Microbiology articles within Nature Communications

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  • Article
    | Open Access

    Genome sequencing can be used to infer pathogen transmission dynamics and inform public health responses. Here, the authors sequence >1,200 SARS-CoV-2 samples from Victoria, Australia and find genomic support for the effectiveness of social restrictions in reducing transmission.

    • Torsten Seemann
    • , Courtney R. Lane
    •  & Benjamin P. Howden

  • Article
    | Open Access

    COVID-19 disease is less common in children than adults, but the extent to which SARS-CoV-2 infections are missed through symptom-driven testing is not well understood. In this study, the authors show that approximately 1% of children seeking care for reasons other than COVID-19 at a Seattle hospital in March/April 2020 were seropositive for SARS-CoV-2.

    • Adam S. Dingens
    • , Katharine H. D. Crawford
    •  & Jesse D. Bloom

  • Article
    | Open Access

    Bacterial transcriptomic data have been used to predict antibiotic susceptibility in a species- or antibiotic-specific manner. Here, the authors show that global transcriptional disorder is a common stress response in bacteria with low fitness, and present a general approach that can predict bacterial fitness independently of species or type of stress.

    • Zeyu Zhu
    • , Defne Surujon
    •  & Tim van Opijnen

  • Article
    | Open Access

    Gut microbial and metabolite alterations are linked to inflammatory bowel diseases pathogenesis. Here the authors identify functional microbiota signatures that correlate with disease activity by comparing patients with Crohn’s disease undergoing autologous hematopoietic stem cell transplantation who either did not respond to therapy, experienced relapse after remission or maintained remission, and show that these microbial signatures recapitulate disease activity when transferred to mice.

    • Amira Metwaly
    • , Andreas Dunkel
    •  & Dirk Haller

  • Article
    | Open Access

    The mechanism underlying packaging of the 8 segments of the influenza virus genome into virions is not well understood. Here, the authors use a multiplexed FISH assay to monitor the 8 segments in parallel in infected cells suggesting bundling routes during the packaging process.

    • Ivan Haralampiev
    • , Simon Prisner
    •  & Andreas Herrmann

  • Article
    | Open Access

    Here, Giansanti et al. perform a system-wide and time-resolved characterization of the changes in the host cell proteome and phosphoproteome of cells infected with the enterovirus coxsackievirus B3 during a full round of replication and identify mTORC1 signalling as a major regulation network during virus infection.

    • Piero Giansanti
    • , Jeroen R. P. M. Strating
    •  & Frank J. M. van Kuppeveld

  • Article
    | Open Access

    Understanding bacterial adhesion is important in a number of different areas of study. Here using a range of simulations and experimental methods, the authors, report on the molecular mechanism behind the binding of bacteria to cellulose fibers at high shear force in the human gut.

    • Zhaowei Liu
    • , Haipei Liu
    •  & Michael A. Nash

  • Comment
    | Open Access

    Weather may marginally affect COVID-19 dynamics, but misconceptions about the way that climate and weather drive exposure and transmission have adversely shaped risk perceptions for both policymakers and citizens. Future scientific work on this politically-fraught topic needs a more careful approach.

    • Colin J. Carlson
    • , Ana C. R. Gomez
    •  & Sadie J. Ryan

  • Article
    | Open Access

    Coronavirus main protease is essential for viral polyprotein processing and replication. Here Vuong et al. report efficient inhibition of SARS-CoV-2 replication by the dipeptide-based protease inhibitor GC376 and its parent GC373, which were originally used to treat feline coronavirus infection.

    • Wayne Vuong
    • , Muhammad Bashir Khan
    •  & M. Joanne Lemieux

  • Comment
    | Open Access

    There is an urgent need for drugs, therapies and vaccines to be available to protect the human population against COVID-19. One of the first approaches taken in the COVID-19 global response was to consider repurposing licensed drugs. This commentary highlights an extraordinary international collaborative effort of independent researchers who have recently all come to the same conclusion—that chloroquine or hydroxchloroquine are unlikely to provide clinical benefit against COVID-19.

