Ameer, Aqsa and Saleem, Farrukh and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer and Javed, Sundus (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: 110957. ISSN 2352-3409
AI Summary:
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.AI Topics:
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.
Ameer, Aqsa
Author
Saleem, Farrukh and Ameer, Aqsa and Afzal, Farhan and Usman, Muhammad and Irshad, Hamid and Sattar, Sadia and Ijaz, Umer Zeeshan and Javed, Sundus (2025) A cross-sectional survey of poultry management systems, practices and antimicrobial use in relation to disease outbreak in Pakistan. BMC Research Notes, 18: 144. ISSN 1756-0500
Ameer, Aqsa and Saleem, Farrukh and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer and Javed, Sundus (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: 110957. ISSN 2352-3409
Ameer, Aqsa and Saleem, Farrukh and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken caeca from Pakistan. Data In Brief, 54: 110487. ISSN 2352-3409
See full publications listSaleem, Farrukh
Author
Saleem, Farrukh and Ameer, Aqsa and Afzal, Farhan and Usman, Muhammad and Irshad, Hamid and Sattar, Sadia and Ijaz, Umer Zeeshan and Javed, Sundus (2025) A cross-sectional survey of poultry management systems, practices and antimicrobial use in relation to disease outbreak in Pakistan. BMC Research Notes, 18: 144. ISSN 1756-0500
Ameer, Aqsa and Saleem, Farrukh and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer and Javed, Sundus (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: 110957. ISSN 2352-3409
Ameer, Aqsa and Saleem, Farrukh and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken caeca from Pakistan. Data In Brief, 54: 110487. ISSN 2352-3409
See full publications listKeating, Ciara
Author
Ameer, Aqsa and Saleem, Farrukh and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer and Javed, Sundus (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: 110957. ISSN 2352-3409
Ameer, Aqsa and Saleem, Farrukh and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Dataset of 130 metagenome-assembled genomes of healthy and diseased broiler chicken caeca from Pakistan. Data In Brief, 54: 110487. ISSN 2352-3409
Saleem, Farrukh and Ameer, Aqsa and Star-Shirko, Banaz and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Dataset of 569 metagenome-assembled genomes from the caeca of multiple chicken breeds from commercial and backyard farming setups of Pakistan. Data In Brief, 54: 110552. ISSN 2352-3409
See full publications listGundogdu, Ozan
Author
Ameer, Aqsa and Saleem, Farrukh and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer and Javed, Sundus (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: 110957. ISSN 2352-3409
Saleem, Farrukh and Ameer, Aqsa and Star-Shirko, Banaz and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Dataset of 569 metagenome-assembled genomes from the caeca of multiple chicken breeds from commercial and backyard farming setups of Pakistan. Data In Brief, 54: 110552. ISSN 2352-3409
See full publications listIjaz, Umer
Author
Cholet, Fabien and Vignola, Marta and Quinn, Dominic and Ijaz, Umer Z. and Sloan, William T. and Smith, Cindy J. (2025) Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: a meta-analysis. Water Research, 281: 123684. ISSN 0043-1354
Saleem, Farrukh and Ameer, Aqsa and Afzal, Farhan and Usman, Muhammad and Irshad, Hamid and Sattar, Sadia and Ijaz, Umer Zeeshan and Javed, Sundus (2025) A cross-sectional survey of poultry management systems, practices and antimicrobial use in relation to disease outbreak in Pakistan. BMC Research Notes, 18: 144. ISSN 1756-0500
Badar, Ayesha and Aqueel, Rhea and Nawaz, Ali and Ijaz, Umer Zeeshan and Malik, Kauser Abdulla (2025) Microbiota transplantation for Cotton Leaf Curl Disease suppression - core microbiome and transcriptome dynamics. Communications Biology, 8 (1): 380. ISSN 2399-3642
See full publications listJaved, Sundus
Author
Saleem, Farrukh and Ameer, Aqsa and Afzal, Farhan and Usman, Muhammad and Irshad, Hamid and Sattar, Sadia and Ijaz, Umer Zeeshan and Javed, Sundus (2025) A cross-sectional survey of poultry management systems, practices and antimicrobial use in relation to disease outbreak in Pakistan. BMC Research Notes, 18: 144. ISSN 1756-0500
Ameer, Aqsa and Saleem, Farrukh and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer and Javed, Sundus (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: 110957. ISSN 2352-3409
Saleem, Farrukh and Ameer, Aqsa and Star-Shirko, Banaz and Keating, Ciara and Gundogdu, Ozan and Ijaz, Umer Zeeshan and Javed, Sundus (2024) Dataset of 569 metagenome-assembled genomes from the caeca of multiple chicken breeds from commercial and backyard farming setups of Pakistan. Data In Brief, 54: 110552. ISSN 2352-3409
See full publications listAvailable under License Creative Commons Attribution.
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