Ontology highlight
ABSTRACT:
PROVIDER: PRJNA736819 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14784381.fastq.gz | Fastqsanger.gz |
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Project description:The breast milk plays a crucial role in shaping the initial intestinal microbiota and mucosal immunity of the infant. Interestingly, breastfeeding has proven to be protective against the early onset of immune-mediated diseases including type 1 diabetes (T1D). Studies have shown that exosomes from human breast milk (HM) are enriched in immune-modulating miRNAs suggesting that exosomal miRNAs transferred to the infant could play a critical role in the development of the infant’s immune system. In this study, we extracted exosome exosomal microRNAs (exomiRs) from breast milk of type 1 diabetic and healthy lactating mothers, in order to identify any differences in the exomiR content between the two groups
2019-08-01 | E-MTAB-7336 | biostudies-arrayexpress
Project description:Breastfeeding is vital for reducing morbidity and mortality, yet exclusive breastfeeding rates are low, with insufficient milk supply being a major weaning factor whose molecular causes remain largely unknown. In this study, we collected fresh milk samples from 30 lactating individuals, classified as low, normal, or high milk producers at multiple postpartum stages, and conducted extensive genomic and microbiome analysis. Using bulk RNA sequencing on human milk fat globules (MFG), milk cells, and breast tissue, we found that MFG-derived RNA closely resembles RNA from milk luminal cells. Furthermore, bulk and single-cell RNA-seq revealed changes in the transcriptome and cellular content linked to milk production. We identified specific genes and cell-type proportions differing in low and high milk production. Infant microbiome diversity was affected by feeding type, but not by maternal milk supply. This study provides a comprehensive human milk transcriptomic catalog, identifies genes associated with milk production, and highlights MFG as a useful biomarker for milk transcriptome analysis.
2024-11-30 | GSE275626 | GEO
Project description:Breastfeeding is vital for reducing morbidity and mortality, yet exclusive breastfeeding rates are low, with insufficient milk supply being a major weaning factor whose molecular causes remain largely unknown. In this study, we collected fresh milk samples from 30 lactating individuals, classified as low, normal, or high milk producers at multiple postpartum stages, and conducted extensive genomic and microbiome analysis. Using bulk RNA sequencing on human milk fat globules (MFG), milk cells, and breast tissue, we found that MFG-derived RNA closely resembles RNA from milk luminal cells. Furthermore, bulk and single-cell RNA-seq revealed changes in the transcriptome and cellular content linked to milk production. We identified specific genes and cell-type proportions differing in low and high milk production. Infant microbiome diversity was affected by feeding type, but not by maternal milk supply. This study provides a comprehensive human milk transcriptomic catalog, identifies genes associated with milk production, and highlights MFG as a useful biomarker for milk transcriptome analysis.
2024-11-30 | GSE275627 | GEO
Project description:Human milk is highly recommended for infant during the first six month of life by World Healthy Organisation (WHO). Human milk is not only rich in macro-nutritional components, but also rich in cells and molecules. MicroRNAs are small non-coding RNAs, which enriched in human milk. These molecules are vital in enormous biological and cellular functions including immune system and in response to infections. By using deep sequencing method, 770,374,554 raw reads were generated from all samples (n=26). Then, filter analysis was done to remove 81,091,772 (10.5%), and 689,282,782 clean reads (89.5%) were considered as clean reads, which was retained for the subsequent bioinformatics analysis. Annotation and matching reads to miRBase revealed1780 mature known microRNAs identified in human milk cells and lipids derived from healthy, cold and other infection types mothers. In particular, 1680 known microRNAs were determined in infected mothers (n=14), while 1,606 known microRNAs in healthy mothers (n=12). Of these known microRNAs, 453 microRNAs were differentially expressed (p<0.05) between healthy and infected samples. The majority of the highly expressed miRNAs in all samples, in particular top 20 microRNAs, were also differentially expressed between healthy and infections. Further, 592 novel mature microRNA sequences were predicted, with only 65,878 total reads. Amongst the total reads of the novel microRNAs, top 20 novel miRNAs were found to contributed in 73.3% (total reads 48,295) of the total reads (65,878).
