Novel microbial screen for detection of 1,4-butanediol, ethylene glycol, and adipic acid

A novel microbial-screening procedure was developed for separate detection of 1,4-butanediol, ethylene glycol, and adipic acid, three commercially important oxychemicals potentially derivable from bacterial omega-oxidation of n-butanol, ethanol, and hexanoic acid, respectively. The screening method involved postproduction addition of one of several specific Pseudomonas strains which produce a soluble fluorescent pigment during growth on the product of interest. A mutation and selection procedure was developed for isolation of specific strains with phenotypes for growth and pigment production on the desired product (e.g., 1,4-butanediol), but not on its bioconversion substrate (e.g., n-butanol), common by-products (e.g., n-butyrate), or product isomers. Pigment production was growth associated and required cultivation of the screening strains under limiting Fe3+ concentrations. The pigments resembled well-characterized, iron-chelating siderophores produced by other fluorescent pseudomonads. The sensitivity of the assay for product accumulation was enhanced by (i) conducting the screening in microtiter dishes to permit examination of individual isolates of putative producers and to control product diffusion, (ii) using a wavelength cutoff filter to reduce background source light, and (iii) using adapted screening strains which grew at lower (0.3 mM) concentrations of test compounds. The potential utility of the method for detecting a variety of oxidative catabolic products is discussed.     

Enhanced production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) copolymer and antimicrobial yellow pigmentation from Cupriavidus sp. USMAHM13 with antibiofilm capability

Antibiofilm polymers have the ability to inhibit bacterial biofilm formation, which is known to occur ubiquitously in the environment and pose risks of infection. In this study, production of P(3HB-co-4HB) copolymer and antimicrobial yellow pigment from Cupriavidus sp. USMAHM13 are enhanced through medium optimization. Before the improvement of yellow pigment production, screening for the best additional supplement was performed resulting in high-yield yellow pigmentation using yeast extract with optimum concentration of 2?g/L. Effects of different concentrations of 1,4-butanediol, ammonium acetate, and yeast extract were studied using central composite design. Under optimal conditions, 53?wt% of polyhydroxyalkanoate (PHA) content, 0.35?g/L of pigment concentration, and 5.87?g/L of residual biomass were achieved at 0.56?wt% C of 1,4-butanediol, 1.14?g/L of ammonium acetate, and 2?g/L of yeast extract. Antibiofilm tests revealed that the yellow pigment coated on P(3HB-co-4HB) copolymer had significant effect on the inhibition of bacteria proliferation and colonization from 6?hr onward reaching 100% inhibition by 12?hr, hence effectively inhibiting the biofilm formation.     

Elucidating and reprogramming Escherichia coli metabolisms for obligate anaerobic n-butanol and isobutanol production

Elementary mode (EM) analysis based on the constraint-based metabolic network modeling was applied to elucidate and compare complex fermentative metabolisms of Escherichia coli for obligate anaerobic production of n-butanol and isobutanol. The result shows that the n-butanol fermentative metabolism was NADH-deficient, while the isobutanol fermentative metabolism was NADH redundant. E. coli could grow and produce n-butanol anaerobically as the sole fermentative product but not achieve the maximum theoretical n-butanol yield. In contrast, for the isobutanol fermentative metabolism, E. coli was required to couple with either ethanol- or succinate-producing pathway to recycle NADH. To overcome these "defective" metabolisms, EM analysis was implemented to reprogram the native fermentative metabolism of E. coli for optimized anaerobic production of n-butanol and isobutanol through multiple gene deletion (~8-9 genes), addition (~6-7 genes), up- and downexpression (~6-7 genes), and cofactor engineering (e.g., NADH, NADPH). The designed strains were forced to couple both growth and anaerobic production of n-butanol and isobutanol, which is a useful characteristic to enhance biofuel production and tolerance through metabolic pathway evolution. Even though the n-butanol and isobutanol fermentative metabolisms were quite different, the designed strains could be engineered to have identical metabolic flux distribution in "core" metabolic pathways mainly supporting cell growth and maintenance. Finally, the model prediction in elucidating and reprogramming the native fermentative metabolism of E. coli for obligate anaerobic production of n-butanol and isobutanol was validated with published experimental data.     

