Genomic Variation and Phenotypic Diversity of Coffee-Derived Lactiplantibacillus plantarum Isolates

Lactiplantibacillus plantarum exhibits substantial strain-level genomic diversity that may contribute to variation in stress tolerance and functional properties. Five isolates recovered from spontaneously fermented red coffee cherries were analyzed by whole-genome resequencing and phenotypic characterization. Single-nucleotide polymorphisms (SNPs) and short insertions and deletions (InDels) were identified and functionally annotated. SNPs predominated, ranging from 16,865 to 20,280 per isolate, with CATR21 showing the highest SNP and InDel counts. Synonymous variants were the most frequent predicted consequence, followed by upstream and missense variants, whereas high-impact variants were uncommon. Selected isolate-specific missense variants affected atpF and atpB in CATR7, mobQ in CATR14, ptsP in CATR21, and glf and epsC in TYPR1. Phenotypic responses were strain- and condition-dependent. CATR21 exhibited the highest viability at pH 2.5 and the highest 24-h autoaggregation among the coffee-derived isolates. CATR7 showed the highest viability under 1% NaCl and the highest numerical viability under 4% NaCl. Genome-wide variant counts did not show a consistent relationship with the evaluated phenotypic traits. Overall, the combined genomic and phenotypic analyses demonstrated substantial strain-level variability among the coffee-derived L. plantarum isolates across the evaluated conditions.