{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T12:12:37Z","timestamp":1789560757841,"version":"build-2803163510"},"reference-count":45,"publisher":"Elsevier BV","issue":"3","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T00:00:00Z","timestamp":1784246400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005844","name":"Universitas Diponegoro","doi-asserted-by":"publisher","award":["222\\u2013743\/UN7\\u00B7D2\/PP\/IV\/2025"],"award-info":[{"award-number":["222\\u2013743\/UN7\\u00B7D2\/PP\/IV\/2025"]}],"id":[{"id":"10.13039\/501100005844","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Genetic Engineering and Biotechnology"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.1016\/j.jgeb.2026.100775","type":"journal-article","created":{"date-parts":[[2026,8,6]],"date-time":"2026-08-06T18:00:04Z","timestamp":1786039204000},"page":"100775","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comprehensive profiling of antibiotic resistance genes and functional clusters of orthologous groups annotation of gut microbiota in Indonesian Kedu chickens"],"prefix":"10.1016","volume":"24","author":[{"given":"Ikania","family":"Agusetyaningsih","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dela Ayu","family":"Lestari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nuruliarizki Shinta","family":"Pandupuspitasari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Asep","family":"Setiaji","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Syaddad Verahry","family":"Philco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sugiharto","family":"Sugiharto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"11","key":"10.1016\/j.jgeb.2026.100775_bb0005","doi-asserted-by":"crossref","first-page":"427","DOI":"10.3390\/environments12110427","article-title":"Antibiotic resistance genes in food animal production: environmental implications and one health challenges","volume":"12","author":"Wojnarowski","year":"2025","journal-title":"Environments"},{"issue":"2","key":"10.1016\/j.jgeb.2026.100775_bb0010","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.01907-21","article-title":"Metagenomic insights into chicken gut antibiotic resistomes and microbiomes","volume":"10","author":"Yang","year":"2022","journal-title":"Microbiol. Spectrum"},{"key":"10.1016\/j.jgeb.2026.100775_bb0015","article-title":"Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms","volume":"11","author":"Sun","year":"2020","journal-title":"Nat. Commun."},{"issue":"9","key":"10.1016\/j.jgeb.2026.100775_bb0020","first-page":"1167","article-title":"Metagenomic insights into the resistome and microbial community in chickens","volume":"5","author":"Li","year":"2020","journal-title":"Nat. Microbiol."},{"issue":"6","key":"10.1016\/j.jgeb.2026.100775_bb0025","first-page":"445","article-title":"Antibiotic resistance gene reservoir in live poultry markets","volume":"78","author":"Wang","year":"2019","journal-title":"J. Inf. Secur."},{"issue":"2","key":"10.1016\/j.jgeb.2026.100775_bb0030","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.bsheal.2024.02.006","article-title":"The multi-kingdom microbiome catalog of the chicken gastrointestinal tract","volume":"6","author":"Wang","year":"2024","journal-title":"Biosaf Health"},{"key":"10.1016\/j.jgeb.2026.100775_bb0035","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.1038\/s42003-021-02827-2","article-title":"Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes","volume":"4","author":"Feng","year":"2021","journal-title":"Commun Biol"},{"key":"10.1016\/j.jgeb.2026.100775_bb0040","doi-asserted-by":"crossref","DOI":"10.1016\/j.envint.2021.106534","article-title":"More diversified antibiotic resistance genes in chickens and workers of the live poultry markets","volume":"153","author":"Wang","year":"2021","journal-title":"Environ. Int."},{"key":"10.1016\/j.jgeb.2026.100775_bb0045","doi-asserted-by":"crossref","DOI":"10.1016\/j.envint.2020.105649","article-title":"Integrated metagenomic and metatranscriptomic profiling reveals differentially expressed resistomes in human, chicken, and pig gut microbiomes","volume":"138","author":"Wang","year":"2020","journal-title":"Environ. Int."