Transcriptional response of A. muciniphila to growth in mucin rich media.
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB76658 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13293790_1.fastq.gz | Fastqsanger.gz | |||
| ERR13293790_2.fastq.gz | Fastqsanger.gz | |||
| ERR13293791_1.fastq.gz | Fastqsanger.gz | |||
| ERR13293791_2.fastq.gz | Fastqsanger.gz | |||
| ERR13293792_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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
Project description:The intestinal anaerobic bacterium Akkermansia muciniphila is specialized in the degradation of mucins, which are heavily O-glycosylated proteins that constitute the major components of the mucus lining the intestine. Despite that adhesion to mucins is considered critical for the persistence of A. muciniphila in the human intestinal tract, our knowledge of how this intestinal symbiont recognizes and binds to mucins is still limited. Here, we first show that the mucin-binding properties of A. muciniphila are independent of environmental oxygen concentrations and not abolished by pasteurization. We then dissected the mucin-binding properties of pasteurized A. muciniphila by use of a recently developed cell-based mucin array that enables display of the tandem repeats of human mucins with distinct O-glycan patterns and structures. We found that A. muciniphila recognizes the unsialylated LacNAc (Galβ1-4GlcNAc1-R) disaccharide selectively on core2 and core3 O-glycans. This disaccharide epitope is abundantly found on human colonic mucins capped by sialic acids, and we demonstrated that endogenous A. muciniphila neuraminidase activity can uncover the epitope and promote binding. In summary, our study provides insights into the mucin-binding properties important for colonization of a key mucin-foraging bacterium.
2024-05-30 | PXD051738 | Pride
Project description:Akkermansia muciniphila, a bacterium, is associated with good health, but data are lacking whether it confers health benefits on children in low income countries and by which mechanisms. In a case-control study of children <5 years old with (n=1717) or without (n=1524) diarrhea, the presence of A. muciniphila reduces the odds ratio of symptoms of diarrhea from six diarrheal pathogens. A. muciniphila is found more frequently among children who are growing well compared with those who are growing poorly. In silico analysis of 1487 A. muciniphila genomes revealed the presence of DNA encoding the peptide larazotide known to benefit human health by improving tight junctions. Although previously considered synthetic, we demonstrated that larazotide is secreted by A. muciniphila. Larazotide is found in the nucleus of colonic epithelial cells and its exogenous application alters gene expression. When larazotide is applied to colonic organoid cultures, the amount of mucin (MUC2) is increased significantly (p<0.005). Our analyses are consistent with A. muciniphila secreting larazotide and intestinal epithelial cells responding by increasing MUC2, potentially creating a positive feedback loop that increases mucin production, which may itself increase abundance of the mucin-metabolizing A. muciniphila. This cycle may confer positive health outcomes for children.
2021-05-25 | GSE175488 | 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:Akkermansia muciniphila, a mucin-degrading microbe found in the human gut, is often associated with positive health outcomes. The abundance of Akkermansia muciniphila is modulated by the presence and accessibility of nutrients, which can be derived from diet or host glycoproteins. In particular, the ability to degrade host mucins, a class of proteins carrying densely O-glycosylated domains, provides a competitive advantage in the sustained colonization of niche mucosal environments. Although Akkermansia muciniphila is known to rely on mucins as a carbon and nitrogen source, the enzymatic machinery used by this microbe to process mucins in the gut is not yet fully characterized. Here, we focus on the mucin-selective metalloprotease, Amuc_0627 (AM0627), which is known to cleave between adjacent residues carrying truncated core 1 O-glycans. We showed that this enzyme is capable of degrading purified mucin 2 (MUC2), the major protein component of mucus in the gut. An X-ray crystal structure of AM0627 (1.9 Å resolution) revealed O-glycan binding residues that are conserved between structurally characterized enzymes from the same family. We further rationalized the substrate cleavage motif using molecular modeling to identify nonconserved glycan-interacting residues. Mutagenesis of these residues resulted in altered substrate preferences down to the glycan level, providing insight into the structural determinants of O-glycan recognition.
2022-06-09 | PXD032164 | Pride
Project description:Growth to mid exponential phase in M9 minimal media supplemented with 0.5% maltose versus growth in rich LB media Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Media: M9 minimal media with 0.5% maltose Keywords: Logical Set
2006-05-20 | GSE4876 | GEO
Project description:Growth to mid exponential phase in M9 minimal media supplemented with 0.5% lactate versus growth in rich LB media Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Media: M9 minimal media with 0.5% lactate Keywords: Logical Set
2006-05-20 | GSE4875 | GEO
Project description:Akkermansia muciniphila, a mucin-degrading microbe found in the human gut, is often associated with positive health outcomes. The abundance of Akkermansia muciniphila is modulated by the presence and accessibility of nutrients, which can be derived from diet or host glycoproteins. In particular, the ability to degrade host mucins, a class of proteins carrying densely O-glycosylated domains, provides a competitive advantage in the sustained colonization of niche mucosal environments. Although Akkermansia muciniphila is known to rely on mucins as a carbon and nitrogen source, the enzymatic machinery used by this microbe to process mucins in the gut is not yet fully characterized. Here, we focus on the mucin-selective metalloprotease, Amuc_0627 (AM0627), which is known to cleave between adjacent residues carrying truncated core 1 O-glycans. We showed that this enzyme is capable of degrading purified mucin 2 (MUC2), the major protein component of mucus in the gut. An X-ray crystal structure of AM0627 at 1.9 Å resolution revealed O-glycan binding residues that are conserved between structurally characterized enzymes from the same family. We further rationalized the substrate cleavage motif using molecular modeling to identify nonconserved glycan-interacting residues. Mutagenesis of these residues resulted in altered substrate preferences down to the glycan level, providing insight into the structural determinants of O-glycan recognition.
2022-08-28 | PXD031225 | Pride
Project description:In this study, we attempted to identify a new probiotic effector molecule of A. muciniphila that plays a role in modulating host cells through secretome analysis. We performed proteomic profiling of secretome of A. muciniphila cultivated under basal medium and BHI medium (supplemented with 0.2% mucin) using nanoflow liquid chromatography-tandem mass spectrometry (nLC-MS/MS).
2024-03-14 | PXD042323 | Pride
Project description:Growth to mid exponential phase in M9 minimal media supplemented with 0.5% maltose versus growth in rich LB media Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Media: M9 minimal media with 0.5% maltose Computed
2006-05-20 | E-GEOD-4876 | biostudies-arrayexpress