Influence of sugar source (lactose,glucose, galactose) on 2,3-butanediol production by Klebsiella oxytoca NRRL-B199

The ability of Klebsiella oxytoca NRRL-B199 to use either lactose or the mixture of glucose and galactose as substrate for the production of 2,3-butanediol was studied in batch fermentations with different conditions of aeration and pH. 2,3-butanediol was undetected, or present in minute concentration in the fermentation broths with lactose, while it was the main product from glucose+galactose with final concentrations of up to 18.8 g/l in media at pH 6.0. Under conditions optimal for 2,3-butanediol synthesis, when aeration limited growth, the rate of biomass growth was more tightly related to the aeration rate in lactose medium than in glucose+galactose medium. These relations suggest that the growth rate is very low on lactose but still considerable on glucose+galactose when aeration rate tends toward zero. Correspondingly, the metabolism is more oxidative in the former medium, yielding mainly acetate as product.Abbreviations CDW cell dry weight     

Effects of introducing heterologous pathways on microbial metabolism with respect to metabolic optimality

Although optimality of microbial metabolism under genetic and environmental perturbations is well studied, the effects of introducing heterologous reactions on the overall metabolism are not well understood. This point is important in the field of metabolic engineering because heterologous reactions are more frequently introduced into various microbial hosts. The genome-scale metabolic simulations of Escherichia coli strains engineered to produce 1,4-butanediol, 1,3-propanediol, and amorphadiene suggest that microbial metabolism shows much different responses to the introduced heterologous reactions in a strain-specific manner than typical gene knockouts in terms of the energetic status (e.g., ATP and biomass generation) and chemical production capacity. The 1,4-butanediol and 1,3-propanediol producers showed greater metabolic optimality than the wild-type strains and gene knockout mutants for the energetic status, while the amorphadiene producer was metabolically less optimal. For the optimal chemical production capacity, additional gene knockouts were most effective for the strain producing 1,3-propanediol, but not for the one producing 1,4-butanediol. These observations suggest that strains having heterologous metabolic reactions have metabolic characteristics significantly different from those of the wild-type strain and single gene knockout mutants. Finally, comparison of the theoretically predicted and ¹³C-based flux values pinpoints pathways with non-optimal flux values, which can be considered as engineering targets in systems metabolic engineering strategies. To our knowledge, this study is the first attempt to quantitatively characterize microbial metabolisms with different heterologous reactions. The suggested potential reasons behind each strain’s different metabolic responses to the introduced heterologous reactions should be carefully considered in strain designs.     

Microbial production of diols as platform chemicals: recent progresses

Diols are chemicals with two hydroxyl groups which have a wide range of appealing applications as chemicals and fuels. In particular, four diol compounds, namely 1,3-propanediol (1,3-PDO), 1,2-propanediol (1,2-PDO), 2,3-butanediol (2,3-BDO) and 1,4-butanediol (1,4-BDO) can be biotechnologically produced by direct microbial bioconversion of renewable materials. These diols are considered as platform green chemicals. We review and discuss here the recent development in the microbial production of these diols, especially regarding the engineering of production strains and optimization of the fermentation processes.     

Use of respiratory quotient as a control parameter for optimum oxygen supply and scale-up of 2,3-butanediol production under microaerobic conditions

