Comprehensive pan‐genome analysis of Lactiplantibacillus plantarum complete genomes
Open accessAbstract
AIMS: The aim of this work was to refine the taxonomy and the functional characterization of publicly available Lactiplantibacillus plantarum complete genomes through a pan-genome analysis. Particular attention was paid in depicting the probiotic potential of each strain. METHODS AND RESULTS: Complete genome sequence of 127 L. plantarum strains, without detected anomalies, was downloaded from NCBI. Roary analysis of L. plantarum pan-genome identified 1436 core, 414 soft core, 1858 shell and 13,203 cloud genes, highlighting the 'open' nature of L. plantarum pan-genome. Identification and characterization of plasmid content, mobile genetic elements, adaptative immune system and probiotic marker genes (PMGs) revealed unique features across all the L. plantarum strains included in the present study. Considering our updated list of PMGs, we determined that approximatively 70% of the PMGs belongs to the core/soft-core genome. CONCLUSIONS: The comparative genomic analysis conducted in this study provide new insights into the genomic content and variability of L. plantarum. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provides a comprehensive pan-genome analysis of L. plantarum, including the largest number (N = 127) of complete L. plantarum genomes retrieved from publicly available repositories. Our effort aimed to determine a solid reference panel for the future characterization of newly sequenced L. plantarum strains useful as probiotic supplements.
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The study by [40] did not associate a gene or group of genes with documented probiotic functions for the L. plantarum strains.
“In fact, this study did not associate a gene or group of genes with documented probiotic functions for the L. plantarum strains.”
From Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese (2024) · cites this paper as [40]
The Results section (‘Probiotic marker genes’ in L. plantarum pan-genome; page not provided) identifies 75 genes associated with probiotic-related functions and examines their presence across strains. It specifically links bshA to bile tolerance, xylA to gut persistence, and srtA to adhesion, contrary to the claim that the study made no such associations. (LLM, conf=0.90)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredThe genes gbuB, bshA, gla2, and xylA were not detected in any of the genomes evaluated.
“The genes gbuB, bshA, gla2, and xylA were not detected in any of the genomes evaluated.”
From Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese (2024) · cites this paper as [40]
In Results, Table 2 lists all four genes as present in at least one of the 127 genomes: gbuB in 33, bshA in 1, gla_2 in 4, and xylA in 3. The accompanying ‘Probiotic marker genes’ text also explicitly says bshA, xylA, and gla_2 were present in some strains. No page number is provided in our copy. (LLM, conf=0.95)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredThe list of strains that harbored any of these 12 genes did not include the model probiotic L. plantarum WCFS1.
“For instance, the list of strains that harbored any of these 12 genes did not include the model probiotic L. plantarum WCFS1 [40].”
From Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese (2024) · cites this paper as [40]
Table 2 in the Results section lists 12 probiotic marker genes, and WCFS1 does not appear among the strains named. However, five rows list strains in which a gene is absent, so the table is not solely a list of strains that harbored these genes. (LLM, conf=0.84)
Experimental — accuracy not yet measuredMost of these genes were found in all the L. plantarum genomes used in the study by [40].
“Most of these genes were found in all the L. plantarum genomes used in this study [40].”
From Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese (2024) · cites this paper as [40]
The Results section on probiotic marker genes (page unavailable) reports that approximately 70% of the considered genes occur in 95–100% of the strains studied. This supports their widespread presence, but not the claim that most were found in every genome. (LLM, conf=0.85)
Experimental — accuracy not yet measuredCarpi et al. generated an updated list of 'probiotic marker genes', including genes putatively accountable for stress resistance (osmotic, acid, oxidative, temperature), adhesion capacity, intestinal persistence and bile salt hydrolase activity.
“Based on such findings, Carpi et al. [40] generated an updated list of ‘probiotic marker genes’, including genes putatively accountable for stress resistance (osmotic, acid, oxidative, temperature), adhesion capacity, intestinal persistence and bile salt hydrolase activity.”
From Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese (2024) · cites this paper as [40]
In total, 75 probiotic marker genes have been reported, of which about 70% correspond to genes located in the core/soft core genome, while 12 genes are located in the shell/cloud genome.
“In total, 75 probiotic marker genes have been reported, of which about 70% correspond to genes located in the core/soft core genome [40], while 12 genes (Supplementary Table S2) are located in the shell/cloud genome.”
From Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese (2024) · cites this paper as [40]
A recent study identified 75 'probiotic marker' genes in the genomes of L. plantarum.
“this study identified 75 “probiotic marker” genes in the genomes of L. plantarum.”
From Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese (2024) · cites this paper as [40]
12 genes (bshA, ClpP1, oppA3, oppA4, xylA, srtA, gbuB, gla2, dps, glf, glpF1, and cbh/bsh) were located in the shell and cloud genome, showing that they were only present in some strains.
“On the other hand, 12 genes (bshA, ClpP1, oppA3, oppA4, xylA, srtA, gbuB, gla2, dps, glf, glpF1, and cbh/bsh) were located in the shell and cloud genome, showing that they were only present in some strains [40].”
From Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese (2024) · cites this paper as [40]
Of the 75 'probiotic marker' genes, 70% corresponded to genes located in the core and soft-core genome.
“Of the 75 “probiotic marker” genes, 70% corresponded to genes located in the core and soft-core genome.”
From Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese (2024) · cites this paper as [40]
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“54C vs. 55A 98.7297 55A vs. WCFS1 98.8804 In total, 75 probiotic marker genes have been reported, of which about 70% correspond to genes located in the core/soft core genome [40], while 12 genes (Supplementary Table S2) are located in the shell/cloud genome.”
InfluentialHuang, Y., Meng, K., Liu, G., Chen, Z., Han, Y., Yang, P., Zhang, R., & Cai, H. (2025) · Biology · doi:10.3390/biology14091167 · Cited by 7 · see citing works
- Authors
- Carpi, F. M., Coman, M. M., Silvi, S., Picciolini, M., Verdenelli, M. C., & Napolioni, V.
- Affiliations
- Synbiotec S.r.l Camerino Italy
- Università di Camerino (IT)
- Independent Researcher Gubbio Italy
- Corresponding author
- Verdenelli, Maria Cristina
- Venue
- Journal of Applied Microbiology
- Publisher
- Oxford University Press (OUP)
- Published
- 2021-07-24
- Volume
- 132
- Issue
- 1
- Pages
- 592-604
- ISSN
- 1364-5072 (ISSN-L)
- 1365-2672
- PMC
- PMC9290807
- OpenAlex
- W3177542363
- Cited by
- 72
- References
- 34
- Citations by year
- 2026: 16 · 2025: 15 · 2024: 16 · 2023: 17 · 2022: 8
- FWCI
- 7.01
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Journal of Applied Microbiology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Unicam Scientific Publications (University of Camerino) (submittedVersion, other-oa)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- Lactobacillus plantarum, pan-genome, probiotic potential, core genome, plasmids, mobile genetic elements, adaptive immunity, strain differences, lactic acid bacteria
- MeSH terms
- Lactobacillaceae, Genome, Bacterial, Sequence Analysis, DNA, Probiotics, Genomics, Lactiplantibacillus plantarum
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