Fecal metagenomic dataset of autoimmune diseases. Fecal metagenomic dataset of patients with autoimmune diseases and healthy controls

Recruitment was conducted at the Second Affiliated Hospital of Dalian Medical University and the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine. Patients with autoimmune diseases were enrolled based on confirmed diagnoses by licensed physicians, adhering to the 2019 European League Against Rheumatism/American College of Rheumatology (EULAR/ACR) classification criteria for ankylosing spondylitis (AS), systemic lupus erythematosus (SLE), and primary Sjögren’s syndrome (pSS). Exclusion criteria included diabetes, severe hypertension, severe obesity or metabolic syndrome, inflammatory bowel disease (IBD), cancers, abnormal liver or kidney function, and recent use of antibiotics or probiotic products within the preceding four weeks. Based on these criteria, the study included 130 AS patients, 73 SLE patients, 66 pSS patients, and 118 healthy controls for further analysis. Fecal samples were collected from participants, temporarily stored on dry ice, and transported to the laboratory within 24 hours, where they were stored at -80°C until further processing. DNA extraction was performed using the TIANamp Stool DNA Kit (TIANGEN, China), and DNA quality was evaluated using the Qubit 2.0 Fluorometer. Metagenomic sequencing libraries were prepared using the NEB Next Ultra DNA Library Prep Kit (NEB, USA) following the manufacturer’s protocol, with unique index codes assigned to each sample. Library quality was verified using an Agilent 2100 Bioanalyzer. Indexed samples were clustered on a cBot Cluster Generation System using an Illumina PE Cluster Kit (Illumina, USA) according to the manufacturer’s instructions. After cluster generation, DNA libraries were sequenced on the Illumina NovaSeq platform, producing 150 bp paired-end reads.

本研究的受试者招募工作于大连医科大学附属第二医院与贵州中医药大学附属第二医院开展。纳入经执业医师确诊的自身免疫性疾病患者，所有患者均符合2019年欧洲抗风湿病联盟/美国风湿病学会（European League Against Rheumatism/American College of Rheumatology, EULAR/ACR）发布的强直性脊柱炎（ankylosing spondylitis, AS）、系统性红斑狼疮（systemic lupus erythematosus, SLE）及原发性干燥综合征（primary Sjögren’s syndrome, pSS）分类标准。本研究的排除标准包括：糖尿病、重度高血压、重度肥胖或代谢综合征、炎症性肠病（inflammatory bowel disease, IBD）、恶性肿瘤、肝肾功能异常，以及入组前4周内使用过抗生素或益生菌制剂。按照上述筛选标准，本研究最终纳入130例AS患者、73例SLE患者、66例pSS患者，以及118名健康对照者，用于后续分析。研究人员收集所有受试者的粪便样本，临时置于干冰中保存，并于24小时内运送至实验室，随后在-80℃条件下冷冻储存直至后续实验处理。DNA提取采用中国天根生化（TIANGEN）的TIANamp粪便DNA提取试剂盒完成，使用Qubit 2.0荧光定量仪对提取得到的DNA质量进行评估。宏基因组测序文库的构建采用美国纽英伦生物（NEB）的NEB Next Ultra DNA文库制备试剂盒，严格遵循厂商提供的实验操作流程，并为每个样本分配唯一的索引标签。使用Agilent 2100生物分析仪验证构建完成的文库质量。将带有索引标签的样本使用Illumina PE簇生成试剂盒（Illumina，美国）在cBot簇生成系统上完成集群扩增，操作流程严格依照厂商说明书执行。集群扩增完成后，在Illumina NovaSeq测序平台上进行高通量测序，最终产出150 bp双端读长序列数据。