Butyric acid and hydrogen production by Clostridium tyrobutyricum ATCC 25755 and mutants

Hydrogen production pathways in Clostridia and their improvement by metabolic engineering

Biological production of hydrogen has a tremendous potential as an environmentally sustainable technology to generate a clean fuel. Among the different available methods to produce biohydrogen, dark fermentation features the highest productivity and can be used as a means to dispose of organic waste biomass. Within this approach, Clostridia have the highest theoretical H2 production yield. Nonetheless, most strains show actual yields far lower than the theoretical maximum: improving their efficiency becomes necessary for achieving cost-effective fermentation processes. This review aims at providing a survey of the metabolic network involved in H2 generation in Clostridia and strategies used to improve it through metabolic engineering. Together with current achievements, a number of future perspectives to implement these results will be illustrated.

Development of inducible promoters for regulating gene expression in Clostridium tyrobutyricum for biobutanol production

Clostridium tyrobutyricum is an anaerobe known for its ability to produce short-chain fatty acids, alcohols, and esters. We aimed to develop inducible promoters for fine-tuning gene expression in C. tyrobutyricum. Synthetic inducible promoters were created by employing an Escherichia coli lac operator to regulate the thiolase promoter (PCathl) from Clostridium acetobutylicum, with the best one (LacI-Pto4s) showing a 5.86-fold dynamic range with isopropyl β- d-thiogalactoside (IPTG) induction. A LT-Pt7 system with a dynamic range of 11.6-fold was then created by combining LacI-Pto4s with a T7 expression system composing of RNA polymerase (T7RNAP) and Pt7lac promoter. Furthermore, two inducible expression systems BgaR-PbgaLA and BgaR-PbgaLB with a dynamic range of ~40-fold were developed by optimizing a lactose-inducible expression system from Clostridium perfringens with modified 5' untranslated region (5' UTR) and ribosome-binding site (RBS). BgaR-PbgaLB was then used to regulate the expressions of a bifunctional aldehyde/alcohol dehydrogenase encoded by adhE2 and butyryl-CoA/acetate Co-A transferase encoded by cat1 in C. tyrobutyricum wild type and Δcat1::adhE2, respectively, demonstrating its efficient inducible gene regulation. The regulated cat1 expression also confirmed that the Cat1-catalyzed reaction was responsible for acetate assimilation in C. tyrobutyricum. The inducible promoters offer new tools for tuning gene expression in C. tyrobutyricum for industrial applications.

Clostridium strain FAM25158, a unique endospore-forming bacterium related to Clostridium tyrobutyricum and isolated from Emmental cheese shows low tolerance to salt

The genus Clostridium is a large and diverse group of species that can cause food spoilage, including late blowing defect (LBD) in cheese. In this study, we investigated the taxonomic status of strain FAM25158 isolated from Emmental cheese with LBD using a polyphasic taxonomic and comparative genomic approach. A 16S rRNA gene sequence phylogeny suggested affiliation to the Clostridium sensu stricto cluster, with Clostridium tyrobutyricum DSM 2637T being the closest related type strain (99.16% sequence similarity). Average Nucleotide Identity (ANI) analysis revealed that strain FAM25158 is at the species threshold with C. tyrobutyricum, with ANI values ranging from 94.70 to 95.26%, while the digital DNA-DNA hybridization values were below the recommended threshold, suggesting that FAM25158 is significantly different from C. tyrobutyricum at the genomic level. Moreover, comparative genomic analysis between FAM25158 and its four closest C. tyrobutyricum relatives revealed a diversity of metabolic pathways, with FAM25158 differing from other C. tyrobutyricum strains by the presence of genes such as scrA, srcB, and scrK, responsible for sucrose utilization, and the absence of many important functional genes associated with cold and osmolality adaptation, which was further supported by phenotypic analyses. Surprisingly, strain FAM25158 exhibited unique physiologic traits, such as an optimal growth temperature of 30°C, in contrast to its closest relatives, C. tyrobutyricum species with an optimal growth temperature of 37°C. Additionally, the growth of FAM25158 was inhibited at NaCl concentrations higher than 0.5%, a remarkable observation considering its origin from cheese. While the results of this study provide novel information on the genetic content of strain FAM25158, the relationship between its genetic content and the observed phenotype remains a topic requiring further investigation.

Bioinformatics and metabolic flux analysis highlight a new mechanism involved in lactate oxidation in Clostridium tyrobutyricum

Climate change and environmental issues compel us to find alternatives to the production of molecules of interest from petrochemistry. This study aims at understanding the production of butyrate, hydrogen, and CO₂ from the oxidation of lactate with acetate in Clostridium tyrobutyricum and thus proposes an alternative carbon source to glucose. This specie is known to produce more butyrate than the other butyrate-producing clostridia species due to a lack of solvent genesis phase. The recent discoveries on flavin-based electron bifurcation and confurcation mechanism as a mode of energy conservation led us to suggest a new metabolic scheme for the formation of butyrate from lactate-acetate co-metabolism. While searching for genes encoding for EtfAB complexes and neighboring genes in the genome of C. tyrobutyricum, we identified a cluster of genes involved in butyrate formation and another cluster involved in lactate oxidation homologous to Acetobacterium woodii. A phylogenetic approach encompassing other butyrate-producing and/or lactate-oxidizing species based on EtfAB complexes confirmed these results. A metabolic scheme on the production of butyrate, hydrogen, and CO₂ from the lactate-acetate co-metabolism in C. tyrobutyricum was constructed and then confirmed with data of steady-state continuous culture. This in silico metabolic carbon flux analysis model showed the coherence of the scheme from the carbon recovery, the cofactor ratio, and the ATP yield. This study improves our understanding of the lactate oxidation metabolic pathways and the role of acetate and intracellular redox balance, and paves the way for the production of molecules of interest as butyrate and hydrogen with C. tyrobutyricum.