    • S. G. P. Funnell
    • , W. E. Dowling
    •  & C. M. Coleman

  • Article
    | Open Access

    Here Zhao et al. report a promising broad-spectrum antiviral alkaline peptide—P9R—that is active against several respiratory, pH-dependent viruses, including Influenza and SARS-CoV-2. P9R interferes with virus internalization by binding to the virus and subsequent inhibition of endosomal acidification.

    • Hanjun Zhao
    • , Kelvin K. W. To
    •  & Kwok-Yung Yuen

  • Article
    | Open Access

    Bats are a likely reservoir of zoonotic coronaviruses (CoVs). Here, analyzing bat CoV sequences in China, the authors find that alpha-CoVs have switched hosts more frequently than betaCoVs, identify a bat family and genus that are highly involved in host-switching, and define hotspots of CoV evolutionary diversity.

    • Alice Latinne
    • , Ben Hu
    •  & Peter Daszak

  • Article
    | Open Access

    In the fly Drosophila melanogaster commensal bacteria and dietary essential amino acids control food choice behavior. Here, by using chemically defined diets and metabolomics, the authors show that Acetobacter pomorum (Ap) and Lactobacilli plantarum (Lp) engage in a mutualistic metabolic relationship to overcome detrimental diets, and identify Ap as the bacterium altering the host’s feeding decisions.

    • Sílvia F. Henriques
    • , Darshan B. Dhakan
    •  & Carlos Ribeiro

  • Article
    | Open Access

    Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are members of the complex II superfamily. Here, the authors present the 2.8 Å cryo-EM structure of Mycobacterium smegmatis Sdh2, which reveals membrane-anchored SdhF as a component of the complex and they discuss the electron/proton transfer pathway in the Sdh2 trimer.

    • Hongri Gong
    • , Yan Gao
    •  & Zihe Rao

  • Article
    | Open Access

    Swarming bacterial populations can exhibit antibiotic resistance, despite sustaining considerable cell death. Here, Bhattacharyya et al. show that killed cells release periplasmic protein AcrA, which activates efflux pumps on the surface of live cells, thus enhancing antibiotic resistance in the surviving cells.

    • Souvik Bhattacharyya
    • , David M. Walker
    •  & Rasika M. Harshey

  • Article
    | Open Access

    Herpes simplex virus establishes lifelong latency in ganglionic neurons, which are the source for recurrent infection. Here Aubert et al. report a promising antiviral therapy based on gene editing with adeno-associated virus-delivered meganucleases, which leads to a significant reduction in ganglionic HSV loads and HSV reactivation.

    • Martine Aubert
    • , Daniel E. Strongin
    •  & Keith R. Jerome

  • Article
    | Open Access

    Herpesvirus virions have an outer lipid membrane dotted with glycoproteins that enable fusion with cell membranes to initiate entry and establish infection. Here the authors elucidate the structural mechanism of a neutralizing antibody derived from a patient infected by the herpesvirus varicella-zoster virus and targeted to its fusogen, glycoprotein-B.

    • Stefan L. Oliver
    • , Yi Xing
    •  & Ann M. Arvin

  • Article
    | Open Access

    Influenza viruses are believed to transmit through the air as respiratory droplets or aerosols. In the guinea pig model, Asadi et al. show that influenza virus can also be transmitted as aerosolized fomites, which are microscopic dust particles stirred up from a virus-contaminated environment.

    • Sima Asadi
    • , Nassima Gaaloul ben Hnia
    •  & Nicole M. Bouvier

  • Article
    | Open Access

    Bacteria can form wall-deficient variants, or L-forms, that divide by a simple mechanism that does not require the FtsZ-based cell division machinery. Here, Wu et al. study L-forms in microfluidic systems to show the importance of geometric effects for cell growth, chromosome segregation and cell division.

    • Ling Juan Wu
    • , Seoungjun Lee
    •  & Jeff Errington

  • Article
    | Open Access

    Staphylococcus aureus is thought to divide in three alternating orthogonal planes over three consecutive divisions. Here the authors dispel this idea, showing that one out of the multiple planes perpendicular to the septum can be used in daughter cells irrespective of its orientation in relation to the penultimate division plane.

