Prophages
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB52388 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR9613060_1.fastq.gz | Fastqsanger.gz | |||
| ERR9613060_2.fastq.gz | Fastqsanger.gz | |||
| ERR9613070_1.fastq.gz | Fastqsanger.gz | |||
| ERR9613070_2.fastq.gz | Fastqsanger.gz | |||
| ERR9613080_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Akkermansia muciniphila is recognized as a promising probiotic that improves the symptoms of a variety of diseases. However, the role and mechanism of A. muciniphila in regulating intestinal homeostasis remain to be explored. Here, we discovered that A. muciniphila was dramatically increased during colitis recovery, and its colonization greatly increased goblet cells to protect the intestinal barrier in mice. Amuc_0904, a previously uncharacterized A. muciniphila outer membrane protein, was identified to induce goblet cell differentiation.
2025-02-05 | GSE288821 | GEO
Project description:Extracellular vesicles derived from milk are known to play a significant role in regulating gut microbiota. However, few studies have focused on the effects of these vesicles on specific bacterial species. This study aimed to investigate how bovine colostrum-derived extracellular vesicles (BCEVs) affect the growth and viability of commensal bacteria, specifically Akkermansia muciniphila. BCEVs and A. muciniphila were co-cultured to measure growth rates using spectrophotometry, and cell viability was assessed at the endpoints. Additionally, to determine whether BCEVs enhance the survival of A. muciniphila in the presence of Caco-2 cells, an anaerobic co-culture experiment was conducted to determine the specific interaction between intestinal epithelial cells and gut microbiota using a Transwell system. The results showed that co-culture with BCEVs increased the growth rate and viability of A. muciniphila. Consistent with this, increased viability of A. muciniphila was observed when it was co-cultured with Caco-2 cells. Transcriptomic analysis revealed that BCEVs regulate nitrogen metabolism in A. muciniphila, enhancing the growth rate and viability. Thus, regulating beneficial gut bacteria, such as A. muciniphila, through BCEVs presents a novel biological approach that positively impacts human health.
2025-07-17 | GSE272132 | GEO
Project description:Group B Streptococcus (GBS) is an opportunistic pathogen that colonizes the vaginal tract and can be transmitted to the fetus or newborn resulting in infection. Previously we identified that Akkermansia muciniphila alters the dynamics of GBS vaginal colonization. Here we determine that A. muciniphila promotes GBS aggregation and attachment to human vaginal epithelial cells (hVECs). RNA-sequencing analysis revealed that A. muciniphila changed expression of 258 unique GBS genes during hVEC colonization, with many involved in cell wall/membrane/envelope biogenesis. We demonstrate that A. muciniphila-mediated increases in GBS aggregation and attachment to hVECs are dependent on GBS capsule and pili, respectively. Lastly, we found that A. muciniphila promoted GBS aggregation in the murine vaginal lumen and continual treatment with A. muciniphila reduced GBS vaginal persistence. Our results highlight the dynamic impact of a commensal organism on GBS colonization, as well as demonstrate the probiotic potential of A. muciniphila in the vaginal environment.
2026-04-15 | GSE306314 | GEO
Project description:Akkermansia muciniphila is recognized as a promising probiotic that improves the symptoms of a variety of diseases. However, the role and mechanism of A. muciniphila in regulating intestinal homeostasis remain to be explored. Here, we discovered that A. muciniphila was dramatically increased during colitis recovery, and its colonization greatly increased goblet cells to protect the intestinal barrier in mice. Amuc_0904, a previously uncharacterized A. muciniphila outer membrane protein, was identified to induce goblet cell differentiation.We want to find the receptors that 904 interacts with cells to explore the detailed mechanism.
2024-09-02 | PXD055466 | Pride
Project description:Commensal-specific T cells contribute to tissue homeostasis within the intestines, and can influence disease pathology in the context of both cancer and autoimmunity. Antigen presenting cells play a critical role in influencing the differentiation of these T cells, but how the complex network of antigen presenting cells in the intestines drives commensal-specific T cells towards a variety of differentiation trajectories remains poorly understood. We examined the priming of T cells specific for the intestinal commensal bacterial species Akkermansia muciniphila, using the LIPSTIC system combined with single-cell RNA-sequencing to identify the APCs that prime A. muciniphila-specific T cells both at homeostasis when it elicits T follicular helper cells, and during inflammation, when it also elicits TH17 and TH1 cells. We found that A. muciniphila-specific T cells were primed by several transcriptionally distinct subpopulations of migratory cDC2s in both contexts. The identity of these subpopulations did not change with inflammation, but the distribution of presentation across the subpopulations shifted, with increased presentation by inflammatory cDC2s favoring TH1 and TH17 polarization. These results reveal how distinct T cell differentiation trajectories can be determined through varied interactions with multiple, functionally distinct subpopulations of APCs.
