Examination of the microbiota of normal cow milk using MinION^TM nanopore sequencing

Abstract

The aim of this study was to evaluate the microbiota of normal milk in dairy cows and their relationship with host factors, such as the age of the cow (Age), somatic cell counts in milk (SCCs), and days in milk (DIM). We investigated 48 milk samples from 22 cows with no systemic or local clinical signs using MinION TM nanopore sequencing for a 16S rRNA gene amplicon. Bacterial richness was positively correlated with the DIM (p = 0.043), and both the Shannon-Wiener Index and Simpson's Index, which are metrics of alpha-diversity, were also significantly positively correlated with the SCC (p < 0.001). The composition ratios of both Actinobacteria at the phylum level and Kocuria spp. at the genus level in the milk microbiota were significantly correlated with the SCC (p < 0.001 and p < 0.001, respectively). In the beta-diversity test, the one-way analysis of similarities test showed a significant difference (p = 0.0051) between the low-and high-SCC groups. This study clarified that the composition of the normal milk microbiota in this herd was related to the SCC. It also raised the possibility of variations in bacterial genera in the normal milk microbiota between the low-and high-SCC groups.However, to clarify the actual condition of the milk microbiota and to elucidate the relationship with the SCC, it is necessary to perform further analyses taking into account not only the relative abundance, but also the absolute abundance of microbes.

Fecal microbiota colonization dynamics in dairy heifers associated with early-life rumen microbiota modulation and gut health

“…Enterococci are commonly found in the feces of pre-ruminant calves ( Devriese et al, 1992 ) and are facultatively anaerobic, lactic acid-producing bacteria that are capable of utilizing various sugars ( Švec and Devriese, 2015 ). Kocuria are typically associated with the skin microbial community and have been found among udder skin microbiota ( Braem et al, 2013 ) and in milk of cows ( Quigley et al, 2013 ; Shinozuka et al, 2021 ). The colostrum-related ASVs disappeared from the fecal community after weaning, which indicates that they had a functional role only during the pre-weaning period.…”

“…Compared with milk bacteria, the milk archaea have been less studied. However, recent evidence suggests that there is a rich community of archaea in milk ( Hoque et al, 2019 ; Shinozuka et al, 2021 ), and archaea have also been found in the uterus ( Yeoman et al, 2018 ) and GI tract of calves right after birth ( Guzman et al, 2015 ). Our results suggest that colostrum could serve as a seeding source for some archaea, but the majority were seeded from young animal rumen early in life and remained in the large intestine thereafter.…”

Regression tree analysis of the relationship between the concentrations of antimicrobial components and the microbiota of normal milk from dairy cows

“…A comprehensive analysis of the microbiota in the milk samples was performed based on previously reported methods [ 46 ] as follows. DNA was previously isolated from each milk sample using ISOSPIN Fecal DNA (Nippon Gene, Tokyo, Japan) according to the manufacturer’s instructions that included an initial bead-beating step.…”

A culture-, amplification-independent, and rapid method for identification of pathogens and antibiotic resistance profile in bovine mastitis milk

“…MinION sequencing is a promising approach for rapid diagnosis of pathogen and antibiotic resistance profiles as well as better clinical management of mastitis A growing body of literature emphasized the applicability of MinION sequencing and its advantages for the infectious disease diagnostics (Petersen et al, 2019;Mongan et al, 2020;Taxt et al, 2020;Avershina et al, 2021;Ciuffreda et al, 2021). However, the use of MinION sequencing in food microbiology and veterinary medicine fields so far has been very limited to a few studies (Catozzi et al, 2020;Azinheiro et al, 2021;Shinozuka et al, 2021). Identifying causative pathogens in mastitis-infected animals is a challenging task, and previous research has documented that some of the causative pathogens are not detectable using conventional diagnostic methods (Taponen et al, 2009;Kuehn et al, 2013;Addis et al, 2016).…”