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Title: Methods for automated genome-scale metabolic model reconstruction

Abstract

In the era of next-generation sequencing and ubiquitous assembly and binning of metagenomes, new putative genome sequences are being produced from isolate and microbiome samples at ever-increasing rates. Genome-scale metabolic models have enormous utility for supporting the analysis and predictive characterization of these genomes based on sequence data. As a result, tools for rapid automated reconstruction of metabolic models are becoming critically important for supporting the analysis of new genome sequences. Many tools and algorithms have now emerged to support rapid model reconstruction and analysis. We are comparing and contrasting the capabilities and output of a variety of these tools, including ModelSEED, Raven Toolbox, PathwayTools, SuBliMinal Toolbox and merlin.

Authors:
 [1];  [2];  [2];  [1]
  1. Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division
  2. Univ. of Minho, Braga (Portugal). Centre of Biological Engineering
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1493924
Grant/Contract Number:  
[AC02-06CH11357]
Resource Type:
Accepted Manuscript
Journal Name:
Biochemical Society Transactions
Additional Journal Information:
[ Journal Volume: 46; Journal Issue: 4]; Journal ID: ISSN 0300-5127
Publisher:
Portland Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; genome annotation; genome-scale metabolic model; metabolic network

Citation Formats

Faria, José P., Rocha, Miguel, Rocha, Isabel, and Henry, Christopher S. Methods for automated genome-scale metabolic model reconstruction. United States: N. p., 2018. Web. doi:10.1042/BST20170246.
Faria, José P., Rocha, Miguel, Rocha, Isabel, & Henry, Christopher S. Methods for automated genome-scale metabolic model reconstruction. United States. doi:10.1042/BST20170246.
Faria, José P., Rocha, Miguel, Rocha, Isabel, and Henry, Christopher S. Tue . "Methods for automated genome-scale metabolic model reconstruction". United States. doi:10.1042/BST20170246. https://www.osti.gov/servlets/purl/1493924.
@article{osti_1493924,
title = {Methods for automated genome-scale metabolic model reconstruction},
author = {Faria, José P. and Rocha, Miguel and Rocha, Isabel and Henry, Christopher S.},
abstractNote = {In the era of next-generation sequencing and ubiquitous assembly and binning of metagenomes, new putative genome sequences are being produced from isolate and microbiome samples at ever-increasing rates. Genome-scale metabolic models have enormous utility for supporting the analysis and predictive characterization of these genomes based on sequence data. As a result, tools for rapid automated reconstruction of metabolic models are becoming critically important for supporting the analysis of new genome sequences. Many tools and algorithms have now emerged to support rapid model reconstruction and analysis. We are comparing and contrasting the capabilities and output of a variety of these tools, including ModelSEED, Raven Toolbox, PathwayTools, SuBliMinal Toolbox and merlin.},
doi = {10.1042/BST20170246},
journal = {Biochemical Society Transactions},
number = [4],
volume = [46],
place = {United States},
year = {2018},
month = {7}
}

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Free Publicly Available Full Text
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Cited by: 8 works
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Works referenced in this record:

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  • DOI: 10.1038/nbt.1666

Efficiently gap-filling reaction networks
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ScrumPy: metabolic modelling with Python
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  • Karp, P. D.; Paley, S. M.; Krummenacker, M.
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Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
journal, November 2016

  • Wattam, Alice R.; Davis, James J.; Assaf, Rida
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Reconstructing genome-scale metabolic models with merlin
journal, April 2015

  • Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.
  • Nucleic Acids Research, Vol. 43, Issue 8
  • DOI: 10.1093/nar/gkv294

In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production
journal, November 2005

  • Bro, Christoffer; Regenberg, Birgitte; Forster, Jochen
  • Metabolic Engineering, Vol. 8, Issue 2, p. 102-111
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WoLF PSORT: protein localization predictor
journal, May 2007

  • Horton, P.; Park, K. -J.; Obayashi, T.
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Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering
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  • Microbial Cell Factories, Vol. 11, Issue 1
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Re-annotation of the genome sequence of Helicobacter pylori 26695
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KBase: The United States Department of Energy Systems Biology Knowledgebase
journal, July 2018

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  • Nature Biotechnology, Vol. 36, Issue 7
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The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum
journal, March 2013


The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
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Application of Genome-Scale Metabolic Models in Metabolic Engineering
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A systematic comparison of the MetaCyc and KEGG pathway databases
journal, January 2013


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journal, May 2014

  • Dias, Oscar; Pereira, Rui; Gombert, Andreas K.
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  • DOI: 10.1002/biot.201300242