},{"issue":"5","key":"10.1016\/j.jgeb.2026.100775_bb0050","doi-asserted-by":"crossref","DOI":"10.1099\/mic.0.001333","article-title":"Role of bacterial efflux pumps in antibiotic resistance, virulence, and strategies to discover novel efflux pump inhibitors","volume":"169","author":"Gaurav","year":"2023","journal-title":"Microbiology (Reading)"},{"issue":"4","key":"10.1016\/j.jgeb.2026.100775_bb0055","doi-asserted-by":"crossref","first-page":"795","DOI":"10.3390\/molecules23040795","article-title":"Antibiotic use in agriculture and its consequential resistance in environmental sources: potential public health implications","volume":"23","author":"Manyi-Loh","year":"2018","journal-title":"Molecules"},{"issue":"7","key":"10.1016\/j.jgeb.2026.100775_bb0060","doi-asserted-by":"crossref","first-page":"479","DOI":"10.3390\/vetsci10070479","article-title":"Meta-analysis on the global prevalence of tetracycline resistance in Escherichia coli isolated from beef cattle","volume":"10","author":"Messele","year":"2023","journal-title":"Vet Sci"},{"issue":"Pt A","key":"10.1016\/j.jgeb.2026.100775_bb0065","article-title":"Strict relationship between class 1 integrons and resistance to sulfamethoxazole in Escherichia coli","volume":"161","author":"Santos","year":"2021","journal-title":"Microb. Pathog."},{"issue":"1","key":"10.1016\/j.jgeb.2026.100775_bb0070","doi-asserted-by":"crossref","first-page":"7","DOI":"10.3892\/br.2021.1490","article-title":"Mechanisms of gram-positive vancomycin resistance (review)","volume":"16","author":"Selim","year":"2022","journal-title":"Biomed Rep"},{"issue":"1","key":"10.1016\/j.jgeb.2026.100775_bb0075","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1186\/s40168-024-01800-5","article-title":"Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition","volume":"12","author":"Li","year":"2024","journal-title":"Microbiome"},{"issue":"3","key":"10.1016\/j.jgeb.2026.100775_bb0080","doi-asserted-by":"crossref","first-page":"402","DOI":"10.3390\/ph18030402","article-title":"Combating antibiotic resistance: mechanisms, multidrug-resistant pathogens, and novel therapeutic approaches: an updated review","volume":"18","author":"Elshobary","year":"2025","journal-title":"Pharmaceuticals"},{"issue":"13","key":"10.1016\/j.jgeb.2026.100775_bb0085","doi-asserted-by":"crossref","first-page":"5776","DOI":"10.3390\/app14135776","article-title":"Antibiotic resistance in the farming environment","volume":"14","author":"Karwowska","year":"2024","journal-title":"Appl. Sci."},{"key":"10.1016\/j.jgeb.2026.100775_bb0090","doi-asserted-by":"crossref","DOI":"10.1016\/j.microb.2025.100515","article-title":"Prevalence and antimicrobial resistance in enterococci isolated from semi-intensive and free-range poultry farms in peri-urban Wakiso and rural Soroti, Uganda","volume":"8","author":"Ochieng","year":"2025","journal-title":"Microbe"},{"issue":"1","key":"10.1016\/j.jgeb.2026.100775_bb0095","doi-asserted-by":"crossref","first-page":"10034","DOI":"10.1038\/s41467-024-54459-9","article-title":"Evidence of horizontal gene transfer and environmental selection impacting antibiotic resistance evolution in soil-dwelling Listeria","volume":"15","author":"Goh","year":"2024","journal-title":"Nat. Commun."},{"issue":"1","key":"10.1016\/j.jgeb.2026.100775_bb0100","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1186\/s40104-022-00786-0","article-title":"Production systems and important antimicrobial resistant-pathogenic bacteria in poultry: a review","volume":"13","author":"Mak","year":"2022","journal-title":"J Anim Sci Biotechnol"},{"key":"10.1016\/j.jgeb.2026.100775_bb0105","article-title":"A review of current bacterial resistance to antibiotics in food animals","volume":"13","author":"Xu","year":"2022","journal-title":"Front. Microbiol."},{"issue":"12","key":"10.1016\/j.jgeb.2026.100775_bb0110","doi-asserted-by":"crossref","first-page":"1664","DOI":"10.3390\/antibiotics12121664","article-title":"Analysis of resistance gene diversity in the intestinal microbiome of broilers from two types of broiler farms in Hebei Province, China","volume":"12","author":"Liang","year":"2023","journal-title":"Antibiotics (Basel)."