Microbiology techniques articles within Nature Communications

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  • Article
    | Open Access

    Mycobacterium abscessus is considered an emerging pathogen, given its prevalence in patients with pulmonary diseases, such as cystic fibrosis. Here, authors perform a genomic analysis on sequential isolates obtained from patients with persistent infections of M. abscessus.

    • Sergio Buenestado-Serrano
    • , Miguel Martínez-Lirola
    •  & Darío García de Viedma

  • Article
    | Open Access

    Population level transcriptomics measurements miss bacterial heterogeneity. Here the authors report smRandom-seq, a droplet-based high-throughput single-microbe RNA-seq assay, using random primers for in situ cDNA generation, droplets for single-microbe barcoding, and CRISPR-based rRNA depletion.

    • Ziye Xu
    • , Yuting Wang
    •  & Yongcheng Wang

  • Article
    | Open Access

    High-yield production of well-performing protein materials is challenging due to their high molecular weights and repetitive sequences. Here the authors develop a method to boost the strength of low molecular-weight protein materials by bi-terminal fusion of intrinsically-disordered mussel foot protein fragments, while achieving high yield.

    • Jingyao Li
    • , Bojing Jiang
    •  & Fuzhong Zhang

  • Article
    | Open Access

    Spatial analysis of microbiomes at single cell resolution is challenging. Here the authors report a highly multiplexed method for spatial profiling, sequential error-robust fluorescence in situ hybridisation (SEER-FISH), and show that this allows mapping of microbial communities at micron-scale.

    • Zhaohui Cao
    • , Wenlong Zuo
    •  & Lei Dai

  • Article
    | Open Access

    Here, using Citrobacter rodentium colonization of mice as a model, the authors characterize the impact of pathogen dose on the number of bacteria that initiate infection in the mouse gut, providing a framework for quantifying the host bottlenecks that eliminate pathogens to protect from infection.

    • Ian W. Campbell
    • , Karthik Hullahalli
    •  & Matthew K. Waldor

  • Article
    | Open Access

    Engineering enzymes to accept noncanonical cofactor biomimetics is difficult. Here, the authors establish a self-sufficient growth selection method and demonstrate its application in engineering the Lactobacillus pentosus NADH oxidase to efficiently recycle reduced nicotinamide mononucleotide (NMNH).

    • Edward King
    • , Sarah Maxel
    •  & Han Li

  • Article
    | Open Access

    A challenge in synthetic biology is the empirical characterisation of genetic parts. Here the authors present FPCountR, a validated method and accompanying R package that enables the precise quantification of fluorescent protein reporters per bacterial cell to be enumerated in ‘proteins per cell’ or nanomolar units without requiring protein purification.

    • Eszter Csibra
    •  & Guy-Bart Stan

  • Article
    | Open Access

    Rapid antibiotic susceptibility testing (AST) is needed. Here the authors report a method for phenotypic AST at the single cell level, using a microfluidic chip that allows for subsequent genotyping with in situ FISH; they apply this to a mixed sample of 7 species and 4 antibiotics.

    • Vinodh Kandavalli
    • , Praneeth Karempudi
    •  & Johan Elf

  • Article
    | Open Access

    Most attempts to co-cultivate the artificial microbial communities fail mostly due to the mismatched rates of consumption and production of nutrients among subpopulations. Here, the authors develop a microbial swarmbot mediated spatial segregation method to assemble stably coexisting consortia with both flexibility and precision.

    • Lin Wang
    • , Xi Zhang
    •  & Zhuojun Dai

  • Article
    | Open Access

    Small-scale bioreactors are increasingly used in quantitative biology. Here, the authors report ReacSight, a software solution to connect reactor arrays with sensitive measurement devices using low-cost pipetting robots and provide applications leveraging optogenetic control in yeast.

    • François Bertaux
    • , Sebastián Sosa-Carrillo
    •  & Gregory Batt

  • Article
    | Open Access

    Safely opening university campuses has been a major challenge during the COVID-19 pandemic. Here, the authors describe a program of public health measures employed at a university in the United States which, combined with other non-pharmaceutical interventions, allowed the university to stay open in fall 2020 with limited evidence of transmission.

    • Diana Rose E. Ranoa
    • , Robin L. Holland
    •  & Martin D. Burke

  • Article
    | Open Access

    Heterologous expression of recombinant proteins often results in misfolding, aggregation and degradation. Here, we show an in vivo dual-biosensor system that simultaneously assesses protein translation and protein folding, thereby enabling rapid screening of expression strains as well as mutant libraries.

    • Ariane Zutz
    • , Louise Hamborg
    •  & Alex Toftgaard Nielsen

  • Article
    | Open Access

    Here, Broszeit et al. show that circulating A/H3N2 viruses have evolved binding specificity to α2,6-sialosides on extended LacNAc moieties and therefore cannot agglutinate erythrocytes. Applying glycan remodeling allows to install functional receptors on erythrocytes and promotes identification of newly circulating variants to facilitate vaccine design.

    • Frederik Broszeit
    • , Rosanne J. van Beek
    •  & Geert-Jan Boons

  • Article
    | Open Access

    The current biorefineries yield lignin with inadequate fractionation for bioconversion, yet substantial changes of these biorefinery designs could jeopardize carbohydrate efficiency and increase capital costs. Here the authors resolve the dilemma by designing ‘plug-in processes of lignin’ to enable economic waste valorization.

