Genomic and metabolic features of Tetragenococcus halophilus as revealed by pan-genome and transcriptome analyses

The genomic and metabolic diversity and features of Tetragenococcus halophilus, a moderately halophilic lactic acid bacterium, were investigated by pan-genome, transcriptome, and metabolite analyses. Phylogenetic analyses based on the 16S rRNA gene and genome sequences of 15 T. halophilus strains revealed their phylogenetic distinctness from other Tetragenococcus species. Pan-genome analysis of the T. halophilus strains showed that their carbohydrate metabolic capabilities were diverse and strain dependent. Aside from one histidine decarboxylase gene in one strain, no decarboxylase gene associated with biogenic amine production was identified from the genomes. However, T. halophilus DSM 20339T produced tyramine without a biogenic amine-producing decarboxylase gene, suggesting the presence of an unidentified tyramine-producing gene. Our reconstruction of the metabolic pathways of these strains showed that T. halophilus harbors a facultative lactic acid fermentation pathway to produce l-lactate, ethanol, acetate, and CO2 from various carbohydrates. The transcriptomic analysis of strain DSM 20339T suggested that T. halophilus may produce more acetate via the heterolactic pathway (including d-ribose metabolism) at high salt conditions. Although genes associated with the metabolism of glycine betaine, proline, glutamate, glutamine, choline, and citrulline were identified from the T. halophilus genomes, the transcriptome and metabolite analyses suggested that glycine betaine was the main compatible solute responding to high salt concentration and that citrulline may play an important role in the coping mechanism against high salinity-induced osmotic stresses. Our results will provide a better understanding of the genome and metabolic features of T. halophilus, which has implications for the food fermentation industry. •The genomic and metabolic features of Tetragenococcus halophilus were investigated.•T. halophilus performs a facultative lactate fermentation with diverse carbohydrates.•T. halophilus may harbor as yet unidentified biogenic amine-producing genes.•Glycine betaine and citrulline may play important roles for coping with osmotic stresses.