The respiratory quotient (RQ) was found to be a suitable control parameter for optimum oxygen supply for the production of 2,3-butanediol + acetoin under microaerobic conditions. In laboratory scale continuous cultures optimum production of 2,3-butanediol + acetoin was obtained at an RQ value between 4.0 to 4.5. This agreed well with optimum RQ value (4.0) stoichiometrically derived from the bioreactions involved. In fed-batch cultures product concentrations as high as 102.9 g/L (96.0 g/L butanediol + 6.9 g/L acetoin) can be achieved within 32 h cultivation with an RQ control algorithm for oxygen supply. Under similar conditions only 85.7 g/L product (77.6 g/L butanediol + 8.1 g/L acetoin) was obtained with control of constant oxygen supply rate throughout the cultivation.In pilot scale batch cultures under identical oxygen supply rate the achievable RQ value was found to be strongly influenced by the reactor type and scale. The initial oxygen supply rate influenced the achievable RQ as well. However, in all the reactors studied the specific product formation rate of cells in the exponential growth phase was only a function of RQ. The same optimum RQ value as found in continuous cultures was obtained. It was thus concluded that RQ can be used as a control parameter for optimum production of 2,3-butanediol + acetoin in both laboratory and pilot plant scale reactors. (c) 1994 John Wiley & Sons, Inc.     

Growth, pigment production and protease activity of Monascus purpureus as affected by salt, sodium nitrite, polyphosphate and various sugars

The effect of different levels of salt, sodium nitrite, polyphosphate and various sugars on growth, pigment production, protease activity and culture pH caused by Monascus purpureus was studied in broth medium and ground meat. The addition of sodium chloride (> 50.0 g l(-1)) and polyphosphate (> 3.0g l(-1)) to broth medium decreased mycelial growth, pigment production and protease activity of M. purpureus, whereas low concentrations of sodium nitrite (< 0.2 g l(-1)) promoted mycelial growth and pigment production. When the basal medium and ground meat contained salt, 150.0 g l(-1), the mould growth was stopped. The medium with fructose as carbon source proved to be the most suitable for mycelium growth and pigment production, with maltose and glucose being the second most productive. When sucrose and lactose were used as carbon sources, mycelium growth and pigment production were inhibited but the protease activity increased significantly. The mould showed more tolerance to salt and polyphosphate in ground meat than in broth medium and used sucrose as a carbon source as well as glucose for growth and pigment production in the meat mixture.     

Comprehensive analysis of metabolic sensitivity of 1,4-butanediol producing Escherichia coli toward substrate and oxygen availability

Nowadays, chemical production of 1,4-butanediol is supplemented by biotechnological processes using a genetically modified Escherichia coli strain, which is an industrial showcase of successful application of metabolic engineering. However, large scale bioprocess performance can be affected by presence of physical and chemical gradients in bioreactors which are a consequence of imperfect mixing and limited oxygen transfer. Hence, upscaling comes along with local and time dependent fluctuations of cultivation conditions. This study emphasizes on scale-up related effects of microbial 1,4-butanediol production by comprehensive bioprocess characterization in lab scale. Due to metabolic network constraints 1,4-butanediol formation takes place under oxygen limited microaerobic conditions, which can be hardly realized in large scale bioreactor. The purpose of this study was to assess the extent to which substrate and oxygen availability influence the productivity. It was found, that the substrate specific product yield and the production rate are higher under substrate excess than under substrate limitation. Furthermore, the level of oxygen supply within microaerobic conditions revealed strong effects on product and by-product formation. Under strong oxygen deprivation nearly 30% of the consumed carbon is converted into 1,4-butanediol, whereas an increase in oxygen supply results in 1,4-butanediol reduction of 77%. Strikingly, increasing oxygen availability leads to strong increase of main by-product acetate as well as doubled carbon dioxide formation. The study provides clear evidence that scale-up of microaerobic bioprocesses constitute a substantial challenge. Although oxygen is strictly required for product formation, the data give clear evidence that terms of anaerobic and especially aerobic conditions strongly interfere with 1,4-butanediol production.     

Biodegradation of Aliphatic-Aromatic Copolyesters by Thermomonospora fusca and Other Thermophilic Compost Isolates

Random aliphatic-aromatic copolyesters synthesized from 1,4-butanediol, adipic acid, and terephthalic acid (BTA) have excellent thermal and mechanical properties and are biodegradable by mixed cultures (e.g., in compost). Over 20 BTA-degrading strains were isolated by using compost as a microbial source. Among these microorganisms, thermophilic actinomycetes obviously play an outstanding role and appear to dominate the initial degradation step. Two actinomycete strains exhibited about 20-fold higher BTA degradation rates than usually observed in a common compost test. These isolates were identified as Thermomonospora fusca strains. They appeared to be particularly suitable for establishment of rapid degradation tests and were used in comparative studies on the biodegradation of various polyesters.     

