Microbiology articles within Nature Communications

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  • 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

  • Article
    | Open Access

    The pathogen Campylobacter jejuni invades intestinal cells after secreting protein effectors into the host cell cytosol via the flagellum. Here, Negretti et al. show that one of these effectors, CiaD, binds to host protein IQGAP1, thus leading to unconstrained activity of small GTPase Rac1, which modulates actin reorganization and bacterial internalization.

    • Nicholas M. Negretti
    • , Christopher R. Gourley
    •  & Michael E. Konkel

  • Article
    | Open Access

    Koalas are susceptible to neoplasms, which are related to infection with the Koala retrovirus. Here, the authors use DNA sequencing to show that the retroviral insertion sites cluster near known cancer genes and demonstrate a high mutational load associated with the germline invasion of the virus.

    • Gayle K. McEwen
    • , David E. Alquezar-Planas
    •  & Alex D. Greenwood

  • Article
    | Open Access

    Understanding a complex microbial ecosystem such as the human gut microbiome requires information about both microbial species and the metabolites they produce and secrete. Here, the authors propose an ecology-based computational method to predict hundreds of new experimentally untested cross-feeding interactions in the human gut microbiome.

    • Akshit Goyal
    • , Tong Wang
    •  & Sergei Maslov

  • Article
    | Open Access

    Non-human primates are important animal models for studying SARS-CoV-2 infection. Here, Salguero et al. directly compare rhesus and cynomolgus macaques and show that both species represent COVID-19 disease of mild clinical cases, and provide a lung histopathology scoring system.

    • Francisco J. Salguero
    • , Andrew D. White
    •  & Miles W. Carroll

  • Article
    | Open Access

    NK cells control SIV infection in secondary lymphoid tissues in the natural host that typically doesn’t progress toward disease. Here the authors show that this control is associated with terminal NK cell differentiation and improved MHC-E-dependent activity lacking in pathogenic SIV infection.

    • Nicolas Huot
    • , Philippe Rascle
    •  & Michaela Müller-Trutwin

  • Article
    | Open Access

    The Pseudomonas aeruginosa lytic polysaccharide monooxygenase CbpD, prevalent in clinical isolates, has been proposed to act as a virulence factor. Here, the authors combine structural work, in silico simulations, enzymatic activity and in vitro and in vivo experiments to further delineate the role of CbpD and show that its deletion renders P. aeruginosa unable to establish a lethal systemic infection, leading to enhanced bacterial clearance in a mouse model of infection.

    • Fatemeh Askarian
    • , Satoshi Uchiyama
    •  & Gustav Vaaje-Kolstad

  • Article
    | Open Access

    In several bacteria, cyclic di-AMP mediates potassium (K+) and osmotic homeostasis. Here, the authors show that DarB, a Bacillus subtilis protein previously reported to bind cyclic di-AMP, interacts with the (p)ppGpp synthetase/hydrolase Rel in a K+-dependent manner in turn leading to Rel-dependent accumulation of pppGpp under conditions of K+ starvation.

    • Larissa Krüger
    • , Christina Herzberg
    •  & Jörg Stülke

  • Article
    | Open Access

    The N cycle involves complex, microbially-mediated shuttling between ammonium, nitrite and nitrate, with climatically important greenhouse gas byproducts. Here the authors use isotope labeling experiments in river sediments and find a cryptic new step in the N cycle between nitrification and the removal of fixed N through N2 gas production.

    • Liao Ouyang
    • , Bo Thamdrup
    •  & Mark Trimmer

  • Article
    | Open Access

    MXenes have emerged as potential antimicrobial materials. Here, the authors report on the creation of a Schottky junction to increase the charge separation between MXenes and semiconductor to increase photodynamic creation of reactive oxygen species under near infrared irradiation for antibacterial purposes.

    • Jianfang Li
    • , Zhaoyang Li
    •  & Shuilin Wu

  • Article
    | Open Access

    Plasmodium falciparum secretes extracellular vesicles (EVs) while growing inside red blood cells (RBCs). Here the authors show that these EVs contain assembled and functional 20S proteasome complexes that remodel the cytoskeleton of naïve human RBCs, priming the RBCs for parasite invasion.

    • Elya Dekel
    • , Dana Yaffe
    •  & Neta Regev-Rudzki

  • Article
    | Open Access

    Antimicrobial resistance is a major global health threat and its development is promoted by antibiotic misuse. Here, the authors present an offline smartphone application for automated and standardized antibiotic susceptibility testing, to be deployed in resource-limited settings.

