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

Ameer, Aqsa; Saleem, Farrukh; Keating, Ciara; Gundogdu, Ozan; Ijaz, Umer Zeeshan; Javed, Sundus

Abstract

The article presents a processed dataset from amplicon sequencing of the V4 region of the 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. 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. 16S rRNA gene amplicon sequencing of caecal DNA from day old and mature chicken samples (22 weeks for Naked Neck, Black Australorp, Rhode Island Red and White Layer; 8 weeks for Broiler) of the four groups was performed. The paired-end reads from all the samples were quality trimmed, error corrected, and overlapped, on which unique Operational Taxonomic Units (OTUs) were obtained at 99 % similarity. Using predictive modelling, the MetaCyc functional pathways, as well as KEGG orthologs were also recovered. The generated data may be used to explore microbial interactions in gastrointestinal tract with respect to NDV vaccination and infection, together with increased understanding of chicken health and productivity.

Citation

Ameer, A., Saleem, F., Keating, C., Gundogdu, O., Ijaz, U. Z., & Javed, S. (2024). Dataset of 16S rRNA gene sequences of 111 healthy and Newcastle disease infected caecal samples from multiple chicken breeds of Pakistan. Data in Brief, 57, Article 110957. https://doi.org/10.1016/j.dib.2024.110957

• Journal Article Type: Article
• Acceptance Date: Sep 16, 2024
• Online Publication Date: Sep 24, 2024
• Publication Date: Dec 1, 2024
• Deposit Date: Oct 16, 2024
• Publicly Available Date: Oct 17, 2024
• Journal: Data in brief
• Electronic ISSN: 2352-3409
• Publisher: Elsevier
• Peer Reviewed: Peer Reviewed
• Volume: 57
• Article Number: 110957
• DOI: https://doi.org/10.1016/j.dib.2024.110957
• Keywords: Operational Taxonomic Units, Poultry, Infection, Gut Microbiome, Vaccination
• Public URL: https://durham-repository.worktribe.com/output/2960901