Environmental sustainability of food production and consumption in the Nordic and Baltic region - a scoping review for Nordic Nutrition Recommendations 2023

This scoping review examines environmental impacts related to food production and consumption in Nordic and Baltic countries. The overarching advice to all Nordic and Baltic countries, in line with the current body of scientific literature, is to shift to a more plant-based dietary pattern and avoid food waste. Taking into account current consumption patterns, there is a high potential and necessity to shift food consumption across the countries to minimise its environmental impact. More specifically, a substantial reduction in meat and dairy consumption and increased consumption of legumes/pulses, whole grains, vegetables, fruits, nuts, and seeds are suggested as a priority intervention. Reducing the environmental impacts of seafoods is also key and suggestions include a shift to seafoods with lower environmental impacts such as seaweed and bivalves. As part of the suggested transition to a more plant-based diet, the scope for increasing the provision of plant-based foods through increasing the cultivation of legumes/pulses, vegetables, and grains and through feed-to-food shifts within the region should be explored.

Genetic Circuits for Feedback Control of Gamma-Aminobutyric Acid Biosynthesis in Probiotic Escherichia coli Nissle 1917

Engineered microorganisms such as the probiotic strain Escherichia coli Nissle 1917 (EcN) offer a strategy to sense and modulate the concentration of metabolites or therapeutics in the gastrointestinal tract. Here, we present an approach to regulate the production of the depression-associated metabolite gamma-aminobutyric acid (GABA) in EcN using genetic circuits that implement negative feedback. We engineered EcN to produce GABA by overexpressing glutamate decarboxylase and applied an intracellular GABA biosensor to identify growth conditions that improve GABA biosynthesis. We next employed characterized genetically encoded NOT gates to construct genetic circuits with layered feedback to control the rate of GABA biosynthesis and the concentration of GABA produced. Looking ahead, this approach may be utilized to design feedback control of microbial metabolite biosynthesis to achieve designable smart microbes that act as living therapeutics.

Expectations for employing Escherichia coli Nissle 1917 in food science and nutrition

As a promising probiotic strain, Escherichia coli Nissle 1917 (EcN) has been demonstrated to confer beneficial effects on intestinal health, immune function, and pathogen prevention. Additionally, EcN has also been widely studied due to its clear genomic information, tractable gene regulation, and simple growth conditions. This review summarizes the various applications potential of EcN in food science and nutrition, including inflammation prevention, tumor-targeting therapy, antibacterial agents for food, and nutrient production with a focus on specific case studies. Moreover, we highlight the major challenges of employing EcN in food science and nutrition, including regulatory approval, stability during food processing, and consumer acceptance. Finally, we conclude with a discussion on perspectives related to employing EcN in food science and nutrition.

Engineering Escherichia coli Nissle 1917 as a microbial chassis for therapeutic and industrial applications

Genetically engineered microbes, especially Escherichia coli, have been widely used in the biosynthesis of proteins and metabolites for medical and industrial applications. As a traditional probiotic with a well-established safety record, E. coli Nissle 1917 (EcN) has recently emerged as a microbial chassis for generating living therapeutics, drug delivery vehicles, and microbial platforms for industrial production. Despite the availability of genetic tools for engineering laboratory E. coli K-12 and B strains, new genetic engineering systems are still greatly needed to expand the application range of EcN. In this review, we have summarized the latest progress in the development of genetic engineering systems in EcN, as well as their applications in the biosynthesis and delivery of valuable small molecules and biomacromolecules of medical and/or industrial interest, followed by a glimpse of how this rapidly growing field will evolve in the future.

Genetic circuits for feedback control of gamma-aminobutyric acid biosynthesis in probiotic Escherichia coli Nissle 1917

Engineered microorganisms such as the probiotic strain Escherichia coli Nissle 1917 (EcN) offer a strategy to sense and modulate the concentration of metabolites or therapeutics in the gastrointestinal tract. Here, we present an approach to regulate production of the depression-associated metabolite gamma-aminobutyric acid (GABA) in EcN using genetic circuits that implement negative feedback. We engineered EcN to produce GABA by overexpressing glutamate decarboxylase (GadB) from E. coli and applied an intracellular GABA biosensor to identify growth conditions that improve GABA biosynthesis. We next employed characterized genetically-encoded NOT gates to construct genetic circuits with layered feedback to control the rate of GABA biosynthesis and the concentration of GABA produced. Looking ahead, this approach may be utilized to design feedback control of microbial metabolite biosynthesis to achieve designable smart microbes that act as living therapeutics.

