Recent progress in the metabolic engineering of alkaloids in plant systems

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Highlights► Recent metabolic engineering efforts for plant alkaloids. ► Characterizing, reconfiguring and fine-tuning metabolic ‘parts’ improves titers. ► Additional strategies are necessary to produce ‘unnatural’ natural products.     

The challenges of cellular compartmentalization in plant metabolic engineering

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Highlights► Targeting enzymes to organelles with highest precursor pool affects product yield. ► Targeting of nonendogenous enzymes to organelles is a useful tool for engineering. ► Identification of transporters is central for effective metabolic engineering. ► Advances in metabolomics of isolated organelles will impact engineering strategies. ► Future plant metabolic engineering will include introduction of entire pathways.     

Comparative genomics approaches to understanding and manipulating plant metabolism

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Highlights► Comparative genomics can help predict the function of unknown plant metabolic genes. ► Functional gene annotations are foundational to the construction of metabolic models. ► Models can simulate effects of genetic changes and thus guide metabolic engineering. ► Examples of comparative genomics facilitating gene discovery in plants are presented.     

Stable isotope-assisted metabolomics to detect metabolic flux changes in mammalian cell cultures

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Highlights► Stable isotope-assisted metabolomics is powerful to determine metabolic fluxes. ► Stable isotope-assisted metabolomics is more complex for mammalian cell cultures. ► Biotechnological processes can be improved by assessing metabolic flux changes. ► Metabolic flux analysis is an attractive tool for toxicity studies. ► There is a huge potential for future applications on mammalian systems.     

Metabolic network flux analysis for engineering plant systems

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Highlights► A powerful range of tools has been developed for metabolic network flux analysis. ► These tools yield insights that are used to aid microbial metabolic engineering. ► Plants present great opportunities and special challenges to applying these tools. ► Tool selection and knowledge of plant systems is key to practical success.     

Profiling metabolic networks to study cancer metabolism

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Highlights► Metabolic dependencies that arise in tumors may present new opportunities for therapy. ► Advanced methods in metabolic systems biology can help identify these dependencies. ► Application of isotope tracers to cancer models can facilitates quantitation of fluxes. ► Tumors with compromised TCA metabolism exhibit unique metabolic profiles.     

Enzyme and metabolic engineering for the production of novel biopolymers: crossover of biological and chemical processes

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Highlights► Poly(ω-hydroxy fatty acids) are polyethylene-like biobased polyester. ► Medium-chain-length polyhydroxyalkanoate homopolymers are processed to stretchy film. ► Microbial lactate-based polyesters exhibit transparent and flexible properties. ► Enzyme and metabolic engineering facilitates the expanding of bio-based polymers.     

Pangenomics – an avenue to improved industrial starter cultures and probiotics

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Highlights► Genome sequencing is an efficient, cost-effective way of characterizing microbes. ► Pangenome analysis gives new insight into texture formation in yoghurt. ► Pangenome analysis of probiotic strains has identified new effect or molecules. ► Pangenome analysis gives insight into probiotic–host specificity. ► Future perspectives include improved strains for food fermentations and probiotics.     

Plant genome-scale metabolic reconstruction and modelling

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Highlights► Recent advances have been made on plant genome-scale metabolic reconstruction. ► Cellular compartmentation makes plant genome-scale reconstruction challenging. ► Current reconstructions capture important features of plant metabolism. ► The models have been used to study isolated tissues and tissue interaction. ► We review the challenges and potential of plant reconstruction and modelling.     

Transcriptome data modeling for targeted plant metabolic engineering

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Highlights► Network analysis is essential for data mining of omics-based large-scale data sets. ► Gene coexpression analysis is useful for prediction of gene function. ► Comparative network analysis can reveal common and unique plant metabolic pathways. ► Novel genome editing tools facilitate rational metabolic engineering.     

Network,nodes and nexus: systems approach to multitarget therapeutics

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Highlights► Complex diseases are an outcome of multiple triggers that precipitate into similar phenotypes. ► Systems level understanding can reveal dynamic aspects of disease progression profile. ► Correlation of metabolic remodeling to phenotypic alteration can delineate critical nodes of interventions. ► Multitargeting of key nodes of metabolic networks can be an effective therapeutic strategy. ► Robust and high-throughput data integration in conjunction with simulation would make the drug discovery process more efficient.     

Metabolomics platforms for genome wide association studies—linking the genome to the metabolome

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Highlights► Genome-wide association studies with metabolomics constitute mGWAS. ► mGWAS provide insights into genetic and environmental impact on metabolic processes. ► We review essential strategies for mGWAS. ► Examples of mGWAS in large cohort studies are discussed.     

Metagenomics of microbial life in extreme temperature environments

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Highlights► Metagenomic microbial community characterization. ► Extreme environment microbiology. ► High and low temperature adaptation.     

Towards metagenome-scale models for industrial applications — the case of Lactic Acid Bacteria

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Highlights► Genome-scale metabolic modelling is being increasingly applied in LAB research. ► Novel techniques that broaden applicability of models remain to be applied to LAB. ► Additional constraints allow better predictions of genome-scale metabolic models. ► Novel approaches to move from modelling monocultures to mixed cultures are being developed. ► The feasibility of metagenome-based modelling approaches is being appreciated.     

Bacteria as vitamin suppliers to their host: a gut microbiota perspective

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Highlights► Humans lack the biosynthetic capacity for most vitamins. ► Vitamins must thus be provided exogenously by nutritionally balanced diets. ► Members of the human gut microbiota can supply their host with microbially synthesized vitamins. ► Fermented milks with high levels of B-group vitamins can be produced by lactic acid.     

Environmental factors influencing the efficacy of probiotic bacteria

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Highlights► Probiotics are living cells and not typical food ingredients. ► Probiotics rapidly adapt to changing conditions in consumer products and the gut. ► Processing, consumer product, and host differences might influence probiotic efficacy. ► Clinical studies should include measurements of probiotic effector expression levels.     

Gut metabotypes govern health effects of dietary polyphenols

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Highlights► Health effects of dietary polyphenols often depend on multiple metabolic processes. ► Gut metabotypes with specific polyphenol metabolism patterns can be differentiated. ► Physiologically achievable concentrations of relevant metabolites should be tested. ► Novel products and applications can exploit polyphenol–microbiota interactions.     

Biological conversion of carbon dioxide and hydrogen into liquid fuels and industrial chemicals

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Highlights► Electrofuels are non-photosynthetic, energy-dense fuels made from carbon dioxide. ► Herein, we review electrofuel production in hydrogen-utilizing organisms. ► We review both current and emerging electrofuel platforms and organisms. ► New advancements in genetic tools for electrofuel host organisms are examined.     

Microbe–microbe interactions in mixed culture food fermentations

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Highlights► Microbial interactions in food fermentations are crucial for product functionality. ► Complex microbial consortia tolerate more variation in the environment. ► Knowledge of communities of fermenting microbes drives diversification of starter cultures. ► Use of complex starter cultures requires new propagation methodologies. ► Immobilised cell technology is a high potential solution for propagating complex cultures.