Mammary microbiome of lactating organic dairy cows varies by time, tissue site, and infection status.

Tucker Andrews,John W Barlow,Thomas R Weicht,Deborah A Neher,Juan J Loor

doi:10.1371/journal.pone.0225001

Abstract

Infections of the cow udder leading to mastitis and reducing milk quality are a critical challenge facing all dairy farmers. Mastitis may be linked to the ecological disruption of an endogenous mammary microbial community, suggesting an ecosystems approach to management and prevention of this disease. The teat end skin represents a first point of host contact with mastitis pathogens and may offer an opportunity for microbially mediated resistance to infection, yet we know little about the microbial community of teat end skin or its potential interaction with the microbial community of intramammary milk of organic dairy cattle. High-throughput sequencing of marker genes for bacterial and fungal communities was used to characterize the skin and milk microbiome of cows with both a healthy and infected gland (i.e., udder quarter) and to assess the sharing of microbial DNA between these tissue habitat sites. The mammary microbiome varied among cows, through time, and between skin and milk. Microbiomes of milk from healthy and infected quarters reflected a diverse group of microbial DNA sequences, though milk had far fewer operational taxonomic units (OTUs) than skin. Milk microbiomes of infected quarters were generally more variable than healthy quarters and were frequently dominated by a single OTU; teat end skin microbiomes were relatively similar between healthy and infected quarters. Commonly occurring genera that were shared between skin and milk of infected glands included Staphylococcus spp. bacteria and Debaryomyces spp. fungi. Commonly occurring genera that were shared between skin and milk of healthy glands included bacteria SMB53 (Clostridiaceae) and Penicillium spp. fungi. Results support an ecological interpretation of the mammary gland and the notion that mastitis can be described as a dysbiosis, an imbalance of the healthy mammary gland microbiome.

Highlights

Mastitis remains one of the most common and costly health concerns of dairy cattle in the United States (US) and globally
Library size for negative control sham swab and blank samples ranged from 23–5812 16S rRNA sequence reads and 1–811 ITS sequence reads; no consistent trends in operational taxonomic units (OTUs) diversity were observed among control samples
While 250 of the 281 OTUs observed in control samples were observed in the skin swab and milk samples, the mean read number for OTUs in controls was 2% of the mean read number for OTUs in the skin swab and milk samples, suggesting limited contamination during collection and processing of swab and milk samples

Summary

Methods

We adopt the term “habitat state” to generally describe the two habitats (teat apex skin and teat cistern milk) in either the healthy or infected state. The four habitat states sampled were teat end skin and teat cistern milk of a mammary gland (individual udder quarter) observed in either a healthy or infected state. A more precise but less concise description of the samples would be “cisternal milk sample from a gland defined as infected” for infected milk, or “teat end skin swab sample from a gland defined as uninfected” for healthy teat, etc. The a priori design of the observational study was to collect teat swab and milk samples from healthy and infected mammary quarters during the grazing season on a single dairy herd over two years to compare composition of bacterial and fungal communities in these four sample types.

Results

Discussion

Conclusion