Microbiology

  • Article
    | Open Access

    Rearrangement hot spots (Rhs) proteins are bacterial polymorphic toxin systems. Here, the authors show that Rhs1 forms a complex with the Type VI secretion system (T6SS) spike protein VgrG and the EagR chaperone. They also present the cryo-EM structure of the Rhs1-EagR complex and propose a model for Rhs loading and delivery by the T6SS.

    • Dukas Jurėnas
    • , Leonardo Talachia Rosa
    •  & Eric Cascales
  • Article
    | Open Access

    Whether there are conserved nucleic acid (NA) binding proteins across species is not fully known. Using data from human, mouse and fly, the authors identify common binders, implicate TAOKs and show that these kinases bind NAs across species and promote virus defence in mammalian cells.

    • Friederike L. Pennemann
    • , Assel Mussabekova
    •  & Andreas Pichlmair
  • Article
    | Open Access

    Current HCV nucleic acid-based diagnosis is largely performed in centralised laboratories. Here, the authors present a pan-genotypic RNA assay, based on reverse transcriptase loop mediated isothermal amplification and develop a low-cost prototype paper-based lateral flow device for point-of-care use, providing a visually read result within 40 min.

    • Weronika Witkowska McConnell
    • , Chris Davis
    •  & Jonathan M. Cooper
  • Article
    | Open Access

    The host range of bacteriophages defines their impact on bacterial ecology and diversity. Here, Göller et al. isolate 94 staphylococcal phages from wastewater and determine their host range on 117 staphylococci from 29 species, revealing a predominant multi-species host range and thus great potential for horizontal gene transfer.

    • Pauline C. Göller
    • , Tabea Elsener
    •  & Elena Gómez-Sanz
  • Perspective
    | Open Access

    Cooperation is vulnerable to cheating, and both cooperation and cheating may be especially common in viruses. Here, Leeks et al. place diverse examples of viral cooperation and cheating within an evolutionary framework, highlighting opportunities emerging from greater synthesis of virology and evolutionary theory.

    • Asher Leeks
    • , Stuart A. West
    •  & Melanie Ghoul
  • Article
    | Open Access

    Spread of bloodborne infections, such as HCV and HIV, is a problem, particularly amongst people who inject drugs (PWID). Here, the authors describe and then confirm in observational PWID cohorts that those with more non-pathogenic viruses in plasma were more likely later to acquire HCV than PWID who had fewer of these non-pathogenic viruses.

    • Abraham J. Kandathil
    • , Andrea L. Cox
    •  & David L. Thomas
  • Article
    | Open Access

    Malnourished children experience a high burden of intestinal pathogens that exacerbate growth stunting, and preventing this pathogen overgrowth has proved challenging. Here the authors show that diet-specific bacterial crossfeeding contributes to the overgrowth of intestinal pathogens during child malnutrition.

    • K. E. Huus
    • , T. T. Hoang
    •  & B. B. Finlay
  • Article
    | Open Access

    Germination of Bacillus subtilis spores in response to L-alanine requires a putative membrane receptor consisting of three proteins. Here, Artzi et al. use evolutionary co-variation analysis and functional assays of mutants to provide evidence that one of the proteins, GerAB, likely acts as the L-alanine sensor.

    • Lior Artzi
    • , Assaf Alon
    •  & David Z. Rudner
  • Article
    | Open Access

    Whether gut microbes drive cognitive differences in natural populations of animals remains unknown. Here, Li et al. demonstrate a causal link between increased symbiotic Lactobacillus Firm-5 species (L. apis) and improved long-term memory in bumblebees.

    • Li Li
    • , Cwyn Solvi
    •  & Wei Zhao
  • Article
    | Open Access

    Microbial ecosystem-based bioproduction requires the regulation of phenotypic structure of microbial populations. Here, the authors report the construction of a programmed lysis system and its ability for reprograming microbial cooperation in poly(lactate-co-3-hydroxybutyrate) and butyrate production by E. coli strains.

    • Wenwen Diao
    • , Liang Guo
    •  & Liming Liu
  • Article
    | Open Access

    Hydrothermal vents are biogeochemically important, but their contribution to the carbon cycle is poorly constrained. Here the authors build a biogeochemical model that estimates autotrophic and heterotrophic production rates of microbial communities within hydrothermal plumes along mid-ocean ridges.

    • Cécile Cathalot
    • , Erwan G. Roussel
    •  & Pierre-Marie Sarradin
  • Article
    | Open Access

    Bone implants with antibacterial and osteogenic properties are important for clinical applications, but creating both properties simultaneously remains challenging. Here, the authors demonstrate a self-activating implant using a hydroxyapatite and molybdenum disulfide coating which accelerates bone regeneration and at the same time prevents bacterial infection.