Wastewater-derived biohydrogen: Critical analysis of related enzymatic processes at the research and large scales

Organic-rich wastewater is a feasible feedstock for biohydrogen production. Numerous review on the performance of microorganisms and the diversity of their communities during a biohydrogen process were published. However, there is still no in-depth overview of enzymes for biohydrogen production from wastewater and their scale-up applications. This review aims at providing an insightful exploration of critical discussion in terms of: (i) the roles and applications of enzymes in wastewater-based biohydrogen fermentation; (ii) systematical introduction to the enzymatic processes of photo fermentation and dark fermentation; (iii) parameters that affect enzymatic performances and measures for enzyme activity/ability enhancement; (iv) biohydrogen production bioreactors; as well as (v) enzymatic biohydrogen production systems and their larger scales application. Furthermore, to assess the best applications of enzymes in biohydrogen production from wastewater, existing problems and feasible future studies on the development of low-cost enzyme production methods and immobilized enzymes, the construction of multiple enzyme cooperation systems, the study of biohydrogen production mechanisms, more effective bioreactor exploration, larger scales enzymatic biohydrogen production, and the enhancement of enzyme activity or ability are also addressed.

Processing of Biomass Prior to Hydrogen Fermentation and Post-Fermentative Broth Management

Using bioconversion and simultaneous value-added product generation requires purification of the gaseous and the liquid streams before, during, and after the bioconversion process. The effect of diversified process parameters on the efficiency of biohydrogen generation via biological processes is a broad object of research. Biomass-based raw materials are often applied in investigations regarding biohydrogen generation using dark fermentation and photo fermentation microorganisms. The literature lacks information regarding model mixtures of lignocellulose and starch-based biomass, while the research is carried out based on a single type of raw material. The utilization of lignocellulosic and starch biomasses as the substrates for bioconversion processes requires the decomposition of lignocellulosic polymers into hexoses and pentoses. Among the components of lignocelluloses, mainly lignin is responsible for biomass recalcitrance. The natural carbohydrate-lignin shields must be disrupted to enable lignin removal before biomass hydrolysis and fermentation. The matrix of chemical compounds resulting from this kind of pretreatment may significantly affect the efficiency of biotransformation processes. Therefore, the actual state of knowledge on the factors affecting the culture of dark fermentation and photo fermentation microorganisms and their adaptation to fermentation of hydrolysates obtained from biomass requires to be monitored and a state of the art regarding this topic shall become a contribution to the field of bioconversion processes and the management of liquid streams after fermentation. The future research direction should be recognized as striving to simplification of the procedure, applying the assumptions of the circular economy and the responsible generation of liquid and gas streams that can be used and purified without large energy expenditure. The optimization of pre-treatment steps is crucial for the latter stages of the procedure.

Organic waste recycling for carbon smart circular bioeconomy and sustainable development: A review

The development of sustainable and low carbon impact processes for a suitable management of waste and by-products coming from different factors of the industrial value chain like agricultural, forestry and food processing industries. Implementing this will helps to avoid the negative environmental impact and global warming. The application of the circular bioeconomy (CB) and the circular economic models have been shown to be a great opportunity for facing the waste and by-products issues by bringing sustainable processing systems which allow to the value chains be more responsible and resilient. In addition, biorefinery approach coupled to CB context could offer different solution and insights to conquer the current challenges related to decrease the fossil fuel dependency as well as increase efficiency of resource recovery and processing cost of the industrial residues. It is worth to remark the important role that the biotechnological processes such as fermentative, digestive and enzymatic conversions play for an effective waste management and carbon neutrality.

Debottlenecking the biological hydrogen production pathway of dark fermentation: insight into the impact of strain improvement

Confronted with the exhaustion of the earth’s fossil fuel reservoirs, bio-based process to produce renewable energy is receiving significant interest. Hydrogen is considered as an attractive energy carrier that can replace fossil fuels in the future mainly due to its high energy content, recyclability and environment-friendly nature. Biological hydrogen production from renewable biomass or waste materials by dark fermentation is a promising alternative to conventional routes since it is energy-saving and reduces environmental pollution. However, the current yield and evolution rate of fermentative hydrogen production are still low. Strain improvement of the microorganisms employed for hydrogen production is required to make the process competitive with traditional production methods. The present review summarizes recent progresses on the screening for highly efficient hydrogen-producing strains using various strategies. As the metabolic pathways for fermentative hydrogen production have been largely resolved, it is now possible to engineer the hydrogen-producing strains by rational design. The hydrogen yields and production rates by different genetically modified microorganisms are discussed. The key limitations and challenges faced in present studies are also proposed. We hope that this review can provide useful information for scientists in the field of fermentative hydrogen production.

Hydrogen can be generated by microorganisms.

Dark fermentation is efficient for biological hydrogen production.

Strain improvement is critical to enhancing hydrogen-producing ability.

Subchronic feeding, allergenicity, and genotoxicity safety evaluations of single strain bacterial protein

Microbial proteins are potentially important alternatives to animal protein. A safety assessment was conducted on a Clostridium protein which can serve as a high-quality protein source in human food. A battery of toxicity studies was conducted comprising a 14-day dose-range finding dietary study in rats, 90-day dietary study in rats and in vitro genotoxicity studies. The allergenic potential was investigated by bioinformatics analysis. In the 90-day feeding study, rats were fed diets containing 0, 5.0, 7.5, and 10% Clostridium protein. The Clostridium protein-containing diets were well-tolerated and no adverse effects on the health or growth were observed. Significant reductions in neutrophil counts were observed in all female rats compared to controls, which were slightly outside of reference ranges. These effects were not deemed to be adverse due to the absence of comparable findings in male rats and high physiological variability of measured values within groups. A No-Observed-Adverse-Effect-Level (NOAEL) of at least 10% Clostridium protein, the highest dose tested and corresponding to 5,558 and 6,671 mg/kg body weight/day for male and female rats, respectively, was established. No evidence of genotoxicity was observed and the allergenic potential was low. These results support the use of Clostridium protein as a food ingredient.

