A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production

Production of Succinic Acid by Metabolically Engineered Actinobacillus succinogenes from Lignocellulosic Hydrolysate Derived from Barley Straw

Succinic acid is an industrially important component that plays a key role in food additives, dietary supplements, and precursors for biodegradable polymers. Due to environmental and economic issues, succinic acid production has become increasingly attractive. This work aimed to improve succinic acid production from lignocellulosic biomass in Actinobacillus succinogenes through genetic modifications and fermentation strategies. Firstly, the effects on succinic acid production by overexpressing genes encoding phosphoenol carboxylase, malate dehydrogenase, and fumarase were evaluated in batch fermentations of engineered A. succinogenes strains. The engineered A. succinogenes expressing PCK, MDH, and FUM (AS-PMF) showed a 1.3-fold increase in succinic acid production compared to the wild-type strain. Subsequently, the fed-batch fermentation with MgCO3 was carried out using AS-PMF, which led to producing 50 g/l of succinic acid with 0.79 g/g of yield. Finally, 22.2 g/l of succinic acid with 0.64 g/g of yield was achieved in batch fermentation from lignocellulosic hydrolysate of barley straw. These results support that sustainable succinic acid from agricultural wastes might be a promising strategy for industrial applications.

Recent advances in bio-based production of top platform chemical, succinic acid: an alternative to conventional chemistry

Succinic acid (SA) is one of the top platform chemicals with huge applications in diverse sectors. The presence of two carboxylic acid groups on the terminal carbon atoms makes SA a highly functional molecule that can be derivatized into a wide range of products. The biological route for SA production is a cleaner, greener, and promising technological option with huge potential to sequester the potent greenhouse gas, carbon dioxide. The recycling of renewable carbon of biomass (an indirect form of CO2), along with fixing CO2 in the form of SA, offers a carbon-negative SA manufacturing route to reduce atmospheric CO2 load. These attractive attributes compel a paradigm shift from fossil-based to microbial SA manufacturing, as evidenced by several commercial-scale bio-SA production in the last decade. The current review article scrutinizes the existing knowledge and covers SA production by the most efficient SA producers, including several bacteria and yeast strains. The review starts with the biochemistry of the major pathways accumulating SA as an end product. It discusses the SA production from a variety of pure and crude renewable sources by native as well as engineered strains with details of pathway/metabolic, evolutionary, and process engineering approaches for enhancing TYP (titer, yield, and productivity) metrics. The review is then extended to recent progress on separation technologies to recover SA from fermentation broth. Thereafter, SA derivatization opportunities via chemo-catalysis are discussed for various high-value products, which are only a few steps away. The last two sections are devoted to the current scenario of industrial production of bio-SA and associated challenges, along with the author's perspective.

Natural Extracts for Antibacterial Applications

Bacteria-induced epidemics and infectious diseases are seriously threatening the health of people around the world. In addition, antibiotic therapy has been inducing increasingly more serious bacterial resistance, which makes it urgent to develop new treatment strategies to combat bacteria, including multidrug-resistant bacteria. Natural extracts displaying antibacterial activity and good biocompatibility have attracted much attention due to greater concerns about the safety of synthetic chemicals and emerging drug resistance. These antibacterial components can be isolated and utilized as antimicrobials, as well as transformed, combined, or wrapped with other substances by using modern assistive technologies to fight bacteria synergistically. This review summarizes recent advances in natural extracts from three kinds of sources-plants, animals, and microorganisms-for antibacterial applications. This work discusses the corresponding antibacterial mechanisms and the future development of natural extracts in antibacterial fields.

Asuc_0142 of Actinobacillus succinogenes 130Z is the l-aspartate/C4-dicarboxylate exchanger DcuA

Anaerobic bacteria often use antiporters DcuB (malate/succinate antiport) or DcuA (l-aspartate/succinate antiport) for the excretion of succinate during fumarate respiration. The rumen bacterium Actinobacillus succinogenes is able to produce large amounts of succinate by fumarate respiration, using the DcuB-type transporter DcuE for l-malate/succinate antiport. Asuc_0142 was annotated as a second DcuB-type transporter. Deletion of Asuc_0142 decreased the uptake rate for l-[14C]aspartate into A. succinogenes cells. Properties of transport by heterologously expressed Asuc_0142 were investigated in an Escherichia coli mutant deficient of anaerobic C4DC transporters. Expression of Asuc_0142 resulted in high uptake activity for l-[14C]fumarate or l-[14C]aspartate, but the former showed a strong competitive inhibition by l-aspartate. In E. coli loaded with l-[14C]aspartate, [14C]succinate or [14C]fumarate, extracellular C4DCs initiated excretion of the intracellular substrates, with a preference for l-aspartateex/succinatein or l-aspartateex/fumaratein antiport. These findings indicate that Asuc_0142 represents a DcuA-type transporter for l-aspartate uptake and l-aspartateex/C4DCin antiport, differentiating it from the DcuB-type transporter DcuE for l-malateex/succinatein antiport. Sequence analysis and predicted structural characteristics confirm structural similarity of Asuc_0142 to DcuA, and Asuc_0142 was thus re-named as DcuAAs. The bovine rumen fluid contains l-aspartate (99.6 µM), whereas fumarate and l-malate are absent. Therefore, bovine rumen colonisers depend on l-aspartate as an exogenous substrate for fumarate respiration. A. succinogenes encodes HemG (protoporphyrinogen oxidase) and PyrD (dihydroorotate dehydrogenase) for haem and pyrimidine biosynthesis. The enzymes require fumarate as an electron acceptor, suggesting an essential role for l-aspartate, DcuAAs, and fumarate respiration for A. succinogenes growing in the bovine rumen.

