Investigation of the viral and bacterial microbiota in intestinal samples from mink (<i>Neovison vison</i>) with pre-weaning diarrhea syndrome using next generation sequencing

Pre-weaning diarrhea (PWD) in mink kits is a common multifactorial syndrome on commercial mink farms. Several potential pathogens such as astroviruses, caliciviruses, Escherichia coli and Staphylococcus delphini have been studied, but the etiology of the syndrome seems complex. In pooled samples from 38 diarrheic and 42 non-diarrheic litters, each comprising of intestinal contents from 2–3 mink kits from the same litter, the bacterial populations were studied using Illumina Next Generation Sequencing technology and targeted 16S amplicon sequencing. In addition, we used deep sequencing to determine and compare the viral intestinal content in 31 healthy non-diarrheic and 30 diarrheic pooled samples (2–3 mink kits from the same litter per pool). The results showed high variations in composition of the bacterial species between the pools. Enterococci, staphylococci and streptococci dominated in both diarrheic and non-diarrheic pools. However, enterococci accounted for 70% of the reads in the diarrheic group compared to 50% in the non-diarrheic group and this increase was at the expense of staphylococci and streptococci which together accounted for 45% and 17% of the reads in the non-diarrheic and diarrheic group, respectively. Moreover, in the diarrheic pools there were more reads assigned to Clostridia, Escherichia-Shigella and Enterobacter compared to the non-diarrheic pools. The taxonomically categorized sequences from the virome showed that the most prevalent viruses in all pools were caliciviruses and mamastroviruses (almost exclusively type 10). However, the numbers of reads assigned to caliciviruses were almost 3 times higher in the diarrheic pools compared the non-diarrheic pools and Sapporo-like caliciviruses were more abundant than the Norwalk-like caliciviruses. The results from this study have contributed to the insight into the changes in the intestinal microbiota associated with the PWD syndrome of mink.水貂幼崽断奶前腹泻（Pre-weaning diarrhea, PWD）是商业化水貂养殖场中常见的多因素综合征。目前已有多项研究针对星状病毒（astroviruses）、杯状病毒（caliciviruses）、大肠杆菌（Escherichia coli）与海豚葡萄球菌（Staphylococcus delphini）等多种潜在病原体展开探索，但该综合征的病因仍较为复杂。本研究采集了38份腹泻组与42份非腹泻组的混合肠道样本，每份样本由同窝2~3只水貂幼崽的肠道内容物混合而成，利用Illumina下一代测序技术（Illumina Next Generation Sequencing）与靶向16S扩增子测序（targeted 16S amplicon sequencing）对样本中的细菌群落进行分析；此外，本研究还通过深度测序（deep sequencing）对31份健康非腹泻组与30份腹泻组的混合样本（每份同样由同窝2~3只水貂幼崽的肠道内容物混合而成）的肠道病毒组成进行了检测与比较。研究结果显示，各混合样本间的细菌物种组成存在显著差异。肠球菌、葡萄球菌与链球菌在腹泻组与非腹泻组样本中均占优势地位，但腹泻组样本中肠球菌的读段占比达70%，而非腹泻组仅为50%；该占比的提升是以葡萄球菌与链球菌的占比下降为代价的——非腹泻组中二者的总读段占比为45%，而腹泻组仅为17%。此外，相较于非腹泻组，腹泻组样本中隶属于梭菌纲（Clostridia）、埃希氏菌-志贺氏菌属（Escherichia-Shigella）与肠杆菌属（Enterobacter）的读段数量更多。病毒组的分类学注释结果显示，所有混合样本中最普遍的病毒为杯状病毒与哺乳动物星状病毒（mamastroviruses，几乎均为10型）。然而，腹泻组样本中杯状病毒的读段数量几乎是非腹泻组的3倍，且札幌样杯状病毒（Sapporo-like caliciviruses）的丰度高于诺沃克样杯状病毒（Norwalk-like caliciviruses）。本研究结果为深入解析与水貂断奶前腹泻综合征相关的肠道菌群变化提供了重要依据。