Physiological limitations and opportunities in microbial metabolic engineering.

Metabolic engineering can have a pivotal role in increasing the environmental sustainability of the transportation and chemical manufacturing sectors. The field has already developed engineered microorganisms that are currently being used in industrial-scale processes. However, it is often challenging to achieve the titres, yields and productivities required for commercial viability. The efficiency of microbial chemical production is usually dependent on the physiological traits of the host organism, which may either impose limitations on engineered biosynthetic pathways or, conversely, boost their performance. In this Review, we discuss different aspects of microbial physiology that often create obstacles for metabolic engineering, and present solutions to overcome them. We also describe various instances in which natural or engineered physiological traits in host organisms have been harnessed to benefit engineered metabolic pathways for chemical production.

Disinfection and conditions associated with thermo-assisted drying and decontamination inconsistently produce negative PRRSV rRT-PCR results on metal surfaces.

Because contaminated livestock trailers are a significant risk for transmitting viruses between herds, various methods of washing, disinfecting, and thermo-assisted drying and decontamination (TADD) have been evaluated for their effectiveness in inactivating porcine reproductive and respiratory syndrome virus (PRRSV) on contaminated surfaces. Information on when to expect negative qRT-PCR results after adequate trailer sanitation is lacking. The objective of this study was to evaluate whether there are conditions associated with washing-disinfectant-TADD procedures that will consistently produce a negative qRT-PCR result for the purpose of monitoring compliance with trailer sanitation and decontamination protocols for PRRSV on metal surfaces. 144 diamond plate aluminum coupons were spiked with PRRSV or phosphate-buffered saline (PBS) and treated with a designated disinfectant protocol. Disinfectants evaluated included multiple accelerated® hydrogen peroxide (AHP) disinfectants and a quaternary ammonium and glutaraldehyde combination disinfectant. Disinfectant was applied for 5 or 60 minutes of contact time at either 20 °C or -10 °C in a matrix of feces or PBS. All coupons were heated until the surface temperature of the coupon reached 71 °C and then held for 10 minutes to simulate TADD under field conditions. Post-treatment swabs for all treatment groups, except negative control groups, were positive by PRRSV qRT-PCR. Under the conditions evaluated in this study, consistently negative qRT-PCR results after treatments were not found. Therefore, for the purpose of monitoring compliance with trailer sanitation and decontamination protocols for PRRSV, alternatives to qRT-PCR should be explored.

[Construction and verification of Lactococcus lactis NZ9000 genome-scale metabolic model].

With the advent of the post-genomic era, metabolic engineering of microorganisms plays an increasingly important role in industrial production. The genome-scale metabolic model (GSMM) integrates all known metabolic information in the organism to provide an optimal platform for global understanding of the metabolic state of the organism and rational guidance for metabolic engineering. As a model strain, Lactococcus lactis NZ9000 plays an important role in industrial fermentation, but there is still no specific genome-scale metabolic model for it. Based on genomic function annotation and comparative genomics, we constructed the first genome-scale metabolic model iWK557 of L. lactis NZ9000, which contains 557 genes, 668 metabolites, and 840 reactions, and further verified at both qualitative and quantitative levels, to provide a good tool for rationally guiding metabolic engineering.

Pseudomonas putida KT2440 is HV1 certified, not GRAS.

Pseudomonas putida is rapidly becoming a workhorse for industrial production due to its metabolic versatility, genetic accessibility and stress-resistance properties. The P. putida strain KT2440 is often described as Generally Regarded as Safe, or GRAS, indicating the strain is safe to use as food additive. This description is incorrect. P. putida KT2440 is classified by the FDA as HV1 certified, indicating it is safe to use in a P1 or ML1 environment.

Whole genome sequencing used in an industrial context reveals a Salmonella laboratory cross-contamination.

