Distributed flux balance analysis simulations of serial biomass fermentation by two organisms


Autoři: Edward Vitkin aff001;  Amichai Gillis aff003;  Mark Polikovsky aff003;  Barak Bender aff003;  Alexander Golberg aff003;  Zohar Yakhini aff001
Působiště autorů: Department of Computer Science, Technion – Israel Institute of Technology, Haifa, Israel aff001;  IBM Watson Health, Haifa, Israel aff002;  Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel aff003;  School of Computer Science, The Interdisciplinary Center, Herzliya, Israel aff004
Vyšlo v časopise: PLoS ONE 15(1)
Kategorie: Research Article
doi: 10.1371/journal.pone.0227363

Souhrn

Intelligent biorefinery design that addresses both the composition of the biomass feedstock as well as fermentation microorganisms could benefit from dedicated tools for computational simulation and computer-assisted optimization. Here we present the BioLego Vn2.0 framework, based on Microsoft Azure Cloud, which supports large-scale simulations of biomass serial fermentation processes by two different organisms. BioLego enables the simultaneous analysis of multiple fermentation scenarios and the comparison of fermentation potential of multiple feedstock compositions. Thanks to the effective use of cloud computing it further allows resource intensive analysis and exploration of media and organism modifications. We use BioLego to obtain biological and validation results, including (1) exploratory search for the optimal utilization of corn biomasses—corn cobs, corn fiber and corn stover—in fermentation biorefineries; (2) analysis of the possible effects of changes in the composition of K. alvarezi biomass on the ethanol production yield in an anaerobic two-step process (S. cerevisiae followed by E. coli); (3) analysis of the impact, on the estimated ethanol production yield, of knocking out single organism reactions either in one or in both organisms in an anaerobic two-step fermentation process of Ulva sp. into ethanol (S. cerevisiae followed by E. coli); and (4) comparison of several experimentally measured ethanol fermentation rates with the predictions of BioLego.

Klíčová slova:

Cloud computing – Ethanol – Fermentation – Glucose – Maize – Oxygen – Saccharomyces cerevisiae – Bioenergy feedstock


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Článek vyšel v časopise

PLOS One


2020 Číslo 1