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Previous research on the genomes of SFB from humans, rats, and mice has revealed significant differences among SFB strains associated with various hosts, suggesting that their evolution is closely linked to their relationships with specific hosts. However, the genome of SFB from chickens has not been extensively investigated. In this study, we present the metagenomic reconstruction of an SFB genome derived from the ileum of layer Lohmann Select Leghorn (LSL) chickens. We utilized Hi-C sequencing techniques to assemble the LSL-SFB and annotate the avian SFB from both turkeys and chickens. Our reference-guided consensus assembly, followed by Hi-C scaffolding, produced a high-quality genome for LSL-SFB. Our pangenomic analysis revealed substantial conservation of core gene clusters among mammalian SFB strains, but we also identified a distinct repertoire of genes in chicken and turkey SFB. Furthermore, metabolic network analysis indicated a reduced capacity for biosynthesis, signifying an increased reliance on the host, as shown by the absence of key biosynthetic and utilization pathways. We also discovered a unique flagellin subunit (fliC-2) in chicken SFB from different genetic lines and confirmed its interaction with the chicken flagellin receptor, Toll-like receptor five. This study provides the first high-quality genome and annotation of LSL-SFB, alongside that of turkeys, offering valuable insights into the mechanisms of host specificity and adaptation. Understanding the interactions between host-specific SFB and their hosts, as well as their role in promoting immune maturation, is essential for improving intestinal health.<\/jats:p>","DOI":"10.3390\/microorganisms14020341","type":"journal-article","created":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T12:49:44Z","timestamp":1770036584000},"page":"341","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Sequencing and Analysis of Chicken Segmented Filamentous Bacteria Genome Revealed Unique Avian-Specific Features"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3841-325X","authenticated-orcid":false,"given":"Jared","family":"Meinen-Jochum","sequence":"first","affiliation":[{"name":"Department of Food Science and Human Nutrition, Iowa State University, Ames, IA 50011, USA"},{"name":"Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8743-2847","authenticated-orcid":false,"given":"Viswanathan","family":"Satheesh","sequence":"additional","affiliation":[{"name":"Office of Biotechnology, Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6848-2144","authenticated-orcid":false,"given":"Rick E.","family":"Masonbrink","sequence":"additional","affiliation":[{"name":"Office of Biotechnology, Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonathan","family":"Rodriguez-Gallegos","sequence":"additional","affiliation":[{"name":"Department of Food Science and Human Nutrition, Iowa State University, Ames, IA 50011, USA"},{"name":"Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5555-4949","authenticated-orcid":false,"given":"David A.","family":"Wright","sequence":"additional","affiliation":[{"name":"Office of Biotechnology, DNA Facility, Iowa State University, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8015-9665","authenticated-orcid":false,"given":"Andrew J.","family":"Severin","sequence":"additional","affiliation":[{"name":"Office of Biotechnology, Genome Informatics Facility, Iowa State University, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4967-7173","authenticated-orcid":false,"given":"Melha","family":"Mellata","sequence":"additional","affiliation":[{"name":"Department of Food Science and Human Nutrition, Iowa State University, Ames, IA 50011, USA"},{"name":"Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA 50011, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,2,2]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/nature14027","article-title":"Growth and host interaction of mouse segmented filamentous bacteria in vitro","volume":"520","author":"Schnupf","year":"2015","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1016\/j.cell.2009.09.033","article-title":"Induction of intestinal Th17 cells by segmented filamentous bacteria","volume":"139","author":"Ivanov","year":"2009","journal-title":"Cell"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1016\/j.jim.2015.03.020","article-title":"Induction of Th17 cells by segmented filamentous bacteria in the murine intestine","volume":"421","author":"Farkas","year":"2015","journal-title":"J. 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