Biofuel production improvement with genome-scale models: The role of cell composition

2010 ◽  
Vol 5 (7) ◽  
pp. 671-685 ◽  
Author(s):  
Ryan S. Senger
Keyword(s):  
Biofuel Production ◽  
Cell Composition ◽  
Production Improvement ◽  
Scale Models ◽  
Genome Scale

scholarly journals Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
N. T. Devika ◽  
Karthik Raman
Keyword(s):  
Short Chain Fatty Acids ◽  
Acetate Production ◽  
Scale Models ◽  
Powerful Approach ◽  
Metabolic Models ◽  
Commercial Applications ◽  
Different Strains ◽  
Genome Scale ◽  
Modelling Approach

AbstractBifidobacteria, the initial colonisers of breastfed infant guts, are considered as the key commensals that promote a healthy gastrointestinal tract. However, little is known about the key metabolic differences between different strains of these bifidobacteria, and consequently, their suitability for their varied commercial applications. In this context, the present study applies a constraint-based modelling approach to differentiate between 36 important bifidobacterial strains, enhancing their genome-scale metabolic models obtained from the AGORA (Assembly of Gut Organisms through Reconstruction and Analysis) resource. By studying various growth and metabolic capabilities in these enhanced genome-scale models across 30 different nutrient environments, we classified the bifidobacteria into three specific groups. We also studied the ability of the different strains to produce short-chain fatty acids, finding that acetate production is niche- and strain-specific, unlike lactate. Further, we captured the role of critical enzymes from the bifid shunt pathway, which was found to be essential for a subset of bifidobacterial strains. Our findings underline the significance of analysing metabolic capabilities as a powerful approach to explore distinct properties of the gut microbiome. Overall, our study presents several insights into the nutritional lifestyles of bifidobacteria and could potentially be leveraged to design species/strain-specific probiotics or prebiotics.

scholarly journals BOFdat: generating biomass objective function stoichiometric coefficients from experimental data

2018 ◽  
Author(s):  
Jean-Christophe Lachance ◽  
Jonathan M. Monk ◽  
Colton J. Lloyd ◽  
Yara Seif ◽  
Bernhard O. Palsson ◽  
...  
Keyword(s):  
Experimental Data ◽  
Objective Function ◽  
Source Code ◽  
Cell Composition ◽  
Link Type ◽  
Scale Models ◽  
Relative Abundances ◽  
Genome Scale ◽  
Python Package

AbstractGenome-scale models (GEMs) rely on a biomass objective function (BOF) to predict phenotype from genotype. Here we present BOFdat, a Python package that offers functions to generate biomass objective function stoichiometric coefficients (BOFsc) from macromolecular cell composition and relative abundances of macromolecules obtained from omic datasets. Growth-associated and non-growth associated maintenance (GAM and NGAM) costs can also be calculated by BOFdat.BOFdat is freely available on the Python Package Index (pip install BOFdat). The source code and an example usage (Jupyter Notebook and example files) are available on GitHub (https://github.com/jclachance/BOFdat). The documentation and API are available through ReadTheDocs (https://bofdat.readthedocs.io)[email protected], [email protected], [email protected]

scholarly journals Deciphering the metabolic capabilities of Bifidobacteria using genome-scale metabolic models

2019 ◽  
Author(s):  
N. T. Devika ◽  
Karthik Raman
Keyword(s):  
Short Chain Fatty Acids ◽  
Acetate Production ◽  
Scale Models ◽  
Powerful Approach ◽  
Metabolic Models ◽  
Commercial Applications ◽  
Different Strains ◽  
Genome Scale ◽  
Modelling Approach

ABSTRACTBifidobacteria, the initial colonisers of breastfed infant guts, are considered as the key commensals that promote a healthy gastrointestinal tract. However, little is known about the key metabolic differences between different strains of these bifidobacteria, and consequently, their suitability for their varied commercial applications. In this context, the present study applies a constraint-based modelling approach to differentiate between 36 important bifidobacterial strains, enhancing their genome-scale metabolic models obtained from the AGORA (Assembly of Gut Organisms through Reconstruction and Analysis) resource. By studying various growth and metabolic capabilities in these enhanced genome-scale models across 30 different nutrient environments, we classified the bifidobacteria into three specific groups. We also studied the ability of the different strains to produce short chain fatty acids, finding that acetate production is niche- and strain-specific, unlike lactate. Further, we captured the role of critical enzymes from the bifid shunt pathway, which was found to be essential for a subset of bifidobacterial strains. Our findings underline the significance of analysing metabolic capabilities as a powerful approach to explore distinct properties of the gut microbiome. Overall, our study presents several insights into the nutritional lifestyles of bifidobacteria and could potentially be leveraged to design species/strain-specific probiotics or prebiotics.

