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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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: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:We implemented transcriptomic analyses of blood and hippocampus of old mice treated with Akkermansia muciniphila Membrane Protein for 8 weeks.
2023-08-25 | GSE162123 | GEO
Project description:The impacts of individual commensal microbes on immunity and disease can differ dramatically depending on the surrounding microbial context, yet the specific bacterial combinations that dictate divergent immunological outcomes in humans remain largely undefined. We isolated a novel Allobaculum strain from an inflammatory bowel disease (IBD) patient that elicited antigen-specific mucosal and systemic antibody responses at homeostasis and exacerbated colitis in gnotobiotic mice. Using human microbiota-associated mouse models, we uncovered an inverse correlation between Allobaculum and the taxonomically-divergent immunostimulatory species Akkermansia muciniphila, which was also reflected in human cohorts. Co-colonization with Allobaculum and A. muciniphila reprogrammed the immune responses evoked by each microbe on its own, ameliorated Allobaculum-induced colitis, and blunted A. muciniphila-induced T and B cell responses. These studies thus identify a reciprocal ‘epistatic’ interaction between unique immunostimulatory human gut bacteria and establish a generalizable framework to dissect the role of microbial context in strain-specific microbial effects on human disease.
2021-12-01 | GSE179165 | GEO
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
Project description:The human gut includes plasma cells (PCs) expressing immunoglobulin A1 (IgA1) or IgA2, two structurally distinct IgA subclasses with elusive regulation, function and reactivity. We show here that intestinal IgA1+ and IgA2+ PCs co-emerged early in life, comparably accumulated somatic mutations, and were enriched within short-lived CD19+ and long-lived CD19− PC subsets, respectively. IgA2+ PCs were often clonally related to IgA1+ PCs and a subset of them presumably emerged from IgA1+ precursors. Of note, secretory IgA1 (SIgA1) and SIgA2 dually coated a large fraction of mucus-embedded bacteria, including Akkermansia muciniphila. Disruption of homeostasis by inflammatory bowel disease (IBD) increased newly formed and actively proliferating IgA1+ plasmablasts, depleted long-lived IgA2+ PCs, and increased SIgA1+SIgA2+ gut microbiota. Such increase featured enhanced IgA1 reactivity to pathobionts, including Escherichia coli, combined with depletion of beneficial Akkermansia muciniphila. Thus, gut IgA1 and IgA2 emerge from clonally related PCs and show unique changes of both frequency and reactivity in IBD.
2024-10-17 | GSE268929 | GEO
Project description:Kees2018 - Genome-scale constraint-based
model of the mucin-degrader Akkermansia
muciniphila
This model is described in the article:
Model-driven design of a
minimal medium for Akkermansia muciniphila confirms mucus
adaptation.
van der Ark KCH, Aalvink S,
Suarez-Diez M, Schaap PJ, de Vos WM, Belzer C.
Microb Biotechnol 2018 Jan; :
Abstract:
The abundance of the human intestinal symbiont Akkermansia
muciniphila has found to be inversely correlated with several
diseases, including metabolic syndrome and obesity.
A. muciniphila is known to use mucin as sole carbon and
nitrogen source. To study the physiology and the potential for
therapeutic applications of this bacterium, we designed a
defined minimal medium. The composition of the medium was based
on the genome-scale metabolic model of A. muciniphila and
the composition of mucin. Our results indicate that
A. muciniphila does not code for GlmS, the enzyme that
mediates the conversion of fructose-6-phosphate (Fru6P) to
glucosamine-6-phosphate (GlcN6P), which is essential in
peptidoglycan formation. The only annotated enzyme that could
mediate this conversion is Amuc-NagB on locus Amuc_1822. We
found that Amuc-NagB was unable to form GlcN6P from Fru6P at
physiological conditions, while it efficiently catalyzed the
reverse reaction. To overcome this inability,
N-acetylglucosamine needs to be present in the medium for
A. muciniphila growth. With these findings, the
genome-scale metabolic model was updated and used to accurately
predict growth of A. muciniphila on synthetic media. The
finding that A. muciniphila has a necessity for GlcNAc,
which is present in mucin further prompts the adaptation to its
mucosal niche.
This model is hosted on
BioModels Database
and identified by:
MODEL1710040000.
To cite BioModels Database, please use:
Chelliah V et al. BioModels: ten-year
anniversary. Nucl. Acids Res. 2015, 43(Database
issue):D542-8.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2021-02-15 | MODEL1710040000 | BioModels