GNPS - 20250311_infant_serum_metabolomics
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap IQ-X
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Erika Claud
PROVIDER: MSV000097292 | GNPS | Tue Mar 11 14:37:00 GMT 2025
REPOSITORIES: GNPS
Similar Datasets
Project description:Bacterial communities associated with infant prematurity displayed distinct metabolic response, genomic functional pathways, and associated-taxonomic characteristics.
Untargeted metabolomics data from serum samples. Methods included.
2025-03-11 | MSV000097292 | MassIVE
Project description:Microbiota assembly in the infant gut is influenced by time and duration of dietary exposure to breast-milk, infant formula and solid foods. In this randomized controlled intervention study, longitudinal sampling of infant stools (n=998) showed similar development of fecal bacterial communities between formula- and breast-fed infants during the first year of life (N=210). Infant formula supplemented with galacto-oligosaccharides (GOS) was most efficient to sustain high levels of bifidobacteria compared to formula containing B. longum and B. breve or placebo. Metabolite (untargeted) and bacterial profiling (16S rRNA/shallow metagenomics sequencing) revealed 24-hour oscillations and integrated data analysis identified circadian networks. Rhythmicity in bacterial diversity, specific taxa and functional pathways increased with age and was most pronounced following breast-feeding and GOS-supplementation. Circadian rhythms in dominant taxa were discovered ex-vivo in a chemostat model. Hence microbiota rhythmicity develops early in life, likely due to bacterial intrinsic clock mechanism and is affected by diet.
2024-01-10 | MSV000093802 | MassIVE
Project description:Through integrative analysis of enhancer and transcriptomic landscapes of CCA from diverse populations, we identified 3 distinct groups, associated with different etiologies, that were enriched in unique pathways. The first group (ESTRO) displayed aberrant enhancer activation in estrogen signaling, and were comprised of mostly fluke-associated CCAs. Another group (OXPHO) displayed activated oxidative phosphorylation pathways, and were associated with hypermethylated BAP1 and IDH-mutant CCAs. Immune-related pathways were activated in the final group (IMMUN), made up of an immunogenic CCA subtype as well as CCA with aristolochic acid mutational signatures. Drug inhibitors of identified enriched pathways reduced tumor growth in in vitro and in vivo models.
| EGAS00001007309 | EGA
Project description:Whole-genome expression microarray analysis was performed using RNA extracted from skin biopsies sampled from the affected child as well as 4 pooled, healthy controls. The hypothesis was that the downstream effects of the inherited EGFR loss-of-function mutation in the infant would be evident by enriched pathways and processess linked to the cutaneous roles of the epidemermal growth factor receptor (EGFR). Functional analysis of the results identified a multitude of enriched gene ontology (GO) processes, pathways, networks and disease-associated transcripts germane to EGFR signaling in the infant's sample compared to controls. The top 3 up-regulated GO processes were linked to known EGFR functionality: keratinocyte differentiation, keratinization and epidermis development. Innate inflammatory response gene components were among the most significantly up-regulated GO networks. Additionally, regulation of epithelial-to-mesenchymal transition and angiogenesis, processes known to be controlled by EGFR activation, were identified as significantly down-regulated GO pathways and processes, respectively. There was also down-regulation of transcripts that are normally increased in tumors which show gain-of-function mutations in EGFR (e.g. non-small cell lung cancer, colorectal cancer, and glioblastoma). Total RNA extracted from a skin biopsy of the infant was compared to skin biopsies from 4 pooled, healthy controls.
2015-05-26 | E-GEOD-54162 | biostudies-arrayexpress
Project description:We undertook the first systemic proteomic study of a 90-case cohort of triple-negative breast cancer (TNBC) with a panoramic proteome view in quantification, phosphorylation, and DNA-binding capacity. Four integrative subtypes (iP-1-4) were stratified based on the proteome quantification profile and phosphoproteome, each of which exhibited distinct molecular, pathway, and network characteristics. Integrated network analyses of 3 proteomic datasets, together with those of genome and transcriptome from the same cohort, revealed holistic views of altered cellular processes and their regulation by/of upstream/downstream molecules, pathways and functional communities in the background of an integrated molecular network.
