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

Efficient methane fermentation from the waste of a novel straw alkali-heat pretreatment-butyric acid fermentation process

ABSTRACTThe butyric acid biorefinery technology for straw is highly significant for environmental protection and the restructuring of the energy system. However, this process produces waste from alkali-heat pretreatment (PW) and butyric acid fermentation (FW). In this study, the feasibility of methane fermentation from the wastes was confirmed, with the methane production from PW and FW of 351.1 ± 11.8 and 741.5 ± 14.2 mLCH4/gVS, respectively. The initial pH and VFW/VPW of methane fermentation using the mixed waste of PW and FW were optimized at 7.5 and 1.8, respectively. The methane fermentation using the mixed waste was also verified by operating two anaerobic digesters in sequencing batch mode. At the VFW/VPW of 0.25 (actual ratio), methane production was 301.20 mLCH4/gVS with the waste load of 0.64 kgVS/m³/d. When the VFW/VPW was 1.8 (optimal ratio), methane production reached 396.45 mLCH4/gVS at the waste load of 1.20 kgVS/m3/d. This study facilitates the comprehensive utilization of all components within rice straw.

Microbial Cell Factories in the Bioeconomy Era: From Discovery to Creation

Microbial cell factories (MCFs) are extensively used to produce a wide array of bioproducts, such as bioenergy, biochemical, food, nutrients, and pharmaceuticals, and have been regarded as the "chips" of biomanufacturing that will fuel the emerging bioeconomy era. Biotechnology advances have led to the screening, investigation, and engineering of an increasing number of microorganisms as diverse MCFs, which are the workhorses of biomanufacturing and help develop the bioeconomy. This review briefly summarizes the progress and strategies in the development of robust and efficient MCFs for sustainable and economic biomanufacturing. First, a comprehensive understanding of microbial chassis cells, including accurate genome sequences and corresponding annotations; metabolic and regulatory networks governing substances, energy, physiology, and information; and their similarity and uniqueness compared with those of other microorganisms, is needed. Moreover, the development and application of effective and efficient tools is crucial for engineering both model and nonmodel microbial chassis cells into efficient MCFs, including the identification and characterization of biological parts, as well as the design, synthesis, assembly, editing, and regulation of genes, circuits, and pathways. This review also highlights the necessity of integrating automation and artificial intelligence (AI) with biotechnology to facilitate the development of future customized artificial synthetic MCFs to expedite the industrialization process of biomanufacturing and the bioeconomy.

Production of a Bacteriocin Like Protein PEG 446 from Clostridium tyrobutyricum NRRL B-67062

Clostridium tyrobutyricum strain NRRL B-67062 was previously isolated from an ethanol production facility and shown to produce high yields of butyric acid. In addition, the cell-free supernatant of the fermentation broth from NRRL B-67062 contained antibacterial activity against certain Gram-positive bacteria. To determine the source of this antibacterial activity, we report the genome and genome mining of this strain. The complete genome of NRRL B-67062 showed one circular chromosome of 3,242,608 nucleotides, 3114 predicted coding sequences, 79 RNA genes, and a G+C content of 31.0%. Analyses of the genome data for genes potentially associated with antimicrobial features were sought after by using BAGEL-4 and anti-SMASH databases. Among the leads, a polypeptide of 66 amino acids (PEG 446) contains the DUF4177 domain, which is an uncharacterized highly conserved domain (pfam13783). The cloning and expression of the peg446 gene in Escherichia coli and Bacillus subtilis confirmed the antibacterial property against Lactococcus lactis LM 0230, Limosilactobacillus fermentum 0315-25, and Listeria innocua NRRL B-33088 by gel overlay and well diffusion assays. Molecular modeling suggested that PEG 446 contains one alpha-helix and three anti-parallel short beta-sheets. These results will aid further functional studies and facilitate simultaneously fermentative production of both butyric acid and a putative bacteriocin from agricultural waste and lignocellulosic biomass materials.

Metabolic and Bioprocess Engineering of Clostridium tyrobutyricum for Butyl Butyrate Production on Xylose and Shrimp Shell Waste

Microbial conversion of agri-food waste to valuable compounds offers a sustainable route to develop the bioeconomy and contribute to sustainable biorefinery. Clostridium tyrobutyricum displays a series of native traits suitable for high productivity conversion of agri-food waste, which make it a promising host for the production of various compounds, such as the short-chain fatty acids and their derivative esters products. In this study, a butanol synthetic pathway was constructed in C. tyrobutyricum, and then efficient butyl butyrate production through in situ esterification was achieved by the supplementation of lipase into the fermentation. The butyryl-CoA/acyl-CoA transferase (cat1) was overexpressed to balance the ratio between precursors butyrate and butanol. Then, a suitable fermentation medium for butyl butyrate production was obtained with xylose as the sole carbon source and shrimp shell waste as the sole nitrogen source. Ultimately, 5.9 g/L of butyl butyrate with a selectivity of 100%, and a productivity of 0.03 g/L·h was achieved under xylose and shrimp shell waste with batch fermentation in a 5 L bioreactor. Transcriptome analyses exhibited an increase in the expression of genes related to the xylose metabolism, nitrogen metabolism, and amino acid metabolism and transport, which reveal the mechanism for the synergistic utilization of xylose and shrimp shell waste. This study presents a novel approach for utilizing xylose and shrimp shell waste to produce butyl butyrate by using an anaerobic fermentative platform based on C. tyrobutyricum. This innovative fermentation medium could save the cost of nitrogen sources (~97%) and open up possibilities for converting agri-food waste into other high-value products.

