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 PICRUSt analysis was used to infer functional capabilities of the microbial communities. This approach infers the functional capacity of the microbiota by prediction of functional genes that typically are associated with different taxa. Although the biological relevance of this approach is still unclear, LEfSe analysis identified several functional gene categories that were enriched in healthy and diarrheic calves. Diarrheic calves had decreased abundances of genes responsible for metabolism of various vitamins (eg, folate, panthotenate), amino acids (eg, valine, leucine, isoleucine, glycine, serine, threonine) and carbohydrate metabolism. This imbalance might indicate that free vitamin and nutrient availability is altered in diarrheic calves. Alterations in amino acid metabolism have been observed in dogs with chronic diarrhea caused by idiopathic inflammatory bowel disease, 53 in cats with acute diarrhea, 54 and in humans with gut inflammation, 67 suggesting that amino acid dysmetabolism may be an important feature of dysbiosis-associated diseases. Increased relative abundances of genes associated with porphyrin and chlorophyll metabolism also were present in diarrheic calves. Porphyrins are tetrapyrroles that bind covalently to a metal (iron, to form cytochromes, peroxidase, catalase, myoglobin, and hemoglobin; copper or nickel, to form molecules for electron transport in methanogenic bacteria). 68 In nonphotosynthetic eukaryotes such as animals, insects, fungi, and protozoa, as well as in the a-Proteobacteria group of bacteria, the committed step for porphyrin biosynthesis is the formation of d-aminolevulinic acid by the reaction of the amino acid glycine with succinyl CoA from the citric acid cycle. 68 Metabolites such as daminolevulinic acid potentially could be used as a marker of increased abundance of Proteobacteria and therefore dysbiosis. However, PICRUSt is only a predictor of metagenomic function, and metabolomic approaches are preferred to identify factual changes in metabolic function of microbiota of diarrheic calves and identify markers of unstable gut microbiota.