Applied microbiology articles within Nature Communications

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  • Article
    | Open Access

    Microbial heparin bioproduction is hampered by the difficulty of recombinant expression of active heparan sulfate N-deacetylase/N-sulfotransferase. Here, the authors solve the problem by developing a cellular system-based semisynthetic strategy and achieve the production of active heparin by engineered E. coli.

    • Jian-Qun Deng
    • , Yi Li
    •  & Ju-Zheng Sheng

  • Article
    | Open Access

    Pseudomonas putida is becoming a host of choice for the valorization of lignocellulosic substrates. Here, the authors provide insight into the adaptation of this bacterium to the non-native substrate D-xylose, enabled by metabolic engineering and adaptive laboratory evolution.

    • Pavel Dvořák
    • , Barbora Burýšková
    •  & Martin Benešík

  • Article
    | Open Access

    While tricarboxylic acid cycle (TCA cycle) is required for heterotrophic microbes, it reduces carbon yield of industrial products due to the release of excess CO2. Here, the authors construct an E. coli strain without a functional TCA cycle and demonstrate its feasibility as a chassis strain for production of four separate compounds.

    • Hang Zhou
    • , Yiwen Zhang
    •  & Baixue Lin

  • Article
    | Open Access

    The Wolbachia cifA and cifB genes generate cytoplasmic incompatibility (CI) in insect hosts but the role of cifA is still debated. Here, the authors report the transgenic recapitulation of CI in the major arbovirus vector Aedes aegypti and provide evidence for cifA inhibiting cifB toxicity in the male germline.

    • Cameron J. McNamara
    • , Thomas H. Ant
    •  & Steven P. Sinkins

  • Article
    | Open Access

    Synthetic microbial communities are suitable for mixed substrates fermentation and long metabolic pathway engineering. Here, the authors combine fermentation experiments with mathematical modeling to reveal the effect of compositional and temporal changes on division of labor in cellulosic ethanol production using two yeast strains.

    • Jonghyeok Shin
    • , Siqi Liao
    •  & Yong-Su Jin

  • Article
    | Open Access

    No consensus exists on the computationally tractable use of dynamic models for strain design. To tackle this, the authors report a framework, nonlinear-dynamic-model-assisted rational metabolic engineering design, for efficiently designing robust, artificially engineered cellular organisms.

    • Bharath Narayanan
    • , Daniel Weilandt
    •  & Vassily Hatzimanikatis

  • Article
    | Open Access

    Ajmaline is an antiarrhythmic monoterpenoid indole alkaloid produced by the root of Rauwolfia serpentina. Here, the authors complete the ajmaline biosynthetic pathway by identifying two reductases and two esterases, and achieve the de novo ajmaline biosynthesis by engineering Baker’s yeast.

    • Jun Guo
    • , Di Gao
    •  & Yang Qu

  • Article
    | Open Access

    Cellular heterogeneity in cell populations of isogenic origin is driven by diverse factors such as nutrient availability and interactions with neighbouring cells. Here, Hu et al. study plasmid retention dynamics in yeast populations, and show that the exchange of complementary metabolites between plasmid-carrying prototrophs and plasmid-free auxotrophs allows the latter to proliferate in selective environments.

    • Kevin K. Y. Hu
    • , Ankita Suri
    •  & Victoria S. Haritos

  • Article
    | Open Access

    Microbial communities are the siege of complex metabolic interactions including cooperation and competition. Here, the authors report the utilization of optogenetics and spatial light-patterning to activate the expression of the invertase SUC2 at selected locations and selectively switch cooperation and competition roles of the yeast cells.

    • Matthias Le Bec
    • , Sylvain Pouzet
    •  & Pascal Hersen

  • Article
    | Open Access

    Cheese fermentation and flavour formation are the result of complex biochemical reactions driven by the activity of multiple microorganisms. Here, the authors identify microbial interactions as a mechanism underlying flavour formation in Cheddar cheese.

    • Chrats Melkonian
    • , Francisco Zorrilla
    •  & Ahmad A. Zeidan

  • Article
    | Open Access

    One-carbon substrates are attractive feedstocks for circular bioeconomy. Here, the authors design an erythrulose monophosphate (EuMP) cycle for formaldehyde assimilation, demonstrate the activity of the core reactions in E. coli, and show its integration with pathway reactions existed in pentose phosphate pathway and glycolysis.

    • Tong Wu
    • , Paul A. Gómez-Coronado
    •  & Hai He

  • Article
    | Open Access

    Redox imbalance limits succinic acid (SA) biosynthesis from glucose via the reductive tricarboxylic acid (TCA) cycle in yeast. Here, the authors engineering the aerobic yeast Yarrowia lipolytica for efficient SA production without pH control via coupling the oxidative and reductive TCA cycle for NADH regeneration in mitochondria.