Engineering of Clostridium tyrobutyricum for butyric acid and butyl butyrate production from cassava starch

Clostridium tyrobutyricum has been successfully engineered to produce butyrate, butanol, butyl butyrate, and γ-aminobutyric acid. It would be interesting to produce bio-chemicals and bio-fuels directly using starch from non-food crop, e.g., cassava, by engineered C. tyrobutyricum. In this study, heterologous α-amylases were screened and expressed in C. tyrobutyricum, resulting in successfully starch hydrolyzation. Furthermore, α-glucosidase (AgluI) was co-expressed with α-amylases, resulting in enhancement in the capacity of starch hydrolyzation and butyrate production. When increasing the cassava starch concentration to 100 g/L, the engineered strain CTAA05 produced 27.0 g/L butyrate. In addition, when introducing butyl butyrate synthetic pathway, strain MU3-AAV produced 26.8 g/L butyl butyrate with 100 g/L cassava starch as substrate. This study showed a generalizable framework to engineered anaerobes for anaerobic production of bio-chemicals and bio-fuels from starchy biomass.

Anaerobic fermentation of organic solid waste: Recent updates in substrates, products, and the process with multiple products co-production

The effective conversion and recycling of organic solid waste contribute to the resolution of widespread issues such as global environmental pollution, energy scarcity and resource depletion. The anaerobic fermentation technology provides for the effective treatment of organic solid waste and the generation of various products. The analysis, which is based on bibliometrics, concentrates on the valorisation of affordable and easily accessible raw materials with high organic matter content as well as the production of clean energy substances and high value-added platform products. The processing and application status of fermentation raw materials such as waste activated sludge, food waste, microalgae and crude glycerol are investigated. To analyse the status of the preparation and engineering applications of the products, the fermentation products biohydrogen, VFAs, biogas, ethanol, succinic acid, lactic acid, and butanol are employed as representatives. Simultaneously, the anaerobic biorefinery process with multiple product co-production is sorted out. Product co-production can reduce waste discharge, enhance resource recovery efficiency, and serve as a model for improving anaerobic fermentation economics.

De novo biosynthesis of butyl butyrate in engineered Clostridium tyrobutyricum

Butyl butyrate has broad applications in foods, cosmetics, solvents, and biofuels. Microbial synthesis of bio-based butyl butyrate has been regarded as a promising approach recently. Herein, we engineered Clostridium tyrobutyricum ATCC 25755 to achieve de novo biosynthesis of butyl butyrate from fermentable sugars. Through introducing the butanol synthetic pathway (enzyme AdhE2), screening alcohol acyltransferases (AATs), adjusting transcription of VAAT and adhE2 (i.e., optimizing promoter), and efficient supplying butyryl-CoA, an excellent engineered strain, named MUV3, was obtained with ability to produce 4.58 g/L butyl butyrate at 25 °C with glucose in serum bottles. More NADH is needed for butyl butyrate synthesis, thus mannitol (the more reduced substrate) was employed to produce butyl butyrate. Ultimately, 62.59 g/L butyl butyrate with a selectivity of 95.97%, and a yield of 0.21 mol/mol was obtained under mannitol with fed-batch fermentation in a 5 L bioreactor, which is the highest butyl butyrate titer reported so far. Altogether, this study presents an anaerobic fermentative platform for de novo biosynthesis of butyl butyrate in one step, which lays the foundation for butyl butyrate biosynthesis from renewable biomass feedstocks.

Metabolic Engineering of Microorganisms to Produce Pyruvate and Derived Compounds

Pyruvate is a hub of various endogenous metabolic pathways, including glycolysis, TCA cycle, amino acid, and fatty acid biosynthesis. It has also been used as a precursor for pyruvate-derived compounds such as acetoin, 2,3-butanediol (2,3-BD), butanol, butyrate, and L-alanine biosynthesis. Pyruvate and derivatives are widely utilized in food, pharmaceuticals, pesticides, feed additives, and bioenergy industries. However, compounds such as pyruvate, acetoin, and butanol are often chemically synthesized from fossil feedstocks, resulting in declining fossil fuels and increasing environmental pollution. Metabolic engineering is a powerful tool for producing eco-friendly chemicals from renewable biomass resources through microbial fermentation. Here, we review and systematically summarize recent advances in the biosynthesis pathways, regulatory mechanisms, and metabolic engineering strategies for pyruvate and derivatives. Furthermore, the establishment of sustainable industrial synthesis platforms based on alternative substrates and new tools to produce these compounds is elaborated. Finally, we discuss the potential difficulties in the current metabolic engineering of pyruvate and derivatives and promising strategies for constructing efficient producers.

Deciphering of the Mannitol Metabolism Pathway in Clostridium tyrobutyricum ATCC 25755 by Comparative Transcriptome Analysis

Clostridium tyrobutyricum has great potential for bio-based chemicals and biofuel production from mannitol; however, the mannitol metabolic pathway and its metabolic regulatory mechanism have not been elucidated. To this end, the RNA-seq analysis on the mid-log growth phase of C. tyrobutyricum grown on mannitol or xylose was performed. Comparative transcriptome analysis and co-transcription experiment indicated that mtlARFD, which encodes the mannitol-specific IIA component, transcription activator, mannitol-specific IIBC components, and mannitol-1-phosphate 5-dehydrogenase, respectively, formed a polycistronic operon and could be responsible for mannitol uptake and metabolism. In addition, comparative genomic analysis of the mtlARFD organization and the MtlR protein structural domain among various Firmicutes strains identified the putative cre (catabolite-responsive element) sites and conserved phosphorylation sites, but whether the expression of mannitol operon was affected by CcpA- and MtlR-mediated metabolic regulation during mixed substrate fermentation needs to be further verified experimentally. Based on the gene knockout and complementation results, the predicted mannitol operon mtlARFD was confirmed to be responsible for mannitol utilization in C. tyrobutyricum. The results of this study could be used to enhance the mannitol metabolic pathway and explore the potential metabolic regulation mechanism of mannitol during mixed substrate fermentation.

