title: Metabolic modeling of common Escherichia coli strains in human gut microbiome.
abstract: The recent high-throughput sequencing has enabled the composition of Escherichia coli strains in the human microbial community to be profiled en masse. However, there are two challenges to address: (1) exploring the genetic differences between E. coli strains in human gut and (2) dynamic responses of E. coli to diverse stress conditions. As a result, we investigated the E. coli strains in human gut microbiome using deep sequencing data and reconstructed genome-wide metabolic networks for the three most common E. coli strains, including E. coli HS, UTI89, and CFT073. The metabolic models show obvious strain-specific characteristics, both in network contents and in behaviors. We predicted optimal biomass production for three models on four different carbon sources (acetate, ethanol, glucose, and succinate) and found that these stress-associated genes were involved in host-microbial interactions and increased in human obesity. Besides, it shows that the growth rates are similar among the models, but the flux distributions are different, even in E. coli core reactions. The correlations between human diabetes-associated metabolic reactions in the E. coli models were also predicted. The study provides a systems perspective on E. coli strains in human gut microbiome and will be helpful in integrating diverse data sources in the following study.
authors.affiliation: Kunming Biological Diversity Regional Center of Instruments, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
authors.forename: Yue-Dong
authors.identifier: 0000-0002-0403-5329
authors.initials: YD
authors.lastname: Gao
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Eastern Jiaochang Road, Kunming, Yunnan 650223, China.
authors.forename: Yuqi
authors.identifier: 0000-0003-0730-5854
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Eastern Jiaochang Road, Kunming, Yunnan 650223, China ; Kunming Institute of Zoology, Chinese University of Hongkong, Joint Research Center for Bio-Resources and Human Disease Mechanisms, Kunming 650223, China.
authors.forename: Jingfei
authors.initials: J
authors.lastname: Huang
mesh_terms: D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism / Q000472:pathogenicity; D041981:Gastrointestinal Tract / Q000382:microbiology; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D064307:Microbiota; D008954:Models, Biological