Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process

Biotechnology for Biofuels
Sabine KochSteffen Klamt

Abstract

Microbial communities are ubiquitous in nature and play a major role in ecology, medicine, and various industrial processes. In this study, we used stoichiometric metabolic modeling to investigate a community of three species, Desulfovibrio vulgaris, Methanococcus maripaludis, and Methanosarcina barkeri, which are involved in acetogenesis and methanogenesis in anaerobic digestion for biogas production. We first constructed and validated stoichiometric models of the core metabolism of the three species which were then assembled to community models. The community was simulated by applying the previously described concept of balanced growth demanding that all organisms of the community grow with equal specific growth rate. For predicting community compositions, we propose a novel hierarchical optimization approach: first, similar to other studies, a maximization of the specific community growth rate is performed which, however, often leads to a wide range of optimal community compositions. In a secondary optimization, we therefore also demand that all organisms must grow with maximum biomass yield (optimal substrate usage) reducing the range of predicted optimal community compositions. Simulating two-species as well as three-speci...Continue Reading

References

Oct 12, 1965·Proceedings of the Royal Society of London. Series B, Containing Papers of a Biological Character·S J Pirt
Feb 17, 1998·Applied and Environmental Microbiology·M Loferer-KrössbacherR Psenner
Nov 15, 2002·Nature·Jörg StellingErnst Dieter Gilles
Apr 8, 2003·Trends in Biotechnology·Nathan D PriceBernhard O Palsson
Feb 1, 1989·Applied and Environmental Microbiology·M J TattonM L Parker
Mar 14, 2007·Molecular Systems Biology·Sergey StolyarDavid A Stahl
Apr 6, 2007·BMC Systems Biology·Steffen KlamtErnst D Gilles
Oct 19, 2007·Nature·Peter J TurnbaughJeffrey I Gordon
Jul 1, 2008·Nature Reviews. Microbiology·Rudolf K ThauerReiner Hedderich
Jul 11, 2008·The ISME Journal·Richard D BardgettNicholas J Ostle
Jul 8, 2009·Journal of Bacteriology·Christopher B WalkerDavid A Stahl
Sep 25, 2009·Applied Microbiology and Biotechnology·Peter Weiland
Mar 10, 2010·Nature Biotechnology·Jeffrey D OrthBernhard Ø Palsson
Oct 1, 2010·Biotechnology and Bioengineering·Timothy J Hanly, Michael A Henson
Oct 12, 2010·Science·Donald E CanfieldPaul G Falkowski
Dec 14, 2011·Nature Communications·Shiri FreilichEytan Ruppin
Feb 10, 2012·PLoS Computational Biology·Ali R Zomorrodi, Costas D Maranas
Mar 14, 2012·Nature Reviews. Genetics·Ilseung Cho, Martin J Blaser
Jul 17, 2012·Nature Reviews. Microbiology·Karoline Faust, Jeroen Raes
Jun 7, 2013·PloS One·Ruchir A KhandelwalFrank J Bruggeman
Apr 20, 2014·ACS Synthetic Biology·Ali R ZomorrodiCostas D Maranas
Jul 6, 2014·PLoS Computational Biology·Hsuan-Chao ChiuElhanan Borenstein

❮ Previous
Next ❯

Citations

Jul 5, 2016·Scientific Reports·Alice Julien-LaferrièreMarie-France Sagot
Jul 25, 2019·Brazilian Dental Journal·Suelen Aline de Lima BarrosGelson Luís Adabo
Nov 14, 2018·Bioinformatics·Beatriz García-JiménezJuan Nogales
Feb 10, 2019·Microbial Cell Factories·Garrett W RoellYinjie J Tang
Jun 24, 2017·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Daniel J Cook, Jens Nielsen
Jul 14, 2020·Frontiers in Bioengineering and Biotechnology·Denny Popp, Florian Centler
Jun 4, 2019·Frontiers in Microbiology·Sören WeinrichFlorian Centler
Mar 16, 2018·Biochemical Society Transactions·Antonella Succurro, Oliver Ebenhöh
Jan 12, 2021·Computational and Structural Biotechnology Journal·Beatriz García-JiménezJuan Nogales

❮ Previous
Next ❯

Software Mentioned

MATLAB package
CellNetAnalyzer
OptDeg
OptCom

Related Concepts

Related Feeds

Biofuels (ASM)

Biofuels are produced through contemporary processes from biomass rather than geological processes involved in fossil fuel formation. Examples include biodiesel, green diesel, biogas, etc. Discover the latest research on biofuels in this feed.