Microbiology articles within Nature Communications

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  • 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

  • Article
    | Open Access

    Infections with bacteria of the genus Sarcina are associated with gastric diseases of unclear etiology. Here, Owens et al. show that infection with a distinct Sarcina species is strongly associated with a lethal disease that affects sanctuary chimpanzees in Sierra Leone.

    • Leah A. Owens
    • , Barbara Colitti
    •  & Tony L. Goldberg

  • Article
    | Open Access

    It is unclear how gut-dwelling E. coli bacteria often emerge to cause systemic infection in chickens. Here, Mageiros et al. use population genomics and pangenome-wide association studies to identify genetic elements associated with pathogenicity in avian E. coli.

    • Leonardos Mageiros
    • , Guillaume Méric
    •  & Samuel K. Sheppard

  • Article
    | Open Access

    Establishing the natural history of COVID-19 requires longitudinal data from population-based cohorts. Here, the authors use linked primary care, testing, and hospital data to describe the disease in ~100,000 individuals with a COVID-19 diagnosis among a population of ~5.5 million in Catalonia, Spain.

    • Edward Burn
    • , Cristian Tebé
    •  & Talita Duarte-Salles

  • Article
    | Open Access

    Nanozymes have been used for antibacterial applications but have potential toxicity to mammalian cells. Here the authors suggest that nanozymes that generate surface bound reactive oxygen species disrupt bacterial cell walls but not mammalian cells walls due to the different particle uptake mechanisms.

    • Feng Gao
    • , Tianyi Shao
    •  & Lihua Yang

  • Article
    | Open Access

    Transfer of a host’s microbiota by faecal microbiota transplantation has shown benefit in the context of recurrent Clostridioides difficle infection. Here the authors shows the inflammatory status of the recipient can impact on engraftment and the efficacy of the introduced microbiota in a model of C.difficile infection.

    • Eric R. Littmann
    • , Jung-Jin Lee
    •  & Michael C. Abt

  • Article
    | Open Access

    To obtain optimal yield and productivity in bioproduction, expression of pathway genes must be appropriately coordinated. Here, the authors report repurposing of base editors for simultaneous regulation of multiple gene expression and demonstrate its application in industrially important and model microorganisms.

    • Yu Wang
    • , Haijiao Cheng
    •  & Yanhe Ma

  • Article
    | Open Access

    Early prediction and diagnosis of sepsis, which is critical in reducing mortality, is challenging as many of its signs and symptoms are similar to other less critical conditions. Here, the authors develop an artificial intelligence algorithm which uses both structured data and unstructured clinical notes to predict sepsis.

    • Kim Huat Goh
    • , Le Wang
    •  & Gamaliel Yu Heng Tan

  • Article
    | Open Access

    Microbial symbionts can help their hosts metabolise diverse diets. A study on herbivorous turtle ants identifies the cuticular components which are nitrogen-enriched by gut bacteria, highlighting the role of symbionts in insect evolution.

    • Christophe Duplais
    • , Vincent Sarou-Kanian
    •  & Corrie S. Moreau

  • Article
    | Open Access

    The COVID-19 epidemic began later in Russia than many European countries, possibly due to restrictions on travel from China. Here, the authors analyze whole genome sequences sampled early in the epidemic in Russia, and find that most strains were not linked to China.

    • Andrey B. Komissarov
    • , Ksenia R. Safina
    •  & Georgii A. Bazykin

  • Article
    | Open Access

    Here, using in vitro assays and structural analysis, the authors characterize the anti-SARS-CoV-2 properties of two small molcules, showing these to bind and target the virus main protease (Mpro), and to exhibit a synergistic antiviral effect when combined with remdesivir in vitro.

    • Shin-ichiro Hattori
    • , Nobuyo Higashi-Kuwata
    •  & Hiroaki Mitsuya

  • Article
    | Open Access

    Fungi may have evolved up to 2.4 billion years ago, but it is unclear when they first colonized land. Here Gan and colleagues report filamentous Ediacaran microfossils from South China that may represent early terrestrial fungi.

