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
AI Summary:
The article focuses on the recovery of prokaryotic organisms, including bacteria and archaea, from 9 different groups of chicken raised in different farm setups in Pakistan.AI Topics:
This article focuses the recovery of prokaryotic organisms including bacteria and archaea from 9 different groups of chicken raised in different farm setups in Pakistan. The groups comprise of three different breeds (Broilers, White Layers, and Black Australorp) of chicken raised in different farming setups that include antibiotic-free control, commercial (open and controlled shed), and backyard farms. We have recovered 569 Metagenomics-Assembled Genomes (MAGs) with a completeness of ≥50% and contamination of ≤10%. For each MAG, functional annotations were obtained that include KEGG modules, carbohydrate active enzymes (CAZymes), peptidases, geochemical cycles, antibiotic resistance genes, stress genes, and virulence genes. Furthermore, two different sets of Single Copy Genes (SCGs) were used to construct the phylogenetic trees. Based on the reconstructed phylogeny, phylogenetic gain of each MAG is calculated to give an account of novelty.
Saleem, 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 listAmeer, 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 listStar-Shirko, Banaz
Author
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 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.
Download (1MB) | Preview
 |