the physiological, metabolic, immunological, and digestion and nutritional uptake functions of the host[1]. Disruption of the gut microbiota structure that results in the elimination of subsets of beneficial bacteria, often leads to pathogen overgrowth, in conjunction with significant loss of microbial diversity[8] Factors such as diet[9,10,11], rearing conditions[12], host genetics[13] and age[9,14,15,16,17,18] can have an effect on poultry gut microbiota diversity, composition, and community structure. The aim of this study was to thoroughly characterize the caecal microbiota in two breeds of chickens fed with different diets and bred under different production systems throughout their complete lifespan; Ross-308 broilers reared for 42 days, as the fast-growing breed used in intensive chicken meat production, and a slow-growing breed (Sasso-T451A) reared in a free-range system for 84 days. The effect of breed, diet and production system was assessed to obtain a comprehensive knowledge of how microbiota develops as chickens grow in the different phases of their productive life, and the following questions were addressed: (i) How do caecal microbial communities change during the productive life of chickens? (ii) Does supplementation of diet with calcium butyrate and dry whey influence the caecal microbial community patterns in broilers? iii) Do caecal microbiome temporal dynamics vary between fast-growing and slow-growing breeds? iv) Which microbial taxa are representative of each age-group? (v) Is there a core microbiota for all age-groups in each breed, and a core microbiota for both breeds throughout their productive life? (vi) Which taxa tend to coexist with Campylobacter in the chicken caeca?
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