Microbiology articles within Nature Communications

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  • Article
    | Open Access

    DNA primases initiate a short primer before handing off to DNA polymerases to continue replication. Here the authors reveal a unique ability of archaeal primases to first synthesize RNA before stochastically incorporating a deoxyribonucleotide and further extending the primer as DNA.

    • Mark D. Greci
    • , Joseph D. Dooher
    •  & Stephen D. Bell

  • Article
    | Open Access

    SARS-CoV-2 infection can lead to progressive pathology in patients with COVID-19, but information for this disease progression is sparse. Here the authors use multi-omics approach to profile the immune responses of patients, assessing immune repertoire and effects of tocilizumab treatments, to find a dyssynchrony between innate and adaptive immunity in progressive COVID-19.

    • Avraham Unterman
    • , Tomokazu S. Sumida
    •  & Charles S. Dela Cruz

  • Article
    | Open Access

    Adverse events resulting from COVID-19 vaccination are a public health concern and it is not known whether pre-existing conditions may impose an increased risk. Here, using electronic health records from Hong Kong, the authors show that adverse events are rare for all groups, and there is no evidence of risk modification due to multimorbidity.

    • Francisco Tsz Tsun Lai
    • , Lei Huang
    •  & Ian Chi Kei Wong

  • Article
    | Open Access

    Microbial communities employ a variety of strategies to compete against competitors sharing their niche, for instance, by producing antibiotics. This study reveals that antibiotics produced by Bacillus subtilis act synergistically to eliminate phylogenetically distinct competitors and are regulated accordingly.

    • Harsh Maan
    • , Maxim Itkin
    •  & Ilana Kolodkin-Gal

  • Article
    | Open Access

    In this case study of a patient with fracture-related pandrug-resistant Klebsiella pneumoniae infection after long-term antibiotic therapy, the authors use a combination therapy of pre-adapted bacteriophage and antibiotics resulting in clinical, microbiological and radiological improvement.

    • Anaïs Eskenazi
    • , Cédric Lood
    •  & Jean-Paul Pirnay

  • Article
    | Open Access

    Understanding the interactions between bacteria and their viruses (phages) in natural communities is a major challenge. Here, the authors isolate and study large numbers of marine Vibrio bacteria and their phages, and find that lytic interactions are sparse and many phages are host-strain-specific, but nevertheless recombination between some phages is common.

    • Kathryn M. Kauffman
    • , William K. Chang
    •  & Libusha Kelly

  • Article
    | Open Access

    An increasing prevalence of Gram-negative bacteria increases the interest in nanotherapies to treat antibiotic resistance. Here, the authors examine the antimicrobial activity of polymyxin-loaded cubosomes and explore a polytherapy treatment of pathogens with cubosomes in combination with polymyxin.

    • Xiangfeng Lai
    • , Mei-Ling Han
    •  & Hsin-Hui Shen

  • Article
    | Open Access

    Genome folding in the nucleus plays an important role in regulating gene expression. Here the authors show that 3D genome architecture also plays an important role for gene expression adaptability for the Epstein-Barr Virus (EBV), a virus that is associated with cancer. They also observe major changes in the fold of the EBV chromosome between silent and transcriptional active viral genomes.

    • Sarah M. Morgan
    • , Hideki Tanizawa
    •  & Italo Tempera

  • Article
    | Open Access

    Coenzyme A (CoA) is an essential metabolite found in all organisms and its synthesis involves five conserved enzymatic steps and uses pantothenate (Pan) as a precursor. Here, Lunghi et al. examine the Pan synthesis pathway in Toxoplasma gondii and find that Pan is crucial for the establishment of chronic but not acute infection.

    • Matteo Lunghi
    • , Joachim Kloehn
    •  & Dominique Soldati-Favre

  • Article
    | Open Access

    Many microbiome differential abundance methods are available, but it lacks systematic comparison among them. Here, the authors compare the performance of 14 differential abundance testing methods on 38 16S rRNA gene datasets with two sample groups, and show ALDEx2 and ANCOM-II produce the most consistent results.

    • Jacob T. Nearing
    • , Gavin M. Douglas
    •  & Morgan G. I. Langille

  • Article
    | Open Access

    Reactive school class closures have been widely implemented to mitigate COVID-19 outbreaks. Here, the authors show that, compared to symptom-prompted PCR testing, screening for cases in schools with antigen tests leads to greater reductions in infection rates in both students and the wider community.

    • Quan-Hui Liu
    • , Juanjuan Zhang
    •  & Marco Ajelli

  • Article
    | Open Access

    Influenza viruses carry their own RNAdependent RNA-polymerase that is highly conserved and a promising anti-viral target. Combining functional and structural data, Keown et al. characterise the inhibitory effect of nanobodies on 1918 pandemic H1N1 influenza strain polymerase complex and identify sensitive sites interfering with polymerase activity in vitro.