Clostridium as microbial cell factory to enable the sustainable utilization of three generations of feedstocks

The sustainable production of chemicals and biofuels from non-fossil carbon sources is considered key to reducing greenhouse gas (GHG) emissions. Clostridium sp. can convert various substrates, including the 1st-generation (biomass crops), the 2nd-generation (lignocellulosic biomass), and the 3rd-generation (C1 gases) feedstocks, into high-value products, which makes Clostridia attractive for biorefinery applications. However, the complexity of lignocellulosic catabolism and C1 gas utilization make it difficult to construct efficient production routes. Accordingly, this review highlights the advances in the development of three generations of feedstocks with Clostridia as cell factories. At the same time, more attention was given to using agro-industrial wastes (lignocelluloses and C1 gases) as the feedstocks, for which metabolic and process engineering efforts were comprehensively analyzed. In addition, the challenges of using agro-industrial wastes are also discussed. Lastly, several new synthetic biology tools and regulatory strategies are emphasized as promising technologies to be developed to address the aforementioned challenges in Clostridia and realize the efficient utilization of agro-industrial wastes.

Exploiting the Type I-B CRISPR Genome Editing System in Thermoanaerobacterium aotearoense SCUT27 and Engineering the Strain for Enhanced Ethanol Production

Thermoanaerobacterium aotearoense strain SCUT27 is a potential industrial biofuel-producing strain because of its broad substrate spectrum, especially the ability to co-use glucose and xylose. The bottleneck hindering the development of strain SCUT27 is the lack of selective markers for polygene manipulation in this thermophilic bacterium. In this study, the endogenous type I-B clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system was developed for multiplex genome editing of strain SCUT27. The protospacer-adjacent motif was identified by in silico analysis and verified with orotidine-5'-phosphate decarboxylase (pyrF) or lactate dehydrogenase (ldh) as the editing target. The type I-B CRISPR/Cas system was functional in strain SCUT27 with 58.3% to 100% editing efficiency. A multiplex genome editing method based on thymidine kinase (tdk) as a negative selection marker was developed, and strain SCUT27/Δtdk/Δldh/ΔargR, in which ldh and the arginine repressor (argR) were knocked out successively, was successfully obtained. Strain SCUT27/Δtdk/Δldh/ΔargR exhibited prominent advantages over wild-type SCUT27 in ethanol production, with significantly improved ability to metabolize xylose. IMPORTANCE Thermophilic microbes have attracted great attention as potential candidates for production of biofuels and chemicals from lignocellulose because of their thermal tolerance and wide substrate spectra. The ability to edit multiple genes using the native type I-B CRISPR/Cas system would speed up engineering of Thermoanaerobacterium aotearoense strain SCUT27 for higher ethanol production from lignocellulosic hydrolysates. Here, we produced a mutant strain, T. aotearoense SCUT27/Δtdk/Δldh/ΔargR, using the native CRISPR/Cas system. The engineered strain showed satisfactory performance with improved ethanol productivity from various lignocellulosic hydrolysates. Our data lay the foundations for development of this thermophilic microbe into an excellent ethanol producer using lignocellulosic hydrolysates. The methods described here may also provide a reference to develop multigene editing methods for other microorganisms.

Elimination of carbon catabolite repression in Clostridium tyrobutyricum for enhanced butyric acid production from lignocellulosic hydrolysates

Clostridium tyrobutyricum, a gram-positive anaerobic bacterium, is recognized as the promising butyric acid producer. But, the existence of carbon catabolite repression (CCR) is the major drawback for C. tyrobutyricum to efficiently use the lignocellulosic biomass. In this study, the xylose pathway genes were first identified and verified. Then, the potential regulatory mechanisms of CCR in C. tyrobutyricum were proposed and the predicted engineering targets were experimental validated. Inactivation of hprK blocked the CcpA-mediated CCR and resulted in simultaneous conversion of glucose and xylose, although xylose consumption was severe lagging behind. Deletion of xylR further shortened the lag phase of xylose utilization. When hprK and xylR were inactivated together, the CCR in C. tyrobutyricum was completely eliminated. Consequently, ATCC 25755/ΔhprKΔxylR showed significant increase in butyrate productivity (1.8 times faster than the control) and excellent butyric acid fermentation performance using both mixed sugars (11.0-11.9 g/L) and undetoxified lignocellulosic hydrolysates (12.4-13.4 g/L).

Rewiring the microbial metabolic network for efficient utilization of mixed carbon sources

Carbon sources represent the most dominant cost factor in the industrial biomanufacturing of products. Thus, it has attracted much attention to seek cheap and renewable feedstocks, such as lignocellulose, crude glycerol, methanol, and carbon dioxide, for biosynthesis of value-added compounds. Co-utilization of these carbon sources by microorganisms not only can reduce the production cost but also serves as a promising approach to improve the carbon yield. However, co-utilization of mixed carbon sources usually suffers from a low utilization rate. In the past few years, the development of metabolic engineering strategies to enhance carbon source co-utilization efficiency by inactivation of carbon catabolite repression has made significant progress. In this article, we provide informative and comprehensive insights into the co-utilization of two or more carbon sources including glucose, xylose, arabinose, glycerol, and C1 compounds, and we put our focus on parallel utilization, synergetic utilization, and complementary utilization of different carbon sources. Our goal is not only to summarize strategies of co-utilization of carbon sources, but also to discuss how to improve the carbon yield and the titer of target products.

