Fecal microbiome profiles of neonatal dairy calves with gastrointestinal disease

Primary author: Giovana Slanzon
Co-author(s): Lindsay Parrish; Sophie Trombetta; William Sischo; Craig McConnel
Faculty sponsor: Dr. Craig Stephen McConnel

Primary college/unit: College of Veterinary Medicine
Campus: Pullman


Gastrointestinal disease is the most common illness in preweaned dairy calves. Studies have associated fecal microbiome composition with health status, but changes in the microbiome across varying levels of GI disease remain unclear. Our objective was to show a correlation between clinical symptoms and shifts in the microbiome composition. Calves (n=360) were enrolled in a sampling scheme of repeat fecal collections throughout 5-15 d of age. Daily evaluations assessed health status based on clinical signs and treatments. Calves with fecal scores of 3 (loose) or 4 (watery) were diagnosed with diarrhea and classified as bright-sick (BS) or depressed-sick (DS) according to their behavior and appetite. Calves with fecal scores <3 and no clinical illness were classified as healthy. Sixty-one fecal samples from healthy calves and 30 samples from diarrheic calves were selected to represent different breeds and ages. The V3-V4 region of the 16S rRNA gene was sequenced and analyzed using DADA2 pipeline. The ASV table was used to compare the taxonomic profiles, differences were identified by LEfSe (p2). Healthy calves had greater enrichment of the families Bifidobacteriaceae, Bacteroidaceae, Prevotellaceae, Eubacteriaceae, Ruminococcaceae, Erysipelotrichaceae. In BS calves Listeriaceae, Clostridiaceae and Lachnospiraceae were more enriched. DS calves had enriched Lactobacillaceae, Streptococcaceae and Enterobacteriaceae in their microbiome. Breed differences included the association of Bacteroidaceae, Eubacteriaceae, Erysipelotrichaceae and Fusobacteriaceae with healthy Jersey calves. Bifidobacteriaceae was more enriched in healthy Holstein calves. On the other hand, Enterobacteriaceae was associated with DS Holstein calves. For DS Jersey calves, the order Lactobacillales was enriched.