    • Bruno M. Saraiva
    • , Moritz Sorg
    •  & Mariana G. Pinho

  • Article
    | Open Access

    A vaccine preventing infection and transmission of SARS-CoV-2 is needed. Here, Wu et al. generate an adenovirus-vector vaccine expressing SARS-CoV-2 spike protein and show that a single dose of mucosal vaccination protects mice and ferrets from infection and inhibits virus replication in the upper respiratory tract.

    • Shipo Wu
    • , Gongxun Zhong
    •  & Wei Chen

  • Article
    | Open Access

    The cause of clonal expansions in the HIV reservoir remains unclear. Here, Gantner et al. perform single-cell TCR sequencing on longitudinal samples from eight individuals on antiretroviral therapy and find that antigens inducing clonal expansions of memory cells are major contributors to the HIV reservoir.

    • Pierre Gantner
    • , Amélie Pagliuzza
    •  & Nicolas Chomont

  • Article
    | Open Access

    Neutralizing antibody titers in SARS-CoV-2 infected or vaccinated people are an important measure for vaccine development and public health decision-making. Here, the authors develop a fluorescence based SARS-CoV-2 assay to determine neutralizing antibody titers in COVID-19 patient sera in a high throughput set-up.

    • Antonio E. Muruato
    • , Camila R. Fontes-Garfias
    •  & Pei-Yong Shi

  • Article
    | Open Access

    Astroviruses are common human pathogens and their genomes contain three known protein-coding genes. Here, Lulla et al. report a fourth, previously overlooked gene encoding protein XP which has a viroporin-like activity that is important for efficient production and/or release of virus particles.

    • Valeria Lulla
    •  & Andrew E. Firth

  • Article
    | Open Access

    The latent human immunodeficiency virus (HIV) reservoir in patients poses a problem for HIV cure. Here, Li et al. show that a combination of compounds inducing viral reactivation and cell death, inhibiting autophagy and blocking new infections can eliminate HIV infection in 50% of humanized HIV infected mice and in blood samples from infected patients.

    • Min Li
    • , Wei Liu
    •  & Jin Wang

  • Article
    | Open Access

    Antibiotics targeting protein translation interact in hard-to-predict ways. Here, Kavčič et al. interpret these interactions in terms of translation bottlenecks, the kinetics of drug uptake and target binding, bacterial growth laws, and a model of queued traffic progression.

    • Bor Kavčič
    • , Gašper Tkačik
    •  & Tobias Bollenbach

  • Article
    | Open Access

    Plasmodium infection activates signaling pathways in a-nucleated erythrocytes. Here, Adderley et al. use a comprehensive antibody microarray to show that infection extensively modulates host cell signalling and that the host receptor tyrosine kinase c-MET supports Plasmodium falciparum proliferation.

    • Jack D. Adderley
    • , Simona John von Freyend
    •  & Christian Doerig

  • Article
    | Open Access

    Some bacterial lineages appear to be pre-disposed to evolving antibiotic resistance. Here, the authors show that differential expression of an efflux pump causes widespread variation in evolvability across Staphylococcus aureus isolates, and chemical inhibition of the pump prevents resistance evolution.

    • Andrei Papkou
    • , Jessica Hedge
    •  & R. Craig MacLean

  • Article
    | Open Access

    The evolutionary relationships within Archaea remain unresolved. Here, the authors used genomic approaches to study the Undinarchaeota, a previously uncharacterized clade of DPANN, shed light on their position in an updated archaeal phylogeny and illuminate the history of archaeal genome evolution.

    • Nina Dombrowski
    • , Tom A. Williams
    •  & Anja Spang

  • Article
    | Open Access

    Plasmodium falciparum chloroquine resistance transporter (PfCRT) mediates multidrug resistance, but its natural function remains unclear. Here, Shafik et al. show that PfCRT transports host-derived peptides of 4-11 residues but not other ions or metabolites, and that drug-resistance-conferring PfCRT mutants have reduced peptide transport.

    • Sarah H. Shafik
    • , Simon A. Cobbold
    •  & Rowena E. Martin

  • Article
    | Open Access

    Lipo-chitooligosaccharides (LCOs) are signaling molecules produced by certain bacteria and fungi that establish symbiotic relationships with plants. Here, the authors show that LCOs are produced also by many other, non-symbiotic fungi, and regulate fungal growth and development.