Socio-Economic and Environmental Impacts of Biomass Valorisation: A Strategic Drive for Sustainable Bioeconomy

In the late twentieth century, the only cost-effective opportunity for waste removal cost at least several thousand dollars, but nowadays, a lot of improvement has occurred. The biomass and waste generation problems attracted concerned authorities to identify and provide environmentally friendly sustainable solutions that possess environmental and economic benefits. The present study emphasises the valorisation of biomass and waste produced by domestic and industrial sectors. Therefore, substantial research is ongoing to replace the traditional treatment methods that potentially acquire less detrimental effects. Synthetic biology can be a unique platform that invites all the relevant characters for designing and assembling an efficient program that could be useful to handle the increasing threat for human beings. In the future, these engineered methods will not only revolutionise our lives but practically lead us to get cheaper biofuels, producing bioenergy, pharmaceutics, and various biochemicals. The bioaugmentation approach concomitant with microbial fuel cells (MFC) is an example that is used to produce electricity from municipal waste, which is directly associated with the loading of waste. Beyond the traditional opportunities, herein, we have spotlighted the new advances in pertinent technology closely related to production and reduction approaches. Various integrated modern techniques and aspects related to the industrial sector are also discussed with suitable examples, including green energy and other industrially relevant products. However, many problems persist in present-day technology that requires essential efforts to handle thoroughly because significant valorisation of biomass and waste involves integrated methods for timely detection, classification, and separation. We reviewed and proposed the anticipated dispensation methods to overcome the growing stream of biomass and waste at a distinct and organisational scale.

Recent advances in n-butanol and butyrate production using engineered Clostridium tyrobutyricum

Acidogenic clostridia naturally producing acetic and butyric acids has attracted high interest as a novel host for butyrate and n-butanol production. Among them, Clostridium tyrobutyricum is a hyper butyrate-producing bacterium, which re-assimilates acetate for butyrate biosynthesis by butyryl-CoA/acetate CoA transferase (CoAT), rather than the phosphotransbutyrylase-butyrate kinase (PTB-BK) pathway widely found in clostridia and other microbial species. To date, C. tyrobutyricum has been engineered to overexpress a heterologous alcohol/aldehyde dehydrogenase, which converts butyryl-CoA to n-butanol. Compared to conventional solventogenic clostridia, which produce acetone, ethanol, and butanol in a biphasic fermentation process, the engineered C. tyrobutyricum with a high metabolic flux toward butyryl-CoA produced n-butanol at a high yield of > 0.30 g/g and titer of > 20 g/L in glucose fermentation. With no acetone production and a high C4/C2 ratio, butanol was the only major fermentation product by the recombinant C. tyrobutyricum, allowing simplified downstream processing for product purification. In this review, novel metabolic engineering strategies to improve n-butanol and butyrate production by C. tyrobutyricum from various substrates, including glucose, xylose, galactose, sucrose, and cellulosic hydrolysates containing the mixture of glucose and xylose, are discussed. Compared to other recombinant hosts such as Clostridium acetobutylicum and Escherichia coli, the engineered C. tyrobutyricum strains with higher butyrate and butanol titers, yields and productivities are the most promising hosts for potential industrial applications.

Production of isopropyl and butyl esters by Clostridium mono-culture and co-culture

Production of esters from the acetone-butanol-ethanol (ABE) fermentation by Clostridium often focuses on butyl butyrate, leaving acetone as an undesired product. Addition of butyrate is also often needed because ABE fermentation does not produce enough butyrate. Here we addressed the problems using Clostridium beijerinckii BGS1 that preferred to produce isopropanol instead of acetone, and co-culturing it with Clostridium tyrobutyricum ATCC 25,755 that produced butyrate. Unlike acetone, isopropanol could be converted into ester using lipase and acids . C. tyrobutyricum ATCC 25,755 produced acids at pH 6, while C. beijerinckii BGS1 produced mainly solvents at the same pH. When the two strains were co-cultured, more butyrate was produced, leading to a higher titer of esters than the mono-culture of C. beijerinckii BGS1. As the first study reporting the production of isopropyl butyrate from the Clostridium fermentation, this study highlighted the potential use of lipase and co-culture strategy in ester production.

Isolation of Clostridium from Yunnan-Tibet hot springs and description of Clostridium thermarum sp. nov. with lignocellulosic ethanol production

Lignocellulose is considered a major source of renewable energy that serve as an alternative to the fossil fuels. Members of the genus Clostridium are some of the many microorganisms that have the ability to degrade lignocellulose efficiently to sugar, which can be further converted to biofuel. In this study, we isolated twelve Clostridium strains from hot spring samples of Yunnan and Tibet, of which isolates SYSU GA15002^T and SYSU GA17076 showed low 16S rRNA gene sequence identity profiles to any of the validly named Clostridium strains (<94.0%). Studies using a polyphasic taxonomy approach concluded that the two isolates represent one novel species of the genus Clostridium, for which we propose the name Clostridium thermarum sp. nov., with SYSU GA15002^T as the type strain of the species. Isolate SYSU GA15002^T has an optimum growth temperature at 45°C. Fermentation of the substrates cellobiose, cellulose, xylan and untreated straw powder by this strain results in the production of ethanol, along with acetate and formate. The complete pathways for the conversion of cellulose and xylan to ethanol is also predicted from the genome of isolate SYSU GA15002^T, which revealed a single step conversion of lignocellulosic biomass through consolidated bioprocessing. This paper is a comprehensive study encompassing isolation, polyphasic taxonomy, lignocellulose biodegradation and the genomic information of Clostridium in Yunnan-Tibet hot springs.

