Microbiology articles within Nature Communications

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  • 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

    Erythromycin esterases (Eres) cleave the macrolactone ring of macrolides, a class of widely used antibiotics. Structures of EreC, in silico flexible docking studies and previous mutagenesis data lead to the proposal of a detailed catalytic mechanism for the Ere family of enzymes.

    • Michał Zieliński
    • , Jaeok Park
    •  & Albert M. Berghuis

  • Article
    | Open Access

    Vaccines that interrupt malaria transmission will be important tools for malaria elimination. Here the authors identify a human monoclonal antibody from Pfs230 vaccinated individuals that blocks transmission of Plasmodium falciparum to mosquitoes in a complement-dependent manner and reacts with gamete surface.

    • Camila H. Coelho
    • , Wai Kwan Tang
    •  & Patrick E. Duffy

  • Article
    | Open Access

    Antibodies plays critical roles in the adaptive immune response to infectious agents including malaria. Here the authors defined antibody interactions with -Fcγ-receptors expressed on immune cells with sporozoites of Plasmodium falciparum, and identified specific target epitopes of antibodies.

    • Gaoqian Feng
    • , Bruce D. Wines
    •  & James G. Beeson

  • Article
    | Open Access

    T cells compose a critical component of the immune response to coronavirus infection with SARS-CoV-2. Here the authors characterise the T cell response to SARS CoV-2 in patients and their close contacts, and show the presence of SARS-CoV-2 specific T cells in the absence of detectable virus infection.

    • Zhongfang Wang
    • , Xiaoyun Yang
    •  & Pixin Ran

  • Article
    | Open Access

    Here, via screening of a polypeptide library from bronchoalveolar lavage, the authors identify and characterize α1-antitrypsin (α1AT) as SARS-CoV-2 inhibitor and show that α1AT binds and inactivates the serine protease TMPRSS2, which enzymatically primes the SARS-CoV-2 spike protein for membrane fusion.

    • Lukas Wettstein
    • , Tatjana Weil
    •  & Jan Münch

  • Article
    | Open Access

    The top down cheminformatics method is usually used for the reconstitution of heterologous pathway to produce plant natural products. Here, the authors report a bottom up computational workflow for the identification of potential products and the enzymes required to make them in a noscapine pathway in yeast.

    • Jasmin Hafner
    • , James Payne
    •  & Christina Smolke

  • Article
    | Open Access

    Long-distance extracellular electron transfer has been observed in Gram-negative bacteria. Here, Yang et al. show that a filamentous, unicellular Gram-positive bacterium is capable of bidirectional extracellular electron transfer, and forms centimetre-range conductive networks consisting of 1mm-long cells and conductive appendages.

    • Yonggang Yang
    • , Zegao Wang
    •  & Mingdong Dong

  • Article
    | Open Access

    In Pseudomonas aeruginosa, the protein AlpA activates the expression of the alp locus in response to DNA damage, leading to lysis in a subset of cells and enhancing virulence of other, surviving cells. Here, the authors show that AlpA acts as an antiterminator rather than a transcriptional activator.

    • Jennifer M. Peña
    • , Samantha M. Prezioso
    •  & Simon L. Dove

  • Article
    | Open Access

    Here, the authors report the isolation and characterization of two human monoclonal antibodies (mAbs) from immunized mice with trimeric spike ectodomains of three human betacoronaviruses HCoV-OC43, SARS-CoV and MERSCoV, and show that while exhibiting cross-reactivity, the mAbs only neutralize MERS-CoV but not SARS-CoV nor SARS-CoV-2, likely due to the subtle epitope differences in the spike S2 fusion subunit.

    • Chunyan Wang
    • , Rien van Haperen
    •  & Berend-Jan Bosch

  • Article
    | Open Access

    Influenza C virus contains a single surface glycoprotein, the haemagglutinin-esterase-fusion (HEF) protein, that mediates receptor binding, receptor destruction, and membrane fusion activities. Here, the authors apply electron cryotomography of whole virus together with subtomogram averaging to determine the HEF structure and lattice organisation on the viral membrane and they discuss mechanistic implications for virus budding and membrane fusion.

    • Steinar Halldorsson
    • , Kasim Sader
    •  & Peter B. Rosenthal

  • Article
    | Open Access

    Viruses rely on host metabolism for replication. Here, the authors perform transcriptional and metabolomic analyses at 8 hours after SARS-CoV-2 infection and find that the virus alters host folate and one-carbon metabolism at a post-transcriptional level.

    • Yuchen Zhang
    • , Rui Guo
    •  & Benjamin E. Gewurz

  • Article
    | Open Access

    Many bacterial pathogens use a type III secretion system (T3SS) to inject effector proteins into host cells. Here, Wimmi et al. show that the external pH regulates the assembly of T3SS cytosolic components in intestinal pathogens, thus preventing T3SS activity in the stomach and allowing T3SS reactivation in the intestine.

