Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Sequencing of total RNA in mouse ileum to evaluate effect of IFNg and Akkermansia muciniphila on host gene expression

ABSTRACT: 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

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER: xiaoxi dong

PROVIDER: E-MTAB-3633 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

Dataset Information

Sequencing of total RNA in mouse ileum to evaluate effect of IFNg and Akkermansia muciniphila on host gene expression

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