Bacteriology articles within Nature Communications

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  • Article
    | Open Access

    Synthesis of lipopolysaccharides, essential components for most gram-negative bacteria, is under tight control. Here, authors use in vitro reconstitution and structural approaches to elucidate some of these regulatory mechanisms involving essential membrane proteins LapB and YejM.

    • Sheng Shu
    •  & Wei Mi

  • Article
    | Open Access

    Antibiotics of the β-lactam class inhibit bacterial cell wall synthesis by targeting penicillin-binding proteins (PBPs). Here, Sacco et al. study the four PBPs present in the pathogen C. difficile, revealing unique structural features and shedding light on the mechanisms underlying β-lactam resistance in this organism.

    • Michael D. Sacco
    • , Shaohui Wang
    •  & Yu Chen

  • Article
    | Open Access

    The genus Bordetella includes environmental bacteria as well as human pathogens. Here, the authors present a large database of environmental and clinical Bordetella isolates and genome sequences, and develop genotyping systems to facilitate evolutionary and epidemiological studies.

    • Sébastien Bridel
    • , Valérie Bouchez
    •  & Sylvain Brisse

  • Article
    | Open Access

    The bacterial respiratory electron transport system (ETS) is branched to allow condition-specific modulation of energy metabolism. Here the authors examine the systems level properties of aerobic electron transport system using adaptive laboratory evolution and multi-omics analyses.

    • Amitesh Anand
    • , Arjun Patel
    •  & Bernhard O. Palsson

  • Article
    | Open Access

    A subset of uropathogenic Escherichia coli are able to halt division and grow into highly filamentous cells during infection of bladder epithelial cells. Here, authors aim to determine the mechanism, and understand the dynamics of cell division machinery during infection-related filamentation.

    • Bill Söderström
    • , Matthew J. Pittorino
    •  & Iain G. Duggin

  • Article
    | Open Access

    Quorum-sensing bacteria produce and secrete autoinducers that trigger a behavioral change in the population when reaching a certain threshold. Here, Bettenworth et al. show that autoinducer synthase gene expression in Sinorhizobium meliloti occurs in asynchronous stochastic pulses, and that physiological cues modulate pulse frequency and, consequently, response behavior dynamics. Frequency-modulated pulsing in autoinducer synthase gene expression thus represents a time-based mechanism for information integration and collective decision-making.

    • Vera Bettenworth
    • , Simon van Vliet
    •  & Anke Becker

  • Article
    | Open Access

    The host environment can impact the outcomes of antimicrobial therapies through unclear mechanisms. Here, Ledger et al. show that human serum reduces the efficacy of the antibiotic daptomycin against Staphylococcus aureus by inducing specific pathways leading to changes in the composition of the bacterial membrane and cell wall.

    • Elizabeth V. K. Ledger
    • , Stéphane Mesnage
    •  & Andrew M. Edwards

  • Article
    | Open Access

    Orthologs of natural competence genes are conserved in non-competent bacterial species, suggesting they have a role other than in transformation. Here, the authors show that competence induction in Staphylococcus aureus occurs in response to reactive oxygen species and host defenses that compromise bacterial respiration during infection, leading to increased DNA and glucose uptake and glycolytic flux.

    • Mar Cordero
    • , Julia García-Fernández
    •  & Daniel Lopez

  • Article
    | Open Access

    Cells of the predatory bacterium Bdellovibrio bacteriovorus, which invades and replicates within the periplasm of other bacteria, have a characteristic curved rod shape. Here, Banks et al. show that a peptidoglycan hydrolase is required for the curved shape, and this facilitates invasion of prey cells.

    • Emma J. Banks
    • , Mauricio Valdivia-Delgado
    •  & R. Elizabeth Sockett

  • Article
    | Open Access

    Vancomycin-resistant Enterococcus faecium is an important healthcare-associated pathogen and genomic analyses could inform targeted interventions. Here, the authors optimise an analysis pipeline for identification of putative transmission events using core genome multilocus sequence type clustering and split kmer analysis.

    • Charlie Higgs
    • , Norelle L. Sherry
    •  & Benjamin P. Howden

  • Article
    | Open Access

    Microbial communities employ a variety of strategies to compete against competitors sharing their niche, for instance, by producing antibiotics. This study reveals that antibiotics produced by Bacillus subtilis act synergistically to eliminate phylogenetically distinct competitors and are regulated accordingly.

    • Harsh Maan
    • , Maxim Itkin
    •  & Ilana Kolodkin-Gal

  • 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

    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

    Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a major pathogen of humans and animals with a reported incidence in Australia three times higher than the UK and USA. Here, the authors report the circulation, antimicrobial resistance signatures, and effects on host cells, of three Salmonella4,[5],12:i:- lineages within Australia.

