Van Beeck, W. | Search bioRxiv

bioRxiv2025

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

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.

microbiology↗

bioRxiv2025

From Diversity to Dominance: How Salt and CO2 Shape LAB-dominated Ecosystems in Vegetable Fermentations

Research on microbial ecosystems is often challenging due to high diversity of microbial taxa present and the complexity of controlling environmental variables. To address these challenges, fermented foods are simpler and more reproducible model ecosystems, where both community composition and environmental factors can be more precisely controlled and manipulated. In this study, we focused on fermented vegetables which are typically dominated by lactic acid bacteria (LAB). It is not completely understood why lactic acid bacteria (LAB) consistently drive the spontaneous fermentation of vegetables such as cabbage and carrots and how variables such as vegetable substrates, salt addition, and carbon dioxide levels can impact microbial community dynamics. Here, we explored the temporal microbial dynamics in standardized fermentations of 11 different vegetables (including beetroot, bell pepper, cabbage, carrot, cucumber, fennel, green asparagus, leek, parsnip, sunroot, and tomato), revealing a consistent dominance of Leuconostoc and other LAB. Additionally, we investigated the impact of varying salt concentrations, demonstrating that lower salt levels resulted in a delayed appearance of the typically dominant LAB community, while simultaneously revealing a higher abundance of Weissella and various Enterobacterales taxa. These effects imposed by reduced salt concentrations were mitigated by CO2 injection, which reverted the enhanced Enterobacterales levels and increased the overall abundance of Lactobacillales. This study demonstrates how targeted manipulation of environmental parameters, such as salinity and gas composition, can be used to uncover ecological principles governing microbial succession and community assembly in reproducible fermentation-based model ecosystems. ImportanceUnderstanding the ecological principles that shape microbial community assembly is essential for advancing our knowledge of microbial ecosystems. Fermented vegetables, increasingly popular among the general population, provide tractable and reproducible model systems to study microbial succession under controlled environmental conditions. By systematically manipulating variables such as vegetable type, salinity and gas composition, we uncovered the effect of these factors on the microbial dynamics throughout the fermentation. These insights not only contribute to a better understanding of the microbial ecology of these man-made food systems but also suggest directions for novel strategies to optimize fermentation processes for producing faster, safer, and more flavorful foods.

microbiology↗