},{"issue":"1","key":"10.1016\/j.jgeb.2026.100775_bb0115","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1038\/s41522-024-00497-6","article-title":"Bacterial capsules: occurrence, mechanism, and function","volume":"10","author":"Gao","year":"2024","journal-title":"NPJ Biofilms Microbiomes"},{"key":"10.1016\/j.jgeb.2026.100775_bb0120","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2025.1633585","article-title":"The AcrAB efflux pump contributes to the virulence of enteroaggregative E. Coli by influencing the aggregative behavior","volume":"15","author":"Laudazzi","year":"2025","journal-title":"Front. Cell. Infect. Microbiol."},{"issue":"1","key":"10.1016\/j.jgeb.2026.100775_bb0125","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/s40168-023-01745-1","article-title":"Metagenome-assembled genome reveals species and functional composition of Jianghan chicken gut microbiota and isolation of Pediococcus acidilactic with probiotic properties","volume":"12","author":"Shen","year":"2024","journal-title":"Microbiome"},{"issue":"8","key":"10.1016\/j.jgeb.2026.100775_bb0130","doi-asserted-by":"crossref","DOI":"10.1007\/s13205-019-1834-1","article-title":"Comparative metagenomic sequencing analysis of cecum microbiotal diversity and function in broilers and layers","volume":"9","author":"Qi","year":"2019","journal-title":"3 Biotech"},{"issue":"20","key":"10.1016\/j.jgeb.2026.100775_bb0135","doi-asserted-by":"crossref","first-page":"13094","DOI":"10.1021\/acsomega.1c00739","article-title":"Alterations and correlations of the gut microbiome, performance, egg quality, and serum biochemical indexes in laying hens with low-protein amino acid-deficient diets","volume":"6","author":"Geng","year":"2021","journal-title":"ACS Omega"},{"issue":"5","key":"10.1016\/j.jgeb.2026.100775_bb0140","doi-asserted-by":"crossref","DOI":"10.1016\/j.psj.2021.101036","article-title":"Amino acid requirements for laying hens: a comprehensive review","volume":"100","author":"Macelline","year":"2021","journal-title":"Poult. Sci."},{"issue":"4","key":"10.1016\/j.jgeb.2026.100775_bb0145","doi-asserted-by":"crossref","DOI":"10.1002\/imt2.198","article-title":"Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition","volume":"3","author":"Ma","year":"2024","journal-title":"Imeta"},{"issue":"7","key":"10.1016\/j.jgeb.2026.100775_bb0150","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a030288","article-title":"Overview of the cytoskeleton from an evolutionary perspective","volume":"10","author":"Pollard","year":"2018","journal-title":"Cold Spring Harb. Perspect. Biol."},{"issue":"1","key":"10.1016\/j.jgeb.2026.100775_bb0155","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/1423-0127-18-23","article-title":"Composition and conservation of the mRNA-degrading machinery in bacteria","volume":"18","author":"Kaberdin","year":"2011","journal-title":"J. Biomed. Sci."},{"issue":"3","key":"10.1016\/j.jgeb.2026.100775_bb0160","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1080\/10409238.2019.1651816","article-title":"Bacterial ribonucleases and their roles in RNA metabolism","volume":"54","author":"Bechhofer","year":"2019","journal-title":"Crit. Rev. Biochem. Mol. Biol."},{"issue":"3","key":"10.1016\/j.jgeb.2026.100775_bb0165","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1038\/nrmicro2261","article-title":"Bacterial nucleoid-associated proteins, nucleoid structure and gene expression","volume":"8","author":"Dillon","year":"2010","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.jgeb.2026.100775_bb0170","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2021.726923","article-title":"Genome-resolved metagenomics of the chicken gut microbiome","volume":"12","author":"Segura-Wang","year":"2021","journal-title":"Front. Microbiol."},{"issue":"2","key":"10.1016\/j.jgeb.2026.100775_bb0175","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1111\/1574-6968.12608","article-title":"The chicken gastrointestinal microbiome","volume":"360","author":"Oakley","year":"2014","journal-title":"FEMS Microbiol. Lett."},{"key":"10.1016\/j.jgeb.2026.100775_bb0180","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/nri2515","article-title":"The gut microbiota shapes intestinal immune responses during health and disease","volume":"9","author":"Round","year":"2009","journal-title":"Nat. Rev. Immunol."