Soybean hulls as carbohydrate feedstock for medium to high-value biomolecule production in biorefineries: A review

Soybean is one of the major world crops, with an annual production of 359 million tons. Each ton of processed soybean generates 50-80 kg of soybean hulls (SHs), representing 5-8% of the whole seed. Due to environmental concerns and great economic potential, the search of SHs re-use solutions are deeply discussed. The lignocellulosic composition of SHs has attracted the attention of the scientific and productive sector. Recently, some studies have reported the use of SHs in the production of medium to high value-added molecules, with potential applications in food and feed, agriculture, bioenergy, and other segments. This review presents biotechnological approaches and processes for the management and exploitation of SHs, including pre-treatment methods and fermentation techniques, for the production of different biomolecules. Great potentialities and innovations were found concerning SH exploration and valorisation of the soybean chain under a biorefinery and circular bioeconomy optic.

Paradigm shift in xylose isomerase usage: a novel scenario with distinct applications

Isomerases are enzymes that induce physical changes in a molecule without affecting the original molecular formula. Among this class of enzymes, xylose isomerases (XIs) are the most studied to date, partly due to their extensive application in industrial processes to produce high-fructose corn sirups. In recent years, the need for sustainable initiatives has triggered efforts to improve the biobased economy through the use of renewable raw materials. In this context, D-xylose usage is crucial as it is the second-most abundant sugar in nature. The application of XIs in biotransforming xylose, enabling downstream metabolism in several microorganisms, is a smart strategy for ensuring a low-carbon footprint and producing several value-added biochemicals with broad industrial applications such as in the food, cosmetics, pharmaceutical, and polymer industries. Considering recent advancements that have expanded the range of applications of XIs, this review provides a comprehensive and concise overview of XIs, from their primary sources to the biochemical and structural features that influence their mechanisms of action. This comprehensive review may help address the challenges involved in XI applications in different industries and facilitate the exploitation of xylose bioprocesses.

Butanol production from Saccharina japonica hydrolysate by engineered Clostridium tyrobutyricum: The effects of pretreatment method and heat shock protein overexpression

Macroalgal biomass is currently considered as a potential candidate for biofuel production. In this study, the effects of pretreatment method and heat shock protein overexpression were investigated for efficient butanol production from Saccharina japonica using engineered Clostridium tyrobutyricum. First, various pretreatment methods including acid hydrolysis, acid hydrolysis and enzymatic saccharification, and ultrasonic-assisted acid hydrolysis were employed to obtain the fermentable sugars, and the resulted hydrolysates were evaluated for butanol fermentation. The results showed that ultrasonic-assisted acid hydrolysate obtained the highest butanol yield (0.26 g/g) and productivity (0.19 g/L⋅h). Then, the effects of homologous or heterologous heat shock protein overexpression on butanol production and tolerance were examined. Among all the engineered strains, Ct-pMA12G exhibited improved butanol tolerance and enhanced butanol production (12.15 g/L butanol with a yield of 0.34 g/g and productivity of 0.15 g/L⋅h) from 1.8-fold concentrated S. japonica hydrolysate, which was the highest level ever reported for macroalgal biomass.

Efficient simultaneous utilization of glucose and xylose from corn straw by Sphingomonas sanxanigenens NX02 to produce microbial exopolysaccharide

Lignocellulosic biomass is a cheap and abundant carbon source in the microbial manufacturing industry. The native co-utilization of glucose and xylose from corn straw total hydrolysate (CSTH) by Sphingomonas sanxanigenens NX02 to produce exopolysaccharide Sanxan was investigated. Batch fermentation demonstrated that, compared to single sugar fermentation, co-substrate of glucose and xylose accelerated cell growth and Sanxan production in the initial 24 h with the same consumption rate. Additionally, NX02 converted CSTH into Sanxan with a yield of 13.10 ± 0.35 g/Kg, which is slightly higher than that of glucose fermentation. Coexistence of three xylose metabolic pathways (Xylose isomerase, Weimberg, and Dahms pathway), incomplete phosphoenolpyruvate-dependent phosphotransferase system, and reinforced fructose metabolism were recognized as the co-utilization mechanism through comparative transcriptome analysis. Therefore, strain NX02 has a prospect of becoming an attractive platform organism to produce polysaccharides and other bio-based products derived from agricultural waste hydrolysate rich in both glucose and xylose.

Effects of benzyl viologen on increasing NADH availability, acetate assimilation, and butyric acid production by Clostridium tyrobutyricum

Clostridium tyrobutyricum produces butyric and acetic acids from glucose. The butyric acid yield and selectivity in the fermentation depend on NADH available for acetate reassimilation to butyric acid. In this study, benzyl viologen (BV), an artificial electron carrier that inhibits hydrogen production, was used to increase NADH availability and butyric acid production while eliminating acetic acid accumulation by facilitating its reassimilation. To better understand the mechanism of and find the optimum condition for BV effect on enhancing acetate assimilation and butyric acid production, BV at various concentrations and addition times during the fermentation were studied. Compared with the control without BV, the addition of 1 μM BV increased butyric acid production from glucose by ∼50% in yield and ∼29% in productivity while acetate production was completely inhibited. Furthermore, BV also increased the coutilization of glucose and exogenous acetate for butyric acid production. At a concentration ratio of acetate (g/L) to BV (mM) of 4, both acetate assimilation and butyrate biosynthesis increased with increasing the concentrations of BV (0-6.25 μM) and exogenous acetate (0-25 g/L). In a fed-batch fermentation with glucose and ∼15 g/L acetate and 3.75 μM BV, butyrate production reached 55.9 g/L with productivity 0.93 g/L/h, yield 0.48 g/g, and 97.4% purity, which would facilitate product purification and reduce production cost. Manipulating metabolic flux and redox balance via BV and acetate addition provided a simple to implement metabolic process engineering approach for butyric acid production from sugars and biomass hydrolysates.

