Intestinal microbiota play an important role in animal health and disease. Until recently, the intestinal microbiota in white spot syndrome virus (WSSV)-infected red swamp crayfish (Procambarus clarkii) at different health statuses have not been studied. This study investigated the intestinal microbiota of healthy crayfish (HC), WSSV-infected active crayfish (IAC) and WSSV-infected diseased crayfish (IDC) by high throughput sequencing technology. The relative abundances of certain phyla changed significantly in WSSV-infected crayfish, shown as decreased Tenericutes and increased Proteobacteria in the IAC and IDC groups and increased Bacteroidetes in the IAC group. More core genera and the significantly increased relative abundance of Anaerorhabdus furcosa resulted in increased intestinal species diversity in the IAC group. The relative abundances of intestinal opportunistic Aeromonas, Citrobacter and WSSV loads significantly increased in the IDC group. The IDC group possessed three significantly increased level-2 KEGG pathways with relative abundances over 5%, including membrane transport, amino acids and carbohydrates metabolism, and the largest increased pathway was glycan biosynthesis and metabolism. The findings provide a basis for developing microbial strategies for the prevention and therapy of WSS disease.

肠道菌群在动物健康和疾病中起着重要作用。直到最近，还没有研究过白斑综合症病毒（WSSV）感染的红色沼泽小龙虾（Procambarus clarkii）在不同健康状况下的肠道菌群。本研究通过高通量测序技术研究了健康小龙虾（HC），WSSV感染的活性小龙虾（IAC）和WSSV感染的患病小龙虾（IDC）的肠道菌群。在WSSV感染的小龙虾中，某些门的相对丰度发生了显着变化，表现为IAC和IDC组的Tenericutes减少，Proteobacteria增多和Bacteroidetes增多在IAC组中。IAC组中更多的核心属和明显的厌氧厌氧菌相对丰富度导致肠道物种多样性增加。IDC组肠道机会性气单胞菌，柠檬酸杆菌和WSSV的相对丰度显着增加。IDC组具有3个显着增加的2级KEGG途径，相对丰度超过5％，包括膜转运，氨基酸和碳水化合物代谢，最大的途径是聚糖的生物合成和代谢。这些发现为制定预防和治疗WSS疾病的微生物策略提供了基础。