A techno-practical method for overcoming the biotoxicity and volatility obstacles of butanol and butyric acid during whole-cell catalysis by Gluconobacter oxydans

BACKGROUND

Butyric acid is a platform chemical material, the production of which has been greatly stimulated by the diverse range of downstream applications in many industries. In particular, higher quality butyric acid used in food and medicine, is more dependent on microbiological production methods. Hence, the bio-oxidation of butanol to butyric acid has been identified as a promising method with good potential economic and environmental benefits. However, both butanol and butyric acid are usually intensively toxic to most microorganisms as well as the bio-oxidation pathway. To develop a green, efficient and competitive microbiological method is the primary work to overcome the bottleneck of butyric acid industry.

RESULT

A combined bioprocess was designed with alternative whole-cell catalysis for butyric acid bio-conversion from butanol by Gluconobacter oxydans in a sealed-oxygen supply bioreactor (SOS). In the operation system, the escape of volatile substrates and toxic chemicals to cells can be avoided by the use of a sealed bioreactor, combined with the rejuvenation of cells by supplying energy co-factors. Finally, during a one-batch whole-cell catalysis, the utilization rate of substrate increased from 56.6 to 96.0% by the simple skill. Additionally, the techno-practical bioprocess can realize the purpose of cell-recycling technology through the rejuvenation effect of co-factor. Finally, we obtained 135.3 g/L butyric acid and 216.7 g/L sorbose during a 60-h whole-cell catalysis. This techno-practical technology provides a promising approach to promote the industrial production of butyric acid with more competitiveness.

CONCLUSION

The techno-practical biotechnology has powerfully promoted the process of butyric acid production by microorganisms, especially makes up for the lack of aerobic fermentation in the industry, and surmounts the shortcomings of traditional anaerobic fermentation. At the same time, this technically practical system provides a promising approach for the promotion of the industrial production of butyric acid in a more competitive manner.

Selective adsorption and recovery of volatile fatty acids from fermented landfill leachate by activated carbon process

An adsorption-desorption process was applied on fermented landfill leachate to adsorb and recover acetic and butyric acid, using activated carbon. In this study, the first, volatile fatty acids adsorption process from fermented leachate was optimized, by investigating various affecting factors such as pH, time, agitation speed, activated carbon dosage, and temperature. The optimum condition for maximum adsorption of 88.94% acetic acid and 98.53% butyric acid, was 19.79 %wt activated carbon dosage, 40.00 rpm of agitation speed, in 9.45 °C and contact time of 179.89 h, while the pH of the substrate was kept fixed at pH:3.0. Results of X-ray fluorescence (XRF) spectrometry, X-ray diffraction (XRD), Fourier transform infrared (FT-IR) and zeta potential revealed that carbon is the dominant component in the adsorbent with a significant effect to remove organic impurities, and it was observed that the activated carbon after the adsorption process showed an amorphous structure peak with a large internal surface area and pore volume. The results exposed that the adsorption on the surface of activated carbon was due to the chemisorption, and the chemisorption mechanism was supported by covalent bonding. The kinetic study displayed excellent fit to Pseudo-second order kinetics model. The second phase of this study was to recover the adsorbed VFAs using multistage desorption unit, in which application of deionized water and ethanol (as desorption agents) resulted in 89.1% of acetic acid and 67.8% of the butyric acid recovery.

Organic acids as antimicrobial food agents: applications and microbial productions

Food safety is a global health and socioeconomic concern since many people still suffer from various acute and life-long diseases, which are caused by consumption of unsafe food. Therefore, ensuring safety of the food is one of the most essential issues in the food industry, which needs to be considered during not only food composition formulation but also handling and storage. For safety purpose, various chemical preservatives have been used so far in the foods. Recently, there has been renewed interest in replacing chemically originated food safety compounds with natural ones in the industry, which can also serve as antimicrobial agents. Among these natural compounds, organic acids possess the major portion. Therefore, in this paper, it is aimed to review and compile the applications, effectiveness, and microbial productions of various widely used organic acids as antimicrobial agents in the food industry.

Efficient resource valorization by co-digestion of food and vegetable waste using three stage integrated bioprocess

During two-stage (Acidogenesis-Methanogenesis) process, solid organics and gaseous by-products are usually left unused. To increase resource recovery efficiency, a three stage process (Hydrolysis/Acidogenesis-Methanogenesis-Composting) was designed. Initially, co-digestion of food waste (FW) and vegetable waste (VW) was carried out in Leach Bed Reactor (LBR) for hydrolysis and acidogenesis, followed by airlift reactor (ALR) for methanogenesis for 21 days using two different feed stocks [2:3 FW:VW~FVW; FW alone]. Off gas from LBR was diverted to ALR to enhance methane recovery. Results depicted that volatile fatty acids (VFA) and biohydrogen production was more for FW fed system, while methane production was higher in FVW fed system. Three different functional zones in three separate chambers significantly accelerated organic removal rate while gas diversion increased overall methane recovery. In third stage, residual solid organic matter from LBR was subjected to aerobic composting and compost with N (%): 2.90 & 2.76; C/N ratio: 18.2 & 20.8 for FVW and FW was recovered. The three-stage process has advantages of zero waste generation and overall process stability, accounting for resource efficient circular loop.