Role of microalgae in circular bioeconomy: from waste treatment to biofuel production

2021 ◽  
Author(s):  
Juliana Botelho Moreira ◽  
Thaisa Duarte Santos ◽  
Jessica Hartwig Duarte ◽  
Priscilla Quenia Muniz Bezerra ◽  
Michele Greque de Morais ◽  
...  
Keyword(s):  
Waste Treatment ◽  
Biofuel Production

scholarly journals Bio-Crude Production Improvement during Hydrothermal Liquefaction of Biopulp by Simultaneous Application of Alkali Catalysts and Aqueous Phase Recirculation

Energies ◽  
2021 ◽  
Vol 14 (15) ◽  
pp. 4492
Author(s):  
Komeil Kohansal ◽  
Kamaldeep Sharma ◽  
Saqib Sohail Toor ◽  
Eliana Lozano Sanchez ◽  
Joscha Zimmermann ◽  
...  
Keyword(s):  
Aqueous Phase ◽  
Hydrothermal Liquefaction ◽  
Biofuel Production ◽  
Hydrothermal Conversion ◽  
Simultaneous Application ◽  
Heating Value ◽  
Production Improvement ◽  
Catalytic Experiment ◽  
Alkali Catalysts ◽  
Alkali Elements

This study focuses on the valorization of the organic fraction of municipal solid waste (biopulp) by hydrothermal liquefaction. Thereby, homogeneous alkali catalysts (KOH, NaOH, K2CO3, and Na2CO3) and a residual aqueous phase recirculation methodology were mutually employed to enhance the bio-crude yield and energy efficiency of a sub-critical hydrothermal conversion (350 °C, 15–20 Mpa, 15 min). Interestingly, single recirculation of the concentrated aqueous phase positively increased the bio-crude yield in all cases, while the higher heating value (HHV) of the bio-crudes slightly dropped. Compared to the non-catalytic experiment, K2CO3 and Na2CO3 effectively increased the bio-crude yield by 14 and 7.3%, respectively. However, KOH and NaOH showed a negative variation in the bio-crude yield. The highest bio-crude yield (37.5 wt.%) and energy recovery (ER) (59.4%) were achieved when K2CO3 and concentrated aqueous phase recirculation were simultaneously applied to the process. The inorganics distribution results obtained by ICP reveal the tendency of the alkali elements to settle into the aqueous phase, which, if recovered, can potentially boost the circularity of the HTL process. Therefore, wise selection of the alkali catalyst along with aqueous phase recirculation assists hydrothermal liquefaction in green biofuel production and environmentally friendly valorization of biopulp.

scholarly journals The role of beekeeping in production of oil crops

2013 ◽  
Vol 7 (4-5) ◽  
pp. 77-82
Author(s):  
Andor Kovács
Keyword(s):  
Sunflower Oil ◽  
Honey Bees ◽  
Energy Production ◽  
Food Industry ◽  
Biofuel Production ◽  
Production Structure ◽  
Ecological Role ◽  
Winter Rape ◽  
Oil Crops

Production of sunflower oil are expected to serve larger and larger extent – over the demand of food industry and chemical industry – biofuel production. This could be especially true for that areas where climate is not allowed to grow winter rape safely and economically. Ecological role of honey-bees can be considered undoubtful in preservation of biodiversity of flora and fauna. I analyse the following problems in our study: • What is the significance of oil plants in European and Hungarian energy production? • How influence pollination the yields and the safety of production of oil plants? • What is the role of oil plants in the development of production structure of beekeeping? • What are the economical advantages of the above-mentioned effects?

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