Diversity of <i>Lactiplantibacillus plantarum</i> in Wild Fermented Food Niches
This study aimed to explore the genetic and functional diversity of <i>Lactiplantibacillus plantarum</i> (<i>Lpb. plantarum</i>) strains from wild fermented foods to identify traits that are useful for food innovation. The growing demand for clean-label, plant-based, and func...
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MDPI AG
2025-05-01
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| Series: | Foods |
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| Online Access: | https://www.mdpi.com/2304-8158/14/10/1765 |
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| author | Ilenia Iarusso Jennifer Mahony Gianfranco Pannella Silvia Jane Lombardi Roberto Gagliardi Francesca Coppola Michela Pellegrini Mariantonietta Succi Patrizio Tremonte |
| author_facet | Ilenia Iarusso Jennifer Mahony Gianfranco Pannella Silvia Jane Lombardi Roberto Gagliardi Francesca Coppola Michela Pellegrini Mariantonietta Succi Patrizio Tremonte |
| author_sort | Ilenia Iarusso |
| collection | DOAJ |
| description | This study aimed to explore the genetic and functional diversity of <i>Lactiplantibacillus plantarum</i> (<i>Lpb. plantarum</i>) strains from wild fermented foods to identify traits that are useful for food innovation. The growing demand for clean-label, plant-based, and functionally enriched fermented foods exposes the limitations of current industrial fermentation practices, which rely on standardized lactic acid bacteria (LAB) strains with limited metabolic plasticity. This constraint hinders the development of new food formulations and the replacement of conventional additives. To address this gap, 343 LAB strains were analyzed, including 69 <i>Lpb plantarum</i> strains, isolated from five minimally processed, spontaneously fermented matrices: fermented millet, kombucha, and sourdough (plant-based), wild fermented mountain milk, and natural whey starter (animal-based). Whole-genome sequencing was performed to assess phylogenetic relationships and to annotate genes encoding carbohydrate-active enzymes (CAZymes) and antimicrobial compounds. The results revealed a marked strain-level diversity. Glycoside hydrolase (GH) families GH13 and GH1 were widely distributed, while GH25 and GH32 showed variable presence across clusters. Strains grouped into clusters enriched with plant-based isolates exhibited distinct CAZyme profiles adapted to complex carbohydrates. Clusters with animal-based strains exhibited a broader gene repertoire related to bacteriocin biosynthesis. These findings highlight the untapped potential of wild fermented food environments as reservoirs of <i>Lpb. plantarum</i> with unique genomic traits. Harnessing this diversity can expand the functional capabilities of starter cultures, promoting more sustainable, adaptive, and innovative fermentation systems. This study underscores the strategic value of underexploited microbial niches in meeting the evolving demands of modern food production. |
| format | Article |
| id | doaj-art-880edf5bbc2b4147ad684690cea37f6b |
| institution | DOAJ |
| issn | 2304-8158 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Foods |
| spelling | doaj-art-880edf5bbc2b4147ad684690cea37f6b2025-08-20T03:14:31ZengMDPI AGFoods2304-81582025-05-011410176510.3390/foods14101765Diversity of <i>Lactiplantibacillus plantarum</i> in Wild Fermented Food NichesIlenia Iarusso0Jennifer Mahony1Gianfranco Pannella2Silvia Jane Lombardi3Roberto Gagliardi4Francesca Coppola5Michela Pellegrini6Mariantonietta Succi7Patrizio Tremonte8Department of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise, Via De 8 Sanctis snc, 86100 Campobasso, ItalySchool of Food and Nutritional Sciences, University College Cork, College Road, T12 K8AF Cork, IrelandDepartment of Science and Technology for Sustainable Development and One Health, Università Campus-Bio-Medico di Roma, Via Alvaro del Portillo 21, 00128 Rome, ItalyDepartment of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise, Via De 8 Sanctis snc, 86100 Campobasso, ItalyScienzanova s.r.l. via Enrico Mattei, 85/87, 86039 Termoli, ItalyDepartment of Agricultural Sciences, University of Naples “Federico II”, Piazza Carlo di Borbone 1, 80055 Portici, ItalyDepartment of Agricultural, Food, Environmental and Animal Science, University of Udine, via Sondrio 2A, 33100 Udine, ItalyDepartment of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise, Via De 8 Sanctis snc, 86100 Campobasso, ItalyDepartment of Agricultural, Environmental and Food Sciences (DiAAA), University of Molise, Via De 8 Sanctis snc, 86100 Campobasso, ItalyThis study aimed to explore the genetic and functional diversity of <i>Lactiplantibacillus plantarum</i> (<i>Lpb. plantarum</i>) strains from wild fermented foods to identify traits that are useful for food innovation. The growing demand for clean-label, plant-based, and functionally enriched fermented foods exposes the limitations of current industrial fermentation practices, which rely on standardized lactic acid bacteria (LAB) strains with limited metabolic plasticity. This constraint hinders the development of new food formulations and the replacement of conventional additives. To address this gap, 343 LAB strains were analyzed, including 69 <i>Lpb plantarum</i> strains, isolated from five minimally processed, spontaneously fermented matrices: fermented millet, kombucha, and sourdough (plant-based), wild fermented mountain milk, and natural whey starter (animal-based). Whole-genome sequencing was performed to assess phylogenetic relationships and to annotate genes encoding carbohydrate-active enzymes (CAZymes) and antimicrobial compounds. The results revealed a marked strain-level diversity. Glycoside hydrolase (GH) families GH13 and GH1 were widely distributed, while GH25 and GH32 showed variable presence across clusters. Strains grouped into clusters enriched with plant-based isolates exhibited distinct CAZyme profiles adapted to complex carbohydrates. Clusters with animal-based strains exhibited a broader gene repertoire related to bacteriocin biosynthesis. These findings highlight the untapped potential of wild fermented food environments as reservoirs of <i>Lpb. plantarum</i> with unique genomic traits. Harnessing this diversity can expand the functional capabilities of starter cultures, promoting more sustainable, adaptive, and innovative fermentation systems. This study underscores the strategic value of underexploited microbial niches in meeting the evolving demands of modern food production.https://www.mdpi.com/2304-8158/14/10/1765lactic acid bacteriaWGS-based annotationkombuchafermented milletsourdoughnatural fermented mountain milk |
| spellingShingle | Ilenia Iarusso Jennifer Mahony Gianfranco Pannella Silvia Jane Lombardi Roberto Gagliardi Francesca Coppola Michela Pellegrini Mariantonietta Succi Patrizio Tremonte Diversity of <i>Lactiplantibacillus plantarum</i> in Wild Fermented Food Niches Foods lactic acid bacteria WGS-based annotation kombucha fermented millet sourdough natural fermented mountain milk |
| title | Diversity of <i>Lactiplantibacillus plantarum</i> in Wild Fermented Food Niches |
| title_full | Diversity of <i>Lactiplantibacillus plantarum</i> in Wild Fermented Food Niches |
| title_fullStr | Diversity of <i>Lactiplantibacillus plantarum</i> in Wild Fermented Food Niches |
| title_full_unstemmed | Diversity of <i>Lactiplantibacillus plantarum</i> in Wild Fermented Food Niches |
| title_short | Diversity of <i>Lactiplantibacillus plantarum</i> in Wild Fermented Food Niches |
| title_sort | diversity of i lactiplantibacillus plantarum i in wild fermented food niches |
| topic | lactic acid bacteria WGS-based annotation kombucha fermented millet sourdough natural fermented mountain milk |
| url | https://www.mdpi.com/2304-8158/14/10/1765 |
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