Comparative genomic and transcriptomic analyses of NaCl-tolerant Staphylococcus sp. OJ82 isolated from fermented seafood

Abstract

Bacteria belonging to the Staphylococcus genus reside in various natural environments; however, only disease-associated Staphylococcus strains have received attention while ecological function and physiologies of non-pathogenic strains were often neglected. Because high level of tolerance against NaCl is a common trait of Staphylococcus, we investigated the characteristics of halotolerance in Staphylococcus sp. OJ82 isolated from fermented seafood containing a high concentration of NaCl. Among the 292 isolates screened, OJ82 showed the highest β-galactosidase and extracellular protease activities under high-salt conditions. Comparative genomic analysis with other Staphylococcus strains showed that (a) replication origins are highly conserved, (b) the OJ82 strain has a high number of amino acid transport- and metabolism-related genes, and (c) OJ82 has many unique proteins (15 %) and 12 prophage-related genomic islands. RNA-seq analysis under high-salt conditions showed that genes involved in cell membranes, transport, osmotic stress, ATP synthesis, and translation are highly expressed. OJ82 may use the ribulose monophosphate pathway to detoxify some toxic intermediates under high-salt conditions. Six new and three known non-coding small RNAs of the OJ82 strain were also found in the RNA-seq analysis. Genomic and transcriptomic analyses identified target β-galactosidase and extracellular protease. Interestingly, the OJ82 strain became resistant to bacteriocin produced by the Bacillus strain only under high-salt conditions. Our data showed that the OJ82 strain adapted to high-salt conditions by expressing core cellular processes (translation, ATP production) and defense genes (membrane synthesis, compatible solute transports, ribulose monophosphate pathway) could survive bacteriocin exposure under high-salt conditions.

Cyclic-di-adenosine monophosphate (c-di-AMP) is required for osmotic regulation inStaphylococcus aureusbut dispensable for viability in anaerobic conditions

“…Compared to other bacteria, S. aureus is extremely tolerant to osmotic stress and as shown here can grow on agar plates containing 2 M NaCl. For S. aureus to be able to divide under these conditions, specific osmotic stress adaption processes are activated and as previously reported a large number of transcriptional changes occur (44,45). While intermediate salt concentrations can rescue the growth of a dacA mutant, the strain might not be able to mount the appropriate stress adaption response under extremely high osmolarity conditions, leading to the observed drop in plating efficiency.…”

Application of molecular tools to elucidate the microbiota of seafood

“…Choi et al . () performed comparative genomic and transcriptomic analyses regarding Staphylococcus sp. OJ82 tolerant to high concentrations of NaCl isolated from fermented seafood, aiming to understand the physiological responses to high saline concentrations.…”

“…The authors indicated that the metagenomic analysis was, thus, successful in understanding alteration in intestinal microbiota after ingestion of the supplemented diet. Choi et al (2014) performed comparative genomic and transcriptomic analyses regarding Staphylococcus sp. OJ82 tolerant to high concentrations of NaCl isolated from fermented seafood, aiming to understand the physiological responses to high saline concentrations.…”

De novo transcriptome analysis of halotolerant bacterium Staphylococcus sp. strain P-TSB-70 isolated from East coast of India: In search of salt stress tolerant genes

“…Recent RNA sequencing by way of high-throughput technology has modernized the study of the microbial transcriptome [22][23][24]. Several researchers have studied the differential gene expression of several bacteria in different stressed conditions through transcriptome profiling since RNA-seq analysis has proved the advantages over the disadvantages through hybridization technique and sequence-based technique [25][26][27][28][29][30].…”

“…is a Gram-positive, mostly non-pathogenic bacteria fitting into the family Staphylococcaceae found worldwide, which is a small constituent of soil microbial flora [32]. The genus Staphylococcus consists of 47 different type species and 24 different subspecies with dependably accessible names [27]. According to Choi and co-workers, resources for isolation of Staphylococcus species comprise of amber [33], insects [34], estuarine and aquatic surface water [35], fermented fish [36], cheese [37], soil, and plant, signifying pervasiveness of the Staphylococcus in the normal environment, while, ecology and physiology of non-pathogenic Staphylococcus in the natural habitat resided ambiguously.…”