Characterization of the Positive Transcription Regulator PfaR for Improving Eicosapentaenoic Acid Production in Shewanella putrefaciens W3-18-1

The biosynthetic pathway of eicosapentaenoic acid (EPA) has previously been reported in marine bacteria, while the regulatory mechanism remains poorly understood. In this study, a putative transcriptional regulator PfaR encoded adjacent to the PFA biosynthesis gene cluster (pfaEABCD) was computationally and experimentally characterized. Comparative analyses on the wild type (WT) strain, in-frame deletion, and overexpression mutants revealed that PfaR positively regulated EPA synthesis at low temperature. RNA-Seq and real-time quantitative PCR analyses demonstrated that PfaR stimulated the transcription of pfaABCD. The transcription start site of pfaR was mapped by using primer extension and highly conserved promoter motifs bound by the housekeeping Sigma 70 factor that were identified in the upstream of pfaR. Moreover, overexpression of PfaR in WT strain W3-18-1 at low temperature could improve EPA productivity from 0.07% to 0.13% (percentage of EPA to dry weight, mg/mg) of dry weight. Taken together, these findings could provide important implications into the transcriptional control and metabolic engineering in terms of EPA productivity for industrial strains. IMPORTANCE We have experimentally confirmed that PfaR is a positive transcription regulator that promotes EPA synthesis at low temperature in Shewanella putrefaciens W3-18-1. Overexpression of PfaR in WT strain W3-18-1 could lead to a 1.8-fold increase in EPA productivity at low temperature. It is further shown that PfaR may be regulated by housekeeping Sigma 70 factor at low temperature.

Recombinant Probiotic Preparations: Current State, Development and Application Prospects

The article is devoted to the latest achievements in the field of research, development, and implementation of various types of medicinal products based on recombinant probiotics. The benefits of probiotics, their modern use in medicine along with the most frequently used genera and species of probiotic microorganisms were highlighted. The medicinal and therapeutic activities of the studied probiotics were indicated. The review suggests various methods of creating recombinant probiotic microorganisms, including standard genetic engineering methods, as well as systems biology approaches and new methods of using the CRISPR-Cas system. The range of potential therapeutic applications of drugs based on recombinant probiotics was proposed. Special attention was paid to modern research on the creation of new, more effective recombinant probiotics that can be used for various therapeutic purposes. Considering the vast diversity of therapeutic applications of recombinant probiotics and ambiguous functions, their use for the potential treatment of various common human diseases (non-infectious and infectious diseases of the gastrointestinal tract, metabolic disorders, and allergic conditions) was investigated. The prospects for creating different types of vaccines based on recombinant probiotics together with the prospects for their implementation into medicine were considered. The possibilities of using recombinant probiotics in veterinary medicine, particularly for the prevention of domestic animal diseases, were reviewed. The prospects for the implementation of recombinant probiotics as vaccines and diagnostic tools for testing certain diseases as well as modeling the work of the human digestive system were highlighted. The risks of creation, application, including the issues related to the regulatory sphere regarding the use of new recombinant microorganisms, which can potentially enter the environment and cause unforeseen circumstances, were outlined.