    • Marco Pascucci
    • , Guilhem Royer
    •  & Mohammed-Amin Madoui

  • Article
    | Open Access

    It is unknown whether capsulized fecal microbiota transplantation (FMT) can modify the microbiota of people with HIV. Here, the authors report the results of a pilot double-blind study, where 30 HIV-infected subjects on ART were randomized to either weekly oral FMT capsules or placebo for 8 weeks, and show that transplanted microbiota successfully engrafts and is able to attenuate HIV-associated dysbiosis.

    • Sergio Serrano-Villar
    • , Alba Talavera-Rodríguez
    •  & Santiago Moreno

  • Article
    | Open Access

    Spores produced by Clostridioides difficile during infection are important for the recurrence of the disease. Here, Castro-Córdova et al. show that the spores gain entry into the intestinal mucosa via pathways dependent on host fibronectin and vitronectin, and spore entry inhibition leads to reduced recurrence of infection in a mouse model.

    • Pablo Castro-Córdova
    • , Paola Mora-Uribe
    •  & Daniel Paredes-Sabja

  • Article
    | Open Access

    Antibiotic therapy can lead to pathogen clearance, but also to alterations in the gut microbiota and systemic immune responses. Here, the authors analyze data from patients with tuberculosis and healthy subjects to show that pathogen clearance and gut microbiota alterations are independently associated with antibiotic-induced changes of the inflammatory response of active tuberculosis.

    • Matthew F. Wipperman
    • , Shakti K. Bhattarai
    •  & Vanni Bucci

  • Article
    | Open Access

    Here, the authors present a pig integrated gene catalog and metagenome-assembled genomes, which they construct from swine gut microbiomes spanning various ages, sexes, breeds, geographical locations, domestication, and gut locations by metagenomic sequencing, providing expanded resources for pig microbiome studies.

    • Congying Chen
    • , Yunyan Zhou
    •  & Lusheng Huang

  • Article
    | Open Access

    The systemic immune features that distinguish COVID-19 from common infections remain incompletely elucidated. Here McClain et al. compare RNA sequencing in peripheral blood between subjects with SARS-CoV-2 and other respiratory infections and demonstrate dysregulated immune responses in COVID-19 with both heterogeneous and conserved components.

    • Micah T. McClain
    • , Florica J. Constantine
    •  & Christopher W. Woods

  • Article
    | Open Access

    Social distancing policies aiming to reduce COVID-19 transmission have been reflected in reductions in human mobility. Here, the authors show that reduced mobility is correlated with decreased transmission, but that this relationship weakened over time as social distancing measures were relaxed.

    • Pierre Nouvellet
    • , Sangeeta Bhatia
    •  & Christl A. Donnelly

  • Article
    | Open Access

    Glycolytic enzymes are challenging drug targets due to their highly conserved active sites and phosphorylated substrates. Here, the authors identify fast acting allosteric inhibitors of Trypanosoma brucei phosphofructokinase that block trypanosome glycolysis and provide cure evidence in murine model.

    • Iain W. McNae
    • , James Kinkead
    •  & Malcolm D. Walkinshaw

  • Article
    | Open Access

    The most advanced P. falciparum circumsporozoite protein (PfCSP)-based malaria vaccine confers partial protection. Here, Pholcharee et al. present crystal structures, binding affinities/kinetics, and in vivo protection of 8 anti-NANP antibodies to understand in vivo protection of PfCSP-targeting antibodies.

    • Tossapol Pholcharee
    • , David Oyen
    •  & Ian A. Wilson

  • Article
    | Open Access

    Phytoplankton account for a large proportion of global primary production and comprise a number of phylogenetically distinct lineages. Here, Uwizeye et al. use FIB-SEM to study ultrastructural plasticity of 7 distinct taxa and describe how subcellular organisation is linked to energy metabolism.

    • Clarisse Uwizeye
    • , Johan Decelle
    •  & Giovanni Finazzi

  • Article
    | Open Access

    Homologous recombination between co-infecting coronaviruses can produce novel pathogens. Here, Wardeh et al. develop a machine learning approach to predict associations between mammals and multiple coronaviruses and hence estimate the potential for generation of novel coronaviruses by recombination.

    • Maya Wardeh
    • , Matthew Baylis
    •  & Marcus S. C. Blagrove

  • Article
    | Open Access

    The role of children in the spread of COVID-19 is not fully understood, and the circumstances under which schools should be opened are therefore debated. Here, the authors demonstrate protocols by which schools in France can be safely opened without overwhelming the healthcare system.

    • Laura Di Domenico
    • , Giulia Pullano
    •  & Vittoria Colizza

  • Article
    | Open Access

    Here, the authors analyze 4907 Circular Metagenome Assembled Genomes from human microbiomes and identify and characterize nearly 600 diverse genomes of crAss-like phages, finding two putative families with unusual genomic features, including high density of self-splicing introns and inteins.

    • Natalya Yutin
    • , Sean Benler
    •  & Eugene V. Koonin

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