    • Tian Gan
    • , Taiyi Luo
    •  & Shuhai Xiao

  • Article
    | Open Access

    Mutualists benefit their partners by providing resources that would be difficult to obtain independently. Here, the authors show in a bacterial community and with mathematical modeling how a mutualist can promote coexistence between competitors by providing them with different limiting resources.

    • Sarah P. Hammarlund
    • , Tomáš Gedeon
    •  & William R. Harcombe

  • Article
    | Open Access

    Bacterial protein FtsZ polymerizes at mid-cell and exhibits treadmilling dynamics, driving the movement of enzymes that synthesize septal peptidoglycan. Here, McCausland et al. combine theoretical modelling with single-molecule imaging of bacteria to show that FtsZ treadmilling drives enzyme movement via a Brownian ratchet mechanism.

    • Joshua W. McCausland
    • , Xinxing Yang
    •  & Jian Liu

  • Article
    | Open Access

    In this study, Omry Koren, Samuli Rautava and colleagues report a sex-specific association between neonatal antibiotic exposure and weight and height gain during the first six years of life and showing that boys but not girls exposed to neonatal antibiotics exhibit impaired weight and height development.

    • Atara Uzan-Yulzari
    • , Olli Turta
    •  & Omry Koren

  • Article
    | Open Access

    The trajectory of the emergence of Zika virus (ZIKV) into the Americas remains unclear. Here, the authors find that four mutations originated before ZIKV introduction to the Americas are direct reversions of previous mutations that accompanied spread many decades ago from ZIKV’s native Africa to Asia, and show in experimental infections of mosquitoes, human cells, and mice that the original mutations reduced fitness for urban transmission, while the reversions restored fitness, likely increasing epidemic risk.

    • Jianying Liu
    • , Yang Liu
    •  & Scott C. Weaver

  • Article
    | Open Access

    Previously, a broadly neutralizing antibody, 3I14, active against groups 1 and 2 influenza A viruses was isolated from human memory B cells and showed protection in mice from lethal viral challenge. Here, Harshbarger and Deming et al. provide the crystal structure of 3I14 Fab in complex with H3, H6, and H10.

    • Wayne D. Harshbarger
    • , Derrick Deming
    •  & Wayne A. Marasco

  • Article
    | Open Access

    Melting of the Greenland Ice Sheet—a threat for sea level rise—is accelerated by ice algal blooms. Here the authors find a link between mineral phosphorus and glacier algae, indicating that dust-derived nutrients aid bloom development, thereby impacting ice sheet melting.

    • Jenine McCutcheon
    • , Stefanie Lutz
    •  & Liane G. Benning

  • Article
    | Open Access

    Photodynamic inactivation is a common antibacterial method but often fails in extremely acidic environments (pH< 4). Here, the authors demonstrate halogenation of fluorescein for the development of a photodynamic agent which works in extremely acidic environments and demonstrate sterilisation applications in fruit juice and in vivo.

    • Ying Wang
    • , Jiazhuo Li
    •  & Peng Wu

  • Article
    | Open Access

    The emergence and spread of artemisinin resistance has compromised antimalarial efficacy. Here, Mok et al. apply quantitative transcriptomics, proteomics, and metabolomics to provide evidence that K13 mutations alter multiple aspects of the parasite’s intra-erythrocytic development to enhance survival following artemisinin treatment.

    • Sachel Mok
    • , Barbara H. Stokes
    •  & David A. Fidock

  • Article
    | Open Access

    Ribosomal RNA (rRNA) expression is regulated at the initiation stage of RNA synthesis. Here, the authors report cryo-EM structures of E. coli RNA polymerase and rRNA promoter complex with DksA/ppGpp on the way to open complex formation, identifying key steps in promoter recognition and opening.

    • Yeonoh Shin
    • , M. Zuhaib Qayyum
    •  & Katsuhiko S. Murakami

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