De novo Assembly and Analysis of Amur Sturgeon (Acipenser schrenckii) Transcriptome in Response to Mycobacterium Marinum Infection to Identify Putative Genes Involved in Immunity.

Fish mycobacteriosis is a common bacterial disease in many species of freshwater and marine fish and has caused severe loss of fish production. Mycobacterium marinum has been the most prevalent pathogen observed in several outbreaks of mycobacteriosis of farmed sturgeons in China. However, the immune responses and pathology of sturgeons in mycobacterial infection are rarely studied. Therefore, we used the Illumina RNA-seq method to analyze the transcriptome profile of Acipenser schrenckii challenged with Mycobacterium marinum. To begin, 168,220 non-redundant contigs were acquired from the infection and control groups, and among these, 33,225 contigs have acquired annotations. A total of 4,043 differently expressed (DE) contigs between the two groups were identified, and among these, 2479 were upregulated and 1564 were down-regulated in the infected fish. A total of 1,340 DE contigs with acquired annotations in KEGG were enriched for 124 pathways including the TNF signaling pathway, and the Toll-like receptor signaling pathway. The roles of DE genes involved in significant pathways and other processes were discussed. The 2,209 DE contigs that have yet to acquire proper annotation may represent candidate genes associated with infection in sturgeons and are expected to serve as immunogenetic resources for further study. To our best knowledge, this is the first transcriptome study on sturgeons under bacterial infection.

High-throughput sequencing reveals the gut and lung prokaryotic community profiles of the Chinese giant salamander (Andrias davidianus).

Increasing attention has been attracted to host microbiota, due to their vital impact on host health. Little is known about the microbiota of the Chinese giant salamander (Andrias davidianus), in spite of the high economic and scientific value of this endangered species. This study was designed to characterise and compare the gut and lung prokaryotic communities of the Chinese giant salamander by high-throughput sequencing. Our study showed that the giant salamander had a lung prokaryotic community that clustered separately from its intestinal microbiota. Statistical analysis (LEfSe) revealed that the bacterial populations were dominated by Geobacter, Sulfurimonas, and Dechloromonas from Proteobacteria phylum, and Corynebacterium from Actinobacteria phylum in the lung, while Parabacteroides, Bacteroides, and PW3 from Bacteroidetes phylum, and Oscillospira from Firmicutes phylum were predominant in the intestine. A particularly innovative finding was the fairly high abundance of Archaea, especially methanogenic Euryarchaeota. The gut dominant Archaea were Methanocorpusculum and Thermoplasmata vadinCA11, while Methanosaeta and Methanoculleus were the main Archaea in the lung. PICRUSt analysis revealed differentiated functional profiles between the intestinal miacrobiota and the lung microbiota. Specially, some microbial metabolic functions were significantly more active in the intestinal microbiota, while the functional genes involved in infectious diseases were much richer in the lung microbiota. This study characterized the prokaryotic microbial community profiles in the gut and lung of the Chinese giant salamander, providing foundational support for future study seeking to understand microbiota of the giant salamander and the role of its microbiota on infectious diseases.

Transcriptomic and proteomic analyses of splenic immune mechanisms of rainbow trout (Oncorhynchus mykiss) infected by Aeromonas salmonicida subsp. salmonicida.

Furunculosis caused by Aeromonas salmonicida subsp. salmonicida is an epidemic disease among salmonids, including rainbow trout (Oncorhynchus mykiss). However, the immune mechanisms that are elicited in rainbow trout against the invasion of A. salmonicida are not yet fully understood. In this study, we examined the spleen to investigate the immune response of rainbow trout at 3days post-infection by A. salmonicida at the transcriptome and proteome levels by using Illumina-seq and iTRAQ methods, respectively. A total of 1036 genes and 133 proteins were found to undergo differential expression during the immune response of the spleen against A. salmonicida infection. Gene ontology and KEGG analysis were conducted among the differentially expressed genes and proteins, revealing that immune system process and response to stimulus were the top two biological processes, and immune system, signaling molecules and interaction, and immune diseases were the differential pathways activated. Correlation analysis of transcriptomic and proteomic results showed 17 proteins (11 upregulated and 6 downregulated) having consistent expression at RNA and protein levels. Moreover, protein-protein interaction analysis showed that diseases, proteasome, aminoacyl-tRNA biosynthesis, and nucleotide metabolism were the main interactions among the consistently expressed proteins. Consequently, these upregulated proteins, namely, ferritin, CD209, IL13Rα1, VDAC2, GIMAP7, PSMA1, and two ANXA11s could be considered as potential biomarkers for rainbow trout immune responses. BIOLOGICAL SIGNIFICANCE: This study provides the first identification of immune markers through an analysis of the differential expression of both genes and their corresponding protein products in the spleen of rainbow trout after infection by A. salmonicida, shedding light on the molecular mechanisms triggered in rainbow trout against A. salmonicida infection and providing new molecular targets for further immunological research in fish.