    • Zhiyong Cui
    • , Yutao Zhong
    •  & Qingsheng Qi

  • Article
    | Open Access

    Microbial rhodopsins are major contributors to global light harvesting on Earth, but their role in carbon fixation is unclear. Here, the authors construct an artificial photosynthesis system by combining rhodopsin with an extracellular electron uptake mechanism for photoelectrosynthetic CO2 fixation in Ralstonia eutropha.

    • Weiming Tu
    • , Jiabao Xu
    •  & Wei E. Huang

  • Article
    | Open Access

    It’s challenging to produce natural products using single strains of engineered microbes fed by renewable carbon sources. Here, the authors assemble a microbial consortium consisting of engineered S. stipitis and S. cerevisiae for streamlined production of (S)-norcoclaurine from glucose and xylose simultaneously.

    • Meirong Gao
    • , Yuxin Zhao
    •  & Zengyi Shao

  • Article
    | Open Access

    One carbon compounds such as CO2, methanol and formate are cost-effective and environmentally friendly microbial feedstocks for biomanufacturing. Here, the authors report the oxygen tolerant reductive glycine pathway in Komagataella phaffii can co-assimilate CO2, methanol and formate.

    • Bernd M. Mitic
    • , Christina Troyer
    •  & Diethard Mattanovich

  • Article
    | Open Access

    Engineering ammonium excretion diazotrophs suffers from severe penalties to the bacteria. Here, the authors utilize a thermo-sensitive glutamine synthetase-based regulatory switch that permits diurnal changes in diazotrophic lifestyle, coincident with seasonal temperatures for cereal cultivation.

    • Yuqian Tang
    • , Debin Qin
    •  & Yi-Ping Wang

  • Article
    | Open Access

    Sufficient supply of sulfonate group donor is critical to biomanufacturing of the sulfate containing compounds. Here, the authors engineer two sulfonate group donor regeneration systems, including 3'-phosphoadenosine-5'-phosphosulfate and the newly discovered 5'-phosphosulfate, to boost biosynthesis of sulfated compounds.

    • Ruirui Xu
    • , Weijao Zhang
    •  & Zhen Kang

  • Perspective
    | Open Access

    The utilization of one-carbon assimilation pathways for bioproduction represents a promising direction towards a more sustainable bio-based economy. Here, the authors compare the thermodynamic efficiencies and energy demand of C1-assimilation pathways and discuss their implementation for energy, material, and food production.

    • Simone Bachleitner
    • , Özge Ata
    •  & Diethard Mattanovich

  • Article
    | Open Access

    Gut microbiota has been reported to influence osteoporosis risk, but the individual species, and underlying mechanisms, remain largely unknown. Here, the authors identify Bacteroides vulgatus and serum valeric acid as potential targets for osteoporosis prevention/treatment.

    • Xu Lin
    • , Hong-Mei Xiao
    •  & Hong-Wen Deng

  • Perspective
    | Open Access

    Using one carbon (C1) molecules as primary feedstock for bioproduction holds great potential for a circular and carbon neutral economy. Here, the authors discuss the potential of merging knowledge gained from natural and synthetic C1-trophic organisms to expedite the development of efficient C1-based biomanufacturing.

    • Enrico Orsi
    • , Pablo Ivan Nikel
    •  & Stefano Donati

  • Article
    | Open Access

    Generating and controlling cell collective behavior is important for synthetic biology and bioproduction. Here, the authors show the diversification dynamic and the fitness cost associated with cell switching are coupled in yeast and bacteria, and demonstrate the feasibility of controlling diversification regimes.

    • Lucas Henrion
    • , Juan Andres Martinez
    •  & Frank Delvigne

  • Article
    | Open Access

    Common methods for water disinfection involve oxidation or irradiation, and are often associated with a high carbon footprint and formation of toxic byproducts. Here, the authors describe a nano-structured material that is highly effective at killing bacteria in water through a hydrodynamic mechanism driven by mild water flow, in the absence of additional energy supply.

    • Lu Peng
    • , Haojie Zhu
    •  & Hong-Ying Hu

  • Article
    | Open Access

    The inherent toxicity of the aromatic compounds to the chassis strain hampers further improvement of bioproduction. Here, the authors show that membrane rigidifying effect of resveratrol can be attenuated by exogenous supplementation of palmitelaidic acid or linoleic acid in fermentation of Corynebacterium glutamicum.

