Composite genome sequence of Bacillus clausii, a probiotic commercially available as Enterogermina®, and insights into its probiotic properties
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Abstract
Background: Some of the spore-forming strains of Bacillus probiotics are marketed commercially as they survive harsh gastrointestinal conditions and bestow health benefits to the host. Results: We report the composite genome of Bacillus clausii ENTPro from a commercially available probiotic Enterogermina ® and compare it with the genomes of other Bacillus probiotics. We find that the members of B. clausii species harbor high heterogeneity at the species as well as genus level. The genes conferring resistance to chloramphenicol, streptomycin, rifampicin, and tetracycline in the B. clausii ENTPro strain could be identified. The genes coding for the bacteriocin gallidermin, which prevents biofilm formation in the pathogens Staphylococcus aureus and S. epidermidis , were also identified. KEGG Pathway analysis suggested that the folate biosynthesis pathway, which depicts one of the important roles of probiotics in the host, is conserved completely in B. subtilis and minimally in B. clausii and other probiotics. Conclusions: We identified various antibiotic resistance, bacteriocins, stress-related, and adhesion-related domains, and industrially-relevant pathways, in the genomes of these probiotic bacteria that are likely to help them survive in the harsh gastrointestinal tract, facilitating adhesion to host epithelial cells, persistence during antibiotic treatment and combating bacterial infections.
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Genomic studies of the composite genome of Bacillus clausii from the probiotic Enterogermina formulation have reported a mobilome enriched with transposons and other mobile genetic elements, along with a novel plasmid sequence.
“Genomic studies of the composite genome of Bacillus clausii from the probiotic Enterogermina® formulation have similarly reported a mobilome enriched with transposons and other mobile genetic elements, along with a novel plasmid sequence.36”
From Safety and efficacy concerns in Indian probiotics: Insights from whole-genome sequencing and <i>in vitro</i> assessment (2026) · cites this paper as [36]
The Results section (‘Genome features of B. clausii ENTPro’; page unavailable) reports a novel plasmid sequence and labels a COG category ‘Mobilome: prophages, transposons.’ It does not report that the ENTPro mobilome is enriched with transposons or other mobile genetic elements, so the enrichment claim is unsupported. (LLM, conf=0.84)
Experimental — accuracy not yet measuredS. boulardii-based products lacked detectable ARGs or virulence factors while exhibiting intrinsic, non-transferable antibiotic resistance, supporting a comparatively favorable safety profile in high-risk clinical settings.
“In contrast to bacterial probiotics, S. boulardii–based products lacked detectable ARGs or virulence factors while exhibiting intrinsic, non-transferable antibiotic resistance, supporting a comparatively favorable safety profile in high-risk clinical settings.4,9,36,37”
From Safety and efficacy concerns in Indian probiotics: Insights from whole-genome sequencing and <i>in vitro</i> assessment (2026) · cites this paper as [36]
The Results section on antibiotic resistance examines Bacillus probiotics, not S. boulardii. Searches for S. boulardii and Saccharomyces boulardii found no passage addressing its resistance genes, virulence factors, transferability of resistance, or safety in high-risk settings. (LLM, conf=0.76)
Experimental — accuracy not yet measuredClinical studies have previously established S. boulardii's efficacy in reducing diarrhea duration in pediatric and adult populations, particularly in the context of antibiotic-associated diarrhea, Helicobacter pylori, and Clostridioides difficile infections.
“Clinical studies have previously established S. boulardii's efficacy in reducing diarrhea duration in pediatric and adult populations, particularly in the context of AAD, Helicobacter pylori, and Clostridioides difficile infections.9,36,37”
From Safety and efficacy concerns in Indian probiotics: Insights from whole-genome sequencing and <i>in vitro</i> assessment (2026) · cites this paper as [36]
The Background discusses Bacillus clausii and its effects on Clostridium difficile toxins, while the cited pediatric diarrhea trial appears only in the References. Searches for S. boulardii and clinical evidence on diarrhea duration found no passage in our copy supporting the claim about children, adults, or the specified infection contexts. (LLM, conf=0.78)
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- Authors
- Khatri, I., Sharma, G., & Subramanian, S.
- Affiliations
- Leiden University Medical Center (NL)
- Institute of Microbial Technology (IN)
- Corresponding author
- Subramanian, Srikrishna
- Venue
- BMC Microbiology
- Published
- 2019-12
- Volume
- 19
- Issue
- 1
- Pages
- 307-307
- ISSN
- 1471-2180 (ISSN-L)
- PMC
- PMC6937992
- OpenAlex
- W2998500456
- Cited by
- 80
- References
- 97
- Citations by year
- 2026: 5 · 2025: 8 · 2024: 15 · 2023: 8 · 2022: 22 · 2021: 15 · 2020: 7
- FWCI
- 8.49
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Microbiology (publishedVersion, cc-by)
- Research Square (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- Council of Scientific Research (CSIR) Network projects (HUM-CSIR-BSC-0119; GAP001)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant-Microbe Interactions and Immunity
- Keywords
- Bacillus clausii, probiotics, antibiotic resistance genes, gallidermin, bacteriocins, folate biosynthesis, biofilm inhibition, gastrointestinal survival, spore-forming bacteria
- MeSH terms
- Bacillus clausii, Whole Genome Sequencing, Bacterial Adhesion, Bacteriocins, Humans, Genome, Bacterial, Probiotics, Drug Resistance, Bacterial, Gastrointestinal Tract
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