Microbial diversity and community composition of caecal microbiota in commercial and indigenous Indian chickens determined using 16s rDNA amplicon sequencing
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Date
2018
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Abstract
Background: The caecal microbiota plays a key role in chicken health and performance, influencing digestion and
absorption of nutrients, and contributing to defence against colonisation by invading pathogens. Measures of
productivity and resistance to pathogen colonisation are directly influenced by chicken genotype, but host driven
variation in microbiome structure is also likely to exert a considerable indirect influence.
Methods: Here, we define the caecal microbiome of indigenous Indian Aseel and Kadaknath chicken breeds and
compare them with the global commercial broiler Cobb400 and Ross 308 lines using 16S rDNA V3-V4 hypervariable
amplicon sequencing.
Results: Each caecal microbiome was dominated by the genera Bacteroides, unclassified bacteria, unclassified
Clostridiales, Clostridium, Alistipes, Faecalibacterium, Eubacterium and Blautia. Geographic location (a measure
recognised to include variation in environmental and climatic factors, but also likely to feature varied management
practices) and chicken line/breed were both found to exert significant impacts (p < 0.05) on caecal microbiome
composition. Linear discriminant analysis effect size (LEfSe) revealed 42 breed-specific biomarkers in the chicken
lines reared under controlled conditions at two different locations.
Conclusion: Chicken breed-specific variation in bacterial occurrence, correlation between genera and clustering of
operational taxonomic units indicate scope for quantitative genetic analysis and the possibility of selective breeding
of chickens for defined enteric microbiota.
Description
TNV_Microbiome_2018_1-13
Keywords
Veterinary Science, Animal Biotechnology