Microbiology articles within Nature Communications

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  • Article
    | Open Access

    Type-III secretion systems (T3SSs) are capable of translocating proteins with high speed while maintaining the membrane barrier for small molecules. Here, a structure-function analysis of the T3SS pore complex elucidates the precise mechanisms enabling the gating and the conformational changes required for protein substrate secretion.

    • Svenja Hüsing
    • , Manuel Halte
    •  & Thibaud T. Renault

  • Article
    | Open Access

    Secondary structures and long-range RNA interactions of the SARS-CoV-2 genome have been investigated by various sequencing methods. Here the authors use an RNA-RNA hybrid sequencing method to predict the secondary and tertiary structure of the SRAS-CoV-2 RNA genome in the virion.

    • Changchang Cao
    • , Zhaokui Cai
    •  & Yuanchao Xue

  • Article
    | Open Access

    Pyrrolysine (Pyl) exists in nature as the 22nd proteinogenic amino acid, but studies of Pyl have been hindered by the difficulty and inefficiency of both its chemical and biological syntheses. Here, the authors developed an improved PANCE approach to evolve the pylBCD pathway for increased production of Pyl proteins in E. coli.

    • Joanne M. L. Ho
    • , Corwin A. Miller
    •  & Matthew R. Bennett

  • Article
    | Open Access

    The ability of the fungal pathogen Candida albicans to undergo yeast-to-hypha transition is believed to be a key virulence factor. Here, Dunker et al. show that a filament-deficient strain is attenuated in a mouse model of intraperitoneal infection, but remains virulent in a mouse model of systemic candidiasis.

    • Christine Dunker
    • , Melanie Polke
    •  & Ilse D. Jacobsen

  • Review Article
    | Open Access

    Antimicrobial resistance is a growing global problem and low dimensional materials have emerged as a potential solution. Here, the authors review the progress which has been made on low dimensional antimicrobials looking at the materials synthesis, modes of action and currently applications.

    • Z. L. Shaw
    • , Sruthi Kuriakose
    •  & Sumeet Walia

  • Article
    | Open Access

    Citrullination is a posttranslational modification of arginines. Here, the authors show that HCMV infection increases citrullination of host and virus proteins to promote infection and that citrullinated interferon-inducible protein IFIT1 is impaired in RNA binding, as a potential mechanism of evasion.

    • Gloria Griffante
    • , Francesca Gugliesi
    •  & Santo Landolfo

  • Article
    | Open Access

    Beneficial plant-microbe interactions are common in nature, but direct evidence for the evolution of mutualism is scarce. Here, Li et al. experimentally evolve a rhizospheric bacterium and find that it can evolve into a mutualist on a relatively short timescale.

    • Erqin Li
    • , Ronnie de Jonge
    •  & Alexandre Jousset

  • Article
    | Open Access

    Effective chemotherapies against tuberculosis must kill the pathogen’s intracellular population. Here, Santucci et al. show that bacterial localisation within human macrophages impact pyrazinamide (PZA) accumulation and efficacy, and that combination with a second antibiotic (bedaquiline) enhances PZA accumulation via a host-dependent process.

    • Pierre Santucci
    • , Daniel J. Greenwood
    •  & Maximiliano G. Gutierrez

  • Article
    | Open Access

    Applying complexome profiling, Evers et al. unravel the composition of mitochondrial oxidative phosphorylation complexes in P. falciparum asexual and sexual blood stages. Abundance of these complexes differs between both stages, supporting the hypothesis that a mitochondrial metabolic switch is central to gametocyte development and functioning.

    • Felix Evers
    • , Alfredo Cabrera-Orefice
    •  & Taco W. A. Kooij

  • Article
    | Open Access

    Bacterial microcompartments (BMCs) are organelles consisting of a protein shell in which certain metabolic reactions take place separated from the cytoplasm. Here, Sutter et al. present a comprehensive catalog of BMC loci, substantially expanding the number of known BMCs and describing distinct types and compartmentalized reactions.

    • Markus Sutter
    • , Matthew R. Melnicki
    •  & Cheryl A. Kerfeld

  • Article
    | Open Access

    Hoshino et al., engineer a human virus receptor, hACE2, and demonstrate its potential for overcoming SARS-CoV-2 mutations that otherwise hinder therapeutic interventions. Overall, the data provide insights in to the therapeutic potential of engineered receptors.