    • Jieni Fu
    • , Weidong Zhu
    •  & Shuilin Wu
  • Article
    | Open Access

    Children often show milder COVID-19 symptoms, but the underlying mechanistic insights are still lacking. Here the authors profile both pediatric and adult cohorts of COVID-19 patients in Brazil to find that children exhibit higher viral load but stronger and biased cellular immunity, thereby serving clues for the differential responses in children.

    • Tiago Fazolo
    • , Karina Lima
    •  & Cristina Bonorino
  • Article
    | Open Access

    In this study, Tran Kiem et al. examine the contribution of different age groups to COVID-19 transmission. Using data from the French epidemic in summer 2020, they report that while individuals aged 80 years and older are more at risk, pandemic control in the absence of vaccines required measures targeted at all age groups.

    • Cécile Tran Kiem
    • , Paolo Bosetti
    •  & Simon Cauchemez
  • Article
    | Open Access

    The RNA genome of the Hepatitis C Virus binds to the liver-specific miR122. Here the authors report the crystal structure of the Ago2:miR122:HCV complex showing that the viral RNA’s structural element traps the Ago2:miR-122 complex on the 5’ end of the viral genome to protect it from degradation.

    • Luca F. R. Gebert
    • , Mansun Law
    •  & Ian J. MacRae
  • Article
    | Open Access

    RNA of some viruses is protected from degradation by a 5′ triphosphate group. Here the authors identify nudix hydrolase 2 (NUDT2) as novel antiviral defense protein that dephosphorylates viral RNA and thereby enables its degradation.

    • Beatrice T. Laudenbach
    • , Karsten Krey
    •  & Andreas Pichlmair
  • Article
    | Open Access

    The bat sarbecovirus RaTG13 is a close relative of SARS-CoV-2, but its spike protein doesn’t efficiently bind human ACE2. Here, the authors show that exchange of spike residue 403 between RaTG13 and SARS-CoV-2 spike proteins affects binding to human ACE2 and entry of pseudotyped viruses.

    • Fabian Zech
    • , Daniel Schniertshauer
    •  & Frank Kirchhoff
  • Article
    | Open Access

    Convalescent plasma (CP) has been trialed as a therapy for SARS-CoV-2 symptoms, but its heterogenous nature precludes uniform outcomes. Here the authors perform deep profiling of CP, as well as plasma of CP recipients before and after transfer, to find CP-mediated, spike/nucleocapsid-focused modulations of humoral responses in the recipient.

    • Jonathan D. Herman
    • , Chuangqi Wang
    •  & Galit Alter
  • Article
    | Open Access

    DNA transfer between two bacterial cells is mediated by the conjugative type 4 secretion systems (T4SSs). Here, the authors report the structure of a complete T4SS outer-membrane core complex (OMCC), revealing distinct C17 and C13 symmetries of its central inner and peripheral outer ring regions, respectively.

    • Himani Amin
    • , Aravindan Ilangovan
    •  & Tiago R. D. Costa
  • Article
    | Open Access

    Vpr is a HIV-1 accessory virulence factor that also interacts with the human DNA repair protein hHR23A. Here, the authors present the structure of Vpr in complex with the C-terminal half of hHR23A comprising the XPC-binding and ubiquitin-associated domains, which reveals that hHR23A interacts with the DCAF1-binding and not the substrate-binding Vpr surface and further illustrates how Vpr acts as a versatile structural adapter that targets diverse DNA repair pathways.

    • In-Ja L. Byeon
    • , Guillermo Calero
    •  & Angela M. Gronenborn
  • Article
    | Open Access

    Resistance-nodulation-cell division (RND)-type tripartite efflux pumps confer multidrug resistance to Gram-negative bacteria. Here, structural and functional analyses of AdeB from Acinetobacter baumannii and AcrB from Escherichia coli provide insight into their different drug-binding and conformational drug transport states.

    • Alina Ornik-Cha
    • , Julia Wilhelm
    •  & Klaas M. Pos
  • Article
    | Open Access

    One might think that complete extinction of a virulent pathogen is the most effective way of saving a population. For a bacteria-phage system, Skanata and Kussell show that sustaining a minimum pathogen level is actually favorable to prevent a complete loss of immunity in the long run.

    • Antun Skanata
    •  & Edo Kussell
  • Article
    | Open Access

    SARS-CoV-2 was detected in mink farms in the Netherlands in the first wave of the pandemic with evidence of human-to-mink and mink-to-human transmission. Here, the authors investigate this outbreak using phylodynamic analysis and show that personnel links and spatial proximity are predictors of transmission between farms.

