Dataset of 16S rRNA sequences of 111 healthy and Newcastle disease infected caecal samples from multiple chicken breeds of Pakistan

The dataset is on amplicon sequencing of V4 region of 16S rRNA gene to recover bacterial and archaeal taxa from the caeca of multiple chicken breeds of Pakistan. These include chicken breeds commonly raised at commercial level, Naked Neck, Black Australorp, Rhode Island Red, White Layer, and Broiler (Ross). All the breeds were challenged with Newcastle Disease Virus (NDV), with vaccination against the disease also explored. This resulted in samples belonging to four treatment groups as: Control; Vaccinated; Vaccinated and Challenged; and Non-vaccinated and Challenged. These were raised on an antibiotic free diet in a semi-controlled farming setup. Additionally, 16S rRNA amplicon sequencing of caecal DNA from day old chicks was done to compare the microbial profiles with the mature chicken sampling of four groups. A total of 11,544,255 paired-end reads from 111 samples were initially obtained. After quality trimming, error correction, and overlapping of paired-end reads, 10,749,141 reads were retained on which Operational Taxonomic Units (OTUs) were obtained at 99% similarity. This resulted in a total of 74,049 unique OTU sequences. Using predictive modelling, the MetaCyc functional pathways, as well as KEGG orthologs were also recovered. The generated data is then helpful to explore microbial interactions in gastrointestinal tract with respect to NDV vaccination and infection, together with increased understanding of chicken health and productivity.