In 2013, during a routine laboratory analysis performed on food samples, one finished product from a European factory was tested positive for Salmonella Hadar. At the same period, one environmental isolate in the same laboratory was serotyped Salmonella Hadar. Prior to this event, the laboratory performed a proficiency testing involving a sample spiked with NCTC 9877 Salmonella Hadar. The concomitance of Salmonella Hadar detection led to the suspicion of a laboratory cross-contamination between the Salmonella Hadar isolate used in the laboratory proficiency testing and the Salmonella Hadar isolate found on the finished product by the same laboratory. Since the classical phenotypic serotyping method is able to attribute a serotype to Salmonella isolates with a common antigenic formula, but cannot differentiate strains of the same serotype within the subspecies, whole genome sequencing was used to test the laboratory cross-contamination hypothesis. Additionally, 12 Salmonella Hadar from public databases, available until the time of the event, were included in the whole genome sequencing analysis to better understand the genomic diversity of this serotype in Europe. The outcome of the analysis showed a maximum of ten single nucleotide polymorphisms (SNPs) between the isolates coming from the laboratory and the finished product, and thus confirmed the laboratory cross-contamination. These results combined with all additional investigations done at the factory, allowed to release finished product batches produced and thus circumvented unnecessary food waste and economic losses for the factory.

Phylogenetic Characterization of Viable but-not-yet Cultured Legionella Groups Grown in Amoebic Cocultures: A Case Study using Various Cooling Tower Water Samples.

　Legionella spp. exist naturally in association with amoeba in water environments and are known to be the etiological agent of a severe form of pneumonia. To detect diverse Legionella populations in cooling tower water systems, amoebic coculturing was performed for 15 water samples obtained from five different kinds of facilities in six geographically different locations. The growth of Legionella in coculture with Acanthamoeba sp. cells was monitored by quantitative PCR targeting Legionella-specific 16S rRNA genes. Seven out of the 15 samples were positive for Legionella growth and subjected to clone library analysis. A total of 333 clones were classified into 14 operational taxonomic units composed of seven known species and seven previously undescribed groups. Four of the seven Legionella-growth-positive samples harbored detectable levels of free-living amoeba and were predominated by either L. drozanskii or L. lytica, by both L. bozemanii and L. longbeachae, or by a not-yet-described group named OTU 4. The Legionella-growth- positive samples contained higher ATP levels (>980 pM) than the growth-negative samples (<160 pM) , suggesting that ATP content would be a good indicator of the presence of viable but nonculturable Legionella populations able to grow with amoeba.

Biological conversion of methane to chemicals and fuels: technical challenges and issues.

Methane is a promising next-generation carbon feedstock for industrial biotechnology due to its low price and huge availability. Biological conversion of methane to valuable products can mitigate methane-induced global warming as greenhouse gas. There have been challenges for the conversion of methane into various chemicals and fuels using engineered non-native hosts with synthetic methanotrophy or methanotrophs with the reconstruction of synthetic pathways for target products. Herein, we analyze the technical challenges and issues of potent methane bioconversion technology. Pros and cons of metabolic engineering of methanotrophs for methane bioconversion, and perspectives on the bioconversion of methane to chemicals and liquid fuels are discussed.

Optimization of laccase production from Marasmiellus palmivorus LA1 by Taguchi method of Design of experiments.

BACKGROUND: Fungal laccase has profound applications in different fields of biotechnology due to its broad specificity and high redox potential. Any successful application of the enzyme requires large scale production. As laccase production is highly dependent on medium components and cultural conditions, optimization of the same is essential for efficient product production. RESULTS: Production of laccase by fungal strain Marasmiellus palmivorus LA1 under solid state fermentation was optimized by the Taguchi design of experiments (DOE) methodology. An orthogonal array (L8) was designed using Qualitek-4 software to study the interactions and relative influence of the seven selected factors by one factor at a time approach. The optimum condition formulated was temperature (28 °C), pH (5), galactose (0.8%w/v), cupric sulphate (3 mM), inoculum concentration (number of mycelial agar pieces) (6Nos.) and substrate length (0.05 m). Overall yield increase of 17.6 fold was obtained after optimization. Statistical optimization leads to the elimination of an insignificant medium component ammonium dihydrogen phosphate from the process and contributes to a 1.06 fold increase in enzyme production. A final production of 667.4 ± 13 IU/mL laccase activity paves way for the application of this strain for industrial applications. CONCLUSION: Study optimized lignin degrading laccases from Marasmiellus palmivorus LA1. This laccases can thus be used for further applications in different scales of production after analyzing the properties of the enzyme. Study also confirmed the use of taguchi method for optimizations of product production.

Monitoring microbial diversity of bioreactors using metagenomic approaches.