    • Yusuke Higuchi
    • , Tatsuya Suzuki
    •  & Atsushi Hoshino

  • Article
    | Open Access

    Type IV pili (T4P) are retractile appendages used by bacteria for DNA uptake and other purposes. T4P extension is thought to occur through the action of a single motor protein, PilB. Here, Ellison et al. show that T4P synthesis in Acinetobacter baylyi depends not only on PilB but also on an additional, distinct motor, TfpB.

    • Courtney K. Ellison
    • , Triana N. Dalia
    •  & Ankur B. Dalia

  • Article
    | Open Access

    Selection of COVID-19 mitigation measures requires balancing health outcomes with economic impacts. Here, the authors derive a system to set triggers for increasing mitigation measures to preserve healthcare capacity, and describe how it has been used to support public health decision making in Austin, Texas.

    • Haoxiang Yang
    • , Özge Sürer
    •  & Lauren Ancel Meyers

  • Article
    | Open Access

    The extracellular Contractile Injection System (eCIS) is a toxin-delivery particle that mediates interactions between bacteria and their invertebrate hosts. Here, the authors catalogue eCIS loci from 1,249 prokaryotic genomes, showing enrichment in non-pathogenic environmental microbes, and identifying eCIS-associated toxins that inhibit the growth of bacteria and/or yeast.

    • Alexander Martin Geller
    • , Inbal Pollin
    •  & Asaf Levy

  • Article
    | Open Access

    COVID-19-related mortality in England shows geographical variation but the reasons for this are not well understood. This study estimated excess mortality in the first wave of the pandemic and found associations with higher density of care homes, overcrowding, and economic deprivation, but not with population density or air pollution.

    • Bethan Davies
    • , Brandon L. Parkes
    •  & Paul Elliott

  • Article
    | Open Access

    Estimating the effectiveness of COVID-19 control measures requires large prospective data including symptoms and personal risk factors. Here, the authors used data from smartphone-based application and found that individual face mask use was associated with a 64% reduced risk of COVID-19 symptoms.

    • Sohee Kwon
    • , Amit D. Joshi
    •  & Andrew T. Chan

  • Article
    | Open Access

    Host cell invasion by Toxoplasma gondii depends on the heavily phosphorylated RON complex, but the relevance and regulation of these modifications are not understood. Here, the authors identify the kinase RON13 as a key virulence factor, determine its structure and show that it phosphorylates the RON complex.

    • Gaëlle Lentini
    • , Rouaa Ben Chaabene
    •  & Dominique Soldati-Favre

  • Article
    | Open Access

    To provide in depth characterization of HIV reservoir cells, the authors here develop a single-cell approach to simultaneously sequence TCR, integration sites and proviral genomes, called STIP-Seq, and show that the translation-competent reservoir mainly consists of proviruses with short deletions at the 5’-end of the genome.

    • Basiel Cole
    • , Laurens Lambrechts
    •  & Linos Vandekerckhove

  • Article
    | Open Access

    CAPPs are putative Primase-Polymerases associated with CRISPR-Cas operons. Here, the authors show CAPPs genetic and physical association with Cas1 and Cas2, their capacity to function as DNA-dependent DNA primases and DNA polymerases, and that Cas1-Cas2 complex adjacent to CAPP has bona fide spacer integration activity.

    • Katerina Zabrady
    • , Matej Zabrady
    •  & Aidan J. Doherty

  • Article
    | Open Access

    Here the authors use microfluidics and single-cell microscopy to quantify the growth dynamics of individual E. coli cells exposed to nutrient fluctuations with periods as short as 30 seconds, finding that nutrient fluctuations reduce growth rates up to 50% compared to a steady nutrient delivery of equal average concentration, implying that temporal variability is an important parameter in bacterial growth.

    • Jen Nguyen
    • , Vicente Fernandez
    •  & Roman Stocker

  • Article
    | Open Access

    Epithelial host defense to rhinovirus infections is enhanced by targeting the mitochondrial metabolic regulator, PGC-1a. Using metabolomics and proteomics, Michi et al show that human airway epithelial cells mount a barrier-protective early glycolysis-shift in response to rhinovirus, and that by targeting PGC-1a early in infection, epithelial barrier function, viral defense and pathology are improved.