Fatty Acid Production by Enhanced Malonyl-CoA Supply in Escherichia coli

The expression of exogenous genes encoding acetyl-CoA carboxylase (Acc) and pantothenate kinase (CoaA) in Escherichia coli enable highly effective fatty acid production. Acc-only strains grown at 37 °C or 23 °C produced an approximately twofold increase in fatty acid content, and additional expression of CoaA achieved a further twofold accumulation. In the presence of pantothenate, which is the starting material for the CoA biosynthetic pathway, the size of the intracellular CoA pool at 23 °C was comparable to that at 30 °C during cultivation, and more than 500 mg/L of culture containing cellular fatty acids was produced, even at 23 °C. However, the highest yield of cellular fatty acids (1100 mg/L of culture) was produced in cells possessing the gene encoding type I bacterial fatty acid synthase (FasA) along with the acc and coaA, when the transformant was cultivated at 30 °C in M9 minimal salt medium without pantothenate or IPTG. This E. coli transformant contained 141 mg/L of oleic acid attributed to FasA under noninducible conditions. The increased fatty acid content was brought about by a greatly improved specific productivity of 289 mg/g of dry cell weight. Thus, the effectiveness of the foreign acc and coaA in fatty acid production was unambiguously confirmed at culture temperatures of 23 °C to 37 °C. Cofactor engineering in E. coli using the exogenous coaA and acc genes resulted in fatty acid production over 1 g/L of culture and could effectively function at 23 °C.

Synechococcus elongatus PCC 7942 as a Platform for Bioproduction of Omega-3 Fatty Acids

Alpha-linolenic acid and stearidonic acid are precursors of omega-3 polyunsaturated fatty acids, essential nutrients in the human diet. The ability of cyanobacteria to directly convert atmospheric carbon dioxide into bio-based compounds makes them promising microbial chassis to sustainably produce omega-3 fatty acids. However, their potential in this area remains unexploited, mainly due to important gaps in our knowledge of fatty acid synthesis pathways. To gain insight into the cyanobacterial fatty acid biosynthesis pathways, we analyzed two enzymes involved in the elongation cycle, FabG and FabZ, in Synechococcus elongatus PCC 7942. Overexpression of these two enzymes led to an increase in C18 fatty acids, key intermediates in omega-3 fatty acid production. Nevertheless, coexpression of these enzymes with desaturases DesA and DesB from Synechococcus sp. PCC 7002 did not improve alpha-linolenic acid production, possibly due to their limited role in fatty acid synthesis. In any case, efficient production of stearidonic acid was not achieved by cloning DesD from Synechocystis sp. PCC 6803 in combination with the aforementioned DesA and DesB, reaching maximum production at 48 h post induction. According to current knowledge, this is the first report demonstrating that S. elongatus PCC 7942 can be used as an autotrophic chassis to produce stearidonic acid.

A comparative study on the genomes, transcriptomes, and metabolic properties of Escherichia coli strains Nissle 1917, BL21(DE3), and MG1655

Escherichia coli is the most well-studied model prokaryote and has become an indispensable host for the biotechnological production of proteins and biochemicals. In particular, the probiotic status of one E. coli strain, E. coli Nissle 1917 (EcN) has helped it become a new favorite amongst synthetic biologists. To broaden its potential applications, here we assemble a comparative study on the genomes, transcriptomes, and metabolic properties of E. coli strains EcN, BL21(DE3), and MG1655. Comparative genomics data suggests that EcN possesses 1404 unique CDSs. In particular, EcN has additional iron transport systems which endow EcN with a higher tolerance to iron scarcity when compared to two other E. coli strains. EcN transcriptome data demonstrates that E. coli strains EcN, BL21(DE3), and MG1655 all have comparable activities of the central metabolic pathway, however only EcN inherits the arginine deiminase pathway. Additionally, we found that EcN displayed a lower expression of ribosomal proteins compared to BL21(DE3) and MG1655. This comparative study on E. coli strains EcN, BL21(DE3), and MG1655 aims to provide a reference for further engineering EcN as a biotechnological tool.

Construction of a sustainable 3-hydroxybutyrate-producing probiotic Escherichia coli for treatment of colitis