Technological advancements in valorization of second generation (2G) feedstocks for bio-based succinic acid production

Succinic acid (SA) is used as a commodity chemical and as a precursor in chemical industry to produce other derivatives such as 1,4-butaneidol, tetrahydrofuran, fumaric acid, and bio-polyesters. The production of bio-based SA from renewable feedstocks has always been in the limelight owing to the advantages of renewability, abundance and reducing climate change by CO₂ capture. Considering this, the current review focuses on various 2G feedstocks such as lignocellulosic biomass, crude glycerol, and food waste for cost-effective SA production. It also highlights the importance of producing SA via separate enzymatic hydrolysis and fermentation, simultaneous saccharification and fermentation, and consolidated bioprocessing. Furthermore, recent advances in genetic engineering, and downstream SA processing are thoroughly discussed. It also elaborates on the techno-economic analysis and life cycle assessment (LCA) studies carried out to understand the economics and environmental effects of bio-based SA synthesis.

Low cost nutrient-rich oil palm trunk bagasse hydrolysate for bio-succinic acid production by Actinobacillus succinogenes

Economical source of succinic acid (SA) is most sought-after as a key platform chemical for a wide range of applications. Low-cost production of bio-succinic acid (bio-SA) from a renewable biomass resource i.e., oil palm trunk (OPT) is reported in this paper. Apart from carbon source, nitrogen source and mineral salts are other important nutrients affecting microbial cell growth and bio-SA biosynthesis by Actinobacillus succinogenes 130Z. In order to access and optimize nutrient requirement of the latter two sources, their effects in terms of types and concentrations were investigated. The findings highlighted the importance of selecting proper nitrogen source in A. succinogenes fermentation. The possibility of producing bio-SA from OPT economically can be achieved through minimal supply of 5 g/L yeast extract compared to that generally supplemented 15 g/L with a similar yield (0.47 g/g). In addition, a higher bio-SA yield (0.49 g/g) was achieved without adding mineral salts, which could further reduce fermentation cost. The use of minimally supplemented hydrolysate resulted in 21.1 g/L of bio-SA with a satisfactory yield (0.58 g/g) in a batch bioreactor system with an estimated 56.4% in cost savings. Conclusively, OPT bagasse hydrolysate is a nutrient-rich feedstock that can be practically utilized for bio-SA production.

Insights on the Advancements of In Silico Metabolic Studies of Succinic Acid Producing Microorganisms: A Review with Emphasis on Actinobacillus succinogenes

Succinic acid (SA) is one of the top candidate value-added chemicals that can be produced from biomass via microbial fermentation. A considerable number of cell factories have been proposed in the past two decades as native as well as non-native SA producers. Actinobacillus succinogenes is among the best and earliest known natural SA producers. However, its industrial application has not yet been realized due to various underlying challenges. Previous studies revealed that the optimization of environmental conditions alone could not entirely resolve these critical problems. On the other hand, microbial in silico metabolic modeling approaches have lately been the center of attention and have been applied for the efficient production of valuable commodities including SA. Then again, literature survey results indicated the absence of up-to-date reviews assessing this issue, specifically concerning SA production. Hence, this review was designed to discuss accomplishments and future perspectives of in silico studies on the metabolic capabilities of SA producers. Herein, research progress on SA and A. succinogenes, pathways involved in SA production, metabolic models of SA-producing microorganisms, and status, limitations and prospects on in silico studies of A. succinogenes were elaborated. All in all, this review is believed to provide insights to understand the current scenario and to develop efficient mathematical models for designing robust SA-producing microbial strains.

Identifying Energy Extraction Optimisation Strategies of Actinobacillus succinogenes

A. succinogenes is well known for utilising various catabolic pathways. A multitude of batch fermentation studies confirm flux shifts in the catabolism as time proceeds. It has also been shown that continuous cultures exhibit flux variation as a function of dilution rate. This indicates a direct influence of the external environment on the proteome of the organism. In this work, ATP production efficiency was explored to evaluate the extent of bio-available energy on the production behaviour of A. succinogenes. It was found that the microbe successively utilised its most-to-least efficient energy extraction pathways, providing evidence of an energy optimisation survival strategy. Moreover, data from this study suggest a pyruvate overflow mechanism as a means to throttle acetic and formic acid production, indicating a scenario in which the external concentration of these acids play a role in the energy extraction capabilities of the organism. Data also indicates a fleeting regime where A. succinogenes utilises an oxidised environment to its advantage for ATP production. Here it is postulated that the energy gain and excretion cost of catabolites coupled to the changing environment is a likely mechanism responsible for the proteome alteration and its ensuing carbon flux variation. This offers valuable insights into the microbe’s metabolic logic gates, providing a foundation to understand how to exploit the system.

