Model-driven approach for the production of butyrate from CO₂/H₂by a novel co-culture ofC. autoethanogenumandC. beijerinckii

Abstract

One-carbon (C1) compounds are promising feedstocks for sustainable production of commodity chemicals. CO2 is a particularly advantageous C1-feedstock since it is an unwanted industrial off-gas that can be converted to valuable products while reducing its atmospheric levels. Acetogens are known microorganisms that can grow on CO2/H2 and syngas converting these substrates into ethanol and acetate. Co-cultivation of acetogens with microbes that can further process such products can expand the variety of products to, for example, medium chain fatty acids (MCFA) and longer chain alcohols. Solventogens are microorganisms known to produce MCFA and alcohols via the acetone, butanol and ethanol (ABE) fermentation in which acetate is a key metabolite. Thus, co-cultivation of a solventogen and acetogen in a consortium provides a potential platform to produce valuable chemicals from CO2. In this study, metabolic modelling was implemented to design a new co-culture of an acetogen and a solventogen to produce butyrate from CO2/H2 mixtures. The model-driven approach suggested the ability of the studied solventogenic species to grow on lactate/glycerol with acetate as co-substrate. This ability was confirmed experimentally by cultivation of Clostridium beijerinckii on these substrates in serum bottles and subsequently in pH-controlled bioreactors. Community modelling also suggested that a novel microbial consortium consisting of the acetogen Clostridium autoethanogenum, and the solventogen C. beijerinckii would be feasible and stable. On the basis of this prediction, a co-culture was experimentally established. C. autoethanogenum grew on CO2/H2 producing acetate and traces of ethanol. Acetate was in turn, consumed by C. beijerinckii together with lactate, producing butyrate. These results show that community modelling of metabolism is a valuable tool to guide the design of microbial consortia for the tailored production of chemicals from renewable resources.

A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia

“…The applicability of these tools to non-model organisms is critical for designing and optimizing synthetic communities. In the past decades, many synthetic communities have been established that do not depend on model organisms and have shown a high potential for producing commodity chemicals [5,[84][85][86][87]. On the other hand, GEMs require accurate genome annotation and curation to properly account for interactions mediated through pathways, but there is still difficulty identifying these components in microbial genomes.…”

“…The error distribution for the different methods was determined (see Methods Section for a description of the normalized error calculation). S. cerevisiae and E. coli biomass concentration increases (5). DFBAlab was the only tool to predict the biomass formation of E. coli somewhat accurately though the simulation differed substantially from hours 5 to 12.5, showing no growth while growth was observed (5B).…”

“…Recent years have seen a soar in the use of multi-species microbial consortia beyond their traditional application in the production of food and beverages [1,2]. For example, microbial consortia are increasingly applied in the production of commodity chemicals [3][4][5], pharmaceuticals [6], or biofuels [7][8][9]; the valorization of waste and emissions [10][11][12], the improvement of sustainable agriculture systems [13][14][15], and applications in health [16] or bioremediation [17][18][19]. Besides the obvious advantage over established industrial processes in terms of sustainability, multi-species consortia offer a number of advantages compared to monocultures.…”