Mouse gut metagenome
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ABSTRACT:
PROVIDER: PRJNA342176 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Peromyscus maniculatus (North American deer mouse) and Peromyscus leucopus (white-footed mouse). Raw sequence reads
| PRJNA494419 | ENA
Project description:The white-footed deermouse Peromyscus leucopus is a primary reservoir for the agents of Lyme disease and other zoonoses in North America. These and other species of Peromyscus are tolerant of the infection by the bacteria, protozoa, and viruses they host. This is mainly by mitigating the damaging effects of the innate immune response. In previous studies we demonstrated differences between P. leucopus and either inbred or outbred M. musculus in the degree of sickness and profiles of biomarkers after exposure to bacterial lipopolysaccharide, a TLR4 agonist. With the objective of developing a method for broadly assessing of innate immunity of capture-release mammals in nature, we evaluated using bulk and single cell RNA-seq primary dermal fibroblast cultures of P. leucopus and M. musculus in their short-term responses to a lipopeptide that is a TLR2 agonist. As we had observed for experimental animals, the fibroblast cultures of the two species displayed both similarities and differences in their responses to the agonist. The notable differences included the greater magnitude of an anti-viral profile of cytokines and other effectors in the deermouse fibroblasts and the occurrence of an interleukin-11 response in the mouse cultures but not deermouse. We also observed in both species' cultures an increased transcription of several types of endogenous retrovirus (ERV) elements after exposure of the cells to the agonist. The P. leucopus cells were distinguished from M. musculus cells in the generally shorter retroviral open reading frames among the differentially expressed sequences. This was consistent with previous findings about ERV transcription in P. leucopus and M. musculus and suggests a greater suppression of ERV activity in P. leuocopus. The results affirm the feasibility of this in vitro model for both laboratory- and field-based studies without need for euthanasia and that inherent differences between deermice and mice in innate immune responses can be demonstrated in primary fibroblasts as well as the animals themselves.
2025-10-22 | GSE302225 | GEO
Project description:Metagenome of gastrointestinal microbiota of Peromyscus leucopus
| PRJNA540317 | ENA
Project description:Age-dependent changes of the gut-associated microbiome have been linked to increased frailty and systemic inflammation. This study found that age-associated changes of the gut microbiome of BALB/c and C57BL/6 mice could be reverted by co-housing of aged (22 months old) and adult (3 months old) mice for 30-40 days or faecal microbiota transplantation (FMT) from adult into aged mice. This was demonstrated using high-throughput sequencing of the V3-V4 hypervariable region of bacterial 16S rRNA gene isolated from faecal pellets collected from 3-4 months old adult and 22-23 months old aged mice before and after co-housing or FMT.
2019-05-08 | E-MTAB-7750 | biostudies-arrayexpress
Project description:Gut microbiome research is rapidly moving towards the functional characterization of the microbiota by means of shotgun meta-omics. Here, we selected a cohort of healthy subjects from an indigenous and monitored Sardinian population to analyze their gut microbiota using both shotgun metagenomics and shotgun metaproteomics. We found a considerable divergence between genetic potential and functional activity of the human healthy gut microbiota, in spite of a quite comparable taxonomic structure revealed by the two approaches. Investigation of inter-individual variability of taxonomic features revealed Bacteroides and Akkermansia as remarkably conserved and variable in abundance within the population, respectively. Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the functional activity with the higher expression rate and the lower inter-individual variability in the study cohort, highlighting the key importance of the biosynthesis of this microbial by-product for the gut homeostasis. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several gut microbiota members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis and short-chain fatty acid production). In conclusion, our results provide useful indications regarding the main functions actively exerted by the gut microbiota members of a healthy human cohort, and support metaproteomics as a valuable approach to investigate the functional role of the gut microbiota in health and disease.
2017-07-19 | PXD005780 | Pride
Project description:The gut microbiome is a malleable microbial community that can remodel in response to various factors, including diet, and contribute to the development of several chronic diseases, including atherosclerosis. We devised an in vitro screening protocol of the mouse gut microbiome to discover molecules that can selectively modify bacterial growth. This approach was used to identify cyclic D,L-α-peptides that remodeled the Western diet (WD) gut microbiome toward the low-fat-diet microbiome state. Daily oral administration of the peptides in WD-fed LDLr-/- mice reduced plasma total cholesterol levels and atherosclerotic plaques. Depletion of the microbiome with antibiotics abrogated these effects. Peptide treatment reprogrammed the microbiome transcriptome, suppressed the production of pro-inflammatory cytokines (including interleukin-6, tumor necrosis factor-α and interleukin-1β), rebalanced levels of short-chain fatty acids and bile acids, improved gut barrier integrity and increased intestinal T regulatory cells. Directed chemical manipulation provides an additional tool for deciphering the chemical biology of the gut microbiome and might advance microbiome-targeted therapeutics.
2019-12-31 | GSE104914 | GEO
Project description:The gut microbiome is a malleable microbial community that can remodel in response to various factors, including diet, and contribute to the development of several chronic diseases, including atherosclerosis. We devised an in vitro screening protocol of the mouse gut microbiome to discover molecules that can selectively modify bacterial growth. This approach was used to identify cyclic D,L-α-peptides that remodeled the Western diet (WD) gut microbiome toward the low-fat-diet microbiome state. Daily oral administration of the peptides in WD-fed LDLr-/- mice reduced plasma total cholesterol levels and atherosclerotic plaques. Depletion of the microbiome with antibiotics abrogated these effects. Peptide treatment reprogrammed the microbiome transcriptome, suppressed the production of pro-inflammatory cytokines (including interleukin-6, tumor necrosis factor-α and interleukin-1β), rebalanced levels of short-chain fatty acids and bile acids, improved gut barrier integrity and increased intestinal T regulatory cells. Directed chemical manipulation provides an additional tool for deciphering the chemical biology of the gut microbiome and might advance microbiome-targeted therapeutics.
2019-12-31 | GSE104913 | GEO
Project description:Whole transcriptome RNA sequencing in brain tissue was generated to explore differences between young and old animals of two closely related species of deer mice (genus Peromyscus) that reportedly differ in their lifespans: P. leucopus that lives for up to 8 years and P. maniculatus that exhibits a lifespan of about 4 years.
2021-03-31 | GSE166394 | GEO
Project description:Gut microbiome of targeted-rectal irradiated mice
| PRJNA283782 | ENA
Project description:Gut microbiome analysis of renal failure mice
| PRJDB2888 | ENA