    • Apilaasha Tharmasothirajan
    • , Josef Melcr
    •  & Jan Marienhagen

  • Article
    | Open Access

    Baker’s yeast is a workhorse of industrial biotechnology, but it is not suited to overproduce many bulk bioproducts, especially organic acids. Here, the authors identify Pichia occidentalis as an acid tolerant yeast and engineer it for the production of muconic acid using a newly developed genome editing toolkit.

    • Michael E. Pyne
    • , James A. Bagley
    •  & Vincent J. J. Martin

  • Article
    | Open Access

    In metabolic engineering, releasing of carbon in the form of CO2 leads to significant decrease of atomic economy. Here, the authors construct a carbon-conserving pathway, which converts glucose into acetyl phosphate without carbon loss, with oscillatory system to improve production of multiple target compounds.

    • Likun Guo
    • , Min Liu
    •  & Guang Zhao

  • Article
    | Open Access

    Photosynthetic glucose production is well controlled due to its complex interactions with other cellular processes. Here, the authors identify that the native glucokinase activity is the bottleneck restricting the metabolism potential for glucose synthesis and engineer a cyanobacterium strain that can produce 5 g/L of glucose.

    • Shanshan Zhang
    • , Jiahui Sun
    •  & Xuefeng Lu

  • Article
    | Open Access

    The bacterium Lacticaseibacillus paracasei is used in the food industry and as a probiotic. Here, the authors use multi-omics and high-throughput chromosome conformation capture analyses to investigate the roles of a type of DNA methylation (N6-methyladenine modification) in this organism.

    • Jie Zhao
    • , Meng Zhang
    •  & Wenyi Zhang

  • Article
    | Open Access

    Using synthetic sRNAs to knockdown target genes has been restricted to a limited number of bacteria. Here, the authors develop a broad-host-range synthetic sRNA platform and show its application in 16 bacterial species, including mitigating virulence-associated phenotypes in pathogens and production of chemicals via metabolic engineering.

    • Jae Sung Cho
    • , Dongsoo Yang
    •  & Sang Yup Lee

  • Review Article
    | Open Access

    In this Review article, the authors discuss the potential of microorganisms as a solution to the challenges faced by our food system. Engineered microorganisms can be used to produce enhanced foods and ingredients in a sustainable manner. The technical, economical, and societal limitations are also discussed together with the current and future perspectives.

    • Alicia E. Graham
    •  & Rodrigo Ledesma-Amaro

  • Article
    | Open Access

    Ethylene glycol is an attractive two-carbon alcohol substrate for bioproduction as it can be derived from CO2 or syngas. Here, the authors design a five-step synthetic metabolic pathway in E. coli to enable the carbon-conserving biosynthesis of the platform chemical 2,4-dihydroxybutyric acid from ethylene glycol.

    • Cláudio J. R. Frazão
    • , Nils Wagner
    •  & Thomas Walther

  • Perspective
    | Open Access

    Establishing sustainable approaches for human space exploration is key to achieve independency from terrestrial resources, as well as for ethical considerations. Here the authors highlight microbial biotechnologies that will support sustainable processes for space-based in situ resource utilization and loop-closure, and may be translatable to Earth applications.

    • Rosa Santomartino
    • , Nils J. H. Averesch
    •  & Luis Zea

  • Article
    | Open Access

    Hydroxylation at the C-14 position of triptolide is critical for its potent antitumor activity. Here, the authors report two CYP82Ds catalyze the 14-hydroxylation reaction via metabolic grid and achieve heterologous bioproduction of triptolide precursor in engineered Saccharomyces cerevisiae.

    • Yifeng Zhang
    • , Jie Gao
    •  & Luqi Huang

  • Article
    | Open Access

    Natural antimicrobial metabolites produced by soil microorganisms can be used as green pesticides. Here, the authors isolated a Pseudomonas mosselii strain 923 from rice rhizosphere soils and identify the compound pyrazolotriazine pseudoiodinine inhibits the growth of plant bacterial and fungal pathogens.

    • Ruihuan Yang
    • , Qing Shi
    •  & Gongyou Chen

  • Article
    | Open Access

    Brassinolide (BL) is one of the most active compounds among phytohormone brassinosteroids (BRs) and can be used for plant growth and development regulation. Here, the authors report the construction of an artificial pathway in baker’s yeast for scalable production of 24-epi-ergosterol, a precursor for BL semi-synthesis.

    • Yiqi Jiang
    • , Zhijiao Sun
    •  & Lirong Yang

  • Article
    | Open Access

    Extrusion bioprinting can be used to produce living materials but controlling cell microenvironments is challenging. Here, the authors use a type of core-shell microgel ink that decouples cell culture from material processing to produce functional materials with a range of potential applications.

    • Yangteng Ou
    • , Shixiang Cao
    •  & Tuomas P. J. Knowles

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