Formation of a dynamic membrane altered the microbial community and metabolic flux in fermentative hydrogen production

This study aimed to investigate the relationship among dynamic membrane (DM) formation, metabolic flux, and microbial community population in dark fermentative hydrogen production. A continuously stirred tank reactor was equipped with an external submerged polyester screen mesh and inoculated with heat-treated anaerobic sludge without immobilization. DM was successfully developed on the polyester mesh and provided high-rate hydrogen production at 60.5 L H₂/L.d and 2.39 mol H₂/mol glucose_added. DM formation was along with tightly bound extracellular polymeric substances. Flux balance analysis revealed that formation of DM altered the metabolic pathways for acetic acid production from homoacetogenesis to hydrogenesis. Bacterial community analysis suggested that Sporolactobacillaceae would contributed to this metabolic pathway shift. Nevertheless, lactic acid was not accumulated and assumed to be consumed by hydrogen producers including Clostridia.

Butyric acid: Applications and recent advances in its bioproduction

Butyric acid is an important C4 organic acid with broad applications. It is currently produced by chemosynthesis from petroleum-based feedstocks. However, the fermentative production of butyric acid from renewable feedstocks has received growing attention because of consumer demand for green products and natural ingredients in foods, pharmaceuticals, animal feed supplements, and cosmetics. In this review, strategies for improving microbial butyric acid production, including strain engineering and novel fermentation process development are discussed and compared regarding product yield, titer, purity and productivity. Future perspectives on strain and process improvements for butyric acid production are also discussed.

Production of butyric acid from acid hydrolysate of corn husk in fermentation by Clostridium tyrobutyricum: kinetics and process economic analysis

BACKGROUND

Butyric acid is an important chemical currently produced from petrochemical feedstocks. Its production from renewable, low-cost biomass in fermentation has attracted large attention in recent years. In this study, the feasibility of corn husk, an abundant agricultural residue, for butyric acid production by using Clostridium tyrobutyricum immobilized in a fibrous bed bioreactor (FBB) was evaluated.

RESULTS

Hydrolysis of corn husk (10% solid loading) with 0.4 M H₂SO₄ at 110 °C for 6 h resulted in a hydrolysate containing ~ 50 g/L total reducing sugars (glucose:xylose = 1.3:1.0). The hydrolysate was used for butyric acid fermentation by C. tyrobutyricum in a FBB, which gave 42.6 and 53.0% higher butyric acid production from glucose and xylose, respectively, compared to free-cell fermentations. Fermentation with glucose and xylose mixture (1:1) produced 50.37 ± 0.04 g L^-1 butyric acid with a yield of 0.38 ± 0.02 g g^-1 and productivity of 0.34 ± 0.03 g L^-1 h^-1. Batch fermentation with corn husk hydrolysate produced 21.80 g L^-1 butyric acid with a yield of 0.39 g g^-1, comparable to those from glucose. Repeated-batch fermentations consistently produced 20.75 ± 0.65 g L^-1 butyric acid with an average yield of 0.39 ± 0.02 g g^-1 in three consecutive batches. An extractive fermentation process can be used to produce, separate, and concentrate butyric acid to > 30% (w/v) sodium butyrate at an economically attractive cost for application as an animal feed supplement.

CONCLUSION

A high concentration of total reducing sugars at ~ 50% (w/w) yield was obtained from corn husk after acid hydrolysis. Stable butyric acid production from corn husk hydrolysate was achieved in repeated-batch fermentation with C. tyrobutyricum immobilized in a FBB, demonstrating that corn husk can be used as an economical substrate for butyric acid production.

Biosynthesis of butyric acid by Clostridium tyrobutyricum

Butyric acid (C₃H₇COOH) is an important chemical that is widely used in foodstuffs along with in the chemical and pharmaceutical industries. The bioproduction of butyric acid through large-scale fermentation has the potential to be more economical and efficient than petrochemical synthesis. In this paper, the metabolic pathways involved in the production of butyric acid from Clostridium tyrobutyricum using hexose and pentose as substrates are investigated, and approaches to enhance butyric acid production through genetic modification are discussed. Finally, bioreactor modifications (including fibrous bed bioreactor, inner disk-shaped matrix bioreactor, fibrous matrix packed in porous levitated sphere carriers), low-cost feedstocks, and special treatments (including continuous fermentation with cell recycling, extractive fermentation with solvent, using different artificial electron carriers) intended to improve the feasibility of commercial butyric acid bioproduction are summarized.

Fermentative hydrogen production from Jerusalem artichoke by Clostridium tyrobutyricum expressing exo-inulinase gene

Clostridium tyrobutyricum ATCC25755 has been reported as being able to produce significant quantities of hydrogen. In this study, the exo-inulinase encoding gene cloned from Paenibacillus polymyxa SC-2 was into the expression plasmid pSY6 and expressed in the cells of C. tyrobutyricum. The engineered C. tyrobutyricum strain efficiently fermented the inulin-type carbohydrates from Jerusalem artichoke, without any pretreatment being necessary for the production of hydrogen. A comparatively high hydrogen yield (3.7 mol/mol inulin-type sugar) was achieved after 96 h in a batch process with simultaneous saccharification and fermentation (SSF), with an overall volumetric productivity rate of 620 ± 60 mL/h/L when the initial total sugar concentration of the inulin extract was increased to 100 g/L. Synthesis of inulinase in the batch SSF culture was closely associated with strain growth until the end of the exponential phase, reaching a maximum activity of 28.4 ± 0.26 U/mL. The overall results show that the highly productive and abundant biomass crop Jerusalem artichoke can be a good substrate for hydrogen production, and that the application of batch SSF for its conversion has the potential to become a cost-effective process in the near future.