Production of 2,3-Butanediol from Sucrose by a <Emphasis Type="Italic">Klebsiella</Emphasis> Species

Chemical 2,3-butanediol is an important platform compound possessing diverse industrial applications. So far, it is mainly produced by using petrochemical feedstock which is associated with high cost and adverse environmental impacts. Hence, finding alternative routes (e.g., via fermentation using renewable carbon sources) to produce 2,3-butanediol are urgently needed. In this study, we report a wild-type Klebsiella sp. strain XRM21, which is capable of producing 2,3-butanediol from a wide variety of carbon sources including glucose, sucrose, xylose, and glycerol. Among them, fermentation of sucrose leads to the highest production of 2,3-butanediol. To maximize the production of 2,3-butanediol, fermentation conditions were first optimized for strain XMR21 by using response surface methodology (RSM) in batch reactors. Subsequently, a fed-batch fermentation strategy was designed based on the optimized parameters, where 91.2 g/L of 2,3-butanediol could be produced from substrate sucrose dosing in 100 g/L for three times. Moreover, random mutagenesis of stain XMR21 resulted in a highly productive mutant strain, capable of producing 119.4 and 22.5 g/L of 2,3-butanediol and ethanol under optimized fed-batch fermentation process within 65 h with a total productivity of 2.18 g/L/h, which is comparable to the reported highest 2,3-butanediol concentration produced by previous strains. This study provides a potential strategy to produce industrially important 2,3-butanediol from low-cost sucrose.     

Simultaneous production of 2,3-butanediol, ethanol and hydrogen with a Klebsiella sp. strain isolated from sewage sludge

A Klebsiella sp. HE1 strain isolated from hydrogen-producing sewage sludge was examined for its ability to produce H(2) and other valuable soluble metabolites (e.g., ethanol and 2,3-butanediol) from sucrose-based medium. The effect of pH and carbon substrate concentration on the production of soluble and gaseous products was investigated. The major soluble metabolite produced from Klebsiella sp. HE1 was 2,3-butanediol, accounting for over 42-58% of soluble microbial products (SMP) and its production efficiency enhanced after increasing the initial culture pH to 7.3 (without pH control). The HE1 strain also produced ethanol (contributing to 29-42% of total SMP) and a small amount of lactic acid and acetic acid. The gaseous products consisted of H(2) (25-36%) and CO(2) (64-75%). The optimal cumulative hydrogen production (2.7 l) and hydrogen yield (0.92molH(2)molsucrose(-1)) were obtained at an initial sucrose concentration of 30gCODl(-1) (i.e., 26.7gl(-1)), which also led to the highest production rate for H(2) (3.26mmolh(-1)l(-1)), ethanol (6.75mmolh(-1)l(-1)) and 2,3-butanediol (7.14mmolh(-1)l(-1)). The highest yield for H(2), ethanol and 2,3-butanediol was 0.92, 0.81 and 0.59molmol-sucrose(-1), respectively. As for the overall energy production performance, the highest energy generation rate was 27.7kJh(-1)l(-1) and the best energy yield was 2.45kJmolsucrose(-1), which was obtained at a sucrose concentration of 30 and 20gCODl(-1), respectively.     

Large-scale production of bacterial biomass from methanol for use as milk-replacer

Summary A mixed methanol-utilizing bacterial culture was utilized to produce bacterial biomass as milk replacer. This culture comprised three pure strains: KISRI-5 (NCIB 12135), KISRI-512 (NCIB 12137) and KISRI-5112 (NCIB 12138). Optimal concentrations of methanol (15 g 1^–1) and medium elements as well as optimal growth conditions, e.g., pH (6.8), temperature (38°C), dissolved oxygen and dilution rate, were established. The maximum biomass yield coefficient obtained under optimized conditions was 0.48 g g^–1.· Large-scale production was successfully carried out in a 1500 1 fermenter under chemostat conditions. A good product was obtained having high true protein content (59–62%) and low polysaccharides (5%) without microbial contamination.     

