Milk metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1056541 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Analysis of the effect of bacteriocin RSQ01 on milk preservation from the perspective of flora Metagenome
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Project description:Analysis of the effect of bacteriocin RSQ01 on milk preservation from the perspective of flora Metagenome
| PRJNA951798 | ENA
Project description:Milk is an indispensable source of infant nutrition in all mammals, made up of complex constituents needed for infant nourishment and immunity. Comparison of miRNA profiles between infected and non-infected/control Holstein cattle could provide important information on the differences in composition of milk at the level of miRNA, if any, and broaden our perspective and understanding of the effect of pathology on cellular compositions and functions. In the present study we therefore analyzed the expression profiles of bovine milk exosomal miRNAs during S. uberis infection and identified 328 known miRNAs and 82 high-confidence miRNA candidates by deep sequencing. The top 10 miRNAs in both control and infected replicates accounted for approximately 80% of total counts, which were predicted to target 605 genes using two computational approaches. In addition, 15 significantly differentially expressed miRNAs were identified between control and infected replicates during S. uberis infection, and a total of 1,852 unique genes were predicted to be targeted by these miRNAs. Ingenuity Canonical Pathways and Diseases and Biological Function analyses using IPA indicated that the identified miRNAs targets mainly enriched in regulating the innate and adaptive immune responses in newborns, as well as infant growth and development. The characterization of these miRNAs could contribute to a better understanding of the molecular mechanisms involved in lactation physiology and milk imparted immune function in the dairy cattle.
2017-07-25 | GSE59794 | GEO
Project description:In dairy cows, milk production and composition are affected by numerous factors, including diet. Milk is the body fluid with the highest RNA concentration, including numerous microRNA. These microRNA presence in the different milk compartments is still poorly documented and the effect of feed restriction on milk miRNome has not been described yet. The aim of this study was to describe the effects of feed restrictions of different intensitizes on milk compartment miRNome composition. Two feed restriction trials were performed on lactating dairy cows, one of high intensity and one of moderate intensity. 2 896 mature microRNA were identified in milk, including 1 493 that were already known in bovine specie. Among the 1 095 miRNA that were abundant enough to be informative, 10% were exclusive to one milk compartment and the abundance of 155 varied between compartments, revealing a specific miRNome for each milk fraction. Feed restriction affected differently these miRNome, with microRNA in whole milk and milk extracellular vesicles being the most affected and microRNA in fat globules and exfoliated mammary epithelial cells being relatively or completely unaffected. Target prediction of known microRNA that varied under feed restriction reflected modification of some key pathways for lactation related to milk fat and protein metabolisms, cell cycle and stress responses. These findings open up opportunities for future research on the use of milk miRNA as biomarkers of energy status in dairy cows.
2023-05-31 | GSE207759 | GEO
Project description:Microbial biodiversity analysis in Niger raw milk
| PRJNA510318 | ENA
Project description:Studies of normal human mammary gland development and function have mostly relied on cell culture, limited surgical specimens, and rodent models. Although RNA extracted from human milk has been used to assay the mammary transcriptome non-invasively, the transcriptome derived from the milk fat layer has not been compared with the mammary-derived transcriptome nor have sources of RNA been quantified in milk. In this study the effects of milk collection and processing on RNA quality and origin were assessed in humans and rhesus macaques. Total RNA in milk was quantitated in acridine orange-stained milk using an automated whole slide scanner and custom-built Globulator software. Total RNA extracted from milk fat, cells in milk, and mammary biopsies of lactating rhesus macaques were compared using RNA sequencing and analysis. Compared with human milk, milk from macaques contained similar amounts of RNA-containing cytoplasmic crescents, but more cells. Total RNA extracted from milk fractions was also evaluated for factors that affect RNA quality. Degradation of RNA extracted from human milk fat was positively correlated with geographic distance from collection site, storage time, and sample type. There were no differences in RNA degradation in macaque milk collected after 10 min or 4 hr accumulation, suggesting that degradation of RNA extracted from milk fat may not occur in the mammary gland. Using RNA-Seq, RNA extracted from macaque milk fat and cells in milk more accurately represented RNA from mammary epithelial cells (cells that produce milk) than did RNA from mammary tissue. Mammary epithelium-specific transcripts were more abundant in macaque milk fat whereas adipose or stroma-specific transcripts were more abundant in mammary tissue. Functional analyses confirmed the validity of milk as a source of RNA from mammary epithelial cells. Analysis of highly abundant putative microRNAs in macaque milk fat revealed a potentially novel non-coding RNA species that is conserved in humans. RNA extracted from the milk fat during lactation accurately portrayed the RNA profile of milk-producing mammary epithelial cells. However, this sample type clearly requires protocols that minimize RNA degradation.
2013-12-12 | GSE49765 | GEO