Butyric acid production from lignocellulosic biomass hydrolysates by engineered Clostridium tyrobutyricum overexpressing xylose catabolism genes for glucose and xylose co-utilization

Clostridium tyrobutyricum can utilize glucose and xylose as carbon source for butyric acid production. However, xylose catabolism is inhibited by glucose, hampering butyric acid production from lignocellulosic biomass hydrolysates containing both glucose and xylose. In this study, an engineered strain of C. tyrobutyricum Ct-pTBA overexpressing heterologous xylose catabolism genes (xylT, xylA, and xylB) was investigated for co-utilizing glucose and xylose present in hydrolysates of plant biomass, including soybean hull, corn fiber, wheat straw, rice straw, and sugarcane bagasse. Compared to the wild-type strain, Ct-pTBA showed higher xylose utilization without significant glucose catabolite repression, achieving near 100% utilization of glucose and xylose present in lignocellulosic biomass hydrolysates in bioreactor at pH 6. About 42.6g/L butyrate at a productivity of 0.56g/L·h and yield of 0.36g/g was obtained in batch fermentation, demonstrating the potential of C. tyrobutyricum Ct-pTBA for butyric acid production from lignocellulosic biomass hydrolysates.

Genome Editing in Clostridium saccharoperbutylacetonicum N1-4 with the CRISPR-Cas9 System

Clostridium saccharoperbutylacetonicum N1-4 is well known as a hyper-butanol-producing strain. However, the lack of genetic engineering tools hinders further elucidation of its solvent production mechanism and development of more robust strains. In this study, we set out to develop an efficient genome engineering system for this microorganism based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated 9 (CRISPR-Cas9) system. First, the functionality of the CRISPR-Cas9 system previously customized for Clostridium beijerinckii was evaluated in C. saccharoperbutylacetonicum by targeting pta and buk, two essential genes for acetate and butyrate production, respectively. pta and buk single and double deletion mutants were successfully obtained based on this system. However, the genome engineering efficiency was rather low (the mutation rate is <20%). Therefore, the efficiency was further optimized by evaluating various promoters for guide RNA (gRNA) expression. With promoter P _J23119 , we achieved a mutation rate of 75% for pta deletion without serial subculturing as suggested previously for C. beijerinckii Thus, this developed CRISPR-Cas9 system is highly desirable for efficient genome editing in C. saccharoperbutylacetonicum Batch fermentation results revealed that both the acid and solvent production profiles were altered due to the disruption of acid production pathways; however, neither acetate nor butyrate production was eliminated with the deletion of the corresponding gene. The butanol production, yield, and selectivity were improved in mutants, depending on the fermentation medium. In the pta buk double deletion mutant, the butanol production in P2 medium reached 19.0 g/liter, which is one of the highest levels ever reported from batch fermentations.IMPORTANCE An efficient CRISPR-Cas9 genome engineering system was developed for C. saccharoperbutylacetonicum N1-4. This paves the way for elucidating the solvent production mechanism in this hyper-butanol-producing microorganism and developing strains with desirable butanol-producing features. This tool can be easily adapted for use in closely related microorganisms. As also reported by others, here we demonstrated with solid data that the highly efficient expression of gRNA is the key factor determining the efficiency of CRISPR-Cas9 for genome editing. The protocol developed in this study can provide essential references for other researchers who work in the areas of metabolic engineering and synthetic biology. The developed mutants can be used as excellent starting strains for development of more robust ones for desirable solvent production.

The acquisition of Clostridium tyrobutyricum mutants with improved bioproduction under acidic conditions after two rounds of heavy-ion beam irradiation

End-product inhibition is a key factor limiting the production of organic acid during fermentation. Two rounds of heavy-ion beam irradiation may be an inexpensive, indispensable and reliable approach to increase the production of butyric acid during industrial fermentation processes. However, studies of the application of heavy ion radiation for butyric acid fermentation engineering are lacking. In this study, a second ¹²C⁶⁺ heavy-ion irradiation-response curve is used to describe the effect of exposure to a given dose of heavy ions on mutant strains of Clostridium tyrobutyricum. Versatile statistical elements are introduced to characterize the mechanism and factors contributing to improved butyric acid production and enhanced acid tolerance in adapted mutant strains harvested from the fermentations. We characterized the physiological properties of the strains over a large pH value gradient, which revealed that the mutant strains obtained after a second round of radiation exposure were most resistant to harsh external pH values and were better able to tolerate external pH values between 4.5 and 5.0. A customized second round of heavy-ion beam irradiation may be invaluable in process engineering.

Carbon material distribution and flux analysis under varying glucose concentrations in hydrogen-producing Clostridium tyrobutyricum JM1

Anaerobic glucose metabolism in hydrogen-producing Clostridium tyrobutyricum was investigated in batch culture with varying initial glucose concentrations (27.8-333.6mM). To understand the regulation of metabolism, the carbon material and reduction balances were applied to estimate the carbon flux distribution for the first time, and metabolic flux analysis (MFA) was used to provide qualitative information and guidance for effective metabolic design. The overall flux distribution suggested that C. tyrobutyricum metabolism has a high capacity for the production of butyrate and hydrogen at an initial glucose concentration of 222.4mM, with balanced activities of NADH and ATP.

Butanol production under microaerobic conditions with a symbiotic system of Clostridium acetobutylicum and Bacillus cereus

BACKGROUND

One major problem of ABE (acetone, butanol and ethanol) fermentation is high oxygen sensitivity of Clostridium acetobutylicum. Currently, no single strain has been isolated or genetically engineered to produce butanol effectively under aerobic conditions. In our previous work, a symbiotic system TSH06 has been developed successfully by our group, and two strains, C. acetobutylicum TSH1 and Bacillus cereus TSH2, were isolated from TSH06.