    • Stephan Wimmi
    • , Alexander Balinovic
    •  & Andreas Diepold

  • Article
    | Open Access

    Some bacterial pathogens release NADase enzymes into the host cell that deplete the host’s NAD+ pool, thereby causing rapid cell death. Here, Strømland et al. identify NADases on the surface of fungal spores, and show that the enzymes display unique biochemical and structural properties.

    • Øyvind Strømland
    • , Juha P. Kallio
    •  & Mathias Ziegler

  • Article
    | Open Access

    The circadian factors BMAL1/CLOCK and REV-ERB are master regulators of the human liver transcriptome but their role in hepatitis B virus infection is largely unknown. Here, Zhuang et al. show that REV-ERB regulates hepatitis B virus entry and BMAL1 directly binds HBV DNA and activates viral genome transcription.

    • Xiaodong Zhuang
    • , Donall Forde
    •  & Jane A. McKeating

  • Article
    | Open Access

    Some epidemiological data suggests that SARS-CoV-2 can be transmitted through the air over longer distances. Here, Kutter et al. show in the ferret model that SARS-CoV-2 and SARS-CoV can be transmitted through the air over more than a meter distance, however, data should be interpreted with care, as ferrets are likely more susceptible to coronavirus infections.

    • Jasmin S. Kutter
    • , Dennis de Meulder
    •  & Sander Herfst

  • 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

    Metabolism changes can modulate immune responses in many contexts, and vice versa. Here the authors associate metabolomic, as well as cytokine and chemokine, data from stratified COVID-19 patients to find that arginine, tryptophan and purine metabolic pathways correlate with hyperproliferation, thus hinting at potential therapeutic targets for severe COVID-19 patients.

    • Nan Xiao
    • , Meng Nie
    •  & Zeping Hu

  • Article
    | Open Access

    Mycobacterium tuberculosis forms biofilms in vitro, but it is unclear whether biofilms are also formed during infection in vivo. Here, Chakraborty et al. demonstrate the formation of biofilms in animal models of infection and in patients with tuberculosis, and that biofilm formation can contribute to drug tolerance.

    • Poushali Chakraborty
    • , Sapna Bajeli
    •  & Ashwani Kumar

  • Article
    | Open Access

    HBV covalently closed circular DNA (cccDNA) enables and persists in chronic infection, but the molecular mechanism of its formation is unclear. Here, Wei and Ploss elucidate the detailed kinetics and biochemical steps by which the relaxed circular DNA is converted into cccDNA.

    • Lei Wei
    •  & Alexander Ploss

  • Article
    | Open Access

    The spike glycoprotein in coronaviruses is a key viral protein for cross-species transmission and infection. Here, the authors present the cryo-EM structures of the spike ectodomains from bat and pangolin coronaviruses, compare them with the available SARS-CoV-2 spike structures and discuss implications for the evolution and cross-species transmission of SARS-CoV-2.

    • Shuyuan Zhang
    • , Shuyuan Qiao
    •  & Xinquan Wang

  • Article
    | Open Access

    Effective use of antimicrobials in both humans and animals is essential to help slow the emergence of antimicrobial resistance. Here, Singleton et al. present a randomised controlled trial demonstrating the efficacy of social norm messaging to reduce antibiotic prescription frequency in veterinary surgeries.

    • David A. Singleton
    • , Angela Rayner
    •  & Gina L. Pinchbeck

  • Article
    | Open Access

    Virulent type III secretion systems (T3SSs) or injectisomes enable pathogenic bacteria to inject effector proteins directly into the host cell cytoplasm. Structures of a needle complex engaged with the effector protein reveal the complete secretion channel and provide insights into the mechanism of substrate translocation through T3SSs.

    • Sean Miletic
    • , Dirk Fahrenkamp
    •  & Thomas C. Marlovits

  • Article
    | Open Access

    Enterococcus faecalis is a commensal microorganism of animals, insects and humans, but also a nosocomial pathogen. Here, the authors analyse genomic sequences from E. faecalis isolates from animals and humans, and find that the last common ancestors of multiple hospital-associated lineages date to the pre-antibiotic era.

    • Anna K. Pöntinen
    • , Janetta Top
    •  & Jukka Corander

  • Article
    | Open Access

    Until today effective antivirals for COVID-19 treatment are not widely available. Here, Zhao et al. characterize a dual-functional cross-linking peptide, 8P9R, that can inhibit SARS-CoV-2 virus entry in vitro and suppresses viral replication in vivo in golden Syrian hamster.

    • Hanjun Zhao
    • , Kelvin K. W. To
    •  & Kwok-Yung Yuen

  • Article
    | Open Access

    Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) is important for invasion of reticulocytes and PvRBP2b antibodies correlate with protection. Here, Chan et al. isolate and characterize anti-PvRBP2b human monoclonal antibodies and describe mechanisms by which these antibodies inhibit invasion.

