Microbiology articles within Nature Communications

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  • Article
    | Open Access

    Here, Ferren et al. isolate Syrian hamster brainstem and lung tissue to establish ex vivo culture systems to study SARS-CoV-2 local viral tropism, immune response and tissue pathology. Further, they provide evidence that these systems can be used for screening of anti-viral compounds.

    • Marion Ferren
    • , Valérie Favède
    •  & Cyrille Mathieu

  • Article
    | Open Access

    The skin disease chytridiomycosis is linked to global amphibian declines but effective mitigation measures require improved understanding of the mechanisms underpinning the disease ecology. This study identifies key mediators of interactions between the fungal pathogen and amphibian skin, providing a marker of host colonization that can predict susceptibility between amphibian species.

    • Yu Wang
    • , Elin Verbrugghe
    •  & An Martel

  • Article
    | Open Access

    Two-pore channels (TPCs) are cation channels that localize to acidic organelles to regulate Ca2+ dependent events. Here, Li et al. characterize a TPC from Toxoplasma gondii(TgTPC) that localizes to the apicoplast, is critical for maintaining its integrity and relevant for Ca2+ uptake from the ER through stabilizing inter-organelle contact.

    • Zhu-Hong Li
    • , Thayer P. King
    •  & Silvia N. J. Moreno

  • Article
    | Open Access

    Here, the authors study the impact of Vibrio cholerae’s T6SS on human gut microbiota isolates and show that certain bacteria are protected from T6SS attacks in an immunity protein-independent manner. Specifically, protection occurred through superior T6SS weaponry in members of the Enterobacter cloacae complex and by molecular armors made of membrane-tethered capsular polysaccharides of diverse Klebsiella isolates.

    • Nicolas Flaugnatti
    • , Sandrine Isaac
    •  & Melanie Blokesch

  • Article
    | Open Access

    Understanding the potential impacts of new variants of SARS-CoV-2 is important for pandemic planning. Here, the authors develop a model incorporating hypothetical new variants with varying transmissibility and immune evasion properties, and use it to project possible future epidemic waves in the UK.

    • Louise Dyson
    • , Edward M. Hill
    •  & Matt J. Keeling

  • Article
    | Open Access

    Bacterial biofilms are aggregates of surface-associated cells embedded in an extracellular polysaccharide (EPS) matrix. Here, the authors describe a unique mode of collective movement by self-propelled, surface-associated spherical microcolonies with EPS cores in the gliding bacterium Flavobacterium johnsoniae.

    • Chao Li
    • , Amanda Hurley
    •  & David J. Beebe

  • Article
    | Open Access

    Biofilm formation in Bacillus subtilis requires expression of matrix production genes, which are upregulated by transcriptional activator RemA. Here, the authors show that RemA forms octameric rings with the potential to form a 16-meric superstructure, suggesting that the protein can wrap DNA through a LytTR-related domain.

    • Tamara Hoffmann
    • , Devid Mrusek
    •  & Gert Bange

  • Article
    | Open Access

    Collateral sensitivity-based antibiotic treatments may have the potential to limit the emergence of antimicrobial resistance. Here, the authors use mathematical modelling to study the effects of pathogen- and drug-specific characteristics for different treatment designs on bacterial population dynamics and resistance evolution.

    • Linda B. S. Aulin
    • , Apostolos Liakopoulos
    •  & J. G. Coen van Hasselt

  • Article
    | Open Access

    Several bacteria in the gut microbiota have been associated with colorectal cancer (CRC) but it is not completely clear whether they have a role in tumourigenesis. Here, the authors show enrichment of 12 bacterial taxa in two cohorts of CRC patients and that two Porphyromonas species accelerate CRC onset through butyrate secretion.

    • Shintaro Okumura
    • , Yusuke Konishi
    •  & Eiji Hara

  • Article
    | Open Access

    RNA secondary structure is important for viral replication, transcription and translation. Here the authors employ SPLASH method and map in vivo RNA interactions and dynamics of SARS-CoV-2 RNA genome in different viral life cycles.

