Microbiology articles within Nature Communications

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  • 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

  • Article
    | Open Access

    Here Arndt et al. establish rotating-crystal magneto-optical detection (RMOD) as a near-point-of-care diagnostic tool for malaria detection and report a sensitivity and specificity of 82% and 84%, respectively, as validated by analyzing a clinical population in a high transmission setting in Papua New Guinea.

    • L. Arndt
    • , T. Koleala
    •  & S. Karl

  • Article
    | Open Access

    Colibactin-producing pks+ Escherichia coli are frequent constituents of the human intestinal microbiota. Here, the authors show that short exposure of cells to pks+ E. coli induces chromosomal aberrations, genomic instability, and multiple features of transformation reminiscent of colorectal cancer.

    • Amina Iftekhar
    • , Hilmar Berger
    •  & Thomas F. Meyer

  • Article
    | Open Access

    New Zealand has been relatively successful in controlling COVID-19 due to implementation of strict non-pharmaceutical interventions. Here, the authors demonstrate a striking decline in reports of influenza and other non-influenza respiratory pathogens over winter months in which the interventions have been in place.

    • Q. Sue Huang
    • , Tim Wood
    •  & Richard J. Webby

  • Article
    | Open Access

    The SARS-CoV-2 spike protein contains a multi-basic cleavage site. Here, the authors show how this multi-basic cleavage site affects entry of SARS-CoV-2 into cells and transmission in the hamster model and identify host factors affecting entry of SARS-CoV-2 in a genome-wide CRISPR screen.

    • Yunkai Zhu
    • , Fei Feng
    •  & Rong Zhang

  • Article
    | Open Access

    Here, using the K18-hACE2 transgenic mice model, the authors report the in vivo efficacy of a fully human neutralizing antibody against SARS-CoV-2 and show that when administered before or up to 3 days post infection, treated mice do not exhibit disease symptoms while 80% of control animals succumb to the infection.

    • Ronit Rosenfeld
    • , Tal Noy-Porat
    •  & Ohad Mazor

  • Article
    | Open Access

    During the early phase of the COVID-19 pandemic there was a need for rapid dissemination of clinical findings. Here, Jung, Di Santo et al. perform a systematic review and cohort study providing evidence for lower methodological quality scores and faster time to publication of clinical studies related to COVID-19 than comparable studies.

    • Richard G. Jung
    • , Pietro Di Santo
    •  & Benjamin Hibbert

  • Article
    | Open Access

    Germ-free mosquitoes generated with current methods exhibit developmental deficits. Here, the authors use genetically modified bacteria to allow complete decolonisation at any developmental stage of Aedes aegypti mosquitoes and show that bacteria support larval development by contributing to folate biosynthesis and enhancing energy storage.

    • Ottavia Romoli
    • , Johan Claes Schönbeck
    •  & Mathilde Gendrin

  • Article
    | Open Access

    Dexamethasone has been shown to have survival benefits for critically ill patients hospitalised with COVID-19 in the UK. Here, the authors estimated the number of lives that could be saved through a UK and global roll out of the drug and demonstrate that it is a cost-effective option.

    • Ricardo Águas
    • , Adam Mahdi
    •  & Mesulame Namedre

  • Article
    | Open Access

    Asymptomatic malaria infections contribute to transmission. Here, Sumner et al. infer participant-to-mosquito transmission by sampling naturally-fed mosquitoes from households in Western Kenya and find that asymptomatic infections more than double the odds of transmission to a mosquito compared to symptomatic infections.

    • Kelsey M. Sumner
    • , Elizabeth Freedman
    •  & Steve M. Taylor

  • Article
    | Open Access

    REACT-2 is a large-scale community study of SARS-CoV-2 seroprevalence in England. Here, the authors estimate that 6% of adults in England had been infected by mid-July 2020, with health and long-term care workers and those of Black or South Asian ethnicity disproportionately affected.

    • Helen Ward
    • , Christina Atchison
    •  & Paul Elliott

  • Article
    | Open Access

    Transcription by bacterial RNA polymerase is interrupted by pausing events that play diverse regulatory roles. Here, the authors find that a large number of E. coli sigma70-dependent pauses, clustered at a 10−20-bp distance from promoters, are regulated by Gre cleavage factors constituting a mechanism for rapid response to changing environmental cues.

    • Zhe Sun
    • , Alexander V. Yakhnin
    •  & Mikhail Kashlev

  • Article
    | Open Access

    Salmonella Typhimurium establishes systemic infection by replicating in host macrophages. Here, Jiang et al. show that infected macrophages exhibit upregulated glycolysis and decreased serine synthesis, leading to accumulation of glycolytic intermediates that promote intracellular replication and virulence of S. Typhimurium.

