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Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction

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Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. / El-Semman, Ibrahim E; Karlsson, Fredrik H; Shoaie, Saeed; Nookaew, Intawat; Soliman, Taysir H; Nielsen, Jens.

In: Bmc Systems Biology, Vol. 8, 03.04.2014, p. 41.

Research output: Contribution to journalArticle

Harvard

El-Semman, IE, Karlsson, FH, Shoaie, S, Nookaew, I, Soliman, TH & Nielsen, J 2014, 'Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction', Bmc Systems Biology, vol. 8, pp. 41. https://doi.org/10.1186/1752-0509-8-41

APA

El-Semman, I. E., Karlsson, F. H., Shoaie, S., Nookaew, I., Soliman, T. H., & Nielsen, J. (2014). Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. Bmc Systems Biology, 8, 41. https://doi.org/10.1186/1752-0509-8-41

Vancouver

El-Semman IE, Karlsson FH, Shoaie S, Nookaew I, Soliman TH, Nielsen J. Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. Bmc Systems Biology. 2014 Apr 3;8:41. https://doi.org/10.1186/1752-0509-8-41

Author

El-Semman, Ibrahim E ; Karlsson, Fredrik H ; Shoaie, Saeed ; Nookaew, Intawat ; Soliman, Taysir H ; Nielsen, Jens. / Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. In: Bmc Systems Biology. 2014 ; Vol. 8. pp. 41.

Bibtex Download

@article{a57220b789034c5c8323653aa3663452,
title = "Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction",
abstract = "BACKGROUND: The gut microbiota plays an important role in human health and disease by acting as a metabolic organ. Metagenomic sequencing has shown how dysbiosis in the gut microbiota is associated with human metabolic diseases such as obesity and diabetes. Modeling may assist to gain insight into the metabolic implication of an altered microbiota. Fast and accurate reconstruction of metabolic models for members of the gut microbiota, as well as methods to simulate a community of microorganisms, are therefore needed. The Integrated Microbial Genomes (IMG) database contains functional annotation for nearly 4,650 bacterial genomes. This tremendous new genomic information adds new opportunities for systems biology to reconstruct accurate genome scale metabolic models (GEMs).RESULTS: Here we assembled a reaction data set containing 2,340 reactions obtained from existing genome-scale metabolic models, where each reaction is assigned with KEGG Orthology. The reaction data set was then used to reconstruct two genome scale metabolic models for gut microorganisms available in the IMG database Bifidobacterium adolescentis L2-32, which produces acetate during fermentation, and Faecalibacterium prausnitzii A2-165, which consumes acetate and produces butyrate. F. prausnitzii is less abundant in patients with Crohn's disease and has been suggested to play an anti-inflammatory role in the gut ecosystem. The B. adolescentis model, iBif452, comprises 699 reactions and 611 unique metabolites. The F. prausnitzii model, iFap484, comprises 713 reactions and 621 unique metabolites. Each model was validated with in vivo data. We used OptCom and Flux Balance Analysis to simulate how both organisms interact.CONCLUSIONS: The consortium of iBif452 and iFap484 was applied to predict F. prausnitzii's demand for acetate and production of butyrate which plays an essential role in colonic homeostasis and cancer prevention. The assembled reaction set is a useful tool to generate bacterial draft models from KEGG Orthology.",
keywords = "Bifidobacterium, Butyrates, Gastrointestinal Tract, Genome, Bacterial, Genomics, Models, Biological, Reproducibility of Results, Journal Article, Research Support, Non-U.S. Gov't",
author = "El-Semman, {Ibrahim E} and Karlsson, {Fredrik H} and Saeed Shoaie and Intawat Nookaew and Soliman, {Taysir H} and Jens Nielsen",
year = "2014",
month = apr,
day = "3",
doi = "10.1186/1752-0509-8-41",
language = "English",
volume = "8",
pages = "41",
journal = "Bmc Systems Biology",
issn = "1752-0509",
publisher = "BioMed Central",

