Flow cytometry of mesenteric lymph nodes, small and large intestinal lamina propria, and spinal cord cells from fibre-rich and fiber-free diet-fed gnotobiotic mice at baseline and after experimental autoimmune encephalomyelitis (EAE) induction

We perform profiling of different immune cell populations in the small (SILP) and large intestine lamina propria (CLP), mesenteric lymph nodes (MLN) and spinal cords (SC). We are specifically interested to evaluate the impact of dietary fiber deprivation followed by mucus erosion on the immune cell profiles of T helper cells (Th cells, T cell population) of gnotobiotic mice fed a fiber-rich (FR) or fiber-free (FF) diet. This dataset aims to assess the impact of microbiome and diet on disease course in a mouse model of multiple sclerosis (experimental autoimmune encephalomyelitis, EAE) via T cell populations. Mice are either germ-free or colonized by intragastric gavage with a defined variation of a 14-member synthetic human gut microbiome (doi: 10.1016/j.cell.2016.10.043 and 10.1016/j.xpro.2021.100607): SM01 (Akkermansia muciniphila monocolonisation), SM03 (Bacteroides caccae, Bacteroides thetaiotaomicron, Barnesiella intestinihominis), SM04 (B. caccae, B. thetaiotaomicron, B. intestinihominis, A. muciniphila), SM12 (full community except mucin-specialists B. intestinihominis and A. muciniphila), SM13 (full community except mucin specialist A. muciniphila), or SM14 (full community: Roseburia intestinalis, Faecalibacterium prausnitzii, Marvinbryantia formatexigens, Collinsella aerofaciens, Desulfovibrio piger, B. caccae, B. thetaiotaomicron, Bacteroides ovatus, Bacteroides uniformis, B. intestinihominis, Eubacterium rectale, Clostridium symbiosum, Escherichia coli, and A. muciniphila). At age 5 to 8 weeks, mice were colonized with SM combinations while fed an FR diet. Mice were either maintained on an FR diet or switched to an FF diet at 5 days after initial colonization, until the end of experiment. Baseline samples were collected 20 days following the diet switch. Otherwise, EAE induction was performed 15 days after the diet switch and samples were collected 30 days after the induction.本研究对小肠固有层（small intestine lamina propria, SILP）、大肠固有层（large intestine lamina propria, CLP）、肠系膜淋巴结（mesenteric lymph nodes, MLN）及脊髓（spinal cords, SC）中的不同免疫细胞群进行了免疫细胞谱型分析。本研究重点探究膳食纤维剥夺伴黏液层受损对喂食富含膳食纤维（fiber-rich, FR）或无膳食纤维（fiber-free, FF）饮食的悉生小鼠（gnotobiotic mice）辅助性T细胞（T helper cells, Th cells，T细胞群）免疫细胞谱型的影响。本数据集旨在通过分析T细胞群，探究微生物组与饮食对多发性硬化症（multiple sclerosis, MS）小鼠模型——实验性自身免疫性脑脊髓炎（experimental autoimmune encephalomyelitis, EAE）——病程的影响。实验所用小鼠分为无菌小鼠（germ-free）与经胃内灌胃定植法携带有14株组合式人工合成人肠道微生物群的悉生小鼠两类，相关微生物组的定义已发表于两篇文献（doi: 10.1016/j.cell.2016.10.043及10.1016/j.xpro.2021.100607），具体菌群组合如下：SM01：单定植嗜黏蛋白阿克曼氏菌（Akkermansia muciniphila）；SM03：定植粪便拟杆菌（Bacteroides caccae）、多形拟杆菌（Bacteroides thetaiotaomicron）及肠巴恩斯菌（Barnesiella intestinihominis）；SM04：定植粪便拟杆菌、多形拟杆菌、肠巴恩斯菌及嗜黏蛋白阿克曼氏菌；SM12：包含完整菌群，但缺失黏液降解专性菌肠巴恩斯菌与嗜黏蛋白阿克曼氏菌；SM13：包含完整菌群，但缺失黏液降解专性菌嗜黏蛋白阿克曼氏菌；SM14：包含完整合成菌群，具体为：肠道罗斯氏菌（Roseburia intestinalis）、普拉梭菌（Faecalibacterium prausnitzii）、甲酸解糖Marvinbryantia菌（Marvinbryantia formatexigens）、产气柯林斯菌（Collinsella aerofaciens）、毕氏脱硫弧菌（Desulfovibrio piger）、粪便拟杆菌、多形拟杆菌、卵形拟杆菌（Bacteroides ovatus）、单形拟杆菌（Bacteroides uniformis）、肠巴恩斯菌、直肠真杆菌（Eubacterium rectale）、共生梭菌（Clostridium symbiosum）、大肠杆菌（Escherichia coli）及嗜黏蛋白阿克曼氏菌。实验小鼠于5~8周龄时，经定植上述SM组合菌群并喂食FR饮食完成造模。初始定植5天后，将部分小鼠维持原有FR饮食，其余小鼠切换为FF饮食，直至实验结束。饮食切换20天后采集基线样本。此外，于饮食切换15天后开展EAE造模，并于造模30天后采集样本。