2021-08-24 | PXD028102 |
Project description:Understanding and quantifying the effects of environmental factors influencing the variation of abundance and diversity of microbial communities was a key theme of ecology. For microbial communities, there were two factors proposed in explaining the variation in current theory, which were contemporary environmental heterogeneity and historical events. Here, we report a study to profile soil microbial structure, which infers functional roles of microbial communities, along the latitudinal gradient from the north to the south in China mainland, aiming to explore potential microbial responses to external condition, especially for global climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 5.0, we showed that microbial communities were distinct for most but not all of the sites. Using substantial statistical analyses, exploring the dominant factor in influencing the soil microbial communities along the latitudinal gradient. Substantial variations were apparent in nutrient cycling genes, but they were in line with the functional roles of these genes. 300 samples were collected from 30 sites along the latitudinal gradient, with 10 replicates in every site
2015-05-23 | E-GEOD-69171 | biostudies-arrayexpress
Project description:Background: While the luminal microbiome composition in the human cervicovaginal tract has been defined, the presence and impact of tissue-adherent ectocervical microbiota remain incompletely understood. Studies of luminal and tissue-associated bacteria in the gastrointestinal tract suggest that they may have distinct roles in health and disease. Here, we performed a multi-omics characterization of paired luminal and tissue samples collected from a clinically well-characterized cohort of Kenyan women. Results: We identified a tissue-adherent bacterial microbiome, with a higher alpha diversity than the luminal microbiome, in which dominant genera overall included Gardnerella and Lactobacillus, followed by Prevotella, Atopobium, and Sneathia. About half of the L. iners dominated luminal samples had a corresponding Gardnerella dominated tissue microbiome. Broadly, the tissue-adherent microbiome was associated with fewer differentially expressed host genes than the luminal microbiome. Gene set enrichment analysis revealed that L. crispatus-dominated tissue-adherent communities were associated with protein translation and antimicrobial activity, whereas a highly diverse microbiome was associated with epithelial remodeling and pro-inflammatory pathways. Communities dominated by L. iners and Gardnerella were associated with low host transcriptional activity. Tissue-adherent microbiomes dominated by Lactobacillus and Gardnerella correlated with host protein profiles associated with epithelial barrier stability, and with a more pro-inflammatory profile for the Gardnerella-dominated microbiome group. Tissue samples with a highly diverse composition had a protein profile representing cell proliferation and pro-inflammatory activity. Conclusion: We identified ectocervical tissue-adherent bacterial communities in all study participants. These communities were distinct from cervicovaginal luminal microbiota in a significant proportion of individuals. This difference could possibly explain that L. iners dominant luminal communities have a high probability of transitioning to high diverse bacterial communities including high abundance of Gardnerella. By performing integrative multi-omics analyses we further revealed that bacterial communities at both sites correlated with distinct host gene expression and protein levels. The tissue-adherent bacterial community is similar to vaginal biofilms that significantly impact women’s reproductive and sexual health.
2023-02-10 | GSE194276 | GEO
Project description:The gut microbiome is an emerging factor in the neurobiology of disease. Blood-brain barrier (BBB) integrity is essential for proper brain function. However, the role the initial microbiome plays in BBB and brain development is unclear. In this study, we colonized germ-free pregnant mice with human full-term- or preterm-infant-derived gut microbiota, thereby establishing these communities in the resulting offspring. We discovered that mice harboring a full-term-associated microbiome exhibited stronger memory and learning capabilities and dramatically decreased early-life BBB permeability when compared to those with a prematurity-associated microbiome. Whole-brain single-cell RNA sequencing revealed downregulation of synaptic signaling genes in BBB cell types of mice with the prematurity-associated microbiome, indicating that microbiome maturity influences BBB transcriptional programs that support cognitive development. Comprehensive metagenomics and metabolomics uncovered bacterial populations and genomic pathways corresponding with decreased levels of circulating long-chain acylcarnitines and lysophosphatidylcholines in mice with the full-term-associated microbiome. Our findings highlight the microbiome as a therapeutic target for improving long-term neurodevelopmental outcomes due to its effect on the early-life BBB.
2025-08-18 | GSE291278 | GEO
Project description:Infants suffer disproportionately from respiratory infections and generate reduced vaccine responses compared to adults, although underlying mechanisms remain unclear. In adult mice, lung-localized, tissue-resident memory T cells (TRM) mediate optimal protection to respiratory pathogens. We hypothesized that reduced protection in infancy was due to impaired T effector localization and/or lung TRM establishment. Using an infant mouse model we demonstrate generation of lung-homing, virus-specific T effectors following influenza infection or live-attenuated vaccination, similar to adults. However, infection during infancy generated markedly fewer lung TRM and heterosubtypic protection was reduced compared to adults. Impaired TRM establishment was infant-T cell-intrinsic and infant effectors displayed distinct transcriptional profiles enriched for T-bet-regulated genes. Notably, mouse and human infant T cells exhibited increased T-bet expression following activation and reducing T-bet levels in infant mice enhanced lung TRM establishment. Our findings reveal that infant T cells are intrinsically programmed for short-term responses and targeting key regulators could promote long-term, tissue-targeted protection at this critical life stage.
2017-07-21 | GSE101696 | GEO
Project description:Tibet is one of the most threatened regions by climate warming, thus understanding how its microbial communities function may be of high importance for predicting microbial responses to climate changes. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, aiming to explore potential microbial responses to climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 4.0, we showed that microbial communities were distinct for most but not all of the sites. Substantial variations were apparent in stress, N and C cycling genes, but they were in line with the functional roles of these genes. sixty-three samples were collected from four elevations (3200,3400,3600 and 3800 m) along a Tibetan alpine meadow; Three replicates in each treatment
2013-11-16 | E-GEOD-52425 | biostudies-arrayexpress