2017-12-22 | GSE80546 | GEO
Project description:Human milk (HM) contains an array of regulatory biomolecules including miRNAs, the origin, properties, distribution and functional significance of which are still undetermined. In this study, we used the TaqMan OpenArray System to profile 681 human mature miRNAs in two fractions of HM (cells and lipids) collected from healthy mothers in month 2 of lactation (n=10). Comparisons were performed with maternal peripheral blood mononuclear cells (PBMCs) and plasma collected from the same individuals, as well as with a bovine- and a soy-based infant formulae. HM cells (292 miRNAs) and PBMCs (345 miRNAs) had higher miRNA content than HM lipids (242 miRNAs) and plasma (219 miRNAs), respectively (p<0.05). Despite the wide variation in miRNA profiles and expression between mothers, a strong association was found between HM cells and lipids within a mother, whilst PBMCs and plasma were distinctly different to the two milk fractions, with plasma displaying marked inter-individual variation. Considering the dominance of epithelial cells in mature milk of healthy women, these results suggest that HM cell and lipid miRNAs primarily originate from the mammary epithelium, whilst the maternal circulation may have a smaller contribution. Infant formulae contained very few human miRNA compared to HM. Our findings demonstrate that unlike infant formulae, human milk is a rich source of lactation-specific miRNA, which could be used as a biomarker of the performance and health status of the lactating gland. Given the recently identified stability and gene regulatory functions of food-derived miRNAs, HM miRNAs may contribute to infant protection and development.
2015-03-30 | GSE66358 | GEO
Project description:Analysis of key genes and gene networks determining milk productivity of the dairy HF cows Transcriptomes were compared of in the mammary glands of the healthy lactating Holstein Friesian cows of the high- (average 11097 kg milk/lactation) and low- (average 6956 kg milk/lactation) milk yield.
2011-11-16 | E-GEOD-33680 | biostudies-arrayexpress
Project description:Background: Human milk extracellular vesicles (EVs) affect various cell types in the gastrointestinal tract, including T cells, and play a role in the development of the newborn’s immune system by delivering specific molecular cargo to target cells. Although maternal allergic sensitization alters the composition of milk, it is unknown whether this impacts the function of milk EVs. Therefore, we analyzed the T cell modulatory capacity and compared the protein and miRNA cargo of EVs from milk of allergic and non-allergic mothers. Methods: EVs were isolated from human milk from allergic and non-allergic donors by differential centrifugation, density gradient floatation and size exclusion chromatography. Functional modulation of primary human CD4+ T cells by EVs was assessed in vitro. Proteomic analysis and small RNA sequencing was performed on milk EVs to evaluate protein and miRNA abundance and to identify cellular targets of this EV cargo in relevant T cell signaling pathways. Results: T cell proliferation, activation and cytokine production were suppressed in the presence of milk EVs. Remarkably, milk EVs from allergic mothers modulated T cell activation to a lesser extent than EVs from non-allergic mothers. Integrative multi-omics analysis identified EV cargo of which the cellular targets could be linked to T cell activation-associated processes. Conclusions: Milk EVs from non-allergic mothers are stronger inhibitors of T cell activation compared to milk EVs from allergic mothers. This altered functionality might be linked to small changes in modulation of certain T cell signaling pathways.
2022-10-30 | GSE216498 | GEO
Project description:BACKGROUND: Metagenomic studies carried out in the past decade have led to an enhanced understanding of the gut microbiome in human health, however, the Indian gut microbiome is not well explored yet. We analysed the gut microbiome of 110 healthy individuals from two distinct locations (North-Central and Southern) in India using multi-omics approaches, including 16S rRNA gene amplicon sequencing, whole genome shotgun metagenomic sequencing, and metabolomic profiling of faecal and serum samples. </br> RESULTS: The gene catalogue established in this study emphasizes the uniqueness of the Indian gut microbiome in comparison to other populations. The gut microbiome of the cohort from North-Central India, which was primarily consuming a plant-based diet, was found to be associated with Prevotella, and also showed an enrichment of Branched Chain Amino Acid (BCAA) and lipopolysaccharide (LPS) biosynthesis pathways. In contrast, the gut microbiome of the cohort from Southern India, which was consuming an omnivorous diet, showed associations with Bacteroides, Ruminococcus and Faecalibacterium, and had an enrichment of Short Chain Fatty Acid (SCFA) biosynthesis pathway and BCAA transporters. This corroborated well with the metabolomics results, which showed higher concentration of BCAAs in the serum metabolome of the North-Central cohort and an association with Prevotella. In contrast, the concentration of BCAAs were found higher in the faecal metabolome of the Southern-India cohort, and showed a positive correlation with the higher abundance of BCAA transporters. </br> CONCLUSIONS: The study reveals the unique composition of Indian gut microbiome, establishes the Indian gut microbial gene catalogue, and compares it with the gut microbiome of other populations. The functional associations revealed using metagenomic and metabolomic approaches provide novel insights on the gut-microbe-metabolic axis, which will be useful for future epidemiological and translational researches.
2019-01-04 | MTBLS803 | MetaboLights
Project description:Previous work has demonstrated that elevated maternal lipid intake (particularly from dairy products) is associated with increased lipids and altered fatty acid profile in milk produced by healthy lactating women. We investigate our primary hypothesis that a maternal diet rich in full-fat dairy products would simultaneously increase milk lipid percent and expression of genes related to the uptake and/or de novo biosynthesis of milk lipids.
2015-02-24 | GSE66191 | GEO