Colitis is a common disease of the colon that is very difficult to treat. Probiotic bacteria could be an effective treatment. The probiotic Escherichia coli Nissle 1917 (EcN) was engineered to synthesize the ketone body (R)-3-hydroxybutyrate (3HB) for sustainable production in the gut lumen of mice suffering from colitis. Components of heterologous 3HB synthesis routes were constructed, expressed, optimized, and inserted into the EcN genome, combined with deletions in competitive branch pathways. The genome-engineered EcN produced the highest 3HB level of 0.6 g/L under microaerobic conditions. The live therapeutic was found to colonize the mouse gastrointestinal tract over 14 days, elevating gut 3HB and short-chain-length fatty acid (SCFA) levels 8.7- and 3.1-fold compared to those of wild-type EcN, respectively. The sustainable presence of 3HB in mouse guts promoted the growth of probiotic bacteria, especially Akkermansia spp., to over 31% from the initial 2% of all the microbiome. As a result, the engineered EcN termed EcNL4 ameliorated colitis induced via dextran sulfate sodium (DSS) in mice. Compared to wild-type EcN or oral administration of 3HB, oral EcNL4 uptake demonstrated better effects on mouse weights, colon lengths, occult blood levels, gut tissue myeloperoxidase activity and proinflammatory cytokine concentrations. Thus, a promising live bacterium was developed to improve colonic microenvironments and further treat colitis. This proof-of-concept design can be employed to treat other diseases of the colon.

Heterologous Production of Polyunsaturated Fatty Acids in E. coli Using Δ5-Desaturase Gene from Microalga Isochrysis Sp

Eicosapentaenoic acid (EPA) and arachidonic acid (ARA) are long-chain polyunsaturated fatty acids (PUFAs) that play a significant role in human growth and development, which deficiency can trigger several metabolic-related diseases. Since the availability of PUFA sources is limited, there arises a need to explore alternative sources. Therefore, the present study aimed to investigate whether an Escherichia coli which are engineered with Δ5Des-Iso gene isolated from Isochrysis sp. could be utilized to synthesize PUFAs. Full-length gene Δ5Des-Iso (1149 bp) was isolated from Isochrysis sp. that encodes 382 amino acids and identified as Δ5-desatruase gene using different bioinformatic analysis. Heterologous gene expression was carried out in E. coli having Δ5Des-Iso with precursor fatty acids. The Δ5Des-Iso produced novel fatty acids of EPA (ω-3) and ARA (ω-6) as respective products were identified by GC-MS. Gene expression and PUFA synthesis in E. coli were optimized by temperature, time, and concentrations of precursor fatty acid substrates. Δ5Des-Iso RNA transcript level was inversely proportional to the time and fatty acid synthesis. And, the significant production of EPA (4.1 mg/g) and ARA (8.3 mg/g) in total fatty acids was observed in E. coli grown at 37 °C for 24 h with 25 μM of external fatty acid substrate as an optimum growth conditions. E. coli could be used as alternative organism to synthesis PUFAs and widely applicable in many nutraceuticals and pharmaceuticals industry for human use.

Designer Probiotics: The Next-Gen High Efficiency Biotherapeutics

The probiotic engineering is a cutting edge technology for improving disease diagnosis, treating gastrointestinal disorders and infectious diseases, and improving nutrition and ecological health. Use of bioengineered microorganisms in animals has different targets and prospects owing to differences in their anatomy, physiology, and feeding habits. In ruminants, the bioengineered microorganism is primarily aimed to enhance nutrient utilization, detoxify toxic plant metabolites, and lessen the enteric methanogenesis, while in non-ruminants, the bioengineered microorganisms are aimed to enhance nutrient utilizations, confer protection against pathogens, and inhibit infectious agents.

Highlights

The microorganisms can be engineered to enhance their metabolic efficiency

The bioengineered microorganisms could solve the burgeoning problem of drug-resistant pathogens

The recombinant probiotics are promising therapeutic agents against infectious diseases.

Pathway Grafting for Polyunsaturated Fatty Acids Production in Ashbya gossypii through Golden Gate Rapid Assembly

Here we present a Golden Gate assembly system adapted for the rapid genomic engineering of the industrial fungus Ashbya gossypii. This biocatalyst is an excellent biotechnological chassis for synthetic biology applications and is currently used for the industrial production of riboflavin. Other bioprocesses such as the production of folic acid, nucleosides, amino acids and biolipids have been recently reported in A. gossypii. In this work, an efficient assembly system for the expression of heterologous complex pathways has been designed. The expression platform comprises interchangeable DNA modules, which provides flexibility for the use of different loci for integration, selection markers and regulatory sequences. The functionality of the system has been applied to engineer strains able to synthesize polyunsaturated fatty acids (up to 35% of total fatty acids). The production of the industrially relevant arachidonic, eicosapentanoic and docosahexanoic acids remarks the potential of A. gossypii to produce these functional lipids.