}

RIS (suitable for import to EndNote) Download

TY - JOUR

T1 - Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction

AU - El-Semman, Ibrahim E

AU - Karlsson, Fredrik H

AU - Shoaie, Saeed

AU - Nookaew, Intawat

AU - Soliman, Taysir H

AU - Nielsen, Jens

PY - 2014/4/3

Y1 - 2014/4/3

N2 - BACKGROUND: The gut microbiota plays an important role in human health and disease by acting as a metabolic organ. Metagenomic sequencing has shown how dysbiosis in the gut microbiota is associated with human metabolic diseases such as obesity and diabetes. Modeling may assist to gain insight into the metabolic implication of an altered microbiota. Fast and accurate reconstruction of metabolic models for members of the gut microbiota, as well as methods to simulate a community of microorganisms, are therefore needed. The Integrated Microbial Genomes (IMG) database contains functional annotation for nearly 4,650 bacterial genomes. This tremendous new genomic information adds new opportunities for systems biology to reconstruct accurate genome scale metabolic models (GEMs).RESULTS: Here we assembled a reaction data set containing 2,340 reactions obtained from existing genome-scale metabolic models, where each reaction is assigned with KEGG Orthology. The reaction data set was then used to reconstruct two genome scale metabolic models for gut microorganisms available in the IMG database Bifidobacterium adolescentis L2-32, which produces acetate during fermentation, and Faecalibacterium prausnitzii A2-165, which consumes acetate and produces butyrate. F. prausnitzii is less abundant in patients with Crohn's disease and has been suggested to play an anti-inflammatory role in the gut ecosystem. The B. adolescentis model, iBif452, comprises 699 reactions and 611 unique metabolites. The F. prausnitzii model, iFap484, comprises 713 reactions and 621 unique metabolites. Each model was validated with in vivo data. We used OptCom and Flux Balance Analysis to simulate how both organisms interact.CONCLUSIONS: The consortium of iBif452 and iFap484 was applied to predict F. prausnitzii's demand for acetate and production of butyrate which plays an essential role in colonic homeostasis and cancer prevention. The assembled reaction set is a useful tool to generate bacterial draft models from KEGG Orthology.

AB - BACKGROUND: The gut microbiota plays an important role in human health and disease by acting as a metabolic organ. Metagenomic sequencing has shown how dysbiosis in the gut microbiota is associated with human metabolic diseases such as obesity and diabetes. Modeling may assist to gain insight into the metabolic implication of an altered microbiota. Fast and accurate reconstruction of metabolic models for members of the gut microbiota, as well as methods to simulate a community of microorganisms, are therefore needed. The Integrated Microbial Genomes (IMG) database contains functional annotation for nearly 4,650 bacterial genomes. This tremendous new genomic information adds new opportunities for systems biology to reconstruct accurate genome scale metabolic models (GEMs).RESULTS: Here we assembled a reaction data set containing 2,340 reactions obtained from existing genome-scale metabolic models, where each reaction is assigned with KEGG Orthology. The reaction data set was then used to reconstruct two genome scale metabolic models for gut microorganisms available in the IMG database Bifidobacterium adolescentis L2-32, which produces acetate during fermentation, and Faecalibacterium prausnitzii A2-165, which consumes acetate and produces butyrate. F. prausnitzii is less abundant in patients with Crohn's disease and has been suggested to play an anti-inflammatory role in the gut ecosystem. The B. adolescentis model, iBif452, comprises 699 reactions and 611 unique metabolites. The F. prausnitzii model, iFap484, comprises 713 reactions and 621 unique metabolites. Each model was validated with in vivo data. We used OptCom and Flux Balance Analysis to simulate how both organisms interact.CONCLUSIONS: The consortium of iBif452 and iFap484 was applied to predict F. prausnitzii's demand for acetate and production of butyrate which plays an essential role in colonic homeostasis and cancer prevention. The assembled reaction set is a useful tool to generate bacterial draft models from KEGG Orthology.

KW - Bifidobacterium

KW - Butyrates

KW - Gastrointestinal Tract

KW - Genome, Bacterial

KW - Genomics

KW - Models, Biological

KW - Reproducibility of Results

KW - Journal Article

KW - Research Support, Non-U.S. Gov't

U2 - 10.1186/1752-0509-8-41

DO - 10.1186/1752-0509-8-41

M3 - Article

C2 - 24708835

VL - 8

SP - 41

JO - Bmc Systems Biology

JF - Bmc Systems Biology

SN - 1752-0509

ER -

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