Longitudinal analysis of bovine microbiota in feedlot cattle following treatment with eprinomectin and chlortetracycline

Eprinomectin is used to control parasites in cattle, but data are limited on its longitudinal effects alone or in combination with antimicrobials like chlortetracycline on bovine microbiota. Rumen and fecal samples were collected on day 0 and at 1, 2, 4, and 8 weeks from control steers ( n = 5) or steers administered, eprinomectin (LR, day 0, n = 5), chlortetracycline (CTC, days 0–56, n = 5), or LR and CTC (LR + CTC, n = 5). The V4 hypervariable region of 16S rRNA gene was amplified in extracted DNA and sequenced using Illumina MiSeq. Alpha-diversity in rumen and fecal samples remained consistent ( P > 0.05) across all samplings and treatments. However, permutational multivariate Analysis of variance revealed changes ( P < 0.05) in microbial communities in rumen but not fecal microbiota with LR and CTC. Firmicutes and Bacteroidetes were the dominant phyla in rumen and fecal microbiota in all samples. Prevotella dominated in the rumen, while 5-7N15 ( Bacteroidaceae family) and Oscillospira dominanted in feces. All steers had similar relative abundances of Prevotella in the rumen, and 5-7N15 and Oscillospira in the feces. These findings suggest that eprinomectin and chlortetracycline may alter microbial communities in the rumen, with minimal impact on dominant taxa in feces.