SteadyCom: Predicting microbial abundances while ensuring community stability

PLoS Computational Biology
Siu Hung Joshua ChanCostas D Maranas

Abstract

Genome-scale metabolic modeling has become widespread for analyzing microbial metabolism. Extending this established paradigm to more complex microbial communities is emerging as a promising way to unravel the interactions and biochemical repertoire of these omnipresent systems. While several modeling techniques have been developed for microbial communities, little emphasis has been placed on the need to impose a time-averaged constant growth rate across all members for a community to ensure co-existence and stability. In the absence of this constraint, the faster growing organism will ultimately displace all other microbes in the community. This is particularly important for predicting steady-state microbiota composition as it imposes significant restrictions on the allowable community membership, composition and phenotypes. In this study, we introduce the SteadyCom optimization framework for predicting metabolic flux distributions consistent with the steady-state requirement. SteadyCom can be rapidly converged by iteratively solving linear programming (LP) problem and the number of iterations is independent of the number of organisms. A significant advantage of SteadyCom is compatibility with flux variability analysis. Steady...Continue Reading

References

Feb 17, 1998·Applied and Environmental Microbiology·M Loferer-KrössbacherR Psenner
Dec 4, 2003·Metabolic Engineering·R Mahadevan, C H Schilling
Jan 14, 2004·Genome Research·Anthony P BurgardCostas D Maranas
Apr 16, 2005·Science·Paul B EckburgDavid A Relman
Mar 14, 2007·Molecular Systems Biology·Sergey StolyarDavid A Stahl
Sep 14, 2007·International Journal of Biological Macromolecules·Maria VardakouPaul Christakopoulos
Jan 25, 2008·BMC Systems Biology·Alexei VazquezZoltán N Oltvai
May 24, 2008·Science·Ruth E LeyJeffrey I Gordon
Oct 22, 2008·Journal of Bacteriology·Varun MazumdarDaniel Segrè
Oct 23, 2008·The Journal of Biological Chemistry·Jan Schellenberger, Bernhard Ø Palsson
Dec 2, 2008·Nature·Peter J TurnbaughJeffrey I Gordon
Apr 7, 2009·Applied and Environmental Microbiology·Margreet I PastinkJeroen Hugenholtz
Apr 7, 2010·Science Translational Medicine·Peter J TurnbaughJeffrey I Gordon
May 1, 2010·Current Opinion in Microbiology·Adam M Feist, Bernhard O Palsson
Aug 4, 2010·Proceedings of the National Academy of Sciences of the United States of America·Carlotta De FilippoPaolo Lionetti
Oct 6, 2010·BMC Bioinformatics·Steinn Gudmundsson, Ines Thiele
Apr 22, 2011·Nature·Manimozhiyan ArumugamPeer Bork
Jun 1, 2011·Genome Biology·J Gregory CaporasoRob Knight
Jun 17, 2011·BMC Bioinformatics·Laszlo DavidAlexander Bockmayr
Aug 4, 2011·European Journal of Clinical Nutrition·J ZimmerP Enck
Oct 13, 2011·Molecular Systems Biology·Jeffrey D OrthBernhard Ø Palsson
Dec 14, 2011·Nature Communications·Shiri FreilichEytan Ruppin
Dec 21, 2011·Proceedings of the National Academy of Sciences of the United States of America·Sharon GreenblumElhanan Borenstein
Feb 10, 2012·PLoS Computational Biology·Ali R Zomorrodi, Costas D Maranas
Mar 1, 2012·Nutrition in Clinical Practice : Official Publication of the American Society for Parenteral and Enteral Nutrition·Rosa Krajmalnik-BrownJohn K DiBaise
Mar 13, 2012·Journal of Theoretical Biology·Sayed-Amir MarashiAlexander Bockmayr
Mar 27, 2012·BMC Systems Biology·Milan J A van Hoek, Roeland M H Merks
May 10, 2012·FEMS Microbiology Reviews·Bryan S Griffiths, Laurent Philippot
Jun 16, 2012·Nature·UNKNOWN Human Microbiome Project Consortium
Jul 17, 2012·Nature·Marcus J ClaessonPaul W O'Toole
Sep 5, 2012·Nature Reviews. Gastroenterology & Hepatology·Harry J FlintSylvia H Duncan
Sep 14, 2012·Nature·Catherine A LozuponeRob Knight
Sep 26, 2012·Journal of Computational Chemistry·Elijah RobertsZaida Luthey-Schulten
Jun 7, 2013·PloS One·Ruchir A KhandelwalFrank J Bruggeman
Jul 6, 2013·Science·Jeremiah J FaithJeffrey I Gordon
Jul 17, 2013·Proceedings of the National Academy of Sciences of the United States of America·Roie Levy, Elhanan Borenstein

