Transcriptome analysis unveils survival strategies of Streptococcus parauberis against fish serum

Abstract

Streptococcus parauberis is an important bacterial fish pathogen that causes streptococcosis in a variety of fish species including the olive flounder. Despite its importance in the aquaculture industry, little is known about the survival strategy of S. parauberis in the host. Therefore, the objective of this study was to produce genome-wide transcriptome data and identify key factors for the survival of S. parauberis SPOF3K in its host. To this end, S. parauberis SPOF3K was incubated in olive flounder serum and nutrient-enriched media as a control. Although S. parauberis SPOF3K proliferated in both culture conditions, the transcriptomic patterns of the two groups were very different. Interestingly, the expression levels of genes responsible for the replication of an S. parauberis plasmid in the presence of olive flounder serum were higher than those in the absence of olive flounder serum, indicating that this plasmid may play an important role in the survival and proliferation of S. parauberis in the host. Several ATP-binding cassette transporters known to transport organic substrates (e.g., biotin and osmoprotectants) that are vital for bacterial survival in the host were significantly up-regulated in S. parauberis cultured in serum. In addition, groEL, dnaK operon, and members of the clp protease family, which are known to play important roles in response to various stressors, were up-regulated in S. parauberis incubated in serum, thus limiting damage and facilitating cellular recovery. Moreover, important virulence factors including the hyaluronic acid capsule (has operon), sortase A (srtA), C5a peptidase (scp), and peptidoglycan O-acetyltransferase (oatA) were significantly upregulated in S. paraubers in serum. These results indicate that S. paraubers can resist and evade the humoral immune responses of fish. The transcriptomic data obtained in this study provide a better understanding of the mode of action of S. parauberis in fish.

A genome‐wide association study of the occurrence of genetic variations in Edwardsiella piscicida, Vibrio harveyi, and Streptococcus parauberis under stressed environments

“…This is one of the main reasons why the first step in most GWAS is to classify the phenotypic characteristics or measurements (which can be discrete units [e.g., high, intermediate and low virulence] and/or continuous values) (Chen & Shapiro, 2015). Given Hence, this study attempted to observe SNPs and/or mutations in the same strain with different environments and exposure times through raw sequencing files that had been used for transcriptomic studies (Lee et al, 2021;Montánchez et al, 2019;Yoon et al, 2020).…”

“…In total, 41 FastQ files for transcriptomic studies on E. piscicida, V. harveyi and S. parauberis have been downloaded from a SRA using the SRA-tool kit . The SRR accessions used in this study are summarized in Table 1 (Lee et al, 2021;Montánchez et al, 2019;Yoon et al, 2020). To observe the emergence of genetic variants stimulated by sub-lethal chemicals in E. piscicida, a study on E. piscicida CK108 transcriptomics that compared a control cultured in ordinary liquid media (brain and heart infusion) and treatments cultured in a media supplemented with either 0.0039% formalin or 0.146% phenol were used in this study (Yoon et al, 2020).…”

“…Because big data from next‐generation sequencing (NGS) may contain valuable multidimensional results, these can be interpreted from multiple perspectives. However, in numerous studies, massive sequencing results have mainly been interpreted in a manner consistent with their purposes, which means some results might be important but are overlooked or underestimated (Lee et al, 2021; Montánchez et al, 2019; Yoon et al, 2020). Hence, making the most of released sequences in an open database such as a sequence read archive (SRA) and Genbank is becoming more important, given the release of a tremendous amount of sequencing results every day.…”

“…the importance of the gene for adapting to the surrounding environment. The advance in transcriptomic sequencing technologies can provide valuable information for profiling the sequence dynamics from the survived bacteria even in the same cultures; however, most studies have focussed on mRNA expression in different environments using transcriptomic results(Le et al, 2021;Lee et al, 2021;Montánchez et al, 2019;Yoon et al, 2020).…”

Robust Nanozyme-Enzyme Nanosheets-Based Lactate Biosensor for Diagnosing Bacterial Infection in Olive Flounder (Paralichthys olivaceus)

“…The detection and identification of S. parauberis mainly rely on the clinical symptoms [ 4 ], biochemical characteristics [ 2 ], molecular techniques including genomics [ 5 , 6 , 7 ], proteomics [ 8 ], and conventional polymerase chain reaction (PCR) based on the 23S rRNA region [ 9 , 10 ]. Although PCR is widely used as a standard molecular technique for the diagnosis, it is time-consuming and costly, has a high risk of contamination, and requires careful implementation to achieve sensitivity and specificity [ 11 , 12 , 13 ].…”