Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1268597 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Periapical abscesses, radicular cysts, and periapical granulomas are among the most frequently identified pathological lesions in the alveolar bone. Although many studies have investigated bacterial metagenomics in periapical abscesses, little is known about the genome mining of abundant bacteria of periapical lesions and its correlation to human transcriptome. This study aims to explore the enriched metabolic environment of periapical lesions associated with microbial diversity and their role in lesion progression. Bacterial DNA and human RNA were isolated from periapical lesions and healthy pulp tissue and sequenced using next-generation sequencing. Bacterial sequences were then analyzed to identify secondary metabolites, pathogenic proteins, and their associated metabolic pathways. Integrated bacterial and human metabolic pathways indicated similar pathways in each lesion. Among these pathways, inflammatory response, humoral immune response, and hemopoiesis were enriched in abscesses. NABA matrisome associated, neutrophil degranulation, and P73 pathway were enriched in cysts. Meanwhile, response to bacterium, regulation of immune effector process, and positive regulation of response to external stimulus were enriched in granulomas. In conclusion, this study is the first to elucidate the interplay between microbial and human metabolic activity. These findings have significant clinical implications for the early diagnosis, prevention, and treatment of periapical lesions.
2025-06-25 | GSE299006 | GEO
Project description:Bacterial DNA was detected in both subgingival and carotid plaque samples. The microbial composition differed between subgingival and carotid plaque communities. Alpha diversity analysis revealed significantly higher diversity in subgingival samples compared to carotid plaques (p = 0.039). Beta diversity analysis, including unweighted UniFrac analysis (p<0.001), linear discriminant analysis with effect size estimation, cladogram-based analysis, and principal component analysis, confirmed marked differences between the subgingival and carotid plaque microbiota. However, the study did reveal overlaps in a few individual cases.
2026-04-01 | GSE308470 | GEO
Project description:Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of climate warming and cooling on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles, four years after soil transplant over large transects from northern (N site) to central (NC site) and southern China (NS site) and vice versa. Four years after soil transplant, soil nitrogen components, microbial biomass, community phylogenetic and functional structures were altered. Microbial functional diversity, measured by a metagenomic tool named GeoChip, and phylogenetic diversity are increased with temperature, while microbial biomass were similar or decreased. Nevertheless, the effects of climate change was overridden by maize cropping, underscoring the need to disentangle them in research. Mantel tests and canonical correspondence analysis (CCA) demonstrated that vegetation, climatic factors (e.g., temperature and precipitation), soil nitrogen components and CO2 efflux were significantly correlated to the microbial community composition. Further investigation unveiled strong correlations between carbon cycling genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycling genes and nitrification, which provides mechanistic understanding of these microbe-mediated processes and empowers an interesting possibility of incorporating bacterial gene abundance in greenhouse gas emission modeling.
2013-10-30 | GSE51592 | GEO