RESULTS

Compared with single culture, TSH06 showed promotion on cell growth and solvent accumulation under microaerobic conditions. To simulate TSH06, a new symbiotic system was successfully re-constructed by adding living cells of B. cereus TSH2 into C. acetobutylicum TSH1 cultures. During the fermentation process, the function of B. cereus TSH2 was found to deplete oxygen and provide anaerobic environment for C. acetobutylicum TSH1. Furthermore, inoculation ratio of C. acetobutylicum TSH1 and B. cereus TSH2 affected butanol production. In a batch fermentation with optimized inoculation ratio of 5 % C. acetobutylicum TSH1 and 0.5 % B. cereus TSH2, 11.0 g/L butanol and 18.1 g/L ABE were produced under microaerobic static condition. In contrast to the single culture of C. acetobutylicum TSH1, the symbiotic system became more aerotolerant and was able to produce 11.2 g/L butanol in a 5 L bioreactor even with continuous 0.15 L/min air sparging. In addition, qPCR assay demonstrated that the abundance of B. cereus TSH2 increased quickly at first and then decreased sharply to lower than 1 %, whereas C. acetobutylicum TSH1 accounted for more than 99 % of the whole population in solventogenic phase.

CONCLUSIONS

The characterization of a novel symbiotic system on butanol fermentation was studied. The new symbiotic system re-constructed by co-culture of C. acetobutylicum TSH1 and B. cereus TSH2 showed excellent performance on butanol production under microaerobic conditions. B. cereus TSH2 was a good partner for C. acetobutylicum TSH1 by providing an anaerobic environment. During fermentation process, the high ratio of Clostridium and low ratio of Bacillus composition indicated that this symbiotic system was an effective and easily controlled cultivation model for ABE fermentation under microaerobic conditions.

Rebalancing Redox to Improve Biobutanol Production by Clostridium tyrobutyricum

Biobutanol is a sustainable green biofuel that can substitute for gasoline. Carbon flux has been redistributed in Clostridium tyrobutyricum via metabolic cell engineering to produce biobutanol. However, the lack of reducing power hampered the further improvement of butanol production. The objective of this study was to improve butanol production by rebalancing redox. Firstly, a metabolically-engineered mutant CTC-fdh-adhE2 was constructed by introducing heterologous formate dehydrogenase (fdh) and bifunctional aldehyde/alcohol dehydrogenase (adhE2) simultaneously into wild-type C. tyrobutyricum. The mutant evaluation indicated that the fdh-catalyzed NADH-producing pathway improved butanol titer by 2.15-fold in the serum bottle and 2.72-fold in the bioreactor. Secondly, the medium supplements that could shift metabolic flux to improve the production of butyrate or butanol were identified, including vanadate, acetamide, sodium formate, vitamin B12 and methyl viologen hydrate. Finally, the free-cell fermentation produced 12.34 g/L of butanol from glucose using the mutant CTC-fdh-adhE2, which was 3.88-fold higher than that produced by the control mutant CTC-adhE2. This study demonstrated that the redox engineering in C. tyrobutyricum could greatly increase butanol production.

Butyric acid fermentation from pretreated and hydrolysed wheat straw by an adapted Clostridium tyrobutyricum strain

Butyric acid is a valuable building-block for the production of chemicals and materials and nowadays it is produced exclusively from petroleum. The aim of this study was to develop a suitable and robust strain of Clostridium tyrobutyricum that produces butyric acid at a high yield and selectivity from lignocellulosic biomasses. Pretreated (by wet explosion) and enzymatically hydrolysed wheat straw (PHWS), rich in C6 and C5 sugars (71.6 and 55.4 g l⁻¹ of glucose and xylose respectively), was used as substrate. After one year of serial selections, an adapted strain of C. tyrobutyricum was developed. The adapted strain was able to grow in 80% (v v⁻¹) PHWS without addition of yeast extract compared with an initial tolerance to less than 10% PHWS and was able to ferment both glucose and xylose. It is noticeable that the adapted C. tyrobutyricum strain was characterized by a high yield and selectivity to butyric acid. Specifically, the butyric acid yield at 60–80% PHWS lie between 0.37 and 0.46 g g⁻¹ of sugar, while the selectivity for butyric acid was as high as 0.9–1.0 g g⁻¹ of acid. Moreover, the strain exhibited a robust response in regards to growth and product profile at pH 6 and 7.

2-Keto acids based biosynthesis pathways for renewable fuels and chemicals

Global energy and environmental concerns have driven the development of biological chemical production from renewable sources. Biological processes using microorganisms are efficient and have been traditionally utilized to convert biomass (i.e., glucose) to useful chemicals such as amino acids. To produce desired fuels and chemicals with high yield and rate, metabolic pathways have been enhanced and expanded with metabolic engineering and synthetic biology approaches. 2-Keto acids, which are key intermediates in amino acid biosynthesis, can be converted to a wide range of chemicals. 2-Keto acid pathways were engineered in previous research efforts and these studies demonstrated that 2-keto acid pathways have high potential for novel metabolic routes with high productivity. In this review, we discuss recently developed 2-keto acid-based pathways.