},{"issue":"6","key":"10.1016\/j.jgeb.2026.100775_bb0185","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1016\/j.biotechadv.2012.04.010","article-title":"Microbial carbohydrate esterases deacetylating plant polysaccharides","volume":"30","author":"Biely","year":"2012","journal-title":"Biotechnol. Adv."},{"key":"10.1016\/j.jgeb.2026.100775_bb0190","doi-asserted-by":"crossref","DOI":"10.1186\/1754-6834-6-93","article-title":"Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates","volume":"6","author":"Reyes-Ortiz","year":"2013","journal-title":"Biotechnol. Biofuels"},{"issue":"1","key":"10.1016\/j.jgeb.2026.100775_bb0195","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/s40643-021-00432-z","article-title":"Pectinolytic lyases: a comprehensive review of sources, category, property, structure, and catalytic mechanism of pectate lyases and pectin lyases","volume":"8","author":"Zheng","year":"2021","journal-title":"Bioresour. Bioprocess."},{"issue":"1","key":"10.1016\/j.jgeb.2026.100775_bb0200","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1186\/1754-6834-6-41","article-title":"Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes","volume":"6","author":"Levasseur","year":"2013","journal-title":"Biotechnol. Biofuels"},{"key":"10.1016\/j.jgeb.2026.100775_bb0205","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1038\/nrmicro925","article-title":"Cellulosomes: plant-cell-wall-degrading enzyme complexes","volume":"2","author":"Doi","year":"2004","journal-title":"Nat. Rev. Microbiol."},{"issue":"Pt 3","key":"10.1016\/j.jgeb.2026.100775_bb0210","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1042\/BJ20040892","article-title":"Carbohydrate-binding modules: fine-tuning polysaccharide recognition","volume":"382","author":"Boraston","year":"2004","journal-title":"Biochem. J."},{"key":"10.1016\/j.jgeb.2026.100775_bb0215","doi-asserted-by":"crossref","DOI":"10.1016\/j.phrs.2021.105420","article-title":"The role of short-chain fatty acids in intestinal barrier function, inflammation, oxidative stress, and colonic carcinogenesis","volume":"165","author":"Liu","year":"2021","journal-title":"Pharmacol. Res."},{"key":"10.1016\/j.jgeb.2026.100775_bb0220","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/B978-0-12-407672-3.00003-4","article-title":"Regulation of bacterial pathogenesis by intestinal short-chain fatty acids","volume":"85","author":"Sun","year":"2013","journal-title":"Adv. Appl. Microbiol."},{"issue":"4","key":"10.1016\/j.jgeb.2026.100775_bb0225","doi-asserted-by":"crossref","first-page":"265","DOI":"10.3390\/antibiotics8040265","article-title":"Short chain fatty acids commonly produced by gut microbiota influence Salmonella enterica motility, biofilm formation, and gene expression","volume":"8","author":"Lamas","year":"2019","journal-title":"Antibiotics (Basel)"}],"container-title":["Journal of Genetic Engineering and Biotechnology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1687157X26001198?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1687157X26001198?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T11:53:10Z","timestamp":1789559590000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1687157X26001198"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":45,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2026,9]]}},"alternative-id":["S1687157X26001198"],"URL":"https:\/\/doi.org\/10.1016\/j.jgeb.2026.100775","relation":{},"ISSN":["1687-157X"],"issn-type":[{"value":"1687-157X","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Comprehensive profiling of antibiotic resistance genes and functional clusters of orthologous groups annotation of gut microbiota in Indonesian Kedu chickens","name":"articletitle","label":"Article Title"},{"value":"Journal of Genetic Engineering and Biotechnology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jgeb.2026.100775","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 Published by Elsevier Inc. on behalf of Academy of Scientific Research and Technology.","name":"copyright","label":"Copyright"}],"article-number":"100775"}}