❮ Previous
Next ❯

Citations

Jan 31, 2019·PLoS Computational Biology·Alessandro Di StefanoPietro Liò
Mar 2, 2019·PLoS Computational Biology·Colton J LloydAdam M Feist
May 31, 2019·Biotechnology Journal·Brendan Fu-Long SieowMatthew Wook Chang
Sep 30, 2020·PLoS Computational Biology·James D Brunner, Nicholas Chia
Mar 22, 2020·NPJ Biofilms and Microbiomes·Ioanna ChatzigiannidouNico Boon
Jan 31, 2019·Metabolites·Partho Sen, Matej Orešič
Mar 9, 2019·Applied Microbiology and Biotechnology·Ishu Khangwal, Pratyoosh Shukla
Jul 25, 2019·Nature Microbiology·Manish KumarJens Nielsen
Mar 24, 2020·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Angela E Douglas
Nov 14, 2018·Bioinformatics·Beatriz García-JiménezJuan Nogales
Jan 23, 2020·MSystems·Christian DienerOsbaldo Resendis-Antonio
Dec 24, 2019·Frontiers in Microbiology·Mohammad Mazharul IslamRajib Saha
Apr 4, 2019·PeerJ·Beatriz García-Jiménez, Mark D Wilkinson
Jul 17, 2020·Computational and Structural Biotechnology Journal·Clémence FriouxFalk Hildebrand
Nov 27, 2020·Computational and Structural Biotechnology Journal·Sara Benito-VaquerizoMaria Suarez-Diez
Dec 19, 2020·Computational and Structural Biotechnology Journal·Álvaro AltamiranoDaniel Garrido
Jan 12, 2021·Computational and Structural Biotechnology Journal·Beatriz García-JiménezJuan Nogales
Jan 6, 2021·Nature Ecology & Evolution·Daniel MachadoKiran R Patil
Feb 10, 2021·Current Opinion in Biotechnology·Livia S ZaramelaKarsten Zengler
Jan 26, 2021·Computational and Structural Biotechnology Journal·Humphrey A MabwiKwang Hyun Cha
Jan 22, 2021·Microbiome·Jack Jansma, Sahar El Aidy
Dec 15, 2020·Bioinformatics·Jingyi CaiS H Joshua Chan
Oct 9, 2019·Current Opinion in Biotechnology·Stephen P LillingtonMichelle A O'Malley
Mar 9, 2021·Frontiers in Molecular Biosciences·Fabrice Jean-PierreGeorge A O'Toole
Apr 6, 2019·Current Opinion in Biotechnology·Alexander Eng, Elhanan Borenstein
Apr 23, 2021·Scientific Reports·Miguel Fernández-NiñoAndrés Fernando González Barrios
May 6, 2021·MSystems·Nana Y D AnkrahAngela E Douglas
Jun 16, 2021·PLoS Computational Biology·Pavlos Stephanos Bekiaris, Steffen Klamt
Jun 15, 2021·Molecular Omics·Lillian R DillardJason A Papin
Mar 31, 2021·Annual Review of Biomedical Engineering·Patrick A LeggieriOphelia S Venturelli

❮ Previous
Next ❯

Software Mentioned

LatticeMicrobes
COBRA
CPLEX
COmputation of Microbial Ecosystems ( COMETS )
OptCom
SteadyCom
Matlab
cFBA
FVA

Related Concepts

Related Feeds

Birth Defects

Birth defects encompass structural and functional alterations that occur during embryonic or fetal development and are present since birth. The cause may be genetic, environmental or unknown and can result in physical and/or mental impairment. Here is the latest research on birth defects.