    • Yan Zhang
    • , Kun Huang
    •  & Zhihu Zhao

  • Article
    | Open Access

    Antibodies (Abs) targeting highly conserved epitopes are important tools against emerging virus variants. Here, the authors characterize Abs that recognize a cryptic epitope in the receptor-binding domain of SARS-CoV-2 spike that is well conserved and show that these Abs can neutralize several variants of concerns.

    • Tingting Li
    • , Wenhui Xue
    •  & Ningshao Xia

  • Article
    | Open Access

    Here the authors sequence 16S rRNA and the more variable gyrase B protein-coding gene to profile the gut microbiome of captive great apes, which together with analysis of wild apes and humans, reveal a displacement of bacterial strains normally restricted to their wild conspecifics with those that are otherwise restricted to humans.

    • Alex H. Nishida
    •  & Howard Ochman

  • Article
    | Open Access

    While phosphorylation is an essential post-translational modification in eukaryotes only recently the phosphoproteome of prokaryotes has been provided. Here, Schastnaya et al. mutate 52 phosphosites on 23 E. coli enzymes and apply metabolomics to provide evidence for the functional relevance of bacterial phosphorylation events.

    • Evgeniya Schastnaya
    • , Zrinka Raguz Nakic
    •  & Uwe Sauer

  • Article
    | Open Access

    There has been limited research on the role of the mucosal immune response to SARS-CoV-2 infection. Here, the authors perform a prospective observational household study and find that mucosal antibody responses are associated with decreased viral load and faster resolution of systemic symptoms.

    • Janeri Fröberg
    • , Joshua Gillard
    •  & Dimitri A. Diavatopoulos

  • Article
    | Open Access

    Here, Shaban et al. show that coronaviruses modulate ER stress and the unfolded protein response. The ER stress inducer thapsigargin exerts potent antiviral effects, partially reverses the virus-induced translational shut-down, reprograms the host proteome and suppresses autophagic flux, thereby inhibiting coronavirus replication at multiple levels.

    • Mohammed Samer Shaban
    • , Christin Müller
    •  & Michael Kracht

  • Article
    | Open Access

    Here, Kodama et al. describe the discovery, isolation and characterization of a novel tick-borne orthonairovirus, designated Yezo virus (YEZV), from patients with an acute febrile illness in Japan. Serological testing of wildlife and molecular screening of ticks suggest an endemic circulation of YEZV in Japan.

    • Fumihiro Kodama
    • , Hiroki Yamaguchi
    •  & Keita Matsuno

  • Article
    | Open Access

    Understanding the structural basis for the inhibition of archaeal eukaryotic-like RNA polymerases (RNAPs) during virus infection is of interest for drug design. Here, the authors present the cryo-EM structures of apo Sulfolobus acidocaldarius RNAP and the RNAP complex structures with two regulatory factors, RIP and TFS4 that inhibit transcription and discuss their inhibitory mechanisms.

    • Simona Pilotto
    • , Thomas Fouqueau
    •  & Finn Werner

  • Article
    | Open Access

    Rapid identification of host genes essential for virus replication may expedite the generation of therapeutic interventions. Here the authors generate mutant clonal intestinal organoids for 19 host genes previously implicated in coronavirus biology and identify the cell surface protease TMPRSS2 as a potential therapeutic target.

    • Joep Beumer
    • , Maarten H. Geurts
    •  & Hans Clevers

  • Article
    | Open Access

    Here, cryo-EM reconstructions of human cytomegalovirus (HCMV) virions reveal host tRNAs associated with the virion’s capsid-bound tegument protein, pp150. tRNA recruitment is mediated by the interactions specific for HCMV only, suggesting the explanation for the absence of such tRNA densities in related herpesviruses.