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.

Increased Selectivity for Butanol in Clostridium Pasteurianum Fermentations via Butyric Acid Addition or Dual Feedstock Strategy

Volatility of the petroleum market has renewed research into butanol as an alternate fuel. In order to increase the selectivity for butanol during glycerol fermentation with Clostridium pasteurianum, butyric acid can be added to the medium. In this manuscript, different methods of extracellular butyric acid addition are explored, as well as self-generation of butyric acid fermented from sugars in a co-substrate strategy. Molasses was used as an inexpensive sugar substrate, and the optimal molasses to glycerol ratio was found to allow the butyric acid to be taken back up into the cells and increase the productivity of butanol from all carbon sources. When butyric acid is added directly into the media, there was no significant difference between chemically pure butyric acid, or butyric acid rich supernatant from a separate fermentation. When low concentrations of butyric acid (1 or 2 g/L) are added to the initial media, an inhibitory effect is observed, with no influence on the butanol selectivity. However, when added later to the fermentation, over 1 g/L butyric acid is taken into the cells and increased the relative carbon yield from 0.449 to 0.519 mols carbon in product/mols carbon in substrate. An optimized dual substrate fermentation strategy in a pH-controlled reactor resulted in the relative carbon yield rising from 0.439 when grown on solely glycerol, to 0.480 mols C product/mols C substrate with the dual substrate strategy. An additional benefit is the utilization of a novel source of sugars to produce butanol from C. pasteurianum. The addition of butyric acid, regardless of how it is generated, under the proper conditions can allow for increased selectivity for butanol from all substrates.

Pretreatment and Detoxification of Acid-Treated Wood Hydrolysates for Pyruvate Production by an Engineered Consortium of Escherichia coli

The biorefinery concept makes use of renewable lignocellulosic biomass to produce commodities sustainably. A synthetic microbial consortium can enable the simultaneous utilization of sugars such as glucose and xylose to produce biochemicals, where each consortium member converts one sugar into the target product. In this study, woody biomass was used to generate glucose and xylose after pretreatment with 20% (w/v) sulfuric acid and 60-min reaction time. We compared several strategies for detoxification with charcoal and sodium borohydride treatments to improve the fermentability of this hydrolysate in a defined medium for the production of the growth-associated product pyruvate. In shake flask culture, the highest pyruvate yield on xylose of 0.8 g/g was found using pH 6 charcoal-treated hydrolysate. In bioreactor studies, a consortium of two engineered E. coli strains converted the mixture of glucose and xylose in batch studies to 12.8 ± 2.7 g/L pyruvate in 13 h. These results demonstrate that lignocellulosic biomass as the sole carbon source can be used to produce growth-related products after employing suitable detoxification strategies.

Butyric acid production from spent coffee grounds by engineered Clostridium tyrobutyricum overexpressing galactose catabolism genes

Clostridium tyrobutyricum cannot utilize galactose, which is abundant in lignocellulose and red algae, as a carbon source for butyric acid production. Hence, when using galactose-rich coffee ground hydrolysate as the substrate, the fermentation performance of C. tyrobutyricum is poor. In this work, a recombinant strain, C. tyrobutyricum ATCC 25755/ketp, overexpressing galactose catabolism genes (galK, galE, galT, and galP) from Clostridium acetobutylicum ATCC 824 was constructed for the co-utilization of glucose and galactose. Batch fermentation in the bioreactor showed that ATCC 25755/ketp could efficiently utilize galactose without glucose-induced carbon catabolite repression and consume nearly 100% of the galactose present in the spent coffee ground hydrolysate. Correspondingly, the butyric acid concentration and productivity of ATCC 25755/ketp reached 34.3 g/L and 0.36 g/L·h, respectively, an increase of 78.6% and 56.5% compared with the wild-type strain, indicating its potential for butyric acid production from hydrolysates of inexpensive and galactose-rich biomass.

Direct conversion of untreated cane molasses into butyric acid by engineered Clostridium tyrobutyricum

The sucrose metabolic genes (scrA, scrB and scrK) from C. acetobutylicum ATCC 824 were successfully overexpressed in C. tyrobutyricum ATCC 25755, endowing it with the ability to co-utilize sucrose, fructose and glucose in the cane molasses. As a result, the engineering strain C. tyrobutyricum ATCC 25755/scrBAK produced 18.07 g/L and 18.98 g/L butyric acid when sucrose and cane molasses were used as the carbon source, respectively. Furthermore, the medium composition and initial cane molasses concentration were optimized to make full use of the untreated cane molasses. Based on these results, 45.71 g/L butyric acid with a yield of 0.39 g/g was obtained in fed-batch fermentation, and the feedstock cost of using untreated cane molasses was decreased by ~47% when compared with the conventional glucose fermentation. This study demonstrated the potential application of C. tyrobutyricum ATCC 25755/scrBAK for economic butyric acid production from untreated cane molasses.