One step forward, two steps back: Transcriptional advancements and fermentation phenomena in Actinobacillus succinogenes 130Z

Within the field of bioproduction, non-model organisms offer promise as bio-platform candidates. Non-model organisms can possess natural abilities to consume complex feedstocks, produce industrially useful chemicals, and withstand extreme environments that can be ideal for product extraction. However, non-model organisms also come with unique challenges due to lack of characterization. As a consequence, developing synthetic biology tools, predicting growth behavior, and building computational models can be difficult. There have been many advancements that have improved work with non-model organisms to address broad limitations, however each organism can come with unique surprises. Here we share our work in the non-model bacterium Actinobacillus succinognes 130Z, which includes both advancements in synthetic biology toolkit development and pitfalls in unpredictable fermentation behaviors. To develop a synthetic biology “tool kit” for A. succinogenes, information gleaned from a growth study and antibiotic screening was used to characterize 22 promoters which demonstrated a 260-fold range of fluorescence protein expression. The strongest of the promoters was incorporated into an inducible system for tunable gene control in A. succinogenes using the promoter for the lac operon as a template. This system flaunted a 481-fold range of expression and no significant basal expression. These findings were accompanied by unexpected changes in fermentation products characterized by a loss of succinic acid and increase in lactic acid after approximately 10 months in the lab. During evaluation of the fermentation shifts, new tests of the synthetic biology tools in a succinic acid producing strain revealed a significant loss in their functionality. Contamination and mutation were ruled out as causes and further testing is needed to elucidate the driving factors. The significance of this work is to share a successful tool development strategy that could be employed in other non-model species, report on an unfortunate phenomenon that needs addressed for further development of A. succinogenes, and provide a cautionary tale for those undertaking non-model research. In sharing our findings, we seek to provide tools and necessary information for further development of A. succinogenes as a platform for bioproduction of succinic acid and to illustrate the importance of diligent and long-term observation when working with non-model bacteria.

Succinic acid production from pulp and paper industry waste: A transcriptomic approach

The fermentative production of biobased chemicals and polymers using crude lignocellulose hydrolysates is challenging due to the presence of various inhibitory compounds and multiple sugars. This study evaluates the metabolic response of Actinobacillus succinogenes for the production of succinic acid using spent sulphite liquor (SSL) as feedstock derived from industrial acidic sulphite pulping of Eucalyptus globulus hardwood. A transcriptomic approach led to significant insights on gene regulation of the major metabolic pathways (glycolysis, pentose phosphate pathway, TCA cycle, pyruvate metabolism and oxidative phosphorylation) in batch cultures carried out on SSL and compared with glucose and xylose. Significantly overexpressed genes in SSL compared to glucose and xylose were fructose biphosphate aldolase (> 1.18-fold change) in the catabolism, phosphoenolpyruvate carboxykinase (> 1.59-fold change) and malate dehydrogenase (> 1.49-fold change) in the TCA cycle, citrate lyase (> 1.7-fold change), dihydrolipoamide dehydrogenase (> 0.88-fold change), pyruvate dehydrogenase E2 (> 1.63-fold change) and pyruvate formate lyase (> 0.61-fold change), involved in acetyl-CoA pathways. Finally, C4 tricarboxylic transporters were overexpressed (DCU (> 1.61-fold change) and 0079 (> 4.19-fold change). SSL was responsible for the upregulation of genes involved in the TCA cycle and oxidative phosphorylation, while xylose showed similar results with SSL in the oxidative phosphorylation.

A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production

Enterobacter sp. LU1, a wild-type bacterium originating from goat rumen, proved to be a potential succinic acid producer in previous studies. Here, the first complete genome of this strain was obtained and analyzed from a biotechnological perspective. A hybrid sequencing approach combining short (Illumina MiSeq) and long (ONT MinION) reads allowed us to obtain a single continuous chromosome 4,636,526 bp in size, with an average 55.6% GC content that lacked plasmids. A total of 4425 genes, including 4283 protein-coding genes, 25 ribosomal RNA (rRNA)-, 84 transfer RNA (tRNA)-, and 5 non-coding RNA (ncRNA)-encoding genes and 49 pseudogenes, were predicted. It has been shown that genes involved in transport and metabolism of carbohydrates and amino acids and the transcription process constitute the major group of genes, according to the Clusters of Orthologous Groups of proteins (COGs) database. The genetic ability of the LU1 strain to metabolize a wide range of industrially relevant carbon sources has been confirmed. The genome exploration indicated that Enterobacter sp. LU1 possesses all genes that encode the enzymes involved in the glycerol metabolism pathway. It has also been shown that succinate can be produced as an end product of fermentation via the reductive branch of the tricarboxylic acid cycle (TCA) and the glyoxylate pathway. The transport system involved in succinate excretion into the growth medium and the genes involved in the response to osmotic and oxidative stress have also been recognized. Furthermore, three intact prophage regions ~70.3 kb, ~20.9 kb, and ~49.8 kb in length, 45 genomic islands (GIs), and two clustered regularly interspaced short palindromic repeats (CRISPR) were recognized in the genome. Sequencing and genome analysis of Enterobacter sp. LU1 confirms many earlier results based on physiological experiments and provides insight into their genetic background. All of these findings illustrate that the LU1 strain has great potential to be an efficient platform for bio-based succinate production.