The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks
text, January 2011


    Works referencing / citing this record:

    ScrumPy: metabolic modelling with Python
    journal, January 2006


    Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal
    journal, April 2017

    • Fritzemeier, Claus Jonathan; Hartleb, Daniel; Szappanos, Balázs
    • PLOS Computational Biology, Vol. 13, Issue 4
    • DOI: 10.1371/journal.pcbi.1005494

    Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction: COMMUNITY DATA-DRIVEN METABOLIC NETWORK MODELING
    journal, June 2016

    • Henry, Christopher S.; Bernstein, Hans C.; Weisenhorn, Pamela
    • Journal of Cellular Physiology, Vol. 231, Issue 11
    • DOI: 10.1002/jcp.25428

    High-throughput generation, optimization and analysis of genome-scale metabolic models
    journal, August 2010

    • Henry, Christopher S.; DeJongh, Matthew; Best, Aaron A.
    • Nature Biotechnology, Vol. 28, Issue 9
    • DOI: 10.1038/nbt.1672

    Prediction of protein subcellular localization
    journal, June 2006

    • Yu, Chin-Sheng; Chen, Yu-Ching; Lu, Chih-Hao
    • Proteins: Structure, Function, and Bioinformatics, Vol. 64, Issue 3
    • DOI: 10.1002/prot.21018

    Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
    journal, November 2016

    • Wattam, Alice R.; Davis, James J.; Assaf, Rida
    • Nucleic Acids Research, Vol. 45, Issue D1
    • DOI: 10.1093/nar/gkw1017

    The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
    journal, November 2013

    • Overbeek, Ross; Olson, Robert; Pusch, Gordon D.
    • Nucleic Acids Research, Vol. 42, Issue D1
    • DOI: 10.1093/nar/gkt1226

    The BioPAX community standard for pathway data sharing
    journal, September 2010

    • Demir, Emek; Cary, Michael P.; Paley, Suzanne
    • Nature Biotechnology, Vol. 28, Issue 9
    • DOI: 10.1038/nbt.1666

    Gap Detection for Genome-Scale Constraint-Based Models
    journal, January 2012

    • Brooks, J. Paul; Burns, William P.; Fong, Stephen S.
    • Advances in Bioinformatics, Vol. 2012
    • DOI: 10.1155/2012/323472

    A Genome Scale Model of Geobacillus thermoglucosidasius (C56-YS93) reveals its biotechnological potential on rice straw hydrolysate
    journal, June 2017


    Reconstructing genome-scale metabolic models with merlin
    journal, April 2015

    • Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.
    • Nucleic Acids Research, Vol. 43, Issue 8
    • DOI: 10.1093/nar/gkv294

    Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
    journal, December 2009

    • Karp, P. D.; Paley, S. M.; Krummenacker, M.
    • Briefings in Bioinformatics, Vol. 11, Issue 1
    • DOI: 10.1093/bib/bbp043

    The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    journal, March 2003


    The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks
    journal, June 2011

    • Swainston, Neil; Smallbone, Kieran; Mendes, Pedro
    • Journal of Integrative Bioinformatics, Vol. 8, Issue 2
    • DOI: 10.1515/jib-2011-186

    Genetically engineered bacteria: An emerging tool for environmental remediation and future research perspectives
    journal, July 2011


    Application of Genome-Scale Metabolic Models in Metabolic Engineering
    journal, August 2013

    • Garcia-Albornoz, Manuel Alberto; Nielsen, Jens
    • Industrial Biotechnology, Vol. 9, Issue 4
    • DOI: 10.1089/ind.2013.0011

    Modeling central metabolism and energy biosynthesis across microbial life
    journal, August 2016


    A genome-scale metabolic network reconstruction of tomato ( Solanum lycopersicum L.) and its application to photorespiratory metabolism
    journal, January 2016

    • Yuan, Huili; Cheung, C. Y. Maurice; Poolman, Mark G.
    • The Plant Journal, Vol. 85, Issue 2
    • DOI: 10.1111/tpj.13075

    Fast Reconstruction of Compact Context-Specific Metabolic Network Models
    journal, January 2014


    KBase: The United States Department of Energy Systems Biology Knowledgebase
    journal, July 2018

    • Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S.
    • Nature Biotechnology, Vol. 36, Issue 7
    • DOI: 10.1038/nbt.4163

    The RAST Server: Rapid Annotations using Subsystems Technology
    journal, January 2008

    • Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
    • BMC Genomics, Vol. 9, Issue 1, Article No. 75
    • DOI: 10.1186/1471-2164-9-75

    Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering
    journal, January 2012

    • Ng, Chiam Yu; Jung, Moo-young; Lee, Jinwon
    • Microbial Cell Factories, Vol. 11, Issue 1
    • DOI: 10.1186/1475-2859-11-68

    Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
    journal, August 2011

    • Schellenberger, Jan; Que, Richard; Fleming, Ronan M. T.
    • Nature Protocols, Vol. 6, Issue 9
    • DOI: 10.1038/nprot.2011.308

    Optimization based automated curation of metabolic reconstructions
    journal, January 2007

    • Satish Kumar, Vinay; Dasika, Madhukar S.; Maranas, Costas D.
    • BMC Bioinformatics, Vol. 8, Issue 1
    • DOI: 10.1186/1471-2105-8-212

    WoLF PSORT: protein localization predictor
    journal, May 2007

    • Horton, P.; Park, K. -J.; Obayashi, T.
    • Nucleic Acids Research, Vol. 35, Issue Web Server
    • DOI: 10.1093/nar/gkm259

    A systematic comparison of the MetaCyc and KEGG pathway databases
    journal, January 2013


    The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum
    journal, March 2013


    The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
    journal, December 2007

    • Caspi, R.; Foerster, H.; Fulcher, C. A.
    • Nucleic Acids Research, Vol. 36, Issue Database
    • DOI: 10.1093/nar/gkm900

    iOD907, the first genome-scale metabolic model for the milk yeast Kluyveromyces lactis
    journal, May 2014

    • Dias, Oscar; Pereira, Rui; Gombert, Andreas K.
    • Biotechnology Journal, Vol. 9, Issue 6
    • DOI: 10.1002/biot.201300242

    The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
    journal, January 2003


    TCDB: the Transporter Classification Database for membrane transport protein analyses and information
    journal, January 2006


    The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions
    journal, January 2011

    • Rolfsson, Ottar; Palsson, Bernhard Ø; Thiele, Ines
    • BMC Systems Biology, Vol. 5, Issue 1
    • DOI: 10.1186/1752-0509-5-155

    fastGapFill: efficient gap filling in metabolic networks
    journal, May 2014


    Chance and necessity in the evolution of minimal metabolic networks
    journal, March 2006

    • Pál, Csaba; Papp, Balázs; Lercher, Martin J.
    • Nature, Vol. 440, Issue 7084
    • DOI: 10.1038/nature04568

    The EcoCyc Database
    journal, January 2002


    A metabolic network approach for the identification and prioritization of antimicrobial drug targets
    journal, March 2012

    • Chavali, Arvind K.; D’Auria, Kevin M.; Hewlett, Erik L.
    • Trends in Microbiology, Vol. 20, Issue 3
    • DOI: 10.1016/j.tim.2011.12.004

    KEGG: Kyoto Encyclopedia of Genes and Genomes
    journal, January 1999

    • Ogata, H.; Goto, S.; Sato, K.
    • Nucleic Acids Research, Vol. 27, Issue 1
    • DOI: 10.1093/nar/27.1.29

    Efficiently gap-filling reaction networks
    journal, June 2014


    OptFlux: an open-source software platform for in silico metabolic engineering
    journal, April 2010

    • Rocha, Isabel; Maia, Paulo; Evangelista, Pedro
    • BMC Systems Biology, Vol. 4, Issue 1
    • DOI: 10.1186/1752-0509-4-45

    Systems approach to refining genome annotation
    journal, November 2006

    • Reed, J. L.; Patel, T. R.; Chen, K. H.
    • Proceedings of the National Academy of Sciences, Vol. 103, Issue 46
    • DOI: 10.1073/pnas.0603364103

    Construction and completion of flux balance models from pathway databases
    journal, January 2012


    Integrative genome‐scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery
    journal, January 2011

    • Kim, Hyun Uk; Kim, Soo Young; Jeong, Haeyoung
    • Molecular Systems Biology, Vol. 7, Issue 1
    • DOI: 10.1038/msb.2010.115

    In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production
    journal, November 2005

    • Bro, Christoffer; Regenberg, Birgitte; Forster, Jochen
    • Metabolic Engineering, Vol. 8, Issue 2, p. 102-111
    • DOI: 10.1016/j.ymben.2005.09.007

    A systematic assessment of current genome-scale metabolic reconstruction tools
    journal, August 2019


    Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
    journal, November 2016

    • Magnúsdóttir, Stefanía; Heinken, Almut; Kutt, Laura
    • Nature Biotechnology, Vol. 35, Issue 1
    • DOI: 10.1038/nbt.3703