Phylogenetic diversity of caecal microbiota in krishibro broilers of India

Abstract

Gut microbiota is attributed to the bird’s health, metabolism, immunity and has implications on food safety and public health. Among food producing animals chicken meat is consumed to a large extent across the globe. Improving production performance of food animals could be achieved by understanding and optimizing microbial communities of gastrointestinal tract. To prevent Dysbacteriosis, a common problem in broiler chicken single or a mixture of antibiotics and coccidiostats are supplemented in broiler chicken diets. A total of 120 krishibro broiler chicken of day old were distributed randomly into three groups (CON, ACFG and CFG) with five replicates of eight birds, in each group which were maintained on similar management conditions. Control group (CON) was administered basal diet alone with no antibiotic and no coccidiostat. ACFG group was given antibiotics chlortetracycline, tylosin phosphate and a coccidiostat, amproilum hydrochloride @ 50 g/100 kg feed each. CFG group was supplemented with coccidiostat alone at the above mentioned dose. At 6 weeks of age, one bird per replicate was slaughtered and the caeca luminal contents were collected and pooled in each group. Changes in caecal microbiota composition were studied using amplicon sequencing of V3-V4 region of 16SrRNA gene on Illumine Miseq platform. The sequencing data were uploaded on MG-RAST pipeline. All the birds appeared healthy throughout the experimental period. Caecal microbial diversity revealed bacteria as the major domain. The dominating bacterial phyla in all the groups were Firmicutes and Bacteroidetes accounting to >90% of the caecal microbiome. Higher Firmicutes/Bacteroidetes ratio was seen in CFG group. The phylum Deinococcus-thermus, Chlorobi, Acidobacteria were represented exclusively in ACFG, CFG, CON groups, respectively. ACFG group was dominated by Rikenellaceae where as CFG and CON groups showed Ruminococcaceae as the major group at the family level of classification (Figure). The predominant genera with above 10% abundance in the caecum were Alistipes, Bacteroides and Clostridium in ACFG group, Faecalibacterium and Alistipes in CFG group, Bacteroides and Faecalibacterium in CON group. Hierarchical clustering showed similarities in ACFG and CON groups at phylum level. The phylogeny at genus level showed CFG clustering with CON. Supplementation of coccidiostats alone and antibiotics with coccidiostats influenced the changes in microbiota composition of Krishibro broiler chicken.