With the rapid development of molecular techniques, particularly 'omics' technologies, the field of microbial ecology is growing rapidly. The applications of next generation sequencing have allowed researchers to produce massive amounts of genetic data on individual microbes, providing information about microbial communities and their interactions through in situ and in vitro measurements. The ability to identify novel microbes, functions, and enzymes, along with developing an understanding of microbial interactions and functions, is necessary for efficient production of useful and high value products in bioreactors. The ability to optimize bioreactors fully and understand microbial interactions and functions within these systems will establish highly efficient industrial processes for the production of bioproducts. This chapter will provide an overview of bioreactors and metagenomic technologies to help the reader understand microbial communities, interactions, and functions in bioreactors.

Molecular biological researches of Kuro-Koji molds, their classification and safety.

To assess the position of Kuro-Koji molds in black Aspergillus, we performed sequence analysis of approximately 2500 nucleotides of partial gene fragments, such as histone 3, on a total of 57 Aspergillus strains, including Aspergillus kawachii NBRC 4308, 12 Kuro-Koji molds isolated from awamori breweries in Japan, Aspergillus niger ATCC 1015, and A. tubingensis ATCC10550. Sequence results showed that all black Aspergillus strains could be classified into 3 types, type N which includes A. niger ATCC 1015, type T which includes A. tubingensis ATCC 10550, and type L which includes A. kawachii NBRC 4308. Phylogenetic analysis showed these three types belong to different clusters. All 12 Kuro-Koji molds isolated from awamori breweries were classified as type L, thus we concluded type L represents the industrial Kuro-Koji molds. We found all type L strains lack the An15g07920 gene which is required for ochratoxin A biosynthesis in black Aspergillus. This sequence is present in the genome of A. niger CBS 513.88 and has homology to the polyketide synthase fragment of A. ochraceus which is involved in ochratoxin A biosynthesis. Based on the industrial importance and the safety of Kuro-Koji molds, we propose to classify the type L strains as Aspergillus luchuensis, as initially reported by Dr. Inui.

[Total and allergic morbidity trends in the population residing in the area of microbiological industry].

Due to exposure to emissions from a protein-vitamin concentrate-manufacturing enterprise, the total and allergic morbidity rates remained high in the Blagoveshchensk population during a follow-up, the incidence of asthma and atopic dermatitis being on the rise and that of pollen disease on the decrease. The findings show the need for a further follow-up of the health status of the population of this area, the living conditions in which are risk factors for allergic and toxic allergic diseases even after microbiological industry closure.

[Characteristics of antigenic complexes of Staphylococcus aureus vaccine strains obtained in different cultivation conditions].

AIM: Assessment of characteristics of antigenic complexes of Staphylococcus aureus vaccine strains in different cultivation conditions. MATERIALS AND METHODS: S. aureus vaccine strains (No. 5, 9, 1986, 1991) were grown in liquid nutrient media--full value and semi-synthetic--as well as on solid medium. Reactor cultivation was performed in the fermenter ANKUM-2M. Complex of antigens were obtained by water extraction method applied to staphylococcal biomass inactivated with acetone and assessed by common methods on protein and carbohydrate content; specific activity was assessed by minimal inhibitory dose in passive hemagglutination inhibition assay. Study of acute toxicity was performed on outbred mice. RESULTS: Using strain no. 1991, model of reactor cultivation in full value medium with separation of biomass by microfiltration was validated on the basis of biomass and semiproduct of antigenic complex (acetone powder) yield as well as productivity of biomass cumulation. Study of antigenic complexes obtained from biomass of 4 strains during reactor cultivation compared with complexes extracted from cultures grown on solid medium revealed increased protein and decreased carbohydrate content but similar specific activity. It was demonstrated that complex of antigens obtained from cultures grown either by reactor cultivation or on solid medium were non-toxic. CONCLUSION: New technology for manufacturing staphylococcal complex of antigens with reactor cultivation of vaccine strains in full value medium with subsequent purification of antigenic complex from the biomass by microfiltration was developed. Results of the study demonstrated the usefulness of the developed technology for both further studies on a cellular staphylococcal vaccine and manufacture of staphylococcal component of "Immunovac" vaccine.