Co-valorization of paper mill sludge and corn steep liquor for enhanced n-butanol production with Clostridium tyrobutyricum Δcat1::adhE2

In this study, hyper-butanol producing Clostridium tyrobutyricum Δcat1::adhE2 was used for butanol production from paper mill sludge (PMS) and corn steep liquor (CSL). Our results demonstrated that CSL can not only serve as a cheap nitrogen source, but also provide lactic acid that can be assimilated by C. tyrobutyricum for enhanced butanol production. Through a separate hydrolysis and fermentation, 16.5 g/L butanol with a yield of 0.26 g/g was obtained from PMS hydrolysates supplemented with 5% CSL. Further, a separate repeated hydrolysis was conducted to improve PMS hydrolysis rate and enhance sugar yield. Fermentation using hydrolysates from such process also generated high-level butanol with high yield. Our results suggested an innovative bioprocess for efficient biobutanol production from low-value waste streams.

Production of n-butanol from cassava bagasse hydrolysate by engineered Clostridium tyrobutyricum overexpressing adhE2: Kinetics and cost analysis

The production of biofuels such as butanol is usually limited by the availability of inexpensive raw materials and high substrate cost. Using food crops as feedstock in the biorefinery industry has been criticized for its competition with food supply, causing food shortage and increased food prices. In this study, cassava bagasse as an abundant, renewable, and inexpensive byproduct from the cassava starch industry was used for n-butanol production. Cassava bagasse hydrolysate containing mainly glucose was obtained after treatments with dilute acid and enzymes (glucoamylases and cellulases) and then supplemented with corn steep liquor for use as substrate in repeated-batch fermentation with engineered Clostridium tyrobutyricum CtΔack-adhE2 in a fibrous-bed bioreactor. Stable butanol production with high titer (>15.0 g/L), yield (>0.30 g/g), and productivity (~0.3 g/L∙h) was achieved, demonstrating the feasibility of an economically competitive process for n-butanol production from cassava bagasse for industrial application.

n-Butanol production from lignocellulosic biomass hydrolysates without detoxification by Clostridium tyrobutyricum Δack-adhE2 in a fibrous-bed bioreactor

Acetone-butanol-ethanol fermentation suffers from high substrate cost and low butanol titer and yield. In this study, engineered Clostridium tyrobutyricum CtΔack-adhE2 immobilized in a fibrous-bed bioreactor was used for butanol production from glucose and xylose present in the hydrolysates of low-cost lignocellulosic biomass including corn fiber, cotton stalk, soybean hull, and sugarcane bagasse. The biomass hydrolysates obtained after acid pretreatment and enzymatic hydrolysis were supplemented with corn steep liquor and used in repeated-batch fermentations. Butanol production with high titer (∼15 g/L), yield (∼0.3 g/g), and productivity (∼0.3 g/L∙h) was obtained from cotton stalk, soybean hull, and sugarcane bagasse hydrolysates, while corn fiber hydrolysate with higher inhibitor contents gave somewhat inferior results. The fermentation process was stable for long-term operation without any noticeable degeneration, demonstrating its potential for industrial application. A techno-economic analysis showed that n-butanol could be produced from lignocellulosic biomass using this novel fermentation process at ∼$2.5/gal for biofuel application.

Engineered Thermoanaerobacterium aotearoense with nfnAB knockout for improved hydrogen production from lignocellulose hydrolysates

BACKGROUND

As a renewable and clean energy carrier, the production of biohydrogen from low-value feedstock such as lignocellulose has increasingly garnered interest. The NADH-dependent reduced ferredoxin:NADP⁺ oxidoreductase (NfnAB) complex catalyzes electron transfer between reduced ferredoxin and NAD(P)⁺, which is critical for production of NAD(P)H-dependent products such as hydrogen and ethanol. In this study, the effects on end-product formation of deletion of nfnAB from Thermoanaerobacterium aotearoense SCUT27 were investigated.

RESULTS

Compared with the parental strain, the NADH/NAD⁺ ratio in the ∆nfnAB mutant was increased. The concentration of hydrogen and ethanol produced increased by (41.1 ± 2.37)% (p < 0.01) and (13.24 ± 1.12)% (p < 0.01), respectively, while the lactic acid concentration decreased by (11.88 ± 0.96)% (p < 0.01) when the ∆nfnAB mutant used glucose as sole carbon source. No obvious inhibition effect was observed for either SCUT27 or SCUT27/∆nfnAB when six types of lignocellulose hydrolysate pretreated with dilute acid were used for hydrogen production. Notably, the SCUT27/∆nfnAB mutant produced 190.63-209.31 mmol/L hydrogen, with a yield of 1.66-1.77 mol/mol and productivity of 12.71-13.95 mmol/L h from nonsterilized rice straw and corn cob hydrolysates pretreated with dilute acid.

CONCLUSIONS

The T. aotearoense SCUT27/∆nfnAB mutant showed higher hydrogen yield and productivity compared with those of the parental strain. Hence, we demonstrate that deletion of nfnAB from T. aotearoense SCUT27 is an effective approach to improve hydrogen production by redirecting the electron flux, and SCUT27/∆nfnAB is a promising candidate strain for efficient biohydrogen production from lignocellulosic hydrolysates.

