{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T06:10:16Z","timestamp":1790143816622,"version":"4.0.1"},"reference-count":49,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:00:00Z","timestamp":1790121600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Inroduction<\/jats:title>\n                    <jats:p>\n                      <jats:italic>Burkholderia cepacia<\/jats:italic>\n                      is a representative member of the\n                      <jats:italic>Burkholderia cepacia<\/jats:italic>\n                      complex (Bcc) and is widely distributed in water and soil environments. It has a propensity to form biofilms in water-based products, making it a significant contaminant in the pharmaceutical, cosmetic, and food industries and posing threats to product quality control and public health. Therefore, rapid and accurate species-level identification of\n                      <jats:italic>B. cepacia<\/jats:italic>\n                      is of great importance.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      To achieve rapid and accurate species-level identification of\n                      <jats:italic>B. cepacia<\/jats:italic>\n                      , we performed a pan-genome analysis based on 138 high-quality genome sequences covering\n                      <jats:italic>B. cepacia<\/jats:italic>\n                      and its closely related Bcc species with taxonomic positions validated by average nucleotide identity (ANI) analysis. A conserved core gene encoding a glycosyl hydrolase family 18 (GH18) protein was identified as a species-specific molecular marker. A specific primer pair comprising SEQ ID NO.2 and SEQ ID NO.3 was designed based on this marker and validated with both genome sequences and bacterial pure cultures.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The GH18-encoding gene is highly conserved across 115\n                      <jats:italic>B. cepacia<\/jats:italic>\n                      strains (sequence identities ranging from 90.3 to 100.0%) and is absent in all other Bcc species examined. The primer pair exhibited high inclusivity and exclusivity for\n                      <jats:italic>B. cepacia<\/jats:italic>\n                      . The established PCR method achieved a detection limit of 5 pg\/\u03bcL for pure genomic DNA and 10\n                      <jats:sup>3<\/jats:sup>\n                      CFU\/mL in artificially contaminated water-based personal care and medical device products.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>\n                      The identification of this conserved core gene provides a promising basis for the rapid and accurate species-level detection of\n                      <jats:italic>B. cepacia<\/jats:italic>\n                      . Given the widespread occurrence of\n                      <jats:italic>B. cepacia<\/jats:italic>\n                      in water and soil environments and its ability to form biofilms in water-based products, such a species-specific molecular marker may help improve contamination monitoring and quality control in the pharmaceutical, cosmetic, and food industries, thereby contributing to public health protection.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1915686","type":"journal-article","created":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T05:49:39Z","timestamp":1790142579000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Pan-genome analysis identifies a Burkholderia cepacia-specific gene marker for rapid species-level identification"],"prefix":"10.3389","volume":"17","author":[{"given":"Kun","family":"Cheng","sequence":"first","affiliation":[{"name":"China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries CO., LTD.","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuaicheng","family":"Mu","sequence":"additional","affiliation":[{"name":"China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries CO., LTD.","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huifen","family":"Feng","sequence":"additional","affiliation":[{"name":"China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries CO., LTD.","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui","family":"Liu","sequence":"additional","affiliation":[{"name":"China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries CO., LTD.","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Liu","sequence":"additional","affiliation":[{"name":"China National Accreditation Service for Conformity Assessment","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ling","family":"Li","sequence":"additional","affiliation":[{"name":"China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries CO., LTD.","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiaqi","family":"Liu","sequence":"additional","affiliation":[{"name":"China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries CO., LTD.","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiwei","family":"Wu","sequence":"additional","affiliation":[{"name":"China National Accreditation Service for Conformity Assessment","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanyuan","family":"Ge","sequence":"additional","affiliation":[{"name":"China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries CO., LTD.","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lei","family":"Zhai","sequence":"additional","affiliation":[{"name":"China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries CO., LTD.","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Su","family":"Yao","sequence":"additional","affiliation":[{"name":"China Center of Industrial Culture Collection, China National Research Institute of Food and Fermentation Industries CO., LTD.","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,23]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"416","DOI":"10.1016\/j.jmb.2008.12.045","article-title":"Domain-based and family-specific sequence identity thresholds increase the levels of reliable protein function transfer","volume":"387","author":"Addou","year":"2009","journal-title":"J. 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