Comparative genomics and phenotypic characterization revealing Staphylococcus gallinarum SP6 as a promising candidate starter culture for salted shrimp paste

Staphylococcus gallinarum is a coagulase-negative staphylococcal species commonly found in fermented foods; however, mechanisms underlying its adaptation, safety, and functional role remain poorly understood. The SP6 strain isolated from Vietnamese fermented shrimp paste was identified as halotolerant and proteolytic. Comparative genomic analysis showed that SP6 has the smallest genome (2.8 Mb; 33.1% GC content) among the compared S. gallinarum genomes that display an open pan-genome. The ability of SP6 to grow at 20% NaCl and pH 11.0 may be associated with multiple candidate genes related to osmoprotection, mechanosensing, ion transport, and pH homeostasis. Exposure to 120 mM H₂O₂ resulted in decreased intracellular thiol levels and differential transcript changes, with an apparent increase in katA, no significant change in bshA, and a decrease in brxA relative to the untreated control. Candidate genes were mapped to five putative metabolic routes potentially relevant to shrimp protein degradation and flavor development, including proteolysis, volatile organic compound synthesis, integration of central metabolic pathways via α-ketoglutarate, branched-chain amino acid metabolism, and esterification. No functional virulence determinants, plasmid replicons, and cytotoxicity against the HT-29 cell line were detected, and SP6 was susceptible to most tested antibiotics, supporting a favorable preliminary safety profile. SP6 produced 190.6 ± 14.7 µg/mL of γ-polyglutamic acid (γ-PGA) with antioxidant activity and reduced histamine levels by 49.2 ± 4.0% under the tested in vitro conditions. Candidate genes potentially associated with histamine metabolism were also identified, although their functional contribution to histamine removal remains to be established. These findings support further evaluation of S. gallinarum SP6 for starter-culture applications.