Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction.
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction.
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DOI：
10.1186/1752-0509-8-41
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发表时间：
2014-04-03
影响因子：
--
通讯作者：
Nielsen J
中科院分区：
文献类型：
--
作者：
El-Semman IE;Karlsson FH;Shoaie S;Nookaew I;Soliman TH;Nielsen J
肠道微生物区系作为代谢器官，在人类健康和疾病中发挥着重要作用。元基因组测序显示了肠道微生物区系的失调与肥胖和糖尿病等人类代谢性疾病的关系。建模可能有助于洞察改变的微生物区系的代谢含义。因此，需要快速和准确地重建肠道微生物区系成员的代谢模型，以及模拟微生物群落的方法。整合微生物基因组(IMG)数据库包含近4,650个细菌基因组的功能注释。这一巨大的新基因组信息为系统生物学重建精确的基因组规模代谢模型(GEMS)增加了新的机会。在这里，我们组装了一个反应数据集，其中包含从现有基因组规模的代谢模型中获得的2340个反应，其中每个反应都被分配给KEGG正交学。然后，使用反应数据集重建IMG数据库中可用的肠道微生物的两个基因组规模的代谢模型：青年双歧杆菌L2-32，它在发酵过程中产生醋酸盐；以及普氏杆菌A2-165，它消耗乙酸盐并产生丁酸盐。普氏革兰氏杆菌在克罗恩病患者中含量较少，已被建议在肠道生态系统中发挥抗炎作用。青春假单胞菌模型iBif452由699个反应和611个独特的代谢物组成。普氏肺孢子虫模型iFap484由713个反应和621个独特的代谢物组成。每个模型都用活体数据进行了验证。我们使用OptCom和通量平衡分析来模拟这两种生物如何相互作用。IBif452和iFap484组成的联合体被用来预测普氏假丝酵母菌对乙酸盐的需求和丁酸盐的生产，丁酸盐在结肠稳态和癌症预防中起着至关重要的作用。组装的反应集是从KEGG矫形学生成细菌草稿模型的有用工具。
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). 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. 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.
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影响因子：
64.8
作者：
Arumugam, Manimozhiyan;Raes, Jeroen;Pelletier, Eric;Le Paslier, Denis;Yamada, Takuji;Mende, Daniel R.;Fernandes, Gabriel R.;Tap, Julien;Bruls, Thomas;Batto, Jean-Michel;Bertalan, Marcelo;Borruel, Natalia;Casellas, Francesc;Fernandez, Leyden;Gautier, Laurent;Hansen, Torben;Hattori, Masahira;Hayashi, Tetsuya;Kleerebezem, Michiel;Kurokawa, Ken;Leclerc, Marion;Levenez, Florence;Manichanh, Chaysavanh;Nielsen, H. Bjorn;Nielsen, Trine;Pons, Nicolas;Poulain, Julie;Qin, Junjie;Sicheritz-Ponten, Thomas;Tims, Sebastian;Torrents, David;Ugarte, Edgardo;Zoetendal, Erwin G.;Wang, Jun;Guarner, Francisco;Pedersen, Oluf;de Vos, Willem M.;Brunak, Soren;Dore, Joel;Weissenbach, Jean;Ehrlich, S. Dusko;Bork, Peer
通讯作者：
Bork, Peer
影响因子：
5.8
作者：
Bornstein, Benjamin J.;Keating, Sarah M.;Hucka, Michael
通讯作者：
Hucka, Michael
影响因子：
64.8
作者：
Fukuda, Shinji;Toh, Hidehiro;Ohno, Hiroshi
通讯作者：
Ohno, Hiroshi
影响因子：
5
作者：
DEGNAN, BA;MACFARLANE, GT
通讯作者：
MACFARLANE, GT
影响因子：
4.4
作者：
Falony, Gwen;Calmeyn, Thomas;De Vuyst, Luc
通讯作者：
De Vuyst, Luc