2026-01-05 | GSE313299 | GEO
Project description:Commensal-specific T cells contribute to tissue homeostasis within the intestines, and can influence disease pathology in the context of both cancer and autoimmunity. Antigen presenting cells play a critical role in influencing the differentiation of these T cells, but how the complex network of antigen presenting cells in the intestines drives commensal-specific T cells towards a variety of differentiation trajectories remains poorly understood. We examined the priming of T cells specific for the intestinal commensal bacterial species Akkermansia muciniphila, using the LIPSTIC system combined with single-cell RNA-sequencing to identify the APCs that prime A. muciniphila-specific T cells both at homeostasis when it elicits T follicular helper cells, and during inflammation, when it also elicits TH17 and TH1 cells. We found that A. muciniphila-specific T cells were primed by several transcriptionally distinct subpopulations of migratory cDC2s in both contexts. The identity of these subpopulations did not change with inflammation, but the distribution of presentation across the subpopulations shifted, with increased presentation by inflammatory cDC2s favoring TH1 and TH17 polarization. These results reveal how distinct T cell differentiation trajectories can be determined through varied interactions with multiple, functionally distinct subpopulations of APCs.
2026-01-05 | GSE313298 | GEO
Project description:In this study we performed MeRIP-Seq to study N6-methyl adenosine (m6A) and and N6,2′ -O-dimethyladenosine (m6Am) modification of mRNA. We investigated the effect of the microbiota on the transcriptome and epitranscriptomic modifications in murine liver and cecum. We compared m6A/m modification profiles in cecum of conventionally raised (CONV) and germ-free (GF) mice. We additionally included GF mice colonised with the flora of CONV mice for four weeks (ex-GF), for which show that they exhibit similar patterns of the most abundant genera of gut bacteria as CONV mice. We added mice treated with several antibiotics to deplete the gut flora (abx)and vancomycin treated mice in which the genera Akkermansia, Escherichia/Shigella and Lactobacillus were enriched. Furthermore, we included GF mice colonised with the commensal bacterium Akkermansia muciniphila (Am), Lactobacillus plantarum (Lp) and Escherichia coli Nissle (Ec) and analysed their m6A/m modification profiles. In addition, we analysed changes in m6A/m- modified liver RNA for CONV, GF, and Am, Lp and Ec mice.
2020-02-12 | E-MTAB-6560 | biostudies-arrayexpress
Project description:Total RNA from ileum of three groups of mice are sequenced. The three groups are 1. wild type mice. 2. mice with IFNg gene knockout. 3. IFNg gene knockout mice after colonization of Akkermansia muciniphila
2015-06-05 | E-MTAB-3633 | biostudies-arrayexpress
Project description:To profile the proteome of intestinal epithelial IEC-6 cells in response to treatment with Akkermansia muciniphila, Bifidobacterium longum, or Akkermansia muciniphila + Bifidobacterium longum co-culture. In addition, we also add arabinoxylan (AX) to Akkermansia muciniphila + Bifidobacterium longum combination since we previously found that this glycan enhance their synergistic effect.
2025-09-24 | PXD061633 | Pride
Project description:Epithelial cells of the mammalian intestine are covered with a mucus layer that prevents direct contact with intestinal microbes but also constitutes a substrate for mucus-degrading bacteria. To study the effect of mucus degradation on the host response, germ-free mice were colonized with Akkermansia muciniphila. This anaerobic bacterium belonging to the Verrucomicrobia is specialized in the degradation of mucin, the glycoprotein present in mucus, and found in high numbers in the intestinal tract of human and other mammalian species. Efficient colonization of A. muciniphila was observed with highest numbers in the cecum, where most mucin is produced. In contrast, following colonization by Lactobacillus plantarum, a facultative anaerobe belonging to the Firmicutes that ferments carbohydrates, similar cell-numbers were found at all intestinal sites. Whereas A. muciniphila was located closely associated with the intestinal cells, L. plantarum was exclusively found in the lumen. The global transcriptional host response was determined in intestinal biopsies and revealed a consistent, site-specific, and unique modulation of about 750 genes in mice colonized by A. muciniphila and over 1500 genes after colonization by L. plantarum. Pathway reconstructions showed that colonization by A. muciniphila altered mucosal gene expression profiles toward increased expression of genes involved in immune responses and cell fate determination, while colonization by L. plantarum led to up-regulation of lipid metabolism. These indicate that the colonizers induce host responses that are specific per intestinal location. In conclusion, we propose that A. muciniphila modulates pathways involved in establishing homeostasis for basal metabolism and immune tolerance toward commensal microbiota. Keywords: Analysis of target gene regulation by using microarrays Adult germ-free female NMRI-KI mice (45 – 65 days) were used for bacterial mono-association. Two bacterial strains were used in this study, A. muciniphila MucT (ATTC BAA-835) and L. plantarum WCFS1 (NCIMB 8826). A. muciniphila was grown anaerobically in a basal mucin based medium and L. plantarum was grown anaerobically at 37°C in Man-Rogosa-Sharpe broth (MRS; Le Pont de Claix, France). After 7 days of colonization, mice were killed by cervical dislocation and terminal ileum, cecum and ascending colon specimens were sampled.
2011-09-20 | E-GEOD-18587 | biostudies-arrayexpress