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

Abstract

Bovine mastitis is a widespread infectious disease. In addition to the economic damages associated with reduced milk yield due to mastitis, the problem of food contamination by microorganism metabolites, in particular toxins, is also a concern. Horizontal transfer of microorganisms from animal populations to humans can also be complicated by antibiotic resistance. Therefore, bovine mastitis is relevant to the study of microbiology and veterinary medicine. In this study, we investigated the microbiome of milk samples from healthy cows and cows with different forms of mastitis from individual quarters of the udder of cows during first and second lactation. Total DNA was extracted from milk samples. The V3–V4 regions of the bacterial 16S rRNA genes from each sample were amplified to generate a library via high-throughput sequencing. We revealed significant dominance of several operational taxonomic units (OTUs) corresponding mostly to groups of Staphylococcus aureus, Aerococcus spp., and Streptococcus spp. In addition, we unexpectedly identified Streptococcus thermophilus in samples with high SCC quantities. We found some infectious agents that characterized summer mastitis. We demonstrated that in Central Russia, mastitis is associated with a wide variety of causal organisms. We observed some differences in the diversity of the two investigated farms. However, we did not find any significant difference among healthy, mastitis and subclinical samples according to their SCC status from either farms by principal component analysis. Linear discriminant analysis effect size (LEfSe) confirmed the presence of several indicator genera in farms from Moscow and the Tula Region. These results confirm the complex bacterial etiology of bovine mastitis.

Distinguishing the milk microbiota of healthy goats and goats diagnosed with subclinical mastitis, clinical mastitis, and gangrenous mastitis

“…Studies with cattle ( Oikonomou et al, 2014 ; Sokolov et al, 2021 ), using the V1–V2 and V3–V4 regions, and buffaloes ( Catozzi et al, 2017 ), with respective sequencing of the V1–V2 region, have already highlighted differences among groups of mastitis in alpha diversity, although they were not statistically significant ( Oikonomou et al, 2014 ), as observed in this study with the amplification of the V4 region. The significant distortions of diversity and richness caused in the microbiota by gangrenous mastitis demonstrates that there was an almost complete elimination of bacteria from the microbiota of these affected animals, resulting in a high abundance of pathogenic genera.…”

“…Our data suggest that the progression of subclinical mastitis, from clinical to gangrenous, plays crucial roles in the composition and structure of the bacterial microbiota of goat milk, modifying the richness and diversity and gradually accentuating the condition of dysbiosis, in addition to causing changes in relation to the indigenous microbiota of clinically healthy animals. Studies with cattle (Oikonomou et al, 2014;Sokolov et al, 2021), using the V1-V2 and V3-V4 regions, and buffaloes (Catozzi et al, 2017), with respective sequencing of the V1-V2 region, have already highlighted differences among groups of mastitis in alpha diversity, although they were not statistically significant (Oikonomou et al, 2014), as observed in this study with the amplification of the V4 region. The significant distortions of diversity and richness caused in the microbiota by gangrenous mastitis demonstrates that there was an almost complete elimination of bacteria from the microbiota of these affected animals, resulting in a high abundance of pathogenic genera.…”

“…The distribution of the types of mastitis in the beta diversity analyses shows the separation of the total and partial groups; however, this difficulty in clearly separating the groups and has already been demonstrated in other studies with cattle (Porcellato et al, 2020;Sokolov et al, 2021), and in this study, it may have occurred because those certain samples were collected in the transition of dysbiosis states between types of mastitis and healthy controls. This phenomenon can interfere with several dynamics Metabolic Pathway Abundances by Mastitis Types in Goats.…”

“…The distribution of the types of mastitis in the beta diversity analyses shows the separation of the total and partial groups; however, this difficulty in clearly separating the groups and has already been demonstrated in other studies with cattle ( Porcellato et al, 2020 ; Sokolov et al, 2021 ), and in this study, it may have occurred because those certain samples were collected in the transition of dysbiosis states between types of mastitis and healthy controls. This phenomenon can interfere with several dynamics ( Xia et al, 2018 ), increasing the severity from subclinical to clinical and gangrenous mastitis or jumping between the types, depending on several other factors inherent to the agents, such as location, host, environment, management, and the microbiota and its resilience to previous dysbiosis cases ( Polveiro et al, 2020 ).…”

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

“…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].…”