    • Yun-Tao Liu
    • , David Strugatsky
    •  & Z. Hong Zhou

  • Article
    | Open Access

    Transcription in archaea is known to be regulated through the recruitment of RNA polymerase to promoters. Here, the authors show that the archaeon Saccharolobus solfataricus regulates transcription globally through a rate-limiting promoter-proximal elongation step.

    • Fabian Blombach
    • , Thomas Fouqueau
    •  & Finn Werner

  • Article
    | Open Access

    Implant infection is the most common mode of joint replacement failure with serious complications. Here, the authors report on the in vivo application of a prophylactic coating technology that can incorporate a range of antibiotics and be applied in the operating room prior to implantation.

    • Weixian Xi
    • , Vishal Hegde
    •  & Tatiana Segura

  • Article
    | Open Access

    Studying the role of predator–prey interactions in food-web stability and species coexistence in the environment is arduous. Here, Cohen et al. use a combination of community and single-cell analyses to show that bacterial predators can regulate prey populations in the species-rich environments of wastewater treatment plants.

    • Yossi Cohen
    • , Zohar Pasternak
    •  & Edouard Jurkevitch

  • Article
    | Open Access

    Latitudinal ecosystem boundaries in the global upper ocean may be driven by many factors. Here the authors investigate pole-to-pole eukaryotic phytoplankton metatranscriptomes, gene co-expression networks, and beta diversity, finding that geographic patterns are best explained by temperature gradients.

    • Kara Martin
    • , Katrin Schmidt
    •  & Thomas Mock

  • Article
    | Open Access

    Methyl salicylate ester is a plant metabolite involved in plant-insect and plant-plant interactions. Here, Yu et al. show that a nematode-trapping fungus has potential to produce a related compound, 6-methyl salicylate, which attracts its prey (nematodes) and modulates spore germination and trap formation in the fungus.

    • Xi Yu
    • , Xiaodi Hu
    •  & Reinhard Fischer

  • Article
    | Open Access

    Myeloid cells are implicated in the innate immune and inflammatory response during infection with Chlamydia trachomatis. Here the authors show the evasion of the neutrophil response to infection and concomitant induction of sterile immunity via the purinergic P2X7 receptor.

    • Chunfu Yang
    • , Lei Lei
    •  & Harlan D. Caldwell

  • Article
    | Open Access

    It is unclear how bacterial cells adapt the reversible switching of flagellar motor rotation to environments of different viscosities. Here, Antani et al. show that flagellar mechanosensors allosterically control the motor’s binding affinity for the chemotaxis response regulator, CheY-P, to adapt flagellar switching over varying viscous loads.

    • Jyot D. Antani
    • , Rachit Gupta
    •  & Pushkar P. Lele

  • Article
    | Open Access

    Infection with SARS-CoV2 and the development of Coronavirus disease 2019 (COVID-19) has been linked to induction of autoimmunity and autoantibody production. Here the authors characterise the new-onset IgG autoantibody response in hospitalised patients with COVID-19 which they correlate to the magnitude of the SARS-CoV2 response.

    • Sarah Esther Chang
    • , Allan Feng
    •  & Paul J. Utz

  • Article
    | Open Access

    OqxB is an RND (Resistance-Nodulation-Division) transporter that contributes to the antibiotic resistance in Klebsiella pneumoniae. Here, the authors report structural and functional characterization of OqxB, with insights into its substrate binding pocket and the role in fluoroquinolone resistance.

    • Nagakumar Bharatham
    • , Purnendu Bhowmik
    •  & Satoshi Murakami

  • Article
    | Open Access

    Activated sludge (AS) systems in wastewater treatment plants (WWTPs) contain high concentration of viruses. Here, the authors apply a systematic metagenomic pipeline and retrieve a catalogue of around 50,000 prokaryotic viruses from samples of six WWTPs, revealing a large and uncharacterized viral diversity in AS communities.

