Project description:Aging is associated with declining immunity and inflammation as well as alterations in the gut microbiome with a decrease of beneficial microbes and increase in pathogenic ones. The aim of this study was to investigate aging associated gut microbiome in relation to immunologic and metabolic profile in a non-human primate (NHP) model. 12 old (age>18 years) and 4 young (age 3-6 years) Rhesus macaques were included in this study. Immune cell subsets were characterized in PBMC by flow cytometry and plasma cytokines levels were determined by bead based multiplex cytokine analysis. Stool samples were collected by ileal loop and investigated for microbiome analysis by shotgun metagenomics. Serum, gut microbial lysate and microbe-free fecal extract were subjected to metabolomic analysis by mass-spectrometry. Our results showed that the old animals exhibited higher inflammatory biomarkers in plasma and lower CD4 T cells with altered distribution of naïve and memory T cell maturation subsets. The gut microbiome in old animals had higher abundance of Archaeal and Proteobacterial species and lower Firmicutes than the young. Significant enrichment of metabolites that contribute to inflammatory and cytotoxic pathways was observed in serum and feces of old animals compared to the young. We conclude that aging NHP undergo immunosenescence and age associated alterations in the gut microbiome that has a distinct metabolic profile.
Project description:The microbiome plays a significant role in gut brain communication and is linked to several animal and human diseases. Hypertension is characterized by gut dysbiosis, and this study aimed to determine how the gut microbiome differed between male and female normotensive and hypertensive rodents. WKY is a genetic control for spontaneous hypertensive rats or SHR which is well documented to have elevated blood pressure at approximately 8 to 10 weeks. We compared the microbiome of normotensive and hypertensive rodents using a meta-genomics approach.
Project description:Many previous studies had revealed that gastrointestinal microbiome is changed compositionally and ecologically in patients with colorectal cancer comparing with healthy population. These finding provide us with a new sight to take advantage of gut microbiota. The current study aims to explore new potential biomarkers for early screening and prognostic prediction of colorectal cancer and colorectal polyps by analyzing metagenomics and metabolomics of gut microbiota.
Project description:Microbiome site model is a Named Entity Recognition (NER) model that identifies and annotates the site of microbiome samples in texts. This is the final model version used to annotate metagenomics publications in Europe PMC and enrich metagenomics studies in MGnify with site metadata from literature. For more information, please refer to the following blogs: http://blog.europepmc.org/2020/11/europe-pmc-publications-metagenomics-annotations.html https://www.ebi.ac.uk/about/news/service-news/enriched-metadata-fields-mgnify-based-text-mining-associated-publications
Project description:Microbiome host model is a Named Entity Recognition (NER) model that identifies and annotates the host of microbiome samples in texts. This is the final model version used to annotate metagenomics publications in Europe PMC and enrich metagenomics studies in MGnify with host metadata from literature. For more information, please refer to the following blogs: http://blog.europepmc.org/2020/11/europe-pmc-publications-metagenomics-annotations.html https://www.ebi.ac.uk/about/news/service-news/enriched-metadata-fields-mgnify-based-text-mining-associated-publications
Project description:Microbiome ecoregion model is a Named Entity Recognition (NER) model that identifies and annotates the ecoregion of microbiome samples in texts. This is the final model version used to annotate metagenomics publications in Europe PMC and enrich metagenomics studies in MGnify with ecoregion metadata from literature. For more information, please refer to the following blogs: http://blog.europepmc.org/2020/11/europe-pmc-publications-metagenomics-annotations.html https://www.ebi.ac.uk/about/news/service-news/enriched-metadata-fields-mgnify-based-text-mining-associated-publications
Project description:Microbiome collection date model is a Named Entity Recognition (NER) model that identifies and annotates the collection date of microbiome samples in texts. This is the final model version used to annotate metagenomics publications in Europe PMC and enrich metagenomics studies in MGnify with collection date metadata from literature. For more information, please refer to the following blogs: http://blog.europepmc.org/2020/11/europe-pmc-publications-metagenomics-annotations.html https://www.ebi.ac.uk/about/news/service-news/enriched-metadata-fields-mgnify-based-text-mining-associated-publications
Project description:Microbiome engineered environment model is a Named Entity Recognition (NER) model that identifies and annotates the man-made environment of microbiome samples in texts. This is the final model version used to annotate metagenomics publications in Europe PMC and enrich metagenomics studies in MGnify with engineered metadata from literature. For more information, please refer to the following blogs: http://blog.europepmc.org/2020/11/europe-pmc-publications-metagenomics-annotations.html https://www.ebi.ac.uk/about/news/service-news/enriched-metadata-fields-mgnify-based-text-mining-associated-publications
Project description:Microbiome sample-material model is a Named Entity Recognition (NER) model that identifies and annotates the material of microbiome samples in texts. This is the final model version used to annotate metagenomics publications in Europe PMC and enrich metagenomics studies in MGnify with sample-material metadata from literature.
For more information, please refer to the following blogs:
http://blog.europepmc.org/2020/11/europe-pmc-publications-metagenomics-annotations.html
https://www.ebi.ac.uk/about/news/service-news/enriched-metadata-fields-mgnify-based-text-mining-associated-publications