Improved n-Butanol Production from Clostridium cellulovorans by Integrated Metabolic and Evolutionary Engineering

Clostridium cellulovorans DSM 743B offers potential as a chassis strain for biomass refining by consolidated bioprocessing (CBP). However, its n-butanol production from lignocellulosic biomass has yet to be demonstrated. This study demonstrates the construction of a coenzyme A (CoA)-dependent acetone-butanol-ethanol (ABE) pathway in C. cellulovorans by introducing adhE1 and ctfA-ctfB-adc genes from Clostridium acetobutylicum ATCC 824, which enabled it to produce n-butanol using the abundant and low-cost agricultural waste of alkali-extracted, deshelled corn cobs (AECC) as the sole carbon source. Then, a novel adaptive laboratory evolution (ALE) approach was adapted to strengthen the n-butanol tolerance of C. cellulovorans to fully utilize its n-butanol output potential. To further improve n-butanol production, both metabolic engineering and evolutionary engineering were combined, using the evolved strain as a host for metabolic engineering. The n-butanol production from AECC of the engineered C. cellulovorans was increased 138-fold, from less than 0.025 g/liter to 3.47 g/liter. This method represents a milestone toward n-butanol production by CBP, using a single recombinant clostridium strain. The engineered strain offers a promising CBP-enabling microbial chassis for n-butanol fermentation from lignocellulose.IMPORTANCE Due to a lack of genetic tools, Clostridium cellulovorans DSM 743B has not been comprehensively explored as a putative strain platform for n-butanol production by consolidated bioprocessing (CBP). Based on the previous study of genetic tools, strain engineering of C. cellulovorans for the development of a CBP-enabling microbial chassis was demonstrated in this study. Metabolic engineering and evolutionary engineering were integrated to improve the n-butanol production of C. cellulovorans from the low-cost renewable agricultural waste of alkali-extracted, deshelled corn cobs (AECC). The n-butanol production from AECC was increased 138-fold, from less than 0.025 g/liter to 3.47 g/liter, which represents the highest titer of n-butanol produced using a single recombinant clostridium strain by CBP reported to date. This engineered strain serves as a promising chassis for n-butanol production from lignocellulose by CBP.

Enhanced butyric acid production using mixed biomass of brown algae and rice straw by Clostridium tyrobutyricum ATCC25755

A brown alga Saccharina japonica and rice straw are attractive feedstock for microbial butyric acid production. However, inefficient fermentation of mannitol (a dominant component in S. japonica) and toxicity of inhibitors in lignocellulosic hydrolysate are limitations. This study demonstrated that mixed biomass with S. japonica and rice straw was effective in butyric acid production over those restrictions. Mannitol was consumed only when acetic acid was present. Notably, acetic acid was not produced but consumed along with mannitol. By mixing S. japonica and rice straw to take advantage of glucose and acetic acid in rice straw, Clostridium tyrobutyricum effectively consumed mannitol by utilizing acetic acid in hydrolysate and acetic acid derived from glucose with the enhanced butyric acid production. Furthermore, cell growth was restored owing to the decreased inhibitor concentration. The results demonstrate the potential of butyric acid production from mixed biomass of macroalgae/lignocellulose overcoming the drawbacks of single biomass.

Specific quorum sensing signal molecules inducing the social behaviors of microbial populations in anaerobic digestion

A series of dominant functional floras involved in anaerobic digestion was obtained by subculturing anaerobic sludge with specific substrates, respectively, and their specific quorum sensing signals (AHLs) were identified. It was found that most of the AHLs were secreted in starvation of the functional floras. One or two AHLs were found to have a significant positive correlation with the behavior of hydrolytic-fermentative bacteria, homoacetogens, syntrophic propionate-oxidizing bacteria, syntrophic butyrate-oxidizing bacteria and aceticlastic methanogens, respectively. Hydrogenotrophic methanogens had a various self-organization means and broader relations with the other populations, which was induced by six AHLs at least. Performance of an upflow anaerobic sludge blanket in the startup process revealed that the dominant populations involved in anaerobic digestion would secret specific AHLs to induce K-strategy in resource-limited situation for reproduction and regulating their cooperation. This work presents a novel perspective on the social behaviors of microbial populations in anaerobic digestion.

Metabolic engineering of Clostridium tyrobutyricum for enhanced butyric acid production from undetoxified corncob acid hydrolysate

Resistance to furan derivatives and phenolic compounds plays an important role in the use of lignocellulosic biomass for biological production of chemicals and fuels. This study confirmed that expression of short-chain dehydrogenase/reductase (SDR) from Clostridium beijerinckii NCIMB 8052 significantly improved the tolerance of C. tyrobutyricum to furfural due to the enhanced activity for furfural reduction. And on this basis, co-expression of SDR and heat shock chaperones GroESL could simultaneously enhance the tolerance of C. tyrobutyricum to furan derivatives and phenolic compounds, which were the main inhibitors presented in dilute-acid lignocellulosic hydrolysates. Consequently, the recombinant strain ATCC 25755/sdr+groESL exhibited good performance in butyric acid production with corncob acid hydrolysate as the substrate. Batch fermentation in bioreactor showed that the butyrate produced by ATCC 25755/sdr+groESL was 32.8 g/L, increased by 28.1% as compared with the wild-type strain. Meanwhile, the butyrate productivity increased from 0.19 g/L·h to 0.29 g/L·h.

The significance of proline on lignocellulose-derived inhibitors tolerance in Clostridium acetobutylicum ATCC 824

When lignocellulosic biomass was used for acetone-butanol-ethanol (ABE) fermentation, several lignocellulose-derived inhibitors, which are toxic to Clostridium acetobutylicum, were generated during acid hydrolysis process and seriously hindered the industrialization of lignocellulosic butanol. In this study, an engineered strain 824(proABC) with significantly improved tolerance to multiple lignocellulose-derived inhibitors (formic acid and phenolic compounds) was constructed by strengthening the proline biosynthesis. The engineered strain exhibited more effective synthesis ability of proline and scavenging ability of reactive oxygen species (ROS). Consequently, the butanol produced by 824(proABC) was 1-, 2.4- or 3.4-fold higher than that of the wild type strain when using the undetoxified hydrolysate of soybean straw, rice straw or corn straw as the substrate, respectively. Therefore, enhancing the proline biosynthesis can be used as an effective strategy to improve the tolerance of C. acetobutylicum to multiple lignocellulose-derived inhibitors, and 824(proABC) has great potential to produce butanol from undetoxified lignocellulosic hydrolysates.