    • Jeremy R. Keown
    • , Zihan Zhu
    •  & Jonathan M. Grimes

  • Article
    | Open Access

    Pseudomonas aeruginosa employs lectins to bind to its host cells, and is known to be the major cause of lung infections. Lectin B (LecB) from Pseudomonas aeruginosa binds specifically to galactose and fucose and is important for pathogenicity, adhesion and biofilm formation. In this work, the neutron crystal structure (1.9 Å) of the deuterated LecB/Ca/fucose complex is reported. The structure, in combination with perdeuteration of the ligand and the receptor allowed the observation of hydrogen atoms, protonation states and hydrogen bonds involved in the interaction between pathogenic bacteria and host cells. Thus the study provides structural insights into the mechanism of high affinity binding of LecB to its targets.

    • Lukas Gajdos
    • , Matthew P. Blakeley
    •  & Anne Imberty

  • Article
    | Open Access

    Here, Kim et al. characterize SARS-CoV-2 infection in juvenile, young, and old aged ferrets to provide a further understanding of differences in COVID-19 severity in humans at different ages. Aged ferrets have higher viral loads, shed virus longer, and mimic the transcriptomic profile of severely infected patients.

    • Young-Il Kim
    • , Kwang-Min Yu
    •  & Young Ki Choi

  • Article
    | Open Access

    Efflux transporters of the RND family confer resistance to multiple antibiotics in Gram-negative bacteria. Here, the authors identify pyridylpiperazine-based compounds that potentiate antibiotic activity in E. coli through allosteric inhibition of its primary RND transporter.

    • Coline Plé
    • , Heng-Keat Tam
    •  & Ruben C. Hartkoorn

  • Article
    | Open Access

    A Variant Surface Glycoprotein (VSG) coat protects bloodstream form T. brucei. Applying super-resolution microscopy Budzak et al. characterize a set of nuclear bodies, which associate with the active expression site in bloodstream form T. brucei and highlight the importance of trans-splicing for transcription of VSG.

    • James Budzak
    • , Robert Jones
    •  & Gloria Rudenko

  • Article
    | Open Access

    Streptomyces bacteria undergo two modes of cell division: formation of cross-walls in hyphae, leading to multicellular compartments, and septation for release of unicellular spores. Here, Bush et al. identify a protein that is important for both cell division modes in Streptomyces, likely by contributing to stabilization of the divisome.

    • Matthew J. Bush
    • , Kelley A. Gallagher
    •  & Susan Schlimpert

  • Article
    | Open Access

    The human silencing hub (HUSH) complex, which includes TASOR, deposits repressive marks on HIV proviruses, resulting in gene repression. Here, Matkovic et al. show that TASOR interacts with RNA Polymerase II, predominantly under its elongating state, and RNA degradation proteins to repress HIV provirus expression.

    • Roy Matkovic
    • , Marina Morel
    •  & Florence Margottin-Goguet

  • Article
    | Open Access

    While cross-reactive immunity between human coronavirus and SARS-CoV-2 may contribute to host protection, validating evidences are still scarce. Here the authors assess a cohort of 52 donors with immediate-early contact with SARS-CoV-2 to correlate higher frequency of cross-reactive T cells with lower infection rate.

    • Rhia Kundu
    • , Janakan Sam Narean
    •  & Ajit Lalvani

  • Article
    | Open Access

    The bacterial Cyclic-oligonucleotide-Based Anti-phage Signaling System (CBASS) contains a CD-NTase that synthesizes cyclic di- and tri-nucleotides, and bacterial STING proteins recognize c-di-GMP generated by CD-NTase during phage infection and signal the infected bacteria to commit suicide. Here, the authors provide insights into the molecular basis for c-di-GMP recognition of bacterial STING proteins by determining two STING protein crystal structures with bound c-di-GMP from Prevotella corporis and Myroides sp. ZB35.

    • Tzu-Ping Ko
    • , Yu-Chuan Wang
    •  & Yeh Chen

  • Article
    | Open Access

    Waning immunity to SARS-CoV-2 is of concern. Here the authors follow spike- and nucleocapsid specific immunity in convalescent individuals for 9 months observing a decline in antibody levels but persisting T cell response. Vaccination approximately 11 months after infection boosts antibody and T cell immunity.

    • Nina Koerber
    • , Alina Priller
    •  & Percy A. Knolle

  • Article
    | Open Access

    Here, Kim et al. describe a new kick and kill strategy utilizing a single administration of a protein kinase C modulator and latency reversing agent in combination with injections of allogeneic peripheral blood natural killer cells diminishes the HIV reservoir in HIV-infected humanized mice.