    • Tomás Allen Rush
    • , Virginie Puech-Pagès
    •  & Jean-Michel Ané

  • Article
    | Open Access

    Histones have a role in antimicrobial defense. Here, the authors show that the histone H2A and the antimicrobial peptide LL-37 exert synergistic effects by enhancing bacterial membrane pores and enabling H2A entry into the bacterial cytoplasm, where it reorganizes DNA and inhibits transcription.

    • Tory Doolin
    • , Henry M. Amir
    •  & Albert Siryaporn

  • Article
    | Open Access

    The human antibacterial and immunomodulatory peptide LL-37 is a hCAP-18 protein cleavage product that self-assembles. Here, the authors present the human and gorilla LL-37 (17–29) crystal structures, revealing a self-assembly of amphipathic helices into a densely packed and elongated hexameric structure with a central pore and mutagenesis experiments support the role of self-assembly for antibacterial activity.

    • Yizhaq Engelberg
    •  & Meytal Landau

  • Article
    | Open Access

    The mechanism underlying the cellular entry of Zika virus is not fully understood. Here, the authors use a chemically modified virus and time-resolved proteomics to capture interacting host proteins during virus entry and identify NCAM1 as a ZIKV receptor.

    • Mayank Srivastava
    • , Ying Zhang
    •  & W. Andy Tao

  • Article
    | Open Access

    Here, the authors apply live-cell and in situ fluorescence imaging at the single-molecule level to examine lambda DNA replication in single cells, finding that individual phage DNAs sequester host factors to their own vicinity and confine their replicated DNAs into separate compartments, suggesting that phage decision-making transcripts are spatially organized in separate compartments to allow distinct subcellular decisions to develop.

    • Jimmy T. Trinh
    • , Qiuyan Shao
    •  & Lanying Zeng

  • Article
    | Open Access

    While membrane contact sites between intracellular organelles are abundant, little is known about the contacts between membranes that delimit extracellular junctions within cells, such as intracellular parasites. Here authors demonstrate the segregation of a lipid transporter from a solute transporter in the malarial host-parasite interface.

    • Matthias Garten
    • , Josh R. Beck
    •  & Joshua Zimmerberg

  • Article
    | Open Access

    CRISPR-Cas is a host adaptive immunity system and viruses harbor diverse anti-CRISPR proteins (Acrs). Here, the authors develop a random forest machine-learning approach to predict Acrs, identifying 2500 candidate Acr families, which expand the current repertoire of predicted Acrs by two orders of magnitude.

    • Ayal B. Gussow
    • , Allyson E. Park
    •  & Eugene V. Koonin

  • Article
    | Open Access

    The discovery of aerobic microbial communities in nutrient-poor sediments below the seafloor begs the question of the mechanisms for their persistence. Here the authors investigate subseafloor sediment in the South Pacific Gyre abyssal plain, showing that aerobic microbial life can be revived and retain metabolic potential even from 101.5 Ma-old sediment.

    • Yuki Morono
    • , Motoo Ito
    •  & Fumio Inagaki

  • Article
    | Open Access

    During an ongoing Ebola virus outbreak, infection before onset of protective immunity from vaccination is a possible scenario. Here the authors show in non-human primates that vaccination shortly before treatment with a monoclonal antibody does not negatively affect effectiveness of the antibody therapy.

    • Robert W. Cross
    • , Zachary A. Bornholdt
    •  & Thomas W. Geisbert

  • Article
    | Open Access

    Flagellotropic phages spin down flagella to reach the bacterial surface and must withstand remarkable drag forces. Here authors show how two nested sets of chainmail stabilise the viral head and a beta-hairpin regulates the formation of the robust yet pliable tail, characteristic of siphoviruses.

    • Joshua M. Hardy
    • , Rhys A. Dunstan
    •  & Fasséli Coulibaly

  • Article
    | Open Access

    SARS-CoV-2 expresses a 2′-O RNA methyltransferase (MTase) that is involved in the viral RNA cap formation and therefore a target for antiviral therapy. Here the authors provide the structure of nsp10-nsp16 with the panMTase inhibitor sinefungin and report that the development of MTase inhibitor therapies that target multiple coronoaviruses is feasible.

    • Petra Krafcikova
    • , Jan Silhan
    •  & Evzen Boura

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