Fate of ochratoxin A content in Argentinean red wine during a pilot scale vinification / Evolución del contenido de ocratoxina A en vinos tintos argentinos durante el proceso de vinificación a escala piloto

The aim of this work was to evaluate the fate of ochratoxin A (OTA) content from must to wine during the red wine making process in a pilot scale vinification. The study was done using musts obtained from two red grape varieties (Bonarda and Tempranillo) artificially contaminated with two OTA levels. A duplicate set of tanks of 100 l each was established for each must (Bonarda and Tempranillo). The fermentations were initiated by inoculation of two Saccharomyces spp. strains having different fermentation performance. The must from the Tempranillo variety was spiked with 6 μg/l of OTA while that from the Bonarda variety with 0.3 μg/l of the toxin. Samples were collected at different stages of the process. Performance of the alcoholic and malolactic fermentations was monitored. Titratable and volatile acidity, pH, ethanol, sugar and SO2 concentrations were determined following standard methods proposed by the Office International de la Vigne et du Vin (OIV). OTA analysis was done by HPLC. Detection and quantification limits were 0.01 and 0.1 ng/ml, respectively. The OTA levels during the vinification trials dropped to an average of about 86.5%. The type of Saccharomyces strains used showed no effect on toxin reduction.

El objetivo del presente trabajo fue evaluar la evolución del contenido de ocratoxina A (OTA) en mostos durante un proceso de vinificación a escala piloto. Se utilizaron mostos de dos variedades de uvas tintas (Bonarda y Tempranillo) contaminados artificialmente con dos niveles distintos de OTA. El ensayo fue llevado a cabo por duplicado en tanques de fermentación de 100 l cada uno. La fermentación se inició mediante la inoculación de dos cepas de Saccharomyces spp. con diferentes características fermentativas. El mosto de la variedad Tempranillo fue contaminado con 6 μg/l de OTA y el mosto de la variedad Bonarda con 0,3 μg/l de la toxina. Se colectaron muestras durante los diferentes estadios del proceso de vinificación. Se estableció el avance de dicho proceso sobre la base de la evolución de las fermentaciones alcohólica y maloláctica. Se determinó la acidez total y volátil, el pH y el contenido de etanol, de azúcar y de SO2 siguiendo los protocolos estándares propuestos por la Oficina Internacional de la Vid y el Vino (OIV). El contenido de OTA se evaluó por HPLC. Los límites de detección y cuantificación fueron 0,01 y 0,1 ng/ml, respectivamente. Los niveles de OTA disminuyeron alrededor del 86,5% al final del proceso de vinificación. El tipo de cepa de Saccharomyces spp. utilizada no tuvo efecto sobre la reducción de OTA.

Equalizing growth in high-throughput small scale cultivations via precultures operated in fed-batch mode.

An often underestimated problem when working with different clones in microtiter plates and shake flask screenings is the non-parallel and non-equal growth of batch cultures. These growth differences are caused by variances of individual clones regarding initial biomass concentration, lag-phase or specific growth rate. Problems arising from unequal growth kinetics are different induction points in expression studies or uneven cultivation periods at the time of harvest. Screening for the best producing clones of a library under comparable conditions is thus often impractical or even impossible. A new approach to circumvent the problem of unequal growth kinetics of main cultures is the application of fed-batch mode in precultures in microtiter plates and shake flasks. Fed-batch operation in precultures is realized through a slow-release system for glucose. After differently growing cultures turn to glucose-limited growth, they all consume the same amount of glucose due to the fixed feed profile of glucose provided by the slow-release system. This leads to equalized growth. Inherent advantages of this method are that it is easy to use and requires no additional equipment like pumps. This new technique for growth equalization in high-throughput cultivations is simulated and verified experimentally. The growth of distinctly inoculated precultures in microtiter plates and shake flasks could be equalized for different microorganisms such as Escherichia coli and Hansenula polymorpha.

Fate of ochratoxin A content in Argentinian red wine during a pilot scale vinification.

The aim of this work was to evaluate the fate of ochratoxin A (OTA) content from must to wine during the red wine making process in a pilot scale vinification. The study was done using musts obtained from two red grape varieties (Bonarda and Tempranillo) artificially contaminated with two OTA levels. A duplicate set of tanks of 100 I each was established for each must (Bonarda and Tempranillo). The fermentations were initiated by inoculation of two Saccharomyces spp. strains having different fermentation performance. The must from the Tempranillo variety was spiked with 6 microg/I of OTA while that from the Bonarda variety with 0.3 microg/I of the toxin. Samples were collected at different stages of the process. Performance of the alcoholic and malolactic fermentations was monitored. Titratable and volatile acidity, pH, ethanol, sugar and SO2 concentrations were determined following standard methods proposed by the Office International de la Vigne et du Vin (OIV). OTA analysis was done by HPLC. Detection and quantification limits were 0.01 and 0.1 ng/ml, respectively. The OTA levels during the vinification trials dropped to an average of about 86.5%. The type of Saccharomyces strains used showed no effect on toxin reduction.

