Abstract
The pacific white shrimp, Litopenaeus vannamei, with the largest shrimp industry production in the world, is currently threatened by a severe disease, white feces syndrome (WFS), which cause devastating losses globally, while its causal agents remain largely unknown. Herein, compared to the Control shrimp by metagenomic analysis, we firstly investigated that the altered functions of intestinal microbial community in WFS shrimp were the enrichment of bacterial chemotaxis and flagellar assembly pathways, hinting at a potential role of pathogenic bacteria for growth and development, which might be related to WFS occurrence. Single-molecule real-time (SMRT) sequencing was to further identify the gene structure and gene regulation for more clues in WFS aetiology. Totally 50,049 high quality transcripts were obtained, capturing 39,995 previously mapped and 10,054 newly detected transcripts, which were annotated to 30,554 genes. A total of 158 differentially expressed genes (DEGs) were characterized in WFS shrimp. These DEGs were strongly associated with various immune related genes that regulated the expression of multiple antimicrobial peptides (e.g., antilipopolysaccharide factors, penaeidins, and crustin), which were further experimentally validated using quantitative PCR on transcript level. Collectively, multigene biomarkers were identified to be closely associated with WFS, especially those functional alterations in microbial community and the upregulated immune related gene with antibacterial activities. Our finding not only inspired our cogitation on WFS aetiology from both microbial and host immune response perspectives with combined metagenomic and full-length transcriptome sequencing, but also provided valuable information for enhancing shrimp aquaculture.
Highlights
Aquaculture remains an important source of food and nutrition for millions of people worldwide, which plays an essential role in meeting the urgent global food demand (Low et al, 2017)
There were 68.9 Gb paired-end reads generated from seven Control and six white feces syndrome (WFS) shrimps, with an average of 5.3 ± 0.83 million reads per sample
To explore the difference between the microbial communities of the Control and WFS groups, a principal coordinate analysis (PCoA) as performed using Bray-Curtis distance. It revealed that the bacterial communities in WFS were notably different from those in the Control group (Figure 1B), which was confirmed by analysis of similarities (ANOSIM, P < 0.001)
Summary
Aquaculture remains an important source of food and nutrition for millions of people worldwide, which plays an essential role in meeting the urgent global food demand (Low et al, 2017). Similar results were observed in another study that several distinguished taxa were responsible for WFS, and growth of candidate pathogens contributed to the altered intestinal microbial interaction (Xiong et al, 2018). These studies focused on the interplay between shrimp health and IM dysbiosis. The puzzle about how the shrimp responds to IM alteration remains largely unknown. This insufficiency can be partially attributed to the lack of a sequenced shrimp host genome and genetic regulation. Given that the aetiology of WFS is uncertain, the discovery of shrimp multigene biomarker for identification of WFS should be a major goal of research efforts
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