    • Yiqiang Chen
    • , Yulin Wang
    •  & Tong Zhang

  • Article
    | Open Access

    During herpesvirus infection, most individuals intrinsically suppress a primary infection and therewith preclude potential damage or neurodegeneration of the CNS. Here, Ames et al. show that Optineurin (OPTN), a conserved autophagy receptor, restricts HSV-1 spread, degrades viral VP16 through autophagy and is neuroprotective against HSV infection in vivo.

    • Joshua Ames
    • , Tejabhiram Yadavalli
    •  & Deepak Shukla

  • Article
    | Open Access

    Trends in antimicrobial resistance (AMR) in aquatic food animals are seldom documented, particularly in Asia. Here, Schar et al. review 749 point prevalence surveys, describing AMR trends in Asian aquaculture and fisheries over two decades, and identifying resistance hotspots as well as regions that would benefit most from future surveillance efforts.

    • Daniel Schar
    • , Cheng Zhao
    •  & Thomas P. Van Boeckel

  • Article
    | Open Access

    Here, using metagenomic profiling in 180 individuals from the Democratic Republic of the Congo, the authors find associations between the gut microbiome and konzo, a neurodegenerative disease that mostly affects children and is caused by the consumption improperly processed cassava.

    • Matthew S. Bramble
    • , Neerja Vashist
    •  & Eric Vilain

  • Article
    | Open Access

    The Spike protein of SARS-CoV-2 has a C-terminal cytoplasmic tail. Here the authors show that this tail binds trafficking machinery via sequences that appear optimised to ensure that Spike accumulates at the site of viral budding in the Golgi but that some can also traffic to the cell surface to induce syncytia formation.

    • Jérôme Cattin-Ortolá
    • , Lawrence G. Welch
    •  & Sean Munro

  • Article
    | Open Access

    MERS-CoV is enzootic in dromedary camels, can spread to humans but undergoes limited onward transmission. Here, Schroeder et al. compare clinical isolates of MERS-CoV in vitro and show that the predominantly circulating recombinant lineage 5 possess a fitness advantage over parental lineage 3 and 4 due to reduced activation of innate immune signaling.

    • Simon Schroeder
    • , Christin Mache
    •  & Christian Drosten

  • Comment
    | Open Access

    Synthetic biology has brought about a conceptual shift in our ability to redesign microbial metabolic networks. Combining metabolic pathway-modularization with growth-coupled selection schemes is a powerful tool that enables deep rewiring of the cell factories’ biochemistry for rational bioproduction.

    • Enrico Orsi
    • , Nico J. Claassens
    •  & Steffen N. Lindner

  • Article
    | Open Access

    The biology of the archaeal phylum Woesearchaeota is poorly understood due to the lack of cultured isolates. Here, the authors analyze datasets of Woesearchaeota 16 S rRNA gene sequences and metagenome-assembled genomes to infer global distribution patterns, ecological preferences and metabolic capabilities.

    • Wen-Cong Huang
    • , Yang Liu
    •  & Meng Li

  • Article
    | Open Access

    Trypanosoma brucei undergoes developmental steps during host infection. Here, using oligopeptide-induced differentiation in vitro, authors model replicative ‘slender’ to transmissible ‘stumpy’ bloodstream forms and identify developmental and cell cycle regulators by single cell transcriptomics.

    • Emma M. Briggs
    • , Federico Rojas
    •  & Thomas D. Otto

  • Article
    | Open Access

    M. tuberculosis cytochrome bd oxidase is of interest as a TB drug target. Here, the authors present the 2.5 Å cryo-EM structure of M. tuberculosis cytochrome bd oxidase and identify a disulfide bond within the canonical quinol binding and oxidation domain (Q-loop) and a menaquinone-9 binding site at heme b595.

    • Schara Safarian
    • , Helen K. Opel-Reading
    •  & Hartmut Michel

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