{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T02:44:45Z","timestamp":1785725085007,"version":"3.56.0"},"reference-count":43,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:00:00Z","timestamp":1785542400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan","award":["AP23485953"],"award-info":[{"award-number":["AP23485953"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Monitoring poultry microbiota and antimicrobial resistance genes is important, as they can reflect flock health, farm conditions, and the level of antimicrobial resistance. Although shotgun metagenomics has been widely applied worldwide to investigate poultry microbiota and antimicrobial resistance, comparable baseline datasets describing the cloacal microbiota and resistome of poultry in Kazakhstan are scarce. In this study, taxonomic and resistome profiles were characterized in pooled metagenomes of the cloacal microbiota of chickens sampled from household and industrial poultry farms in Kazakhstan. Cloacal swabs were collected from laying hens, pooled at the house level, and analyzed using high-throughput metagenomic sequencing. Taxonomic profiles were generated at the genus level, and antimicrobial resistance gene signals were summarized by drug class. Compositional patterns were assessed using CLR\/Aitchison ordination, the Mantel test, and Procrustes analysis. The pooled samples exhibited heterogeneous microbiota profiles at the genus level and included taxa of veterinary interest, such as Chlamydia, Avibacterium, and Gallibacterium spp. Resistome profiling revealed a broad but uneven distribution of antimicrobial resistance signals, including those associated with tetracyclines, fluoroquinolones, aminoglycosides, and beta-lactams. Taxonomic and resistome profiles showed preliminary alignment at the matrix level, indicating that resistome variations are partially linked to microbial community structure.<\/jats:p>","DOI":"10.3390\/microorganisms14081689","type":"journal-article","created":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T01:43:27Z","timestamp":1785721407000},"page":"1689","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Pooled Shotgun Metagenomics Reveals Cloacal Microbiota Composition and Resistome Patterns in Chickens from Kazakhstan"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0397-7840","authenticated-orcid":false,"given":"Ilya","family":"Korotetskiy","sequence":"first","affiliation":[{"name":"Department Biochemical Engineering, LLC International Engineering and Technological University, 050060 Almaty, Kazakhstan"},{"name":"JSC Scientific Center for Anti-Infectious Drugs, 050060 Almaty, Kazakhstan"},{"name":"LLP Research and Production Association Kazpharmacom, 040900 Irgeli, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9490-9300","authenticated-orcid":false,"given":"Sergey","family":"Shilov","sequence":"additional","affiliation":[{"name":"JSC Scientific Center for Anti-Infectious Drugs, 050060 Almaty, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatyana","family":"Kuznetsova","sequence":"additional","affiliation":[{"name":"JSC Scientific Center for Anti-Infectious Drugs, 050060 Almaty, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6436-803X","authenticated-orcid":false,"given":"Natalya","family":"Zubenko","sequence":"additional","affiliation":[{"name":"JSC Scientific Center for Anti-Infectious Drugs, 050060 Almaty, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7194-0556","authenticated-orcid":false,"given":"Lyudmila","family":"Ivanova","sequence":"additional","affiliation":[{"name":"JSC Scientific Center for Anti-Infectious Drugs, 050060 Almaty, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena","family":"Solodova","sequence":"additional","affiliation":[{"name":"Department Biochemical Engineering, LLC International Engineering and Technological University, 050060 Almaty, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadezhda","family":"Korotetskaya","sequence":"additional","affiliation":[{"name":"LLP Research and Production Association Kazpharmacom, 040900 Irgeli, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alfia","family":"Tugeyeva","sequence":"additional","affiliation":[{"name":"Department Biochemical Engineering, LLC International Engineering and Technological University, 050060 Almaty, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timur","family":"Izmailov","sequence":"additional","affiliation":[{"name":"LLP Research and Production Association Kazpharmacom, 040900 Irgeli, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,1]]},"reference":[{"key":"ref_1","unstructured":"Food and Agriculture Organization of the United Nations (2026, June 10). 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