{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:27:25Z","timestamp":1792787245407,"version":"4.5.0"},"reference-count":28,"publisher":"American Society for Microbiology","issue":"10","license":[{"start":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T00:00:00Z","timestamp":1791244800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T00:00:00Z","timestamp":1791244800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"name":"Canadian Government | Natural Sciences and Engineering Research Council of Canada","award":["401904"],"award-info":[{"award-number":["401904"]}],"id":[{"id":"https:\/\/ror.org\/01h531d29","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000094","name":"Ontario Ministry of Agriculture, Food and Rural Affairs","doi-asserted-by":"publisher","award":["030537"],"award-info":[{"award-number":["030537"]}],"id":[{"id":"10.13039\/501100000094","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CBS Bio Platforms Canada","award":["055818"],"award-info":[{"award-number":["055818"]}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2026,10,6]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      This study aimed to develop a strain-specific quantitative PCR (qPCR) assay for\n                      <jats:italic toggle=\"yes\">Bacillus subtilis<\/jats:italic>\n                      BS9 and characterize its persistence and spatial distribution in the broiler chicken gastrointestinal tract. Whole-genome sequencing and comparative genomic analysis identified a unique 110-bp sequence within a strain-specific genomic island, which was used to design a highly specific qPCR assay with excellent efficiency and sensitivity. In a 14-day\n                      <jats:italic toggle=\"yes\">in vivo<\/jats:italic>\n                      trial, broiler chicks receiving daily oral doses of BS9 were analyzed using both culture-based methods and the newly developed qPCR. The assay was applied qualitatively, presence or absence, to detect BS9 in intestinal samples. BS9 was detected exclusively in the duodenum, jejunum, and cecum, with no presence in the gizzard or ileum. These findings demonstrate that BS9 exhibits region-specific persistence in the gut, likely reflecting adaptation to distinct physiological niches, which may contribute to its probiotic mechanisms.\n                    <\/jats:p>\n                    <jats:sec>\n                      <jats:title>IMPORTANCE<\/jats:title>\n                      <jats:p>\n                        This work provides the first detailed account of\n                        <jats:italic toggle=\"yes\">B. subtilis<\/jats:italic>\n                        BS9\u2019s spatial persistence in poultry, revealing preferential adherence to specific intestinal regions. The strain-specific qPCR assay developed here offers a precise, culture-independent tool for tracking BS9 in complex gut environments. These insights into the genetic basis and tissue tropism of BS9 persistence advance our understanding of probiotic-host interactions and establish a framework for characterizing novel probiotic strains.\n                      <\/jats:p>\n                    <\/jats:sec>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.00926-26","type":"journal-article","created":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T13:02:53Z","timestamp":1789650173000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Genome-informed qPCR tracking revealed preferential persistence of\n                    <i>Bacillus subtilis<\/i>\n                    BS9 in the broiler chicken gastrointestinal tract"],"prefix":"10.1128","volume":"14","author":[{"given":"Junli","family":"Ni","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01rkwtz72","id-type":"ROR","asserted-by":"publisher"}],"name":"Institute of 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