Integrated knowledge mining,genome-scale modeling,and machine learning for predicting Yarrowia lipolytica bioproduction

Predicting bioproduction titers from microbial hosts has been challenging due to complex interactions between microbial regulatory networks, stress responses, and suboptimal cultivation conditions. This study integrated knowledge mining, feature extraction, genome-scale modeling (GSM), and machine learning (ML) to develop a model for predicting Yarrowia lipolytica chemical titers (i.e., organic acids, terpenoids, etc.). First, Y. lipolytica production data, including cultivation conditions, genetic engineering strategies, and product information, was manually collected from literature (~100 papers) and stored as either numerical (e.g., substrate concentrations) or categorical (e.g., bioreactor modes) variables. For each case recorded, central pathway fluxes were estimated using GSMs and flux balance analysis (FBA) to provide metabolic features. Second, a ML ensemble learner was trained to predict strain production titers. Accurate predictions on the test data were obtained for instances with production titers >1 g/L (R² = 0.87). However, the model had reduced predictability for low performance strains (0.01–1 g/L, R² = 0.29) potentially due to biosynthesis bottlenecks not captured in the features. Feature ranking indicated that the FBA fluxes, the number of enzyme steps, the substrate inputs, and thermodynamic barriers (i.e., Gibbs free energy of reaction) were the most influential factors. Third, the model was evaluated on other oleaginous yeasts and indicated there were conserved features for some hosts that can be potentially exploited by transfer learning. The platform was also designed to assist computational strain design tools (such as OptKnock) to screen genetic targets for improved microbial production in light of experimental conditions.     

Production of 1,3-propanediol, 2,3-butanediol and ethanol by a newly isolated Klebsiella oxytoca strain growing on biodiesel-derived glycerol based media

The production of 1,3-propanediol, 2,3-butanediol and ethanol was studied, during cultivations of strain Klebsiella oxytoca FMCC-197 on biodiesel-derived glycerol based media. Different kinds of glycerol feedstocks and experimental conditions had an important impact upon the distribution of metabolic products; production of 1,3-propanediol was positively influenced by stable pH conditions and by the absence of N₂ gas infusions throughout the fermentation. Thus, during batch bioreactor fermentations conducted at increasing glycerol concentrations, 1,3-propanediol at 41.3 g/L and yield ～47% (w/w) was achieved at initial glycerol concentration ～120 g/L. At even higher initial glycerol media (150 and 170 g/L), growth was not ceased, but 1,3-propanediol production declined. During fed-batch fermentation under optimal experimental conditions, 126 g/L of glycerol were converted into 50.1 g/L of 1,3-propanediol. In this experiment, also 25.2 g/L of ethanol (conversion yield ～20%, w/w) were formed. A batch-bioreactor culture was performed under non-sterilized conditions and the 1,3-propanediol production was almost equivalent to the sterilized process. Concerning 2,3-butanediol formation, the most detrimental parameter was the absence of N₂ sparging and as a result, no 2,3-butanediol was produced. The presence of glucose as co-substrate seriously enhanced 2,3-butanediol production; when commercial glucose was employed as sole substrate, 32.1 g/L of 2,3-butanediol were formed.     

