Date of Award


Document Type


Degree Name

Master of Science (MS)


Plant and Soil Science

First Advisor

Deborah Neher


Infections of the cow udder leading to mastitis and lower milk quality are a critical challenge facing northeast organic dairy farmers. Limited mastitis treatment options are available to organic producers and bedding systems impact cow health, including mastitis risk. Composted bedded pack, a system touted for increased cow comfort and well-being, allows stratified accumulation of bedding and manure in the barn. This method is gaining popularity among organic producers, yet little is known about the microbiota of the accumulated pack and its interaction with the cow mammary gland. An in-depth single farm study was conducted that surveyed bedded pack (microbiome and microarthropod community), dipteran vectors of bacterial mastitis pathogens, and the teat skin and teat cistern milk microbiomes. Comparisons were made with four additional farms utilizing bedded packs to test generality of results.

Few fly pests were observed in the bedded pack. However, bedding on all farms was found to harbor the mesostigmatid mite genus Glyptholaspis, a well-established predator of nematodes and muscid fly larvae, suggesting that predators may suppress populations of biting flies in bedded pack barns. Additionally, the fungivorous genus Rhizoglyphus was commonly abundant in all farms, suggesting that the mite community regulates microbial activity at multiple trophic levels.

High-throughput sequencing of universal marker genes for bacterial and fungal communities was used to characterize the skin and milk microbiome of cows with both a healthy and infected quarter on the case study farm, and the composted bedded pack of all five farms. The bedded pack microbiome varied with bedding material and management style; fungal taxa were primarily yeasts of the Ascomycota; all farms additionally contained anaerobic fungi associated with the bovine rumen. Common bacterial genera included Acinetobacter and Pseudomonas, both of which were also commonly observed on teat skin and in milk. The udder microbiome varied through time and between skin and milk. Both healthy and infected milk microbiomes reflected a diverse group of microbial DNA sequences. Health status of the quarter changed whether taxa were shared between the teat skin, milk, and bedding. Proportion of taxa shared between healthy milk and skin was stable while taxa shared in infected quarters varied widely. Taxa shared among all habitats included yeast genus Debaryomyces and bacteria Acinetobacter guillouiaea.

Results support an ecological interpretation of both the udder and the bedded pack environment and support the notion that mastitis can be described as an imbalance of the healthy mammary gland microbiome. Future work might compare udder health between common bedding practices, investigating the impact of bedding on the microbiota of the mammary gland in the healthy and diseased state.



Number of Pages

137 p.

Included in

Soil Science Commons