    • Zhi-Hua Liu
    • , Naijia Hao
    •  & Joshua S. Yuan

  • Article
    | Open Access

    Understanding the human antibody response to influenza A virus strains is important for vaccine development. Here, Creanga et al. generate a panel of 55 replication-deficient reporter viruses representing diversity of human H1N1 and H3N2, and pandemic subtypes and characterize the neutralization profile of 24 antibodies and polyclonal sera.

    • Adrian Creanga
    • , Rebecca A. Gillespie
    •  & Masaru Kanekiyo

  • Article
    | Open Access

    During Plasmodium intra-erythrocytic developmental, parasites compromise the structural integrity of host red-blood cells. Here, Clark et al. develop a flow cytometric osmotic stability assay to show that P. vivax infection destabilizes host reticulocytes, which are less stable than P. falciparum-infected normocytes.

    • Martha A. Clark
    • , Usheer Kanjee
    •  & Manoj T. Duraisingh

  • Article
    | Open Access

    To obtain optimal yield and productivity in bioproduction, expression of pathway genes must be appropriately coordinated. Here, the authors report repurposing of base editors for simultaneous regulation of multiple gene expression and demonstrate its application in industrially important and model microorganisms.

    • Yu Wang
    • , Haijiao Cheng
    •  & Yanhe Ma

  • Article
    | Open Access

    The intact proviral DNA assay quantifies the genomically intact HIV reservoir, but assay failure due to HIV-1 polymorphism has been observed. Here, the authors report a 28% failure rate in a cohort of people with HIV-1, and note within-host HIV-1 diversity as a further challenge to IPDA accuracy.

    • Natalie N. Kinloch
    • , Yanqin Ren
    •  & R. Brad Jones

  • Article
    | Open Access

    There is an urgent need to develop simple and fast antimicrobial susceptibility tests. Here, Spencer et al. describe a label-free test that can deliver results within an hour, consisting of a 30-min antibiotic treatment followed by single-cell analysis of phenotypic responses with microfluidic impedance cytometry.

    • Daniel C. Spencer
    • , Teagan F. Paton
    •  & Hywel Morgan

  • Article
    | Open Access

    The detection of pathogens in food and clinical samples remains a challenge. Here, Shen et al. present a detection system, involving a combination of nucleic acid-based allosteric probes and CRISPR-Cas13a components, that can detect very low numbers of a bacterial pathogen in milk and serum samples without isolation.

    • Jinjin Shen
    • , Xiaoming Zhou
    •  & Da Xing

  • Article
    | Open Access

    Existing efforts have been focused on one of the elements in the automation of the design, build, test, and learn (DBTL) cycle for biosystems design. Here, the authors integrate a robotic system with machine learning algorithms to fully automate the DBTL cycle and apply it in optimizing the lycopene biosynthetic pathway.

    • Mohammad HamediRad
    • , Ran Chao
    •  & Huimin Zhao

  • Article
    | Open Access

    Stimuli affecting migration of filaria in host tissues are unclear. Using in situ imaging, Kilarski et al. here show that universal adaptations of nematodes allow Litomosoides sigmodontis infective larvae to mechanically break into pre-collecting lymphatics and follow the direction of flow towards the lymph node.

    • Witold W. Kilarski
    • , Coralie Martin
    •  & Melody A. Swartz

  • Article
    | Open Access

    Brown macroalgae is a good candidate feedstock for biorefinery, but the major carbohydrate alginate cannot be digested by current industrial microbes. Here, the authors isolate Vibrio sp. dhg and engineer it to produce value-added biochemicals from alginate using newly developed genetic tools.

    • Hyun Gyu Lim
    • , Dong Hun Kwak
    •  & Gyoo Yeol Jung

  • Article
    | Open Access

    Vector alteration strategies are emerging as attractive tools for malaria transmission control. Here, Shane et al. engineer a bacterial strain, isolated from mosquitoes, to produce an antiplasmodial protein in the presence of blood meal, causing the mosquitoes to become refractory to Plasmodium infection.

    • Jackie L. Shane
    • , Christina L. Grogan
    •  & David J. Lampe

  • Article
    | Open Access

    Bacterial microcompartments (BMCs) are protein-bound organelles encapsulating segments of metabolic pathways. Here the authors utilize specific de novo coiled-coil protein-protein interactions to display proteins on the outer or inner surface of BMCs.

    • Matthew J. Lee
    • , Judith Mantell
    •  & Martin J. Warren

  • Article
    | Open Access

    Targeting tumors with bacteria as vehicles for metabolite therapy suffers from low efficiency and robustness. Here, the authors combine carbon nitride with nitric oxide generation enzyme-positive E. coli for photo-controlled metabolite therapy (PMT) and observe increased effects both in vitro and in tumor-bearing mice.

    • Di-Wei Zheng
    • , Ying Chen
    •  & Xian-Zheng Zhang

  • Article
    | Open Access

    The Trioplex real-time RT-PCR assay was developed for detection of Zika virus infections in areas with dengue and chikungunya transmission. Here, Santiago et al. describe the optimization and clinical performance of the assay, showing high sensitivity for detection and differentiation of the three viruses.

    • Gilberto A. Santiago
    • , Jesús Vázquez
    •  & Jorge L. Muñoz-Jordan

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