    • Lu Lu
    • , Reina S. Sikkema
    •  & Marion P. G. Koopmans
  • Article
    | Open Access

    Phenotypically tolerant, persister bacterial subpopulations can survive transient antibiotic treatment and facilitate resistance evolution. Here, Nordholt et al. show that E. coli can display persistence against a widely used disinfectant and this is associated with alterations in the cell surface and with antibiotic tolerance.

    • Niclas Nordholt
    • , Orestis Kanaris
    •  & Frank Schreiber
  • Article
    | Open Access

    Endogenous ACE2 is a receptor for SARS-CoV-2 and a recombinant soluble ACE2 protein can inhibit SARS-CoV-2 infection acting as a decoy. Here the authors show that B38-CAP, an ACE2-like enzyme but not a decoy for the virus, is protective against SARS-CoV-2-induced lung injury in animal models.

    • Tomokazu Yamaguchi
    • , Midori Hoshizaki
    •  & Keiji Kuba
  • Article
    | Open Access

    After transmission of Plasmodium sporozoites from infected mosquitoes, parasites first infect hepatocytes. Here, Cha et al. identify a sporozoite ligand (phospholipid scramblase) and the hepatocytic receptor (carbamoyl-phosphate synthetase 1) as relevant for hepatocyte invasion and show that an antibody to hepatocyte-binding peptide 1 (HP1), which structurally mimics the sporozoite ligand, partially protects mice from infection.

    • Sung-Jae Cha
    • , Min-Sik Kim
    •  & Marcelo Jacobs-Lorena
  • Review Article
    | Open Access

    Cellular microbiology is a field that combines the study of infection and cell biology. In this review, we highlight emerging technologies and infection models that recently transformed our understanding of the infected cell and may inspire future medicine.

    • Ana Teresa López-Jiménez
    •  & Serge Mostowy
  • Article
    | Open Access

    Here, the authors report quantitative daily gut microbiome variation of individual gut bacterial abundances in healthy individuals, linked to changes in transit time and diet, highlighting the potential need for multiple samplings for microbiome target identification and the development and application of reliable microbiome diagnostics.

    • Doris Vandeputte
    • , Lindsey De Commer
    •  & Jeroen Raes
  • Article
    | Open Access

    Micronutrient supplements are key to global efforts to address child malnutrition. Here, in a cohort of children, previously enrolled into a large cluster randomized controlled trial of micronutrient supplementation in Pakistan, Popovic et al. find that vitamins and iron increase carriage of protozoa and fungi in the gut, potentially disrupting the bacterial microbiome.

    • Ana Popovic
    • , Celine Bourdon
    •  & Lisa G. Pell
  • Article
    | Open Access

    Bioleaching of rare earth elements using microorganisms offers an environmentally friendly alternative to thermochemical extraction. Here, Schmitz et al. generate a whole-genome knockout collection of mutants for one such microorganism, Gluconobacter oxydans, and identify genes affecting the production of acidic biolixiviant and thus bioleaching efficacy.

    • Alexa M. Schmitz
    • , Brooke Pian
    •  & Buz Barstow
  • Article
    | Open Access

    Altered gut microbiome and exacerbation of symptoms at times of psychological stress are feature characteristics of Crohn’s disease. Here authors show in a mouse model that psychological stress impairs IL-22-dependent protective immunity of the ileal mucosa, which allows invasive bacteria to colonise the gut.

    • Christopher R. Shaler
    • , Alexandra A. Parco
    •  & Brian K. Coombes
  • Article
    | Open Access

    How the immune responses induced by SARS-CoV-2 and human coronavirus (hCoV) crosstalk is still unclear. Here the authors profile the humoral responses of prepandemic and SARS-CoV-2-infected donors to find that higher hCoV antibody titers are associated with SARS-CoV-2 negativity, and with reduced hospitalization in SARS-CoV-2 positive patients.

    • Irene A. Abela
    • , Chloé Pasin
    •  & Alexandra Trkola
  • Article
    | Open Access

    Here, the authors develop and characterize a mouse microbiota composed of 15 strains representative of the intestinal microbiota found in C57BL/6J specific opportunistic- and pathogen-free (C57Bl/6J SOPF) mice and derive a new standardized gnotobiotic mouse model, called GM15, which recapitulates the phenotypes of SOPF or SPF animals in different animal facilities with improved reproducibility.

    • Marion Darnaud
    • , Filipe De Vadder
    •  & Andrea Tamellini
  • Article
    | Open Access

    The V3-crown of the HIV-1 envelope protein largely elicits non-neutralizing antibodies. Here, the authors show that the V3-crown can be targeted by broadly neutralizing designed ankyrin repeat proteins recognizing two conformations one of which resembles CCR5- bound V3.

