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bioRxiv · 10.1101/2025.11.19.689190

Variations in cow milk and teat skin microbiota across the lactation cycle with intra-mammary cephalosporin use at dry-off

Van Beeck, W.·Lemos, M.·Niesen, A. M.·Finnegan, P.·Shih, T.·Ho, A.·Rossow, H. A.·Marco, M. L.
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Abstract

Cephalosporins and other broad-spectrum antibiotics are frequently administered prophylactically into the udder when dairy cows end their lactation cycle, termed dry-off, to reduce mastitis risk. However, the use of antibiotics on cows that do not have signs of infection may result in the selection of microbes resistant to antibiotics and negatively alter the udder microbiome composition. In this study, the effects of intramammary cephalosporin therapy with either Cephapirin (CB) or Ceftiofur (CH) on milk and teat skin microbiota were examined for three dairies in California. Bacterial composition was measured for cows with low somatic cell counts (SCC,<100,000 cells /mL) and high, subclinical SCC (>200,000 cells/mL). Samples were collected at dry-off (before treatment), seven days later, and 55-75 Days in Milk (DIM) in the next lactation cycle. The milk and skin microbiota were largely separated based on dairy (milk: R2 = 6.22, skin: R2 = 7.56) and day of sampling (milk: R2 = 4.74 and skin: R2 = 3.77). CB or CH use was associated with a small but significant impact on the milk microbiota beta-diversity (Bray-Curtis, p =0.003, R2= 1.4%) but no effect was observed on the skin. At one dairy (Dairy 3), milk from cows receiving CB and CH had a reduction in proportions of Staphylococcaceae at 55-75DIM compared to untreated cows. Overall, antibiotic use did not result in large significant changes to bacterial diversity in milk or on the teat skin, and instead the microbiota at those sites mainly differed between the time and location of sampling. ImportanceThe use of antibiotics in agriculture is under increasing scrutiny due to the rising spread of antimicrobial resistant bacteria. Our study showed that common preventative antibiotic intramammary treatment of cows with cephalosporins at the end their lactation (dry-off) had minimal effects on the milk and teat skin microbiota on asymptomatic cows with high somatic cell counts.

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Van Beeck, W., Lemos, M., Niesen, A. M., Finnegan, P., Shih, T., Ho, A., Rossow, H. A., Marco, M. L.. 2025-11-19. Variations in cow milk and teat skin microbiota across the lactation cycle with intra-mammary cephalosporin use at dry-off. https://doi.org/10.1101/2025.11.19.689190

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