New coculture system of Clostridium spp. and Megasphaera hexanoica using submerged hollow-fiber membrane bioreactors for caproic acid production

In this study, a coculture bioprocess was developed with Clostridium strains producing butyric acid and Megasphaera hexanoica producing caproic acid from the butyric acid. The two bacterial strains were each cultivated in two submerged hollow-fiber membrane bioreactors (s-HF/MBRs), separately. Each fermentation broth was filtered through the membrane modules, and the filtered broth was either interchanged on another reactor or obtained sequentially through. Using s-HF/MBRs, the caproic acid concentration increased to 10.08 g L^-1, with the fastest productivity of 0.69 g L^-1 h^-1, which higher than that previously reported.

Pretreatment with γ-Valerolactone/[Mmim]DMP and Enzymatic Hydrolysis on Corncob and Its Application in Immobilized Butyric Acid Fermentation

Corncob is a widely available raw material with high carbohydrate and low lignin content. To improve corncob conversion to the fermentable sugars, a novel method encompassing pretreatment using the γ-valerolactone (GVL)/1-methyl-3-methylimidazolium dimethylphosphite ([Mmim]DMP) system integrated with cellulase hydrolysis was developed and optimized. It is confirmed that lignin was extracted efficiently after combined pretreatment and that the subsequent enzymatic saccharification efficiency could be significantly enhanced, resulting in the yield of 94.9% glucose from cellulose and 53.3% xylose from xylan, respectively. Furthermore, the above fermentable sugars were used as carbon source for Clostridium tyrobutyricum immobilized in macroporous Ca-alginate-lignin beads with the extracted lignin as the active ingredient to evaluate the fermentability of butyric acid. The results showed that high butyrate productivity of 0.47 g/L/h and yield of 0.45 g/g were obtained after 10 repeated batches of fermentation, demonstrating an effective process for the production of butyric acid from abundant corncob waste-biomass.

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.

Bioaugmentation with Clostridium tyrobutyricum to improve butyric acid production through direct rice straw bioconversion

One-pot bioconversion is an economically attractive biorefinery strategy to reduce enzyme consumption. Direct conversion of lignocellulosic biomass for butyric acid production is still challenging because of competition among microorganisms. In a consolidated hydrolysis/fermentation bioprocessing (CBP) the microbial structure may eventually prefer the production of caproic acid rather than butyric acid production. This paper presents a new bioaugmentation approach for high butyric acid production from rice straw. By dosing 0.03 g/L of Clostridium tyrobutyricum ATCC 25755 in the CBP, an increase of 226% higher butyric acid was yielded. The selectivity and concentration also increased to 60.7% and 18.05 g/L, respectively. DNA-sequencing confirmed the shift of bacterial community in the augmented CBP. Butyric acid producer was enriched in the bioaugmented bacterial community and the bacteria related to long chain acids production was degenerated. The findings may be useful in future research and process design to enhance productivity of desired bio-products.

Solvent production from xylose

Xylose is the second most abundant sugar derived from lignocellulose; it is considered less desirable than glucose for fermentation, and strategies that specifically increase xylose utilization in wild type or engineered cells are goals for biofuel production. Issues arise with xylose utilization because of carbohydrate catabolite repression, which is the preferential utilization of glucose relative to xylose in fermentations with both pure and mixed cultures. Taken together the low substrate utilization rates and solvent yields with xylose compared to glucose, many industrial fermentations ignore the xylolytic portion of the reaction in lieu of methods to maintain high glucose. This is shortsighted given the massive potential for xylose generation from a number of sustainable biomass feedstocks, based on utilization of the hemicellulose fraction(s) that enter pretreatment. A number of strategies have been developed in recent years to address xylose utilization and solvent production from xylose in systems with just xylose, or in systems with mixtures of glucose plus xylose, which are more typical of pretreated lignocellulose. The approaches vary in terms of complexity, stability, and ease of introduction to existing fermentation infrastructure (i.e., so-called drop-in fermentation strategies). Some approaches can be considered traditional engineering approaches (e.g., change the reaction conditions), while others are more subtle cellular approaches to eliminate the impacts of catabolite repression. Finally, genetic engineering has been used to increase xylose utilization, although this can be considered a relatively nascent approach compared to manipulations completed to date for glucose utilization.

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.

Recent advances and strategies in process and strain engineering for the production of butyric acid by microbial fermentation

Butyric acid is an important platform chemical, which is widely used in the fields of food, pharmaceutical, energy, etc. Microbial fermentation as an alternative approach for butyric acid production is attracting great attention as it is an environmentally friendly bioprocessing. However, traditional fermentative butyric acid production is still not economically competitive compared to chemical synthesis route, due to the low titer, low productivity, and high production cost. Therefore, reduction of butyric acid production cost by utilization of alternative inexpensive feedstock, and improvement of butyric acid production and productivity has become an important target. Recently, several advanced strategies have been developed for enhanced butyric acid production, including bioprocess techniques and metabolic engineering methods. This review provides an overview of advances and strategies in process and strain engineering for butyric acid production by microbial fermentation. Additionally, future perspectives on improvement of butyric acid production are also proposed.