A core microbiota dominates a rich microbial diversity in the bovine udder and may indicate presence of dysbiosis

Abstract

The importance of the microbiome for bovine udder health is not well explored and most of the knowledge originates from research on mastitis. Better understanding of the microbial diversity inside the healthy udder of lactating cows might help to reduce mastitis, use of antibiotics and improve animal welfare. In this study, we investigated the microbial diversity of over 400 quarter milk samples from 60 cows sampled from two farms and on two different occasions during the same lactation period. Microbiota analysis was performed using amplicon sequencing of the 16S rRNA gene and over 1000 isolates were identified using MALDI-TOF MS. We detected a high abundance of two bacterial families, Corynebacteriaceae and Staphylococcaceae, which accounted for almost 50% of the udder microbiota of healthy cows and were detected in all the cow udders and in more than 98% of quarter milk samples. A strong negative correlation between these bacterial families was detected indicating a possible competition. The overall composition of the udder microbiota was highly diverse and significantly different between cows and between quarter milk samples from the same cow. Furthermore, we introduced a novel definition of a dysbiotic quarter at individual cow level, by analyzing the milk microbiota, and a high frequency of dysbiotic quarter samples were detected distributed among the farms and the samples. These results emphasize the importance of deepening the studies of the bovine udder microbiome to elucidate its role in udder health.

Comparative Analysis of Milk Microbiomes and Their Association with Bovine Mastitis in Two Farms in Central Russia

“…Bovine milk microbiome analysis revealed strong variations between quarters, with some quarters clearly dominated by one taxonomic unit, whereas others displayed a more balanced profile. Similarly, a considerable difference in quarter microbiota from the same cow was described in previous work [43] We show in our study that not only a single group of pathogenic microorganisms but several pathogenic genera and species within milk microbiota might be associated with subclinical and clinical bovine mastitis at the same time within one general area of Central Russia.…”

“…The next agent identified in this work was Corynebacterium. In recent studies by Porcellato et al [43] strong negative correlation of Corynebacteriaceae and Staphylococcacea was detected. In contrast, early positive correlations with Staphylococcus were shown for this genus [44].…”

Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk

“…The number of eukaryotic and archaeal reads varied from sample to sample, accounting for up to over 50% of all of the reads. Obviously, the bovine milk microbiome is highly diverse and different from sample to sample [7,12,53], which is reinforced by our study. The advantage of full-length SSU rRNA gene sequencing over short amplicon sequencing approaches is an improved species-level classification, as well as the simultaneous analysis of not only the bacteria present in the sample but also the identification of archaeal and eukaryotic species.…”

“…In short, the amplicon sequencing taxonomic resolution is more or less limited to the genus level. The sequencing of milk samples using short amplicon sequencing was performed intensively before, e.g., by Porcellato et al [7], Taponen et al [8], Metzger et al [9], Cremonesi et al [10], Metzger et al [11], Pang et al [12], Doyle et al [13], Oultram et al [14], Sokolov et al [15] and Li et al [16]. Nevertheless, full-length sequencing approaches are rare and, if published, are mostly performed using long-read sequencers, e.g., Catozzi et al [17].…”

Milk Lymphocyte Profile and Macrophage Functions: New Insights Into the Immunity of the Mammary Gland in Quarters Infected With Corynebacterium Bovis

“…Despite its high prevalence in the etiology of intramammary infections in cattle, C. bovis is considered a minor mastitis pathogen with limited clinical signi cance [5]. From another point of view, it has been considered part of the udder core microbiota with potential protective role against dysbiosis [6][7][8]. This bacterium colonizes the teat apices [9,10], teat canal [11] but can also be isolated from the teat cistern, gland cistern, and mammary parenchyma [12].…”