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Disease outbreak has continued to be a major challenge for shrimp aquaculture industry. In recent years, manipulation of gut microbiota has been shown to improve the health of host shrimp and disease resistance. Therefore, understanding how various factors can shape the gut microbiota of shrimp is crucial for future utilization of gut microbiota as tools for disease controls. The salinity of the rearing environment can potentially affect shrimp gut microbiota as well as the host-microbe interactions. The effects of salinity adaptation on intestinal microbiota and transcriptomes of juvenile black tiger shrimp Penaeus monodon were examined in this experiment. Intestinal microbiota and transcriptomic profiles from juvenile black tiger shrimp of the same cohort adapted to three different salinity levels were examined using 16S rDNA amplicon sequencing and RNA sequencing, respectively. Shrimp were acclimatized from the original 20 ppt salinity to either 10 ppt or 30 ppt over a period of 10 days, and intestinal samples were collected on Day 0, Day 10, and Day 20 after reaching the target salinity. Across all salinity levels, the dominant phyla composition in the intestine of shrimp was relatively similar with Proteobacteria (83.4%), Bacteroidetes (8.1%), Planctomycetes (3.2%), Verrucomicrobia (2.5%), and Firmicutes (1.5%). The most abundant genus was Vibrio. While it can be found at all salinity levels, a relative abundance of Vibrio was lower at 10 ppt than at higher salinity. A shift toward the higher relative abundance of Vibrio ASVs belonging to the Harveyi clade was observed at higher salinity. On the other hand, the relative abundance of Shewanella was higher at 10 ppt than at higher salinity. Other dominant genera in the intestines not affected by the change in salinity were Pseudoaltermonas and Tenacibaculum. The shift in the rearing water microbiota with different salinity levels was also observed. The most abundant intestinal transcripts responding to different salinity levels based on GO classification were intracellular anatomical structure (cellular component), protein binding (molecular function), and organic substance metabolic process (biological function). Genes involved with stress and immune responses were differentially expressed, and correlations between potentially pathogenic Vibrio and genes relating to innate immunity and peritrophic matrix were observed. The results confirmed the influence of rearing water salinity on both the intestinal microbiota and transcriptomes of shrimp. Efforts to shape the microbiota of aquatic animals should take into consideration the rearing salinity to ensure its efficacy. Using multi-omic platform allowed for better understanding of the microbiota and the host-microbe interaction, which will help support the sustainability of aquaculture production.

Background Poor reproductive maturation of the black tiger shrimp (Penaeus monodon) in captivity is one of the serious threats to sustainability of the shrimp farming industry. Understanding molecular mechanisms governing reproductive maturation processes requires the fundamental knowledge of integrated expression profiles in gonads of this economically important species. In P. monodon, a non-model species for which the genome sequence is not available, expressed sequence tag (EST) and cDNA microarray analyses can help reveal important transcripts relevant to reproduction and facilitate functional characterization of transcripts with important roles in male reproductive development and maturation. Results In this study, a conventional testis EST library was exploited to reveal novel transcripts. A total of 4,803 ESTs were unidirectionally sequenced and analyzed in silico using a customizable data analysis package, ESTplus. After sequence assembly, 2,702 unique sequences comprised of 424 contigs and 2,278 singletons were identified; of these, 1,133 sequences are homologous to genes with known functions. The sequences were further characterized according to gene ontology categories (41% biological process, 24% molecular function, 35% cellular component). Through comparison with EST libraries of other tissues of P. monodon, 1,579 transcripts found only in the testis cDNA library were identified. A total of 621 ESTs have not been identified in penaeid shrimp. Furthermore, cDNA microarray analysis revealed several ESTs homologous to testis-relevant genes were more preferentially expressed in testis than in ovary. Representatives of these transcripts, homologs of saposin (PmSap) and Dmc1 (PmDmc1), were further characterized by RACE-PCR. The more abundant expression levels in testis than ovary of PmSap and PmDmc1 were verified by quantitative real-time PCR in juveniles and wild broodstock of P. monodon. Conclusions Without a genome sequence, a combination of EST analysis and high-throughput cDNA microarray technology can be a useful integrated tool as an initial step towards the identification of transcripts with important biological functions. Identification and expression analysis of saposin and Dmc1 homologs demonstrate the power of these methods for characterizing functionally important genes in P. monodon.