Genome-wide comparative analysis of Lactiplantibacillus pentosus isolates autochthonous to cucumber fermentation reveals subclades of divergent ancestry

Authors: Page, Clinton; Perez Diaz, Ilenys; PAN, ECHO - North Carolina State University; BARRANGOU, RODOLPHE - North Carolina State University

Submitted to: Foods
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/13/2023
Publication Date: 6/23/2023
Citation: Page, C.A., Perez Diaz, I.M., Pan, E., Barrangou, R. 2023. Genome-wide comparative analysis of Lactiplantibacillus pentosus isolates autochthonous to cucumber fermentation reveals subclades of divergent ancestry. Foods. 12(13):2455. https://doi.org/10.3390/foods12132455.
DOI: https://doi.org/10.3390/foods12132455

Interpretive Summary: Several lactic acid producing bacteria are naturally present in cucumber, lead the fermentation needed to make pickles and can confer health benefits for consumers. This research studied the natural genetic diversity of a particular species of such bacteria known as Lactiplantibacillus pentosus. Using genome sequences for several clones of such bacterial species we identified key features that can distinguish them from other closely related bacteria and unique characteristics of sibling Lactiplantibacillus pentosus. The ability to distinguish Lactiplantibacillus pentosus siblings enable us to design functional starter cultures for cucumber fermentation that can enhance the quality of pickles and the microbial stability of environmentally compatible-low salt fermentations.

Technical Abstract: Lactiplantibacillus pentosus, 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 L. pentosus and 3 Lactiplantibacillus plantarum 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)5, 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 L. pentosus autochthonous cucumber isolates from olive fermentation isolates into clade A and B, respectively. The L. pentosus 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 L. pentosus subclades identified in the phylogenetic trees constructed. While L. plantarum autochthonous to cucumber fermentation only encode for Type II-A CRISPR arrays, autochthonous L. pentosus clade B codes for Type I-E and L. pentosus clade A hosts both types of arrays. L. pentosus 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 Lactiplantibacillus species, the level of species differentiation in a vegetable fermentation habitat, and diversity profile of relevance in the selection of functional starter cultures.