Identification of Multigene Biomarker for Shrimp White Feces Syndrome by Full-Length Transcriptome Sequencing

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.

Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system

“…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 ). Pacific white shrimp, Litopenaeus vannamei , with the largest production in global shrimp industry, has suffered enormous economic losses due to serious infectious diseases (Zeng et al 2020 ). Diseases caused by viruses and bacteria have been major impact on the sustainable development of the industry, especially the occurrence of white spot syndrome virus (WSSV) (Tassanakajon et al 2018 ).…”

“…Diseases caused by viruses and bacteria have been major impact on the sustainable development of the industry, especially the occurrence of white spot syndrome virus (WSSV) (Tassanakajon et al 2018 ). Recently, newer diseases have emerged, such as early mortality syndrome (EMS), acute hepatopancreatic necrosis disease (AHPND) or hepatopancreas necrosis syndrome (HPNS) (Flegel 2019 ; Huang et al 2016 ), and white feces syndrome (WFS) (Huang et al 2020 ; Zeng et al 2020 ). These diseases occurred in many Asian countries including China, India, Indonesia, Thailand and Vietnam.…”

Intestine Bacterial Community Composition of Shrimp Varies Under Low- and High-Salinity Culture Conditions

“…However, the frequent occurrence of shrimp bacterial diseases, such as early mortality syndrome (EMS), acute hepatopancreatic necrosis disease (AHPND), hepatopancreas necrosis syndrome (HPNS), and white feces syndrome (WFS), has led to enormous economic losses every year worldwide (Sriurairatana et al, 2014;Lee et al, 2015;Choi et al, 2016;Huang et al, 2016;Xiong et al, 2017). In fact, the occurrence of L. vannamei bacterial diseases is closely associated with the obvious shifts in host intestine microbiota (Zhu et al, 2016;Hou et al, 2018;Huang et al, 2020;Zeng et al, 2020). Salinity is a very important abiotic factor affecting the intestine bacterial signatures (Zhang et al, 2016) and health status (Ponce-Palafox et al, 1997) of L. vannamei.…”

Immune responses and immunoprotection in crustaceans with special reference to shrimp

“…Accordingly, many transcriptome studies in different crustaceans have been reported. Recently, transcriptomic approach has been employed in shrimp to understand the correct chronological order of the immune response events (Soo et al 2019) and immune function of haemocytes during pathogen infection and to identify multigene biomarkers of a specific disease (Zeng et al 2020). However, as a wide range of physiological responses including biotic and abiotic stressors, moulting and reproduction modulate the crustacean immune system, application of transcriptomic study is required to understand host responses against varied stressors.…”