Stability and activity of lipase in subcritical 1,1,1,2-tetrafluoroethane (R134a).

The stability and activity of commercial immobilized lipase from Candida antarctica (Novozym 435) in subcritical 1,1,1,2-tetrafluoroethane (R134a) was investigated. The esterification of oleic acid with glycerol was studied as a model reaction in subcritical R134a and in solvent-free conditions. The results indicated that subcritical R134a treatment led to significant increase of activity of Novozym 435, and a maximum residual activity of 300% was measured at 4 MPa, 30 degrees C after 7 h incubation. No deactivation of Novozym 435 treated with subcritical R134a under different operation factors (pressure 2-8 MPa, temperature 30-60 degrees C, incubation time 1-12 h, water content 1:1, 1:2, 1:5 enzyme/water, depressurization rate 4 MPa/1 min, 4 MPa/30 min, 4 MPa/90 min) was observed. While the initial reaction rate was high in subcritical R134a, higher conversion was obtained in solvent-free conditions. Though the apparent conversion of the reaction is lower in subcritical R134a, it is more practicable, especially at low enzyme concentrations desired at commercial scales.

Development and standardization of cyst based liquid formulation of Azospirillum bioinoculant.

Azospirillum bioinoculant is well known for its high nitrogen fixing and plant growth promoting characters. The carrier based bioinoculants generally suffer from shorter shelf life, poor quality, high contamination and low field performance. Therefore, it is necessary to develop alternative new formulation of inoculants where cyst based inoculants can play significant role. The cyst based liquid formulation was developed by inoculating Azospirillum into the cyst inducing minimal salts medium (MSM). One hundred per cent conversion of vegetative cells into cyst cells was noticed in 96 h. The survival of cyst cells in the MSM was observed up to one year and two months and interestingly, the population level of 10(8) was maintained till the final observation. The cyst cells of Azospirillum accumulated poly-beta-hydroxybutyrate (PHB) granules and exhibited desiccation tolerance up to 20 days and temperature tolerance up to 40 degrees C. Thus the cyst based liquid formulation has twin advantage of longer shelf life and tolerance to harmful environmental conditions. Regeneration of cyst cells into vegetative cells in different media viz., tap water, sterile water, rice gruel and nutrient broth was studied. The changes started within 3 h and complete return of vegetative cells was observed at 24 h. Although all the media tested favoured regeneration, comparatively quicker regeneration was observed in nutrient broth and followed by rice gruel. Thus, cyst based liquid formulation of Azospirillum has all the survival advantages and can be used as a potential bioinoculant.

Process Analytical Technology (PAT): batch-to-batch reproducibility of fermentation processes by robust process operational design and control.

The Process Analytical Technology (PAT) initiative of the FDA is a reaction on the increasing discrepancy between current possibilities in process supervision and control of pharmaceutical production processes and its current application in industrial manufacturing processes. With rigid approval practices based on standard operational procedures, adaptations of production reactors towards the state of the art were more or less inhibited for long years. Now PAT paves the way for continuous process and product improvements through improved process supervision based on knowledge-based data analysis, "Quality-by-Design"-concepts, and, finally, through feedback control. Examples of up-to-date implementations of this concept are presented. They are taken from one key group of processes in recombinant pharmaceutical protein manufacturing, the cultivations of genetically modified Escherichia coli bacteria.

[4647-cell culture for preparation of recombinant bivaccine against smallpox and hepatitis B].

The seeding and working banks of a 4647-cell culture have been created. The 4647-cell culture in these banks has a high proliferative activity, as well as the morphology, typical of this line, and the karyotype and the enzymogram, which are characteristic for the cells of an African talapoin (Cercopithecus aethiops). The culture is not contaminated with bacteria, fungi, Mycoplasma, and viruses, including oncoviruses. The deposited 4647 cells have high viral productive properties for the accumulation of the recombinant virus strain b7,5S2-S vaccine and keep the stability of all biological properties during a long-term cultivation. The continuous 4647 cell line was tested at the L. A. Tarasevich State Institute of SK. The seeding and working banks of 4647-cell culture at passages 108 and 128 are recommended as a substrate for cultivation of the strain b7,5S2-S vaccinia, used to prepare a bivaccine against smallpox and hepatitis B.