Supplemental Tables for the Manuscript : Effect of an intramammary lipopolysaccharide challenge on the hindgut microbial composition and fermentation of dairy cattle experiencing intermittent subacute ruminal acidosis

Our hypothesis is that a transient subacute ruminal acidosis (SARA) challenge will result in microbial changes due to large undigested carbohydrates bypassing the rumen and being fermented in the hindgut, and these changes will be more prominent after an LPS challenge due to the systemic effects of the LPS. To test this 18 early-lactating Simmental cows were divided into three groups (n = 6), two were fed a SARA-inducing feeding regime, one was fed a control (CON) diet, with either 60% or 40% concentrate, respectively. On d 30, one SARA group (SARA-LPS) and the CON group (CON-LPS) were intramammarily challenged with a single dose of 50 µg LPS from E. coli (O26:B6), while the remaining six SARA (SARA-PLA) received a placebo. Feces from the cows were collected and analyzed for pH and short chain fatty acids SCFA, as well as DNA was extracted for 16S rRNA analysis. Microbial analysis was performed using QIIME2. The data here is a statistical analysis of the operational taxonomic units (OTUs) that were measured in the feces between dairy cows fed either a control or a SARA challenge diet (Supplementary Table 1), the statistical analysis of the OTUs measured in feces of dairy cows fed control diet and receiving a LPS infusion (CON-LPS) or a SARA diet receiving either a LPS (SARA-LPS) or placebo infusion (SARA-PLA; Supplementary Table 2). As well this repository includes a Spearman's correlation coefficient matrix between statistically significant identified genera of fecal microbes and the fermentation characteristics of feces (short chain fatty acids SCFA; pH).我们的研究假说为：一过性亚急性瘤胃酸中毒（subacute ruminal acidosis, SARA）刺激会因大量未消化碳水化合物绕过瘤胃并在后肠发酵，引发微生物组改变；而由于脂多糖（lipopolysaccharide, LPS）的全身性效应，在脂多糖刺激后这类微生物改变会更为显著。为验证该假说，本研究将18头早期泌乳期西门塔尔奶牛分为3组，每组6头：其中2组饲喂可诱导亚急性瘤胃酸中毒的日粮，精料占比为60%；1组饲喂对照组（control, CON）日粮，精料占比为40%。试验第30天时，1个亚急性瘤胃酸中毒刺激组（SARA-LPS组）与对照组（CON-LPS组）经乳房内注射单剂量50微克大肠杆菌O26:B6来源的脂多糖，剩余6头亚急性瘤胃酸中毒刺激组奶牛（SARA-PLA组）则注射安慰剂。本研究收集了所有奶牛的粪便样品，检测其pH值与短链脂肪酸（short chain fatty acids, SCFA）含量，并提取粪便DNA用于16S rRNA测序分析；微生物组分析采用QIIME2平台完成。本数据集包含两类统计分析结果：其一为饲喂对照日粮或亚急性瘤胃酸中毒刺激日粮的泌乳奶牛粪便中操作分类单元（operational taxonomic units, OTUs）的检测统计分析（详见补充表1）；其二为饲喂对照日粮并接受脂多糖攻毒的奶牛（CON-LPS组）、饲喂亚急性瘤胃酸中毒日粮并分别接受脂多糖攻毒（SARA-LPS组）或安慰剂注射（SARA-PLA组）的奶牛粪便中操作分类单元的检测统计分析（详见补充表2）。此外，本数据集还包含粪便中经统计学鉴定具有显著性差异的菌属与粪便发酵特性（短链脂肪酸含量、pH值）之间的斯皮尔曼相关系数矩阵（Spearman's correlation coefficient matrix）。