    • Li-Jin Chan
    • , Anugraha Gandhirajan
    •  & Wai-Hong Tham

  • Article
    | Open Access

    3-Hydroxypropionic acid (3HP) is an important platform chemical. Here, the authors engineer Halomonas bluephagenesis by deleting newly identified degradation pathway and balancing redox state to achieve high level production of 3HP and its copolymer under open and unsterile conditions.

    • Xiao-Ran Jiang
    • , Xu Yan
    •  & Guo-Qiang Chen

  • Article
    | Open Access

    Industrial sugarcane ethanol fermentations are accomplished by a microbial community dominated by S. cerevisiae and co-occurring bacteria. Here, the authors investigate how microbial community composition contributes to community function and reveal the role of acetaldehyde in improving yeast growth rate and ethanol production.

    • Felipe Senne de Oliveira Lino
    • , Djordje Bajic
    •  & Morten Otto Alexander Sommer

  • Article
    | Open Access

    Integrated studies of matched tissue sites and cell types in COVID-19 patients are important to define the immune mechanisms of pathology. Here, the authors describe an immune signature in fatal COVID-19 patients harmonizing single-cell RNA sequencing of blood and matched BAL cells with deep clinical, immunological and functional data.

    • Pierre Bost
    • , Francesco De Sanctis
    •  & Vincenzo Bronte

  • Article
    | Open Access

    The existence of HIV reservoir and ongoing replication despite antiretroviral therapy (ART) represents a barrier for cure efforts. Here, using SIV/SHIV-infected rhesus macaque suppressed with ART for one year, the authors characterize multiple lymphoid and non-lymphoid tissues and show that while the viral reservoir exhibits a wide anatomic heterogeneity, persistent viral transcription is mainly restricted to secondary lymphoid organs.

    • Anthony M. Cadena
    • , John D. Ventura
    •  & Dan H. Barouch

  • Article
    | Open Access

    The cost and complexity of whole genome sequencing limits its use in identifying and validating sequences used for genetic engineering and synthetic biology. Here the authors present Prymetime, an integrated workflow to sequence engineered strains and identify engineering in metagenomes.

    • Joseph H. Collins
    • , Kevin W. Keating
    •  & Eric M. Young

  • Article
    | Open Access

    Checkpoint blocking therapies are used to treat metastatic melanoma, but can have adverse immune-mediated effects, including liver pathology. Here the authors identify an expanded pool of CD4+ effector memory T cells resulting from prior CMV exposure as a risk factor for this adverse effect in these patients.

    • James A. Hutchinson
    • , Katharina Kronenberg
    •  & Sebastian Haferkamp

  • Article
    | Open Access

    The authors show that the pathogen Staphylococcus aureus induces a distinct airway immunometabolic response, dominated by release of itaconate. This metabolite, in turn, potentiates extracellular polysaccharide synthesis and biofilm formation in S. aureus, which may facilitate chronic infection.

    • Kira L. Tomlinson
    • , Tania Wong Fok Lung
    •  & Sebastián A. Riquelme

  • Article
    | Open Access

    Current vaccine strategies for SARS-CoV-2 focus on eliciting neutralising antibodies to the spike protein (S), but differences in immunogenicity of full-length S versus receptor binding domain (RBD) only aren’t fully understood. Here, the authors show immunogenicity of different prime-boost strategies with S and/or RBD in mice and macaques.

    • Hyon-Xhi Tan
    • , Jennifer A. Juno
    •  & Adam K. Wheatley

  • Article
    | Open Access

    Here, the authors determine seroprevalence of antibodies to SARS-CoV-2 in healthy blood donors in the cities of Wuhan, Shenzhen, and Shijiazhuang in China between January and April 2020. The age- and sex-standardized SARS-CoV-2 seroprevalence among 18–60 year-old adults is, with 2.66%, the highest in Wuhan.

    • Le Chang
    • , Wangheng Hou
    •  & Lunan Wang

  • Article
    | Open Access

    Chondroitin sulfate (CS) is a type of sulfated glycosaminoglycan that is manufactured by extraction from animal tissues for the treatment of osteoarthritis and in drug delivery applications. Here, the authors report the development of single microbial cell factories capable of compete, one-step biosynthesis of animal-free CS production in E. coli.

    • Abinaya Badri
    • , Asher Williams
    •  & Mattheos A. G. Koffas

  • Article
    | Open Access

    Therapeutic application of RNA viruses requires tight control over viral activity. Here the authors design a regulatory switch that enables control over activity with clinically approved HIV protease inhibitors.

    • E. Heilmann
    • , J. Kimpel
    •  & D. von Laer

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