    • Lingyan Jiang
    • , Peisheng Wang
    •  & Lei Wang

  • Article
    | Open Access

    A bat origin for SARS-CoV-2 has been proposed. Here, by sampling wild Rhinolophus acuminatus bats from Thailand, the authors identified a SARS-CoV-2-related coronavirus (SC2r-CoV), designated as RacCS203, with 91.5% genome similarity to SARS-CoV-2, and show that sera obtained from bats and Malayan pangolin neutralize SARS-CoV-2.

    • Supaporn Wacharapluesadee
    • , Chee Wah Tan
    •  & Lin-Fa Wang

  • Article
    | Open Access

    Spread of SARS-CoV-2 in the early phase of the pandemic has been driven by high population susceptibility, but virus sensitivity to climate may play a role in future outbreaks. Here, the authors simulate SARS-CoV-2 dynamics in winter assuming climate dependence is similar to an endemic coronavirus strain.

    • Rachel E. Baker
    • , Wenchang Yang
    •  & Bryan T. Grenfell

  • Article
    | Open Access

    The spatial arrangement of bacterial strains and species within microbial communities is considered crucial for their ecology. Here, Krishna Kumar et al. use a droplet-based printing method to arrange different bacterial genotypes across a sub-millimetre array, and show that micron-scale changes in spatial distributions can drive major shifts in ecology.

    • Ravinash Krishna Kumar
    • , Thomas A. Meiller-Legrand
    •  & Kevin R. Foster

  • Article
    | Open Access

    The humoral immune response to SARS-CoV-2 infection is not yet fully understood. Here, Marot et al. monitor the longitudinal profile and neutralizing activity of IgG, IgA, and IgM among 26 healthcare workers and provide evidence for a short-lasting humoral immune protection due to a decrease of neutralizing antibody titers within 3 months.

    • Stéphane Marot
    • , Isabelle Malet
    •  & Anne-Geneviève Marcelin

  • Article
    | Open Access

    Enzalutamide, an approved drug for prostate cancer, acts on TMPRSS2 expression, a key mediator for SARS-CoV-2 infection. Here, the authors characterize the anti-SARS-CoV-2 effects of Enzalutamide in prostate cancer cells, lung cancer cells, human lung organoids and in hACE2-transduced Tmprss2 knockout mice and show lack antiviral action in human lung cells and human lung organoids, likely due to the AR-independent TMPRSS2 expression in mouse and human lung epithelial cells.

    • Fei Li
    • , Ming Han
    •  & Dong Gao

  • Article
    | Open Access

    It has been suggested that pangolin coronaviruses may be the origin of SARS-CoV-2. Here the authors show that the Pangolin-CoV spike is structurally closely related to the closed form of SARS-CoV-2 spike and exhibits similar binding properties to human and pangolin ACE2; although neither spike binds bat ACE2.

    • Antoni G. Wrobel
    • , Donald J. Benton
    •  & Steven J. Gamblin

  • Article
    | Open Access

    In this single-arm clinical trial, the authors show that treatment of COVID-19 patients with bevacizumab, an anti-vascular endothelial growth factor drug, can improve PaO2/FiO2 ratios and oxygen-support status. Relative to an external control group, bevacizumab shows clinical efficacy by improving oxygenation.

    • Jiaojiao Pang
    • , Feng Xu
    •  & Yihai Cao

  • Article
    | Open Access

    Soil organic matter (SOM) is a huge sink of carbon, but the varied flux dynamics are challenging to predict. Here, the authors present a new model with the complexities of SOM cycling, including parameters for substrate accessibility, microbe diversity, and enzymatic substrate depolymerization.

    • Julien Sainte-Marie
    • , Matthieu Barrandon
    •  & Delphine Derrien

  • Article
    | Open Access

    Pathogenesis of steroid-resistant gut acute graft-versus-host-disease (SR-Gut-aGVHD) remains unclear., Here the authors show in mouse models that dysbiosis caused by the expansion of Th/Tc22, as well as depletion of CX3CR1hi mononuclear phagocytes resulted from the reduction of Th/Tc1, contributes to SR-Gut-aGVHD onset.

    • Qingxiao Song
    • , Xiaoning Wang
    •  & Defu Zeng

  • Article
    | Open Access

    Flavonoids are abundant polyphenols in plants but it is not well understood how their metabolism is initiated by microbes in the human gut. Here, the authors identify and characterise an ene-reductase from the gut bacterium, Flavonifractor plautii ATCC 49531 that catalyses the hydrogenation of the C2–C3 double bond of flavones and flavonols and present its crystal structure.

    • Gaohua Yang
    • , Sen Hong
    •  & Yang Gu

  • Article
    | Open Access

    Mycelial fusion can favour fungal strains that exploit each other, but the mechanism is not well understood. Here, Grum-Grzhimaylo et al. show that different cheater lineages share similar deficiencies in initiating fusion that nevertheless enable them to preferentially obtain the benefits of fusion initiated by wild-type mycelia.

    • Alexey A. Grum-Grzhimaylo
    • , Eric Bastiaans
    •  & Duur K. Aanen

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