    • Jocelyn T. Kim
    • , Tian-Hao Zhang
    •  & Jerome A. Zack

  • Article
    | Open Access

    Structural immunology is critical in understanding the interplay between the immune response and the infective agent but such studies in T cells and SARS-CoV-2 lag behind those of antibodies and B-cell receptors. Here the authors assess recognition of SARS-CoV-2 spike epitopes and their natural variants by public and private T cell receptors.

    • Daichao Wu
    • , Alexander Kolesnikov
    •  & Roy A. Mariuzza

  • Article
    | Open Access

    Here, the authors provide insights into the conformational dynamics of the Beta and Kappa SARS-CoV-2 spike (S) proteins by determining their cryo-EM structures, which revealed a distribution shift towards the open state for both variants compared to the wild-type S protein. They also present the structures of the Kappa and Beta S-ACE2 complexes, where a population shift towards the three receptor-binding domain up conformation was observed. In combination with biochemical data these structures show how the S protein variants efficiently recognize and bind to ACE2.

    • Yifan Wang
    • , Cong Xu
    •  & Yao Cong

  • Article
    | Open Access

    Long non-coding RNAs (lncRNAs) play roles in key cellular processes, but remain largely unexplored in fungal pathogens such as Candida. Here, Hovhannisyan and Gabaldón analyze thousands of sequencing datasets to infer and characterize the lncRNA repertoires of five Candida species, paving the way for their future functional characterization.

    • Hrant Hovhannisyan
    •  & Toni Gabaldón

  • Article
    | Open Access

    The T cell response to Kaposi sarcoma-associated herpesvirus is critical to controlling infection and immunopathology but has been poorly explored in immunocompetent patients. Here the authors characterise the T cell response to the Kaposi sarcoma-associated herpesvirus proteome in immunocompetent patients from rural Uganda.

    • Angela Nalwoga
    • , Romin Roshan
    •  & Denise Whitby

  • Article
    | Open Access

    Oral rotavirus vaccine (ORV) efficacy varies between countries, but underlying reasons aren’t fully understood. In this prospective cohort study, authors show that maternal rotavirus-specific antibodies in serum and breastmilk and pre-vaccination microbiota diversity are negatively correlated with ORV response in India and Malawi but not in the UK.

    • Edward P. K. Parker
    • , Christina Bronowski
    •  & Miren Iturriza-Gómara

  • Article
    | Open Access

    Signals of antimicrobial resistance in pathogen genomes may be detectable before the organism evolves an antimicrobial resistance phenotype. Here, the authors investigate this hypothesis using Mycobacterium tuberculosis data from Peru and identify candidate “pre-resistance” markers.

    • Arturo Torres Ortiz
    • , Jorge Coronel
    •  & Louis Grandjean

  • Article
    | Open Access

    Double membrane vesicles (DMV) are used as replication organelles by several RNA viruses. Applying proteomics and lipidomics, Tabata and Prasad et al. find that two cellular acyltransferases (AGPAT1/2), responsible for synthesis of phosphatidic acid, play a role in the DMV-biogenesis of HCV and SARS-CoV-2, highlighting a common biogenesis mechanism for evolutionary distant positive-strand RNA viruses.

    • Keisuke Tabata
    • , Vibhu Prasad
    •  & Ralf Bartenschlager

  • Article
    | Open Access

    Identifying new SARS-CoV-2 genetic variants of concern is important to inform public health strategies, but distinguishing those causing a significant threat is challenging. Here, the authors develop and evaluate two models for assessing the strength of selection for new variants.

    • Christiaan H. van Dorp
    • , Emma E. Goldberg
    •  & Ethan O. Romero-Severson

  • Article
    | Open Access

    Establishing the relative transmissibility of emerging variants of SARS-CoV-2 is key for pandemic management. Here, the authors use full-population administrative data from Denmark linked to PCR test results and estimate that the Alpha variant was ~60% higher than other strains circulating in early 2021.

    • Frederik Plesner Lyngse
    • , Kåre Mølbak
    •  & Carsten Thure Kirkeby

  • Article
    | Open Access

    Plant roots host diverse fungal communities that affect plant health. Here, Mesny et al. use comparative genomics and transcriptomics of fungal isolates from the Arabidopsis thaliana root mycobiota, together with root colonization assays, to identify genetic determinants of endophytism.

    • Fantin Mesny
    • , Shingo Miyauchi
    •  & Stéphane Hacquard

  • Article
    | Open Access

    The bacterium Legionella pneumophila can cause severe respiratory infection, but is typically a symbiont of free-living amoeba. Here, the authors analyse the genomes of 902 clinical and environmental isolates, and identify a bacterial gene that is strongly associated with human infection and confers resistance to complement-mediated killing.

    • Bryan A. Wee
    • , Joana Alves
    •  & J. Ross Fitzgerald

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