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.     

The emerging field of transport engineering of plant specialized metabolites

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Highlights► Transport engineering has the potential to increase nutritional value of crops. ► Transport engineering can increase yield of synthetic biology approaches. ► Neo-functionalization of primary metabolite transporters to specialized metabolism. ► Elimination of glucosinolate seed accumulation is achieved via transport engineering. ► Glucosinolates in Arabidopsis: a model for transport of specialized metabolites.     

The role of membrane transport in metabolic engineering of plant primary metabolism

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Highlights► The plastidial pyruvate transporter in plants is driven by sodium symport. ► The mitochondrial pyruvate transporter MPC has been identified. ► All transporters needed for a synthetic PEP-CK/C₄ photosynthetic cycle are now known. ► The SWEET proteins define a new class of sugar efflux carriers in plants.     

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.     

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.     

Computational methods for evaluation of cell-based data assessment—Bioconductor

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Highlights► Bioconductor proposes more than 20 R packages for FCM analysis. ► Data infrastructure proposed by flowCore has become the standard for many packages. ► Automated gating is improving but remains an intensive field of research.     

Recent trends in nanopores for biotechnology

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Highlights► Nanopores are single-molecule detectors with exceptional sensitivity and versatility. ► Over the past few years, progress has been made in making and using nanopores in biotechnology. ► Nanopore-based DNA sequencing can revolutionize healthcare by reducing both sequencing costs and time.     

Clawing back: broadening the notion of metal chelators in medicine

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Highlights► Not all chelators are the same: more than metal sequestration and elimination. ► Metal chelates can redistribute metals across biological membranes. ► Metal-chelating fragments provide leads for metalloenzyme inhibition. ► Metal chelation can enhance metal reactivity and thus cytotoxicity. ► Prochelators provide site-activated metal chelation and passivation.     

Progress in understanding and engineering primary plant metabolism

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Highlights► Crop yield depends on efficiency of conversion of light energy into biomass. ► Models have estimated energy conversion efficiency in photosynthesis and metabolism. ► Research is exploring strategies to modify or suppress photorespiration. ► Energy loss during conversion of photosynthate to biomass is also large ► Research is addressing uncertainties over where these losses occur.     

In situ treatment of PCBs by anaerobic microbial dechlorination in aquatic sediment: are we there yet?

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Highlights► Microbial catalysts with different PCB dechlorinating activities are cultured. ► Biostimulation and bioaugmentation has been successful in the laboratory. ► Molecular tools for monitoring dechlorinating bacteria in situ are available. ► Methods to deploy these catalysts in the field are currently under development.     

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.     

Nanotechnology meets electrophysiology

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Highlights► We focus on the latest developments in nanotechnology-based electrophysiology. ► Methods for extracellular recording via nanoFET-based devices are described. ► Metal nanoelectrodes for the recording of electrogenic cells are reviewed. ► The latest developments of intracellular FET-based probes are shortly covered. ► Pioneering electrical scaffold devices for the interfacing with tissues are described.     

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.     

DNA nanotechnology with one-dimensional self-assembled nanostructures

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Highlights► Hybridization chain reactions for amplified DNA detection and DNA assembly. ► Rolling circle amplification-synthesized DNAzyme chains for amplified DNA detection. ► Bi-enzyme cascades and biocatalytic synthesis of metallic nanowires on DNA templates. ► Self-assembled one-dimensional DNA nanostructures for biocatalytic cascades. ► Programmed assembly of metal nanoparticles on one-dimensional DNA nanostructures.     

Engineering plant metabolism into microbes: from systems biology to synthetic biology

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Highlights► Microbial production of pharmaceutical and fuel molecules. ► Systems biology tools advanced our understanding about synthetic pathway design. ► Synthetic biology led us to cell factories tailor-made for chemical production. ► Combinatorial gene assembly for synthetic pathway diversification. ► Engineering static, dynamic and spatial control for better production phenotype.     

Perspectives on the contribution of lactic acid bacteria to cheese flavor development

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Highlights► This review covers current know-how on cheese flavor development. ► Proteolysis, autolysis and amino acid catabolism by lactic acid bacteria are discussed. ► Systems biology approaches will drive future technology improvements. ► Next-generation sequencing holds promise for fast increase in exploitable knowledge. ► Culture heterogeneity may be significant for industrial flavor production by LAB.     

Human milk and related oligosaccharides as prebiotics

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Highlights► The intestinal microbiome is recognized as an important determinant of health. ► Galacto-oligosaccharides are non-digestible carbohydrates. ► Galacto-oligosaccharides stimulate growth and activity of gut bacteria. ► Subtle differences in structure can result in significant differences in activity. ► Less abundant oligosaccharides from bovine milk are similar to those from human milk.     

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.