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Genome-informed qPCR tracking revealed preferential persistence of Bacillus subtilis BS9 in the broiler chicken gastrointestinal tract.

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Τίτλος: Genome-informed qPCR tracking revealed preferential persistence of Bacillus subtilis BS9 in the broiler chicken gastrointestinal tract.
Συγγραφείς: Ni J; Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China., Cai H; Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China., Gelinas A; Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada., Zhan X; Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada.; School of Animal Science and Technology, Foshan University, Foshan, Guangdong, China., Qi N; Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China.; Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada., Kiarie EG; Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada., Li J; Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada.
Πηγή: Microbiology spectrum [Microbiol Spectr] 2026 Oct 06; Vol. 14 (10), pp. e0092626. Date of Electronic Publication: 2026 Sep 17.
Τύπος έκδοσης: Journal Article
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: ASM Press Country of Publication: United States NLM ID: 101634614 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2165-0497 (Electronic) Linking ISSN: 21650497 NLM ISO Abbreviation: Microbiol Spectr Subsets: MEDLINE
Imprint Name(s): Original Publication: Washington, DC : ASM Press, 2013-
Ιατρικοί όροι (MeSH): Chickens*/microbiology , Bacillus subtilis*/genetics , Bacillus subtilis*/isolation & purification , Bacillus subtilis*/classification , Gastrointestinal Tract*/microbiology , Real-Time Polymerase Chain Reaction*/methods, Probiotics/administration & dosage ; Animals ; Genome, Bacterial
Περίληψη: This study aimed to develop a strain-specific quantitative PCR (qPCR) assay for Bacillus subtilis 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 in vivo 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.IMPORTANCEThis work provides the first detailed account of B. subtilis BS9's 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.
Competing Interests: The authors declare no conflict of interest.
Grant Information: 401904 Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC); 030537 Ontario Ministry of Agriculture, Food and Rural Affairs; 055818 CBS Bio Platforms Canada
Contributed Indexing: Keywords: Bacillus subtilis; chicken intestinal tract; persistence; qPCR-based specific detection
Entry Date(s): Date Created: 20260917 Date Completed: 20261007 Latest Revision: 20261007
Update Code: 20261007
DOI: 10.1128/spectrum.00926-26
PMID: 42752246
Βάση Δεδομένων: MEDLINE
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  Data: Genome-informed qPCR tracking revealed preferential persistence of Bacillus subtilis BS9 in the broiler chicken gastrointestinal tract.
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  Data: <searchLink fieldCode="AU" term="%22Ni+J%22">Ni J</searchLink>; Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China.<br /><searchLink fieldCode="AU" term="%22Cai+H%22">Cai H</searchLink>; Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China.<br /><searchLink fieldCode="AU" term="%22Gelinas+A%22">Gelinas A</searchLink>; Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada.<br /><searchLink fieldCode="AU" term="%22Zhan+X%22">Zhan X</searchLink>; Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada.; School of Animal Science and Technology, Foshan University, Foshan, Guangdong, China.<br /><searchLink fieldCode="AU" term="%22Qi+N%22">Qi N</searchLink>; Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China.; Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada.<br /><searchLink fieldCode="AU" term="%22Kiarie+EG%22">Kiarie EG</searchLink>; Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada.<br /><searchLink fieldCode="AU" term="%22Li+J%22">Li J</searchLink>; Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada.
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  Data: <searchLink fieldCode="JN" term="%22101634614%22">Microbiology spectrum</searchLink> [Microbiol Spectr] 2026 Oct 06; Vol. 14 (10), pp. e0092626. <i>Date of Electronic Publication: </i>2026 Sep 17.
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  Data: <i>Original Publication</i>: Washington, DC : ASM Press, 2013-
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  Data: <searchLink fieldCode="MM" term="%22Chickens%22">Chickens*</searchLink>/<searchLink fieldCode="MM" term="%22Chickens+microbiology%22">microbiology</searchLink> <br /><searchLink fieldCode="MM" term="%22Bacillus+subtilis%22">Bacillus subtilis*</searchLink>/<searchLink fieldCode="MM" term="%22Bacillus+subtilis+genetics%22">genetics</searchLink> <br /><searchLink fieldCode="MM" term="%22Bacillus+subtilis%22">Bacillus subtilis*</searchLink>/<searchLink fieldCode="MM" term="%22Bacillus+subtilis+isolation+%26+purification%22">isolation & purification</searchLink> <br /><searchLink fieldCode="MM" term="%22Bacillus+subtilis%22">Bacillus subtilis*</searchLink>/<searchLink fieldCode="MM" term="%22Bacillus+subtilis+classification%22">classification</searchLink> <br /><searchLink fieldCode="MM" term="%22Gastrointestinal+Tract%22">Gastrointestinal Tract*</searchLink>/<searchLink fieldCode="MM" term="%22Gastrointestinal+Tract+microbiology%22">microbiology</searchLink> <br /><searchLink fieldCode="MM" term="%22Real-Time+Polymerase+Chain+Reaction%22">Real-Time Polymerase Chain Reaction*</searchLink>/<searchLink fieldCode="MM" term="%22Real-Time+Polymerase+Chain+Reaction+methods%22">methods</searchLink><br /><searchLink fieldCode="MH" term="%22Probiotics%22">Probiotics</searchLink>/<searchLink fieldCode="MH" term="%22Probiotics+administration+%26+dosage%22">administration & dosage</searchLink> ; <searchLink fieldCode="MH" term="%22Animals%22">Animals</searchLink> ; <searchLink fieldCode="MH" term="%22Genome%2C+Bacterial%22">Genome, Bacterial</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: This study aimed to develop a strain-specific quantitative PCR (qPCR) assay for Bacillus subtilis 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 in vivo 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.IMPORTANCEThis work provides the first detailed account of B. subtilis BS9's 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.
– Name: Abstract
  Label: Competing Interests
  Group: Ab
  Data: The authors declare no conflict of interest.
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  Label: Grant Information
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  Data: 401904 Canadian Government | Natural Sciences and Engineering Research Council of Canada (NSERC); 030537 Ontario Ministry of Agriculture, Food and Rural Affairs; 055818 CBS Bio Platforms Canada
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  Label: Contributed Indexing
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  Data: <i>Keywords: </i>Bacillus subtilis; chicken intestinal tract; persistence; qPCR-based specific detection
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  Data: <i>Date Created: </i>20260917 <i>Date Completed: </i>20261007 <i>Latest Revision: </i>20261007
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  Data: 10.1128/spectrum.00926-26
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  Data: 42752246
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      – SubjectFull: Probiotics administration & dosage
        Type: general
      – SubjectFull: Animals
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