Genome analysis of a wild rumen bacterium Enterobacter aerogenes LU2 - a novel bio-based succinic acid producer

Enterobacter aerogenes LU2 was isolated from cow rumen and recognized as a potential succinic acid producer in our previous study. Here, we present the first complete genome sequence of this new, wild strain and report its basic genetic features from a biotechnological perspective. The MinION single-molecule nanopore sequencer supported by the Illumina MiSeq platform yielded a circular 5,062,651 bp chromosome with a GC content of 55% that lacked plasmids. A total of 4,986 genes, including 4,741 protein-coding genes, 22 rRNA-, 86 tRNA-, and 10 ncRNA-encoding genes and 127 pseudogenes, were predicted. The genome features of the studied strain and other Enterobacteriaceae strains were compared. Functional studies on the genome content, metabolic pathways, growth, and carbon transport and utilization were performed. The genomic analysis indicates that succinic acid can be produced by the LU2 strain through the reductive branch of the tricarboxylic acid cycle (TCA) and the glyoxylate pathway. Antibiotic resistance genes were determined, and the potential for bacteriocin production was verified. Furthermore, one intact prophage region of length ~31,9 kb, 47 genomic islands (GIs) and many insertion sequences (ISs) as well as tandem repeats (TRs) were identified. No clustered regularly interspaced short palindromic repeats (CRISPRs) were found. Finally, comparative genome analysis with well-known succinic acid producers was conducted. The genome sequence illustrates that the LU2 strain has several desirable traits, which confirm its potential to be a highly efficient platform for the production of bulk chemicals.

Microbial energy management-A product of three broad tradeoffs

Wherever thermodynamics allows, microbial life has evolved to transform and harness energy. Microbial life thus abounds in the most unexpected places, enabled by profound metabolic diversity. Within this diversity, energy is transformed primarily through variations on a few core mechanisms. Energy is further managed by the physiological processes of cell growth and maintenance that use energy. Some aspects of microbial physiology are streamlined for energetic efficiency while other aspects seem suboptimal or even wasteful. We propose that the energy that a microbe harnesses and devotes to growth and maintenance is a product of three broad tradeoffs: (i) economic, trading enzyme synthesis or operational cost for functional benefit, (ii) environmental, trading optimization for a single environment for adaptability to multiple environments, and (iii) thermodynamic, trading energetic yield for forward metabolic flux. Consideration of these tradeoffs allows one to reconcile features of microbial physiology that seem to opposingly promote either energetic efficiency or waste.

Compatibility of utilising nitrogen-rich oil palm trunk sap for succinic acid fermentation by Actinobacillus succinogenes 130Z

In this study, the potential of oil palm trunk (OPT) sap as a sole substrate for succinic acid (SA) production was evaluated using Actinobacillus succinogenes 130Z. After OPT sap was characterised, the effects of adding carbonate, yeast extract (YE) and minerals to this medium were investigated in an attempt to develop a low-cost fermentation medium. The OPT sap alone, gave comparable SA yield and productivity (0.54 g/g and 0.35 g/L/h) to those supplemented with YE (0.50 g/g and 0.36 g/L/h) and minerals (0.55 g/g and 0.40 g/L/h). The findings showed that OPT sap has sufficient amount of nutrients for SA biosynthesis by A. succinogenes 130Z and could potentially reduce cost without requiring expensive nutrients supplementation.

Link between Heterotrophic Carbon Fixation and Virulence in the Porcine Lung Pathogen Actinobacillus pleuropneumoniae

Actinobacillus pleuropneumoniae is a capnophilic pathogen of the porcine respiratory tract lacking enzymes of the oxidative branch of the tricarboxylic acid (TCA) cycle. We previously claimed that A. pleuropneumoniae instead uses the reductive branch in order to generate energy and metabolites. Here, we show that bicarbonate and oxaloacetate supported anaerobic growth of A. pleuropneumoniae Isotope mass spectrometry revealed heterotrophic fixation of carbon from stable isotope-labeled bicarbonate by A. pleuropneumoniae, which was confirmed by nano-scale secondary ion mass spectrometry at a single-cell level. By gas chromatography-combustion-isotope ratio mass spectrometry we could further show that the labeled carbon atom is mainly incorporated into the amino acids aspartate and lysine, which are derived from the TCA metabolite oxaloacetate. We therefore suggest that carbon fixation occurs at the interface of glycolysis and the reductive branch of the TCA cycle. The heme precursor δ-aminolevulinic acid supported growth of A. pleuropneumoniae, similar to bicarbonate, implying that anaplerotic carbon fixation is needed for heme synthesis. However, deletion of potential carbon-fixing enzymes, including PEP-carboxylase (PEPC), PEP-carboxykinase (PEPCK), malic enzyme, and oxaloacetate decarboxylase, as well as various combinations thereof, did not affect carbon fixation. Interestingly, generation of a deletion mutant lacking all four enzymes was not possible, suggesting that carbon fixation in A. pleuropneumoniae is an essential metabolic pathway controlled by a redundant set of enzymes. A double deletion mutant lacking PEPC and PEPCK was not impaired in carbon fixation in vitro but showed reduction of virulence in a pig infection model.

High-affinity l-malate transporter DcuE of Actinobacillus succinogenes catalyses reversible exchange of C4-dicarboxylates

Actinobacillus succinogenes is a natural succinate producer, which is the result of fumarate respiration. Succinate production from anaerobic growth with C₄ -dicarboxylates requires transporters catalysing uptake and efflux of C₄ -dicarboxylates. Transporter Asuc_1999 (DcuE) found in A. succinogenes belongs to the Dcu family and was considered the main transporter for fumarate respiration. However, deletion of dcuE affected l-malate uptake of A. succinogenes rather than fumarate uptake. DcuE complemented anaerobic growth of Escherichia coli on l-malate or fumarate; thus, the transporter was characterized in E. coli heterologously. Time-dependent uptake and competitive inhibition assays demonstrated that l-malate is the most preferred substrate for uptake by DcuE. The V_max of DcuE for l-malate was 20.04 μmol/gDW·min with K_m of 57 μM. The V_max for l-malate was comparable to that for fumarate, whereas the K_m for l-malate was 8 times lower than that for fumarate. The catalytic efficiency of DcuE for l-malate was 7.3-fold higher than that for fumarate, showing high efficiency and high affinity for l-malate. Furthermore, DcuE catalysed the reversible exchange of three C₄ -dicarboxylates - l-malate, fumarate and succinate - but the preferred substrate for uptake was l-malate. Under physiological conditions, the C₄ -dicarboxylates were reduced to succinate. Therefore, DcuE is proposed as the l-malate/succinate antiporter in A. succinogenes.

