Genetic, Environmental and Management Influences on Selected Gut Bacterial Populations in Chickens

Abstract

The indigenous gut bacteria of chicken influences both the health and disease. Many factors affect the gut microbiome of commercial chickens. Host-biology and the environment are two key factors recognized as important drivers of the community structure of the gut bacteria. However, compared to mammalian literature, the host genetic and environment have been little explored in productive chickens. Three experiments were designed to study the effects of host-biology and environmental conditions on the gut bacterial composition: 1) two genetically divergent chicken lines (meat-type and egg-type) sharing the same rearing area and diet; 2) individually caged broiler breeder hens maintained with feed-restricted or fed-satiated regimen; and 3) a naturally occurring necrotic enteritis chicken model. In each study the intestinal bacteria population was sequenced with Illumina technology targeting the V4 regions of 16S rRNA bacterial gene to annotate the ecological diversity of the bacterial communities. The rarefaction sequencing depth of the three experiments were: 1) 70,750; 2) 31,000, and 3)18,500 reads/sample. In the first experiment, genetically divergent chickens (broiler- and egg-type) hatched and reared in a common area and fed the same diet developed similar fecal microbial populations but showed significant variations in the abundance of some groups of bacteria as the chickens grew older. Among the observed taxonomic differences, the order Lactobacillales was consistently enriched in broiler-type chickens. In experiment 2, it was found that doubling the feed ration of previously feed-restricted mature broiler hens decreased the proportion of Lactobacillus spp., and mediated few alterations in low abundant groups of bacteria. These alterations suggest a modification in the bacterial functionality. In the third experiment, chickens with necrotic enteritis had reduced species richness and diversity of the ileal and cecal bacterial communities compared to healthy pen-mates. Bacterial alterations in the sick chickens included reduced numbers of the butyrate producer bacteria Ruminococcaceae and increased Clostridiaceae. Within the ileum of “healthy” chickens the proportion of Lactobacillus species was reduced compared to those reported in the literature. This might suggest the environment used in that study was limiting in acquirable Lactobacillus species and so developed an aberrant gut microbiota. Overall these three different types of study designs found that the environmental factors were more influential than the host-genetic background and feed intake on the community structure of the gut bacteria in chickens.