    • Aubrey N. Michi
    • , Bryan G. Yipp
    •  & David Proud

  • Article
    | Open Access

    Here, Geoghegan, Evelyn et al. provide a lattice light-sheet microscopy based 4D imaging pipeline to quantitatively investigate Plasmodium spp. invasion and show that the nascent parasitophorous vacuole is predominantly formed from host’s erythrocyte membrane and undergoes continuous remodeling throughout invasion.

    • Niall D. Geoghegan
    • , Cindy Evelyn
    •  & Kelly L. Rogers

  • Article
    | Open Access

    The concentration of SARS-CoV-2 changes during an individual’s infection, and mutations accumulate as viruses are transmitted between people. Here, the authors use data from Iceland to demonstrate how this information can be exploited at the population-level to determine the phase of the epidemic.

    • Hakon Jonsson
    • , Olafur T. Magnusson
    •  & Kari Stefansson

  • Article
    | Open Access

    Yellow fever virus (YFV) is an arbovirus affecting humans and non-human primates (NHPs) with seasonal transmission. Here Hamlet et al. model the monthly occurrence of YF in humans and NHPs across Brazil and show that seasonality of agriculture is an important predictor of seasonal YF transmission.

    • Arran Hamlet
    • , Daniel Garkauskas Ramos
    •  & Neil M. Ferguson

  • Article
    | Open Access

    Deer mice are natural hosts for a number of human pathogens. Here, Griffin et al. report that intranasal exposure of the North American deer mouse to SARS-CoV-2 results in virus replication and shedding, despite causing only mild or asymptomatic illness. Additionally, infected deer mice can transmit SARS-CoV-2 to naïve deer mice.

    • Bryan D. Griffin
    • , Mable Chan
    •  & Darwyn Kobasa

  • Article
    | Open Access

    High-resolution cryo-EM structures and biochemical analyses of the human mitoribosome, in complex with mitochondria-specific factors mediating mitoribosome recycling, RRFmt and EF-G2mt, offer insight into mechanisms of mitoribosome recycling and resistance to antibiotic fusidic acid.

    • Ravi Kiran Koripella
    • , Ayush Deep
    •  & Rajendra K. Agrawal

  • Article
    | Open Access

    The role of meteorological factors in SARS-COV-2 transmission is not well understood. Here, the authors use county-level data from the United States to the end of 2020 and find evidence of a moderate association between increased transmissibility and cold, dry weather and low ultraviolet radiation.

    • Yiqun Ma
    • , Sen Pei
    •  & Kai Chen

  • Article
    | Open Access

    Here, the authors use simulated quantitative gut microbial communities to benchmark the performance of 13 common data transformations in determining diversity as well as microbe-microbe and microbe-metadata associations, finding that quantitative approaches incorporating microbial load variation outperform computational strategies in downstream analyses, urging for a widespread adoption of quantitative approaches, or recommending specific computational transformations whenever determination of microbial load of samples is not feasible.

    • Verónica Lloréns-Rico
    • , Sara Vieira-Silva
    •  & Jeroen Raes

  • Article
    | Open Access

    Disentangling the impacts of non-pharmaceutical interventions on COVID-19 transmission is challenging as they have been used in different combinations across time and space. This study shows that, early in the epidemic, school/daycare closures and stopping nursing home visits were associated with the biggest reduction in transmission in the United States.

    • Bingyi Yang
    • , Angkana T. Huang
    •  & Derek A. T. Cummings

  • Article
    | Open Access

    Population-based surveys are the gold standard for estimating seroprevalence but are expensive and often only capture a small geographic area or window of time. This study describes a new platform, SCALE-IT, for serosurveillance based on algorithmic sampling of electronic health records, and uses it to estimate the seroprevalence of SARS-CoV-2 in San Francisco.

    • Isobel Routledge
    • , Adrienne Epstein
    •  & Isabel Rodriguez-Barraquer

  • Article
    | Open Access

    Mitochondrial ribosomes (mitoribosomes) are characterized by a distinct architecture and thus biogenesis pathway. Here, cryo-EM structures of mitoribosome large subunit assembly intermediates elucidate final steps of 16 S rRNA folding, methylation and peptidyl transferase centre (PTC) completion, as well as functions of several mitoribosome assembly factors.

    • Caillan Crowe-McAuliffe
    • , Victoriia Murina
    •  & Daniel N. Wilson

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