Opportunities, challenges, and future perspectives of succinic acid production by Actinobacillus succinogenes

Due to environmental issues and the depletion of fossil-based resources, ecofriendly sustainable biomass-based chemical production has been given more attention recently. Succinic acid (SA) is one of the top value added bio-based chemicals. It can be synthesized through microbial fermentation using various waste steam bioresources. Production of chemicals from waste streams has dual function as it alleviates environmental concerns; they could have caused because of their improper disposal and transform them into valuable products. To date, Actinobacillus succinogenes is termed as the best natural SA producer. However, few reviews regarding SA production by A. succinogenes were reported. Herewith, pathways and metabolic engineering strategies, biomass pretreatment and utilization, and process optimization related with SA fermentation by A. succinogenes were discussed in detail. In general, this review covered vital information including merits, achievements, progresses, challenges, and future perspectives in SA production using A. succinogenes. Therefore, it is believed that this review will provide platform to understand the potential of the strain and tackle existing hurdles so as to develop superior strain for industrial applications. It will also be used as a baseline for identification, isolation, and improvement of other SA-producing microbes.

Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z

BACKGROUND

Actinobacillus succinogenes is a promising bacterial catalyst for the bioproduction of succinic acid from low-cost raw materials. In this work, a genome-scale metabolic model was reconstructed and used to assess the metabolic capabilities of this microorganism under producing conditions.

RESULTS

The model, iBP722, was reconstructed based on the functional reannotation of the complete genome sequence of A. succinogenes 130Z and manual inspection of metabolic pathways, covering 1072 enzymatic reactions associated with 722 metabolic genes that involve 713 metabolites. The highly curated model was effective in capturing the growth of A. succinogenes on various carbon sources, as well as the SA production under various growth conditions with fair agreement between experimental and predicted data. Calculated flux distributions under different conditions show that a number of metabolic pathways are affected by the activity of some metabolic enzymes at key nodes in metabolism, including the transport mechanism of carbon sources and the ability to fix carbon dioxide.

CONCLUSIONS

The established genome-scale metabolic model can be used for model-driven strain design and medium alteration to improve succinic acid yields.

Complete Genome Sequence of Actinobacillus succinogenes GXAS137, a Highly Efficient Producer of Succinic Acid

The bacterium Actinobacillus succinogenes GXAS137, an efficient producer of succinic acid, was isolated from bovine rumen in Nanning, Guangxi Province, China. Here, we present the 2.3-Mb genome assembly of this strain, which consists of 2,314,479 bp (G+C content of 44.89%) with a circular chromosome, 2,235 DNA coding sequences, 57 tRNAs, and 15 rRNAs.

John PC, Crowley MF, Bomble YJ. Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes

Succinate is a precursor of multiple commodity chemicals and bio-based succinate production is an active area of industrial bioengineering research. One of the most important microbial strains for bio-based production of succinate is the capnophilic gram-negative bacterium Actinobacillus succinogenes, which naturally produces succinate by a mixed-acid fermentative pathway. To engineer A. succinogenes to improve succinate yields during mixed acid fermentation, it is important to have a detailed understanding of the metabolic flux distribution in A. succinogenes when grown in suitable media. To this end, we have developed a detailed stoichiometric model of the A. succinogenes central metabolism that includes the biosynthetic pathways for the main components of biomass-namely glycogen, amino acids, DNA, RNA, lipids and UDP-N-Acetyl-α-D-glucosamine. We have validated our model by comparing model predictions generated via flux balance analysis with experimental results on mixed acid fermentation. Moreover, we have used the model to predict single and double reaction knockouts to maximize succinate production while maintaining growth viability. According to our model, succinate production can be maximized by knocking out either of the reactions catalyzed by the PTA (phosphate acetyltransferase) and ACK (acetyl kinase) enzymes, whereas the double knockouts of PEPCK (phosphoenolpyruvate carboxykinase) and PTA or PEPCK and ACK enzymes are the most effective in increasing succinate production.

Investigation of putative invasion determinants of Actinobacillus species using comparative genomics

Actinobacillus spp. are Gram-negative bacteria associated with mucosal membranes. While some are commensals, others can cause important human and animal diseases. A. pleuropneumoniae causes severe fibrinous hemorrhagic pneumonia in swine but not systemic disease whereas other species invade resulting in septicemia and death. To understand the invasive phenotype of Actinobacillus spp., complete genomes of eight isolates were obtained and pseudogenomes of five isolates were assembled and annotated. Phylogenetically, A. suis isolates clustered by surface antigen type and were more closely related to the invasive A. ureae, A. equuli equuli, and A. capsulatus than to the other swine pathogen, A. pleuropneumoniae. Using the LS-BSR pipeline, 251 putative virulence genes associated with serum resistance and invasion were detected. To our knowledge, this is the first genome-wide study of the genus Actinobacillus and should contribute to a better understanding of host tropism and mechanisms of invasion of pathogenic Actinobacillus and related genera.

