RECTAL MICROBIOTA DYNAMICS IN PRE-WEANED DAIRY CALVES DEPENDING ON COLOSTRUM INTAKE, PRESENCE OF DIARRHEA AND ANTIBIOTIC TREATMENT

Thesis (Ph.D.), College of Veterinary Medicine, Washington State UniversityThe mammalian intestine microbial community carries out many functions contributing to host's defense from infectious diseases, nutrition, growth, immunodevelopment and immunomodulation. Several factors such as diet, age, antibiotics, and disease can affect microbiota composition and biodiversity. Neonatal diarrhea continues to be a major challenge in dairy calf raising. Diarrhea represents one of the most common causes of calf mortality, and the major cause of morbidity and use of antimicrobial treatment. Contributing to the persistent presence of calf neonatal diarrhea in dairy production is a farm management's flaw in not being able to ensure adequate passive immunity to calves through colostrum feeding. Very little is known on calves' gut microbiota composition, and nothing is known on the impact colostrum has on microbiota; the relationship between microbiota and presence of diarrhea; and the impact of antimicrobial treatment on microbiota. The goal of this study was to explore the effect of colostrum and antimicrobial treatment on calves' fecal rectal microbiota and evaluate microbiota as risk factor for diarrhea and antimicrobial treatment.In a cross-sectional study we assessed the dominant taxa in microbiota from dairy calves during their first month of life and found an age-dependent succession of the dominant microbial community. From a data analysis perspective, principal component analysis was a useful tool to present community structure collected as relative abundance (proportion of taxa in a sample) to subsequent multivariate analyses. In a longitudinal study we investigated age and colostrum effect on the microbial community from dairy calves during the first two weeks of life. This field-based investigation demonstrated significant colostrum-age interaction effect on intestinal microbiota in preweaned dairy calves.We also examined microbiota from 1 and 3 day old calves as risk factor for neonatal diarrhea and antimicrobial treatment. We found significant likelihood of diarrhea and treatment associated with calves' microbiota structures.Finally, effect of antibiotic treatment on microbiota structure and diversity, and microbiota resilience to antibiotic treatment were examined. Antibiotics impacted microbiota structure and biodiversity and the effect was detected immediately after antibiotic administration. Microbiota profile from treated animals returned similar to controls' microbial community by fourteen days after treatment.College of Veterinary Medicine, Washington State Universit