    • Danielle J. Ingle
    • , Rebecca L. Ambrose
    •  & Deborah A. Williamson

  • Article
    | Open Access

    Bacterial cells actively change their size and shape in response to external environments. Here, Shi et al. explore how cells regulate their morphology during rapid environmental changes, showing that the characteristic dynamics of surface area-to-volume ratio are conserved across genetic and chemical perturbations, as well as across species and growth temperatures.

    • Handuo Shi
    • , Yan Hu
    •  & Kerwyn Casey Huang

  • Article
    | Open Access

    Prokaryotic cell transcriptomics has been limited to mixed or sub-population dynamics and individual cells within heterogeneous populations. Here the authors develop a ‘TRANSITomic’ approach to profile transcriptomes of single Burkholderia pseudomallei cells as they transit through host cell infection.

    • Yun Heacock-Kang
    • , Ian A. McMillan
    •  & Tung T. Hoang

  • 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

    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

    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

  • Comment
    | Open Access

    Many newly-discovered microbial phyla have been studied solely by cultivation-independent techniques such as metagenomics. Much of their biology thus remains elusive, because the organisms have not yet been isolated and grown in the lab. Katayama et al. lift the curtain on some intriguing biology by cultivating and studying bacteria from the elusive OP9 phylum (Atribacterota).

    • Muriel C. F. van Teeseling
    •  & Christian Jogler

  • Article
    | Open Access

    In Bacteroidetes, SusCD complexes mediate uptake of large nutrients across the outer membrane. SusCD structures in the apo state and in complex with β2,6 fructo-oligosaccharides reveal several substrate molecules in the binding cavity and suggest details of the pedal bin mechanism employed in glycan import.

    • Declan A. Gray
    • , Joshua B. R. White
    •  & Bert van den Berg

  • Article
    | Open Access

    Chlamydia trachomatis does not possess TrpL-mediated transcription attenuation of its trp operon. Here, the authors show that an iron-dependent regulator, YtgR, acts as a tryptophan-dependent attenuator of the trp operon in this organism, due to translational regulation of YtgR levels via a triple tryptophan motif.

    • Nick D. Pokorzynski
    • , Nathan D. Hatch
    •  & Rey A. Carabeo

  • Article
    | Open Access

    Here, the authors characterize the effects of Lactobacillus casei strains engineered to express pathogenic or non-pathogenic Listeria adhesion protein (LAP) in systemic colonization and protection against lethal Listeria monocytogenes infection in mice and show that these engineered strains can colonize the intestine and prevent dissemination of L. monocytogenes and protect against lethal infection while promoting immunomodulatory effects.

    • Rishi Drolia
    • , Mary Anne Roshni Amalaradjou
    •  & Arun K. Bhunia

  • Article
    | Open Access

    The bacterium Neisseria meningitidis causes life-threatening meningitis and sepsis. Here, Muir et al. construct a complete collection of defined mutants in protein-coding genes of this organism, which they use to identify its essential genome and to shed light on the functions of multiple genes.

    • Alastair Muir
    • , Ishwori Gurung
    •  & Vladimir Pelicic

  • Article
    | Open Access

    The pathogenesis of Streptococcus pyogenes (GAS) causing scarlet fever has been associated with the presence of prophages, such as ΦHKU.vir, and their products. Here, the authors characterize the exotoxins SpeC and Spd1 of ΦHKU.vir and show these to act synergistically to facilitate nasopharyngeal colonization in mice.

    • Stephan Brouwer
    • , Timothy C. Barnett
    •  & Mark J. Walker

  • Article
    | Open Access

    Pandemic cholera was reintroduced to Argentina in 1992, leading to epidemic spread. Here, the authors use whole genome sequencing to show how, over 6 years, epidemic cholera was caused by invariant 7PET lineage Vibrio cholerae, against a background of sporadic disease caused by diverse local strains.

    • Matthew J. Dorman
    • , Daryl Domman
    •  & Nicholas R. Thomson

  • 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

    High levels of Fusobacterium nucleatum have been associated with poor overall survival in patients with colorectal and esophageal cancer. Here, the authors show that F. nucleatum is abundant in breast cancer samples and that the colonization by F. nucleatum accelerates tumor growth and metastasis in preclinical breast cancer models.

    • Lishay Parhi
    • , Tamar Alon-Maimon
    •  & Gilad Bachrach

  • Article
    | Open Access

    Multidrug resistance of the opportunistic pathogen Stenotrophomonas maltophilia is an increasing problem. Here, analyzing strains from 22 countries, the authors show that the S. maltophilia complex is divided into 23 monophyletic lineages and find evidence for intra-hospital transmission.

    • Matthias I. Gröschel
    • , Conor J. Meehan
    •  & Thomas A. Kohl

  • Article
    | Open Access

    Bacteria can produce membranous nanotubes that mediate contact-dependent exchange of molecules between bacterial cells. Here, Baidya et al. show that cell-wall remodelling enzymes from Bacillus subtilis are required for efficient nanotube extrusion and penetration, and can be delivered to other