Succinic acid production from fruit and vegetable wastes hydrolyzed by on-site enzyme mixtures through solid state fermentation

In this study, a novel biorefinery concept of succinic acid (SA) production from fruit and vegetable wastes (FVWs) hydrolyzed by crude enzyme mixtures through solid state fermentation was designed. Enzyme complex solid mashes from various types of FVWs were on-site produced through solid-state fermentation by Aspergillus niger and Rhizopus oryzae. This solid was then added to FVW suspensions and undergo hydrolysis reaction to generate fermentable sugars and other essential nutrients for bacterial growth and product formation. The subsequent fungal hydrolysis produced 12.00g/L glucose and 13.83g/L fructose using 10% mass ratio (w/v) of FVW. Actinobacillus succinogenes used this FVW hydrolysate as the sole feedstock and produced 27.03g/L of succinic acid with high yield and productivity of 1.18gSA/g sugar and 1.28gL^-1h^-1, respectively. This work demonstrated that FVWs can be biotransformed to value added products which have considerable potential economics and environmental meaning.

Continuous succinic acid fermentation by Actinobacillus succinogenes in a packed-bed biofilm reactor

BACKGROUND

Succinic acid is one of the most interesting platform chemicals that can be produced in a biorefinery approach. In this study, continuous succinic acid production by Actinobacillus succinogenes fermentation in a packed-bed biofilm reactor (PBBR) was investigated.

RESULTS

The effects of the operating conditions tested, dilution rate (D), and medium composition (mixture of glucose, xylose, and arabinose-that simulate the composition of a lignocellulosic hydrolysate)-on the PBBR performances were investigated. The maximum succinic acid productivity of 35.0 g L^-1 h^-1 and the maximum SA concentration were achieved at a D = 1.9 h^-1. The effect of HMF and furfural on succinic acid production was also investigated. HMF resulted to reduce succinic acid production by 22.6%, while furfural caused a reduction of 16% in SA production at the same dilution rate.

CONCLUSION

Succinic acid production by A. succinogenes fermentation in a packed-bed reactor (PBBR) was successfully carried out for more than 5 months. The optimal results were obtained at the dilution rate 0.5 h^-1: 43.0 g L^-1 of succinic acid were produced, glucose conversion was 88%; and the volumetric productivity was 22 g L^-1 h^-1.

Transcriptome analysis and anaerobic C4 -dicarboxylate transport in Actinobacillus succinogenes

A global transcriptome analysis of the natural succinate producer Actinobacillus succinogenes revealed that 353 genes were differentially expressed when grown on various carbon and energy sources, which were categorized into six functional groups. We then analyzed the expression pattern of 37 potential C₄‐dicarboxylate transporters in detail. A total of six transporters were considered potential fumarate transporters: three transporters, Asuc_1999 (Dcu), Asuc_0304 (DASS), and Asuc_0270‐0273 (TRAP), were constitutively expressed, whereas three others, Asuc_1568 (DASS), Asuc_1482 (DASS), and Asuc_0142 (Dcu), were differentially expressed during growth on fumarate. Transport assays under anaerobic conditions with [¹⁴C]fumarate and [¹⁴C]succinate were performed to experimentally verify that A. succinogenes possesses multiple C₄‐dicarboxlayte transport systems with different substrate affinities. Upon uptake of 5 mmol/L fumarate, the systems had substrate specificity for fumarate, oxaloacetate, and malate, but not for succinate. Uptake was optimal at pH 7, and was dependent on both proton and sodium gradients. Asuc_1999 was suspected to be a major C₄‐dicarboxylate transporter because of its noticeably high and constitutive expression. An Asuc_1999 deletion (∆1999) decreased fumarate uptake significantly at approximately 5 mmol/L fumarate, which was complemented by the introduction of Asuc_1999. Asuc_1999 expressed in Escherichia coli catalyzed fumarate uptake at a level of 21.6 μmol·gDW⁻¹·min⁻¹. These results suggest that C₄‐dicarboxylate transport in A. succinogenes is mediated by multiple transporters, which transport various types and concentrations of C₄‐dicarboxylates.

Media optimization for economic succinic acid production by Enterobacter sp. LU1

Enterobacter sp. LU1 could efficiently convert glycerol to succinic acid under anaerobic conditions after the addition of lactose. In this study, media constituents affecting both Enterobacter sp. LU1 biomass and succinic acid production were investigated employing response surface methodology (RSM) with central composite design. Statistical methods led to the development of an efficient and inexpensive microbiological media based on crude glycerol, whey permeate as carbon sources and urea as a nitrogen source. The optimized production of bacterial biomass in aerobic conditions was predicted and the interactive effects between crude glycerol, urea and magnesium sulfate were investigated. As a result, a model for predicting the concentration of bacterial biocatalyst biomass was developed with crude glycerol as a sole carbon source. In addition, it was observed that the interactive effect between crude glycerol and urea was statistically significant. Response surface methodology was also employed to develop the model for predicting the concentration of succinic acid produced. Validity of the model was confirmed during verification experiments wherein actual results differed from predicted values by 0.77%. The applied statistical methods proved the feasibility for anaerobic succinic acid production on crude glycerol without expensive yeast extract addition. In conclusion, the RSM method can provide valuable information for succinic acid scale-up fermentation using Enterobacter sp. LU1.

