BioLEGO — a web-based application for biorefinery design and evaluation of serial biomass fermentation

Abstract

The composition of feedstock biomass and the selection of fermenting microorganisms are critical factors in biorefinery design. Feedstock biomass composition is constrained by local supply materials, but microorganism selection affords considerable flexibility. Once biomass feedstock is identified, biorefinery designers need to select optimal fermenting organisms. While fermentation by microorganism communities can increase the range of digested biomass compounds and can be more resistant to infections, it has intrinsic problems in the context of species competition, process design and modeling — issues related to insufficient process control. Using a serial fermentation approach, we offset some of these issues to allow maximal process control, while benefiting from organism diversity to maximize feedstock conversion rates. Here, we describe BioLEGO, a freely available web-based application that enables computer-assisted a single and two-step multiorganism fermentation process design. BioLEGO is based on a modular modeling approach, enabling the generation of different fermentation configurations consisting of independent organism modules. BioLEGO supports the evaluation of possible biomass-to-product yields for biomass mixes or general media and recommends media changes to increase the process efficacy.

Thermochemical hydrolysis of macroalgae Ulva for biorefinery: Taguchi robust design method

“…This methodology enables the prediction of organism growth rates, as well as the prediction of minimal and maximal production rates of various metabolic compounds, based only on reaction stoichiometry and directionality. FBA-based approaches have a wide range of applications, including phenotype analysis, bioengineering and metabolic model reconstructions36373839.…”

“…Specifically, to predict the biofuel molecule production rates, we utilized one-step simulation framework described in previous work39 with metabolic models of S. cerevisiae 41 (original and modified to incorporate Xylose uptake, simulating RN1016 strain), of E. coli 42 and of C. acetobutylicum 43. The composition of the Ulva biomass was based on literature121344 and appears in Table 1.…”

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

“…Serial fermentation is a design approach that offers tighter and more predictable control of inter-organism relations and reactions, thus enabling better process optimization [15][16][17][18]. Briefly, in this process each organism is grown separately.…”

“…In previous work we introduced BioLego-a platform that simulates the efficiency of biomass fermentation in two-step processes [15,16,19]. This current work leverages Microsoft Azure Cloud to enhance the BioLego framework and to allow high-scale simulations, exploring a large multiplicity of scenarios, of the efficiency of biomass fermentation in two-step processes.…”

Carbohydrate-based phenotyping of the green macroalga Ulva fasciata using near-infrared spectrometry: potential implications for marine biorefinery

“…We decided to focus on these molecules as they are the major carbohydrates in the Ulva species. In addition, in our previous work, we showed that the glucose, rhamnose and xylose contents of U. fasciata predict the potential of this feedstock for bioethanol fermentation (Vitkin et al 2015). In addition to examining the potential use of reflectance spectroscopy for deriving different sugar contents, we developed PLS to predict the contents of specific monosaccharides based on whole thalli spectrum features.…”