Fig. 1.

Dairy calf fecal microbiota changes over the first 10 weeks of life. a The diet, sampling, and sequencing scheme for dairy calves (n = 22). TMR indicates a total mixed ration diet. b Boxplots of alpha diversity as measured by Chao1 richness and Shannon diversity index. The Chao1 richness and Shannon index values were presented as the median (central black horizontal line); the lower and upper hinges correspond to the 25th and 75th percentiles. Outliers are displayed as small black circles. c 2-dimensional NMDS of dairy fecal samples based on GUniFrac (stress = 0.16). Subsampling to obtain equal sample size (n = 22) at each time point was completed prior to performing the ordination analysis and PERMANOVA. The centroid of each ellipse represents the group mean, and the shape was defined by the covariance within each group. d Bar plot depicting the relative abundance of bacterial families over time; unclassified taxa and bacterial families which has a relative abundance less than 1% were grouped into “Others”