Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves

Gomez, D.E.; Arroyo, L.G.; Costa, M.C.; Viel, L.; Weese, J.S.

The Jaccard index (a measure of community membership, which only considers the number of shared genera, but not their abundance) and the Yue and Clayton index (a measure of community structure, which considers shared genera and their relative abundances) were calculated. Unweighted unique fraction metric (UNIFRAC) analysis of molecular variance (AMOVA), homogeneity of molecular variance analysis (HOMOVA), and parsimony test were used to compare community membership and structure between groups. The similarity between groups was visualized by dendrograms plotted by FigTree v1.4.0.1. j Clustering of the groups was represented by principal coordinate analysis plotted by a statistical software. k Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) 20 was used to predict the functional gene content in the fecal microbiota based on taxonomy obtained from the Greengenes reference database (http://greengenes.lbl.gov/cgibin/nph-index.cgi). 21 Comparison of the percentages of functional gene content between groups (healthy calves between farms, and healthy and diarrheic calves within farms) was performed by Mann-Whitney U-test, adjusted for multiple comparisons.