Metabolic Engineering of Actinobacillus succinogenes Provides Insights into Succinic Acid Biosynthesis

Actinobacillus succinogenes, a Gram-negative facultative anaerobe, exhibits the native capacity to convert pentose and hexose sugars to succinic acid (SA) with high yield as a tricarboxylic acid (TCA) cycle intermediate. In addition, A. succinogenes is capnophilic, incorporating CO₂ into SA, making this organism an ideal candidate host for conversion of lignocellulosic sugars and CO₂ to an emerging commodity bioproduct sourced from renewable feedstocks. In this work, we report the development of facile metabolic engineering capabilities in A. succinogenes, enabling examination of SA flux determinants via knockout of the primary competing pathways-namely, acetate and formate production-and overexpression of the key enzymes in the reductive branch of the TCA cycle leading to SA. Batch fermentation experiments with the wild-type and engineered strains using pentose-rich sugar streams demonstrate that the overexpression of the SA biosynthetic machinery (in particular, the enzyme malate dehydrogenase) enhances flux to SA. Additionally, removal of competitive carbon pathways leads to higher-purity SA but also triggers the generation of by-products not previously described from this organism (e.g., lactic acid). The resultant engineered strains also lend insight into energetic and redox balance and elucidate mechanisms governing organic acid biosynthesis in this important natural SA-producing microbe.IMPORTANCE Succinic acid production from lignocellulosic residues is a potential route for enhancing the economic feasibility of modern biorefineries. Here, we employ facile genetic tools to systematically manipulate competing acid production pathways and overexpress the succinic acid-producing machinery in Actinobacillus succinogenes Furthermore, the resulting strains are evaluated via fermentation on relevant pentose-rich sugar streams representative of those from corn stover. Overall, this work demonstrates genetic modifications that can lead to succinic acid production improvements and identifies key flux determinants and new bottlenecks and energetic needs when removing by-product pathways in A. succinogenes metabolism.

Adaptation of gut microbiome to different dietary nonstarch polysaccharide fractions in a porcine model

SCOPE

Dietary fibers, consisting of nonstarch polysaccharides (NSPs) were found to modulate the gut microbiota. However, little is known about the role of a separated fiber fraction. Here, we describe a response in gut microbiome to different fiber fractions using a porcine model.

METHODS AND RESULTS

Ileal and cecal digesta were collected from pigs fed with fiber-free diet (FFD) or diet containing 5% cellulose (CEL), xylan (XYL) or β-glucan (GLU). We observed an elevated 16S rRNA gene copies in ileum and cecum digesta after NSP ingestion. Interestingly, we found that cecum digesta contained higher bacterial diversity than ileum digesta. Moreover, NSPs had no significant influence on overall diversity, but acutely altered the abundance of specific bacteria. Importantly, NSPs decreased the abundance of phylum Firmicutes, but increased the phylum Proteobacteria in ileal samples. Among the NSP-treated groups, pigs on CEL-containing diet had exclusively higher abundance of Lactobacillus spp. in the ileum. Whereas, the GLU-treated samples had more Clostridium spp.

CONCLUSION

This study not only indicated how the gut microbiome adapts to the three major NSP fractions, but the results also contribute to our understanding of the role of dietary fibers in modulating gut microbiota and health.

Biotechnological route for sustainable succinate production utilizing oil palm frond and kenaf as potential carbon sources

Due to the world's dwindling energy supplies, greater thrust has been placed on the utilization of renewable resources for global succinate production. Exploration of such biotechnological route could be seen as an act of counterbalance to the continued fossil fuel dominance. Malaysia being a tropical country stands out among many other nations for its plenty of resources in the form of lignocellulosic biomass. To date, oil palm frond (OPF) contributes to the largest fraction of agricultural residues in Malaysia, while kenaf, a newly introduced fiber crop with relatively high growth rate, holds great potential for developing sustainable succinate production, apart from OPF. Utilization of non-food, inexhaustible, and low-cost derived biomass in the form of OPF and kenaf for bio-based succinate production remains largely untapped. Owing to the richness of carbohydrates in OPF and kenaf, bio-succinate commercialization using these sources appears as an attractive proposition for future sustainable developments. The aim of this paper was to review some research efforts in developing a biorefinery system based on OPF and kenaf as processing inputs. It presents the importance of the current progress in bio-succinate commercialization, in addition to describing the potential use of different succinate production hosts and various pretreatments-saccharifications under development for OPF and kenaf. Evaluations on the feasibility of OPF and kenaf as fermentation substrates are also discussed.

Efficient estimation of the maximum metabolic productivity of batch systems

BACKGROUND

Production of chemicals from engineered organisms in a batch culture involves an inherent trade-off between productivity, yield, and titer. Existing strategies for strain design typically focus on designing mutations that achieve the highest yield possible while maintaining growth viability. While these methods are computationally tractable, an optimum productivity could be achieved by a dynamic strategy in which the intracellular division of resources is permitted to change with time. New methods for the design and implementation of dynamic microbial processes, both computational and experimental, have therefore been explored to maximize productivity. However, solving for the optimal metabolic behavior under the assumption that all fluxes in the cell are free to vary is a challenging numerical task. Previous studies have therefore typically focused on simpler strategies that are more feasible to implement in practice, such as the time-dependent control of a single flux or control variable.