Polyunsaturated fatty acids in marine bacteria and strategies to enhance their production

Polyunsaturated fatty acids (PUFAs) play an important role in human diet. Despite the wide-ranging importance and benefits from heart health to brain functions, humans and mammals cannot synthesize PUFAs de novo. The primary sources of PUFA are fish and plants. Due to the increasing concerns associated with food security as well as issues of environmental contaminants in fish oil, there has been considerable interest in the production of polyunsaturated fatty acids from alternative resources which are more sustainable, safer, and economical. For instance, marine bacteria, particularly the genus of Shewanella, Photobacterium, Colwellia, Moritella, Psychromonas, Vibrio, and Alteromonas, are found to be one among the major microbial producers of polyunsaturated fatty acids. Recent developments in the area with a focus on the production of polyunsaturated fatty acids from marine bacteria as well as the metabolic engineering strategies for the improvement of PUFA production are discussed.

Engineering chemical interactions in microbial communities

Microbes living within host-associated microbial communities (microbiotas) rely on chemical communication to interact with surrounding organisms. These interactions serve many purposes, from supplying the multicellular host with nutrients to antagonizing invading pathogens, and breakdown of chemical signaling has potentially negative consequences for both the host and microbiota. Efforts to engineer microbes to take part in chemical interactions represent a promising strategy for modulating chemical signaling within these complex communities. In this review, we discuss prominent examples of chemical interactions found within host-associated microbial communities, with an emphasis on the plant-root microbiota and the intestinal microbiota of animals. We then highlight how an understanding of such interactions has guided efforts to engineer microbes to participate in chemical signaling in these habitats. We discuss engineering efforts in the context of chemical interactions that enable host colonization, promote host health, and exclude pathogens. Finally, we describe prominent challenges facing this field and propose new directions for future engineering efforts.

Enhanced eicosapentaenoic acid production by a new deep-sea marine bacterium Shewanella electrodiphila MAR441T

Omega-3 fatty acids are products of secondary metabolism, essential for growth and important for human health. Although there are numerous reports of bacterial production of omega-3 fatty acids, less information is available on the biotechnological production of these compounds from bacteria. The production of eicosapentaenoic acid (EPA, 20:5ω3) by a new species of marine bacteria Shewanella electrodiphila MAR441T was investigated under different fermentation conditions. This strain produced a high percentage (up to 26%) of total fatty acids and high yields (mg / g of biomass) of EPA at or below the optimal growth temperature. At higher growth temperatures these values decreased greatly. The amount of EPA produced was affected by the carbon source, which also influenced fatty acid composition. This strain required Na+ for growth and EPA synthesis and cells harvested at late exponential or early stationary phase had a higher EPA content. Both the highest amounts (20 mg g-1) and highest percent EPA content (18%) occurred with growth on L-proline and (NH4)2SO4. The addition of cerulenin further enhanced EPA production to 30 mg g-1. Chemical mutagenesis using NTG allowed the isolation of mutants with improved levels of EPA content (from 9.7 to 15.8 mg g-1) when grown at 15°C. Thus, the yields of EPA could be substantially enhanced without the need for recombinant DNA technology, often a commercial requirement for food supplement manufacture.

Genetic engineering of probiotic Escherichia coli Nissle 1917 for clinical application

Escherichia coli strain Nissle 1917 (EcN) has been used as a probiotic. Genetic engineering has enhanced the utility of EcN in several vaccine and pharmaceutical preparations. We discuss in this mini review the genetics and physical properties of EcN. We also discuss the numerous genetic engineering strategies employed for EcN-based vaccine development, including recombinant plasmid transfer, genetic engineering of cryptic plasmids or the EcN chromosome, EcN bacterial ghosts and its outer membrane vesicles. We also provide a current update on the progress and the challenges regarding the use of EcN in vaccine development.