Genome-Wide Comparative Analysis of <i>Lactiplantibacillus pentosus</i> Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry
<i>Lactiplantibacillus pentosus</i>, commonly isolated from commercial cucumber fermentation, is a promising candidate for starter culture formulation due to its ability to achieve complete sugar utilization to an end pH of 3.3. In this study, we conducted a comparative genomic analysis...
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MDPI AG
2023-06-01
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| Series: | Foods |
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| Online Access: | https://www.mdpi.com/2304-8158/12/13/2455 |
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| author | Clinton A. Page Ilenys M. Pérez-Díaz Meichen Pan Rodolphe Barrangou |
| author_facet | Clinton A. Page Ilenys M. Pérez-Díaz Meichen Pan Rodolphe Barrangou |
| author_sort | Clinton A. Page |
| collection | DOAJ |
| description | <i>Lactiplantibacillus pentosus</i>, commonly isolated from commercial cucumber fermentation, is a promising candidate for starter culture formulation due to its ability to achieve complete sugar utilization to an end pH of 3.3. In this study, we conducted a comparative genomic analysis encompassing 24 <i>L. pentosus</i> and 3 <i>Lactiplantibacillus plantarum</i> isolates autochthonous to commercial cucumber fermentation and 47 lactobacillales reference genomes to determine species specificity and provide insights into niche adaptation. Results showed that metrics such as average nucleotide identity score, emulated Rep-PCR-(GTG)<sub>5</sub>, computed multi-locus sequence typing (MLST), and multiple open reading frame (ORF)-based phylogenetic trees can robustly and consistently distinguish the two closely related species. Phylogenetic trees based on the alignment of 587 common ORFs separated the <i>L. pentosus</i> autochthonous cucumber isolates from olive fermentation isolates into clade A and B, respectively. The <i>L. pentosus</i> autochthonous clade partitions into subclades A.I, A.II, and A.III, suggesting substantial intraspecies diversity in the cucumber fermentation habitat. The hypervariable sequences within CRISPR arrays revealed recent evolutionary history, which aligns with the <i>L. pentosus</i> subclades identified in the phylogenetic trees constructed. While <i>L. plantarum</i> autochthonous to cucumber fermentation only encode for Type II-A CRISPR arrays, autochthonous <i>L. pentosus</i> clade B codes for Type I-E and <i>L. pentosus</i> clade A hosts both types of arrays. <i>L. pentosus</i> 7.8.2, for which phylogeny could not be defined using the varied methods employed, was found to uniquely encode for four distinct Type I-E CRISPR arrays and a Type II-A array. Prophage sequences in varied isolates evidence the presence of adaptive immunity in the candidate starter cultures isolated from vegetable fermentation as observed in dairy counterparts. This study provides insight into the genomic features of industrial <i>Lactiplantibacillus</i> species, the level of species differentiation in a vegetable fermentation habitat, and diversity profile of relevance in the selection of functional starter cultures. |
| first_indexed | 2024-03-11T01:42:13Z |
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| institution | Directory Open Access Journal |
| issn | 2304-8158 |
| language | English |
| last_indexed | 2024-03-11T01:42:13Z |
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| spelling | doaj.art-a705af15662c445f9c83e7a06c8667f92023-11-18T16:32:46ZengMDPI AGFoods2304-81582023-06-011213245510.3390/foods12132455Genome-Wide Comparative Analysis of <i>Lactiplantibacillus pentosus</i> Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent AncestryClinton A. Page0Ilenys M. Pérez-Díaz1Meichen Pan2Rodolphe Barrangou3United States Department of Agriculture, Agricultural Research Service, SEA Food Science and Market Quality and Handling Research Unit, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USAUnited States Department of Agriculture, Agricultural Research Service, SEA Food Science and Market Quality and Handling Research Unit, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USADepartment of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USADepartment of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 322 Schaub Hall, Box 7624, Raleigh, NC 27695-7624, USA<i>Lactiplantibacillus pentosus</i>, commonly isolated from commercial cucumber fermentation, is a promising candidate for starter culture formulation due to its ability to achieve complete sugar utilization to an end pH of 3.3. In this study, we conducted a comparative genomic analysis encompassing 24 <i>L. pentosus</i> and 3 <i>Lactiplantibacillus plantarum</i> isolates autochthonous to commercial cucumber fermentation and 47 lactobacillales reference genomes to determine species specificity and provide insights into niche adaptation. Results showed that metrics such as average nucleotide identity score, emulated Rep-PCR-(GTG)<sub>5</sub>, computed multi-locus sequence typing (MLST), and multiple open reading frame (ORF)-based phylogenetic trees can robustly and consistently distinguish the two closely related species. Phylogenetic trees based on the alignment of 587 common ORFs separated the <i>L. pentosus</i> autochthonous cucumber isolates from olive fermentation isolates into clade A and B, respectively. The <i>L. pentosus</i> autochthonous clade partitions into subclades A.I, A.II, and A.III, suggesting substantial intraspecies diversity in the cucumber fermentation habitat. The hypervariable sequences within CRISPR arrays revealed recent evolutionary history, which aligns with the <i>L. pentosus</i> subclades identified in the phylogenetic trees constructed. While <i>L. plantarum</i> autochthonous to cucumber fermentation only encode for Type II-A CRISPR arrays, autochthonous <i>L. pentosus</i> clade B codes for Type I-E and <i>L. pentosus</i> clade A hosts both types of arrays. <i>L. pentosus</i> 7.8.2, for which phylogeny could not be defined using the varied methods employed, was found to uniquely encode for four distinct Type I-E CRISPR arrays and a Type II-A array. Prophage sequences in varied isolates evidence the presence of adaptive immunity in the candidate starter cultures isolated from vegetable fermentation as observed in dairy counterparts. This study provides insight into the genomic features of industrial <i>Lactiplantibacillus</i> species, the level of species differentiation in a vegetable fermentation habitat, and diversity profile of relevance in the selection of functional starter cultures.https://www.mdpi.com/2304-8158/12/13/2455<i>Lactiplantibacillus pentosus</i>comparative genomics<i>Lactiplantibacillus plantarum</i>cucumber fermentationstarter culture |
| spellingShingle | Clinton A. Page Ilenys M. Pérez-Díaz Meichen Pan Rodolphe Barrangou Genome-Wide Comparative Analysis of <i>Lactiplantibacillus pentosus</i> Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry Foods <i>Lactiplantibacillus pentosus</i> comparative genomics <i>Lactiplantibacillus plantarum</i> cucumber fermentation starter culture |
| title | Genome-Wide Comparative Analysis of <i>Lactiplantibacillus pentosus</i> Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry |
| title_full | Genome-Wide Comparative Analysis of <i>Lactiplantibacillus pentosus</i> Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry |
| title_fullStr | Genome-Wide Comparative Analysis of <i>Lactiplantibacillus pentosus</i> Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry |
| title_full_unstemmed | Genome-Wide Comparative Analysis of <i>Lactiplantibacillus pentosus</i> Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry |
| title_short | Genome-Wide Comparative Analysis of <i>Lactiplantibacillus pentosus</i> Isolates Autochthonous to Cucumber Fermentation Reveals Subclades of Divergent Ancestry |
| title_sort | genome wide comparative analysis of i lactiplantibacillus pentosus i isolates autochthonous to cucumber fermentation reveals subclades of divergent ancestry |
| topic | <i>Lactiplantibacillus pentosus</i> comparative genomics <i>Lactiplantibacillus plantarum</i> cucumber fermentation starter culture |
| url | https://www.mdpi.com/2304-8158/12/13/2455 |
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