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Perturbations in early life gut microbiota can have long-term impacts on host health. In this study, we investigated antimicrobial-induced temporal changes in diversity, stability, and compositions of gut microbiota in neonatal veal calves, with the objective of identifying microbial markers that predict diarrhea. A total of 220 samples from 63 calves in first 8 weeks of life were used in this study. The results suggest that increase in diversity and stability of gut microbiota over time was a feature of “healthy” (non-diarrheic) calves during early life. Therapeutic antimicrobials delayed the temporal development of diversity and taxa–function robustness (a measure of microbial stability). In addition, predicted genes associated with beta lactam and cationic antimicrobial peptide resistance were more abundant in gut microbiota of calves treated with therapeutic antimicrobials. Random forest machine learning algorithm revealed that Trueperella , Streptococcus , Dorea , uncultured Lachnospiraceae , Ruminococcus 2, and Erysipelatoclostridium may be key microbial markers that can differentiate “healthy” and “unhealthy” (diarrheic) gut microbiota, as they predicted early life diarrhea with an accuracy of 84.3%. Our findings suggest that diarrhea in veal calves may be predicted by the shift in early life gut microbiota, which may provide an opportunity for early intervention (e.g., prebiotics or probiotics) to improve calf health with reduced usage of antimicrobials.

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The objective of this study was to investigate the effect of one specific strain of yeast, Saccharomyces cerevisiae boulardii CNCM I-1079 (SCB), on the growth performance, health, and fecal bacterial profile of veal calves. A total of 84 animals were enrolled in an experiment at a commercial veal farm for a total of 7 wk. Calves were fed twice a day with a milk replacer meal during the entire experiment and were randomly assigned to receive daily either SCB supplementation (10 × 10 9 cfu/d) or a placebo (CON). Individual feed intake and body weight were monitored on a daily and weekly basis, respectively. Fecal samples were collected at arrival to the veal facility (wk 0) and additional samples were taken on d 14 (wk 2) and d 49 (wk 7). These samples were subjected to 16S rRNA gene amplicon sequencing using Illumina MiSeq (Illumina Inc., San Diego, CA) to examine the bacterial profiles and real-time quantitative PCR to quantify Saccharomyces cerevisiae and specific bacterial groups. The significant increase of S. cerevisiae in the feces of SCB calves at wk 2 and 7 compared with wk 0 (respectively 1.7 × 10 7 , 1.2 × 10 7 , and 2.2 × 10 5 copy number of S. cerevisiae/g of feces) indicates a good survival of that yeast strain along the gastrointestinal tract. Supplementation of SCB did not improve overall growth performance with regard to average daily gain (ADG), final body weight, and feed intake. Nevertheless, a total of 69.1% of nonsupplemented calves had diarrhea and 28.6% experienced severe diarrhea, whereas 50.0% of the calves supplemented with SCB had diarrhea and 9.5% experienced severe diarrhea. With respect to antibiotic use, 89.7% of the diarrheic calves recorded in the CON group were treated, whereas only 66.7% of the SCB diarrheic calves received an antibiotic. In addition, diarrheic calves supplemented with SCB maintained an ADG similar to nondiarrheic animals, whereas the CON diarrheic calves had a significantly lower ADG in comparison with nondiarrheic CON calves. Fecalibacterium was the most predominant bacterial genus in fecal samples of nondiarrheic and diarrheic calves supplemented with SCB, whereas fecal microbiota was predominated by Collinsella in diarrheic calves from the CON group. Live yeast supplementation in milk replacer led to a decrease of diarrhea in milk-fed veal calves and the fecal microbiota of diarrheic calves maintained a healthy community similar to nondiarrheic animals, with Fecalibacterium being the predominant genus.

There is an increasing movement against use of antibiotic growth promoters in animal feed. Prebiotic supplementation is a potential alternative to enhance the host's natural defense through modulation of gut microbiota. In the present study, the effect of mannan oligosaccharide (MOS) and virginiamycin (VIRG) on cecal microbial ecology and intestinal morphology of broiler chickens raised under suboptimal conditions was evaluated. MOS and VIRG induced different bacterial community structures, as revealed by denaturing gradient gel electrophoresis of 16S rDNA. The antibiotic treatment reduced cecal microbial diversity while the community equitability increased. A higher bacterial diversity was observed in the cecum of MOS-supplemented birds. Quantitative polymerase chain reaction results indicated that MOS changed the cecal microbiota in favor of the Firmicutes population but not the Bacteroidetes population. No difference was observed in total bacterial counts among treatments. MOS promoted the growth of Lactobacillus spp. and Bifidobacterium spp. in the cecum and increased villus height and goblet cell numbers in the ileum and jejunum. These results provide a deeper insight into the microbial ecological changes after supplementation of MOS prebiotic in poultry diets.