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.

At Kyoto Encyclopedia of Genes and Genomes (KEGG) level 1, genes associated with metabolism predominated, accounting for 62% (n = 148) overall. Genes encoding genetic information processing (31; 13%), environmental information processing (15; 6%), cellular information processing (15; 6%), and organismal system (immune system, endocrine system, and nervous system; 19; 8%) also were common. At KEGG level 2, 14% (n = 20) of the metabolism genes belonged to xenobiotic biodegradation metabolism, 11% (n = 17) to lipid metabolism, 11% (n = 16) to biosynthesis of secondary metabolites, 10% (n = 15) to carbohydrate metabolism, 9% (n = 14) to amino acid metabolism, 9% (n = 13) to metabolism of terpenoids and polyketides, 8% (n = 12) to metabolism of cofactors and vitamins, 7% (n = 11) to glycan metabolism, 6% (n = 9) metabolism of other amino acids, 5% (n = 8) were unclassified, 5% (n = 8) were related to energy metabolism, and 2% (n = 2) to enzyme families. There were no differences in the percentages of KEGG orthologs from either level 1 or 2 (all adjusted P values >.05). The relative abundances of the 20 most abundant KEGG orthologs are presented in supplemental Fig 1. When comparing healthy and diarrheic calves, LEfSe analysis indicated that porphyrin and chlorophyll metabolism pathway genes were enriched in diarrheic calves from F1. On F2, biosynthesis of vancomycin group antibiotics; valine, leucine, and isoleucine biosynthesis; glycine, serine, and threonine metabolism; folate biosynthesis; pantothenate and CoA biosynthesis; and C5 branched dibasic acid metabolism were enriched in healthy calves, whereas porphyrin and chlorophyll metabolism pathway genes were enriched in diarrheic calves (Fig 10) .