    • Nikolas Friedrich
    • , Emanuel Stiegeler
    •  & Alexandra Trkola
  • Article
    | Open Access

    Many microbes grow diauxically, utilizing resources one at a time rather than simultaneously. This study developed a minimal model of diauxic microbial communities assembling in a serially diluted culture, providing testable predictions for the assembly of natural as well as synthetic communities of diauxically shifting microorganisms.

    • Zihan Wang
    • , Akshit Goyal
    •  & Sergei Maslov
  • Article
    | Open Access

    O’nyong nyong and Chikungunya virus are arboviruses present in Africa but their prevalence is unknown, partly due to high antibody cross-reactivity with one another. Here, the authors develop a statistical model that accounts for cross-reactivity to characterise circulation of both viruses from seroprevalence surveys.

    • Nathanaël Hozé
    • , Issa Diarra
    •  & Simon Cauchemez
  • Article
    | Open Access

    Bacterial biofilms exhibit complex spatiotemporal pattern formation. Here the authors report a collective cell reorientation cascade in growing Vibrio cholerae biofilms that leads to a differentially ordered, spatiotemporally coupled core-rim structure.

    • Japinder Nijjer
    • , Changhao Li
    •  & Jing Yan
  • Article
    | Open Access

    Here the authors provide a detailed virological analysis of thirteen postmortem COVID-19 cases, including presence of replication-competent SARS-CoV-2 in extrapulmonary organs and tissue-specific patterns of SARS-CoV-2 genome diversity of an immunocompromised patient.

    • Jolien Van Cleemput
    • , Willem van Snippenberg
    •  & Linos Vandekerckhove
  • Article
    | Open Access

    Currently, there are no treatments or vaccines against Epstein-Barr virus (EBV) infection. Here, Zhu et al. isolate gH/gL-specific antibodies from infected donors and identify 1D8, that substantially reduces infection levels in both, B- and epithelial cells, and reduces tumor burdens in EBV-challanged humanized mice due to interferance with the gH/gL-mediated membrane fusion and binding.

    • Qian-Ying Zhu
    • , Sisi Shan
    •  & Linqi Zhang
  • Article
    | Open Access

    Several clinical reports have described gastrointestinal symptoms for COVID-19, though whether the virus can replicate within the stomach remains unclear. Here the authors generate gastric organoids from human biopsies and show that the virus can efficiently infect gastric epithelium, suggesting that the stomach might have an active role in fecal-oral transmission.

    • Giovanni Giuseppe Giobbe
    • , Francesco Bonfante
    •  & Paolo De Coppi
  • Article
    | Open Access

    The nucleotidyl cyclase toxin exoenzyme Y (ExoY), which is secreted by the human pathogens Pseudomonas aeruginosa and Vibrio vulnificus is activated by actin. Here, the authors present the cryo-EM structures of PaExoY bound to F-actin and VvExoY in complex with G-actin-profilin. These structures together with molecular dynamics simulations and enzymatic assays provide insights into the activation mechanism for both bacterial cyclase toxin families that interact with either F- or G-actin.

    • Alexander Belyy
    • , Felipe Merino
    •  & Stefan Raunser
  • Article
    | Open Access

    The pathogen Mycobacterium tuberculosis depends on host fatty acids and cholesterol as carbon sources. Here, Beites et al. identify a protein complex that is essential for fatty acid and cholesterol utilization and thus for survival of M. tuberculosis during infection, supporting this pathway as a potential target for tuberculosis drug development.

    • Tiago Beites
    • , Robert S. Jansen
    •  & Sabine Ehrt
  • Article
    | Open Access

    The tuberculosis necrotizing toxin (TNT) is the major cytotoxicity factor of M. tuberculosis (Mtb). Mtb possesses five type VII secretion systems (ESX). Pajuelo et al. show that the ESX-4 system is required for TNT secretion and that ESX-2 and ESX-4 systems work in concert with ESX-1 to permeabilize the phagosomal membrane and enable trafficking of TNT into the cytoplasm of macrophages infected with Mtb.

    • David Pajuelo
    • , Uday Tak
    •  & Michael Niederweis
  • Article
    | Open Access

    Bacteria-based therapy has shown promise for cancer treatment. To enhance tumor accumulation, here the authors describe the design of tumor specific aptamer-conjugated bacteria, to improve intratumor localization and enhance therapeutic efficacy.

    • Zhongmin Geng
    • , Zhenping Cao
    •  & Weihong Tan