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).