In silico and in vivo stability analysis of a heterologous biosynthetic pathway for 1,4-butanediol production in metabolically engineered E. coli

Recently, several approaches have been published in order to develop a functional biosynthesis route for the non-natural compound 1,4-butanediol (BDO) in E. coli using glucose as a sole carbon source or starting from xylose. Among these studies, there was reported as high as 18 g/L product concentration achieved by industrial strains, however BDO production varies greatly in case of the reviewed studies. Our motivation was to build a simple heterologous pathway for this compound in E. coli and to design an appropriate cellular chassis based on a systemic biology approach, using constraint-based flux balance analysis and bi-level optimization for gene knock-out prediction. Thus, the present study reports, at the “proof-of concept” level, our findings related to model-driven development of a metabolically engineered E. coli strain lacking key genes for ethanol, lactate and formate production (ΔpflB, ΔldhA and ΔadhE), with a three-step biosynthetic pathway. We found this strain to produce a limited quantity of 1,4-BDO (.89 mg/L BDO under microaerobic conditions and .82 mg/L under anaerobic conditions). Using glycerol as carbon source, an approach, which to our knowledge has not been tackled before, our results suggest that further metabolic optimization is needed (gene-introductions or knock-outs, promoter fine-tuning) to address the redox potential imbalance problem and to achieve development of an industrially sustainable strain. Our experimental data on culture conditions, growth dynamics and fermentation parameters can consist a base for ongoing research on gene expression profiles and genetic stability of such metabolically engineered E. coli strains.     

粘质沙雷氏菌产2,3-丁二醇培养基的优化

研究了各种碳源、氮源、柠檬酸及无机盐对细胞生长与产物形成的影响,通过单因子、正交及中心组合设计响应面分析优化发酵培养基。结果表明在培养基中添加柠檬酸不但可以促进细胞生长与糖耗速度,还可以缩短发酵周期,提高2,3-丁二醇的产量。采用优化后的培养基,2,3-丁二醇的产量由14.03g/L增加到39.27g/L,提高了近3倍。     

Inhibition of acetate accumulation leads to enhanced production of (R,R)-2,3-butanediol from glycerol in Escherichia coli

This work describes the production of (R,R)-2,3-butanediol in Escherichia coli using glycerol by metabolic engineering approaches. The introduction of a synthetic pathway converting pyruvate to (R,R)-2,3-butanediol into wild-type E. coli strain BW25113 led to the production of (R,R)-2,3-butanediol at a titer of 3.54?g/l and a yield of 0.131?g product/g glycerol (26.7?% of theoretical maximum) with acetate (around 3.00?g/l) as the dominant by-product. We therefore evaluated the impacts of deleting the genes ackA or/and poxB that are responsible for the major by-product, acetate. This increased production of (R,R)-2,3-butanediol to 9.54?g/l with a yield of 0.333?g product/g glycerol (68.0?% of theoretical maximum) in shake flask studies. The utilization of low-priced crude glycerol to produce value-added chemicals is of great significance to the economic viability of the biodiesel industry.     

Effect of restricted aeration on catabolism of cholic acid by two Pseudomonas species.

Examination of some previously isolated bile acid-utilizing Pseudomonas strains showed that Pseudomonas sp. ATCC 31752, together with other fluorescent strains, can be assigned to Pseudomonas putida biotype B, whereas Pseudomonas sp. ATCC 31753, like most other nonfluorescent strains, is an unrecognized phenotype. A study was made of the growth of these two species at 25 degrees C and pH 7.0 in a fermentor with 2.5 g of sodium cholate liter-1 as sole carbon source, and the catabolism of the cholate and its products was followed by high-pressure liquid chromatographic and thin-layer chromatographic examination. At aeration rates of either 150 or 5 ml min-1 liter-1, growth of each species followed the same catabolic pathway. 7 alpha, 12 beta-Dihydroxy-1,4-androstadiene-3,17-dione was the major catabolite formed, with 0.3 g liter-1 being the maximum concentration that accumulated at the higher aeration rate, whereas 1.4 g liter-1 accumulated at the lower aeration rate, irrespective of the species used. The latter yield is sufficiently high to be of potential commercial value if such a catabolite were found to be economically useful for steroid drug manufacture. It is postulated that the rate-limiting step in cholic acid catabolism by these species at the lower aeration rate is 9 alpha-hydroxylation, a step requiring molecular oxygen, hence, the marked effect of oxygen limitation on catabolite accumulation. Another consequence of oxygen limitation is the production of a red pigment in the culture medium, which, however, does not affect catabolite recovery.