Converting carbon dioxide to butyrate with an engineered strain of Clostridium ljungdahlii

Microbial conversion of carbon dioxide to organic commodities via syngas metabolism or microbial electrosynthesis is an attractive option for production of renewable biocommodities. The recent development of an initial genetic toolbox for the acetogen Clostridium ljungdahlii has suggested that C. ljungdahlii may be an effective chassis for such conversions. This possibility was evaluated by engineering a strain to produce butyrate, a valuable commodity that is not a natural product of C. ljungdahlii metabolism. Heterologous genes required for butyrate production from acetyl-coenzyme A (CoA) were identified and introduced initially on plasmids and in subsequent strain designs integrated into the C. ljungdahlii chromosome. Iterative strain designs involved increasing translation of a key enzyme by modifying a ribosome binding site, inactivating the gene encoding the first step in the conversion of acetyl-CoA to acetate, disrupting the gene which encodes the primary bifunctional aldehyde/alcohol dehydrogenase for ethanol production, and interrupting the gene for a CoA transferase that potentially represented an alternative route for the production of acetate. These modifications yielded a strain in which ca. 50 or 70% of the carbon and electron flow was diverted to the production of butyrate with H2 or CO as the electron donor, respectively. These results demonstrate the possibility of producing high-value commodities from carbon dioxide with C. ljungdahlii as the catalyst. Importance: The development of a microbial chassis for efficient conversion of carbon dioxide directly to desired organic products would greatly advance the environmentally sustainable production of biofuels and other commodities. Clostridium ljungdahlii is an effective catalyst for microbial electrosynthesis, a technology in which electricity generated with renewable technologies, such as solar or wind, powers the conversion of carbon dioxide and water to organic products. Other electron donors for C. ljungdahlii include carbon monoxide, which can be derived from industrial waste gases or the conversion of recalcitrant biomass to syngas, as well as hydrogen, another syngas component. The finding that carbon and electron flow in C. ljungdahlii can be diverted from the production of acetate to butyrate synthesis is an important step toward the goal of renewable commodity production from carbon dioxide with this organism.

Blocking the butyrate-formation pathway impairs hydrogen production in Clostridium perfringens

Inactivating competitive pathways will improve fermentative hydrogen production by obligate anaerobes, such as those of genus Clostridium. In our previous study, the hydrogen yield of Clostridium perfringens W13 in which l-lactate dehydrogenase was inactivated increased by 44% when compared with its original strain W12. In this study, we explored whether blocking butyrate formation pathway would increase hydrogen yield. The acetyl-CoA acetyltransferase gene (atoB) encodes the first enzyme in this pathway, which ultimately forms butyrate. Clostridium perfringens W14 and W15 were constructed by inactivating atoB in W13 and W12, respectively. The hydrogen yield of W14 and W15 was 44% and 33% of those of W13 and W12, respectively. Inactivation of atoB decreased the pyruvate synthesis and its conversion to acetyl-CoA in both mutants, and increased ethanol formation in W14 and W15. Proteomic analysis revealed that the expressions of five proteins involved in butyrate formation pathway were up-regulated in W14. Our results suggest that butyrate formation deficiency improved ethanol production but not hydrogen production, indicating the importance of butyrate formation pathway for hydrogen production in C. perfringens.

Co-culturing a novel Bacillus strain with Clostridium tyrobutyricum ATCC 25755 to produce butyric acid from sucrose

BACKGROUND

Currently, the most promising microorganism used for the bio-production of butyric acid is Clostridium tyrobutyricum ATCC 25755T; however, it is unable to use sucrose as a sole carbon source. Consequently, a newly isolated strain, Bacillus sp. SGP1, that was found to produce a levansucrase enzyme, which hydrolyzes sucrose into fructose and glucose, was used in a co-culture with this strain, permitting C. tyrobutyricum ATCC 25755T to ferment sucrose to butyric acid.

RESULTS

B. sp. SGP1 alone did not show any butyric acid production and the main metabolite produced was lactic acid. This allowed C. tyrobutyricum ATCC 25755T to utilize the monosaccharides resulting from the activity of levansucrase together with the lactic acid produced by B. sp. SGP1 to generate butyric acid, which was the main fermentative product within the co-culture. Furthermore, the final acetic acid concentration in the co-culture was significantly lower when compared with pure C. tyrobutyricum ATCC 25755T cultures grown on glucose. In fed-batch fermentations, the optimum conditions for the production of butyric acid were around pH 5.50 and a temperature of 37°C. Under these conditions, the final butyrate concentration was 34.2±1.8 g/L with yields of 0.35±0.03 g butyrate/g sucrose and maximum productivity of 0.3±0.04 g/L/h.

CONCLUSIONS

Using this co-culture, sucrose can be utilized as a carbon source for butyric acid production at a relatively high yield. In addition, this co-culture offers also the benefit of a greater selectivity, with butyric acid constituting 92.8% of the acids when the fermentation was terminated.

Acetate adaptation of clostridia tyrobutyricum for improved fermentation production of butyrate

Clostridium tyrobutyricum ATCC 25755 is an acidogenic bacterium capable of utilizing xylose for the fermentation production of butyrate. Hot water extraction of hardwood lingocellulose is an efficient method of producing xylose where autohydrolysis of xylan is catalysed by acetate originating from acetyl groups present in hemicellulose. The presence of acetic acid in the hydrolysate might have a severe impact on the subsequent fermentations. In this study the fermentation kinetics of C. tyrobutyricum cultures after being classically adapted for growth at 26.3 g/L acetate equivalents were studied. Analysis of xylose batch fermentations found that even in the presence of high levels of acetate, acetate adapted strains had similar fermentation kinetics as the parental strain cultivated without acetate. The parental strain exposed to acetate at inhibitory conditions demonstrated a pronounced lag phase (over 100 hours) in growth and butyrate production as compared to the adapted strain (25 hour lag) or non-inhibited controls (0 lag).

Additional insight into the metabolic pathway of xylose consumption was gained by determining the specific activity of the acetate kinase (AK) enzyme in adapted versus control batches. AK activity was reduced by 63% in the presence of inhibitory levels of acetate, whether or not the culture had been adapted.