RESULTS

This work presents an efficient method for the calculation of a maximum theoretical productivity of a batch culture system using a dynamic optimization framework. The proposed method follows traditional assumptions of dynamic flux balance analysis: first, that internal metabolite fluxes are governed by a pseudo-steady state, and secondly that external metabolite fluxes are dynamically bounded. The optimization is achieved via collocation on finite elements, and accounts explicitly for an arbitrary number of flux changes. The method can be further extended to calculate the complete Pareto surface of productivity as a function of yield. We apply this method to succinate production in two engineered microbial hosts, Escherichia coli and Actinobacillus succinogenes, and demonstrate that maximum productivities can be more than doubled under dynamic control regimes.

CONCLUSIONS

The maximum theoretical yield is a measure that is well established in the metabolic engineering literature and whose use helps guide strain and pathway selection. We present a robust, efficient method to calculate the maximum theoretical productivity: a metric that will similarly help guide and evaluate the development of dynamic microbial bioconversions. Our results demonstrate that nearly optimal yields and productivities can be achieved with only two discrete flux stages, indicating that near-theoretical productivities might be achievable in practice.

Improving succinic acid production by Actinobacillus succinogenes from raw industrial carob pods

Carob pods are an inexpensive by-product of locust bean gum industry that can be used as renewable feedstock for bio-based succinic acid. Here, for the first time, unprocessed raw carob pods were used to extract a highly enriched sugar solution, afterwards used as substrate to produce succinic acid using Actinobacillus succinogenes. Batch fermentations containing 30g/L sugars resulted in a production rate of 1.67gSA/L.h and a yield of 0.39gSA/g sugars. Taking advantage of A. succinogenes' metabolism, uncoupling cell growth from succinic acid production, a fed-batch mode was implemented to increase succinic acid yield and reduce by-products formation. This strategy resulted in a succinic acid yield of 0.94gSA/g sugars, the highest yield reported in the literature for fed-batch and continuous experiments, while maintaining by-products at residual values. Results demonstrate that raw carob pods are a highly efficient feedstock for bio-based succinic acid production.

The pentose phosphate pathway leads to enhanced succinic acid flux in biofilms of wild-type Actinobacillus succinogenes

Increased pentose phosphate pathway flux, relative to total substrate uptake flux, is shown to enhance succinic acid (SA) yields under continuous, non-growth conditions of Actinobacillus succinogenes biofilms. Separate fermentations of glucose and xylose were conducted in a custom, continuous biofilm reactor at four different dilution rates. Glucose-6-phosphate dehydrogenase assays were performed on cell extracts derived from in situ removal of biofilm at each steady state. The results of the assays were coupled to a kinetic model that revealed an increase in oxidative pentose phosphate pathway (OPPP) flux relative to total substrate flux with increasing SA titre, for both substrates. Furthermore, applying metabolite concentration data to metabolic flux models that include the OPPP revealed similar flux relationships to those observed in the experimental kinetic analysis. A relative increase in OPPP flux produces additional reduction power that enables increased flux through the reductive branch of the TCA cycle, leading to increased SA yields, reduced by-product formation and complete closure of the overall redox balance.

Succinic acid production from lignocellulosic hydrolysate by Basfia succiniciproducens

The production of chemicals alongside fuels will be essential to enhance the feasibility of lignocellulosic biorefineries. Succinic acid (SA), a naturally occurring C4-diacid, is a primary intermediate of the tricarboxylic acid cycle and a promising building block chemical that has received significant industrial attention. Basfia succiniciproducens is a relatively unexplored SA-producing bacterium with advantageous features such as broad substrate utilization, genetic tractability, and facultative anaerobic metabolism. Here B. succiniciproducens is evaluated in high xylose-content hydrolysates from corn stover and different synthetic media in batch fermentation. SA titers in hydrolysate at an initial sugar concentration of 60g/L reached up to 30g/L, with metabolic yields of 0.69g/g, and an overall productivity of 0.43g/L/h. These results demonstrate that B. succiniciproducens may be an attractive platform organism for bio-SA production from biomass hydrolysates.

Succinic acid production by Actinobacillus succinogenes from batch fermentation of mixed sugars

Succinic acid production from the monosaccharides xylose, arabinose, glucose, mannose and galactose was studied using the bacterium Actinobacillus succinogenes. In Duran bottle cultures, containing 10 g/L of each of sugar, succinic acid was produced from all sugars except for galactose. The highest succinate yield, 0.56 g/g, was obtained with glucose, whereas the succinate yield was 0.42, 0.38 and 0.44 g/g for xylose, mannose and arabinose, respectively. The specific succinate productivity was 0.7 g/g h for glucose, but below 0.2 g/g h for the other sugars. Batch bioreactor fermentations were carried out using a sugar mixture of the five sugars giving a total concentration of 50 g/L, mimicking the distribution of sugars in spent sulfite liquor (SSL) from Eucalyptus which is rich in xylose. In this mixture, an almost complete conversion of all sugars (except galactose) was achieved resulting in a final succinate concentration of 21.8–26.8 g/L and a total yield of 0.59–0.68 g/g. There was evidence of co-consumption of glucose and xylose, whereas mannose was consumed after glucose. The main by-products were acetate 0.14–0.20 g/g and formate 0.08–0.13 g/g. NADH balance calculations suggested that NADH required for succinate production was not met solely from formate and acetate production, but other means of NADH production was necessary. Results from mixed sugar fermentations were verified using SSL as substrate resulting in a succinate yield of 0.60 g/g. In addition, it was found that CO2 sparging could replace carbonate supply in the form of MgCO3 without affecting the succinate yield.