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Genomic diversity, functional differentiation and prophage dynamics in Lactiplantibacillus paraplantarum

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Abstract

Lactiplantibacillus (L.) paraplantarum is widely distributed in fermented foods and the gastrointestinal tract of mammals. However, its genomic diversity, evolutionary relationships, functional potential, and ecological adaptation strategies remain poorly understood. In this study, 42 genomes [isolated in this study (n = 20) + retrieved from NCBI (n = 22)] were analyzed to characterize species-level genomic structure, metabolic versatility, and prophage diversity. Pan-genome analysis revealed an open pan-genome with extensive accessory gene content. Phylogenomic and Average Nucleotide Identity (ANI) analyses showed that strains clustered by clade rather than by isolation habitat. KEGG and CAZy databases indicated enrichment in carbohydrate metabolism and core glycoside hydrolase families, consistent with a fermentative lifestyle, with distinct clade-associated functional signatures. Prophage ANI analysis demonstrated lineage-structured phage diversity closely aligned with host phylogeny. Prophage-associated functional genes also exhibited clade-specific distribution patterns. Phenotypic validation of selected strains exhibited pronounced condition-dependent phenotypic variation, with carbohydrate source, environmental pH, and simulated gastrointestinal stress significantly influencing acid production, growth performance, and survival in a strain-specific manner. This study provides a genomic and phenotypic framework for understanding clade-associated diversification in L. paraplantarum and supports its application in fermentation and probiotic development.

Data availability

Publicly available genomes retrieved from NCBI are provided with their original NCBI accession numbers (Table S4). The laboratory strains in this study are available upon reasonable request.

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Acknowledgements

This work was supported by the Interdisciplinary Research Fund of Inner Mongolia Agricultural University (Grant No. BR231410), the Science and Technology Program of Inner Mongolia Autonomous Region (Grant No. 2025YFSH0077).

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Author notes

  1. These authors contributed equally: Ruirui Lv, Wenxin Ma.

Authors and Affiliations

  1. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China

    Ruirui Lv, Wenxin Ma, Yan Lei, Mengjun Cui & Xia Chen

  2. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China

    Ruirui Lv, Wenxin Ma, Yan Lei, Mengjun Cui & Xia Chen

  3. Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China

    Ruirui Lv, Wenxin Ma, Yan Lei, Mengjun Cui & Xia Chen

Authors

  1. Ruirui Lv
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  2. Wenxin Ma
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  3. Yan Lei
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  4. Mengjun Cui
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Contributions

Ruirui Lv: Data curation, investigation, methodology, writing—original draft, writing—review and editing. Wenxin Ma: Data curation, methodology, writing— original draft. Yan Lei: Investigation and methodology. Mengjun Cui: Investigation and methodology. Xia Chen: Formal analysis, project administration, supervision, writing—review and editing.

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Xia Chen.

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Lv, R., Ma, W., Lei, Y. et al. Genomic diversity, functional differentiation and prophage dynamics in Lactiplantibacillus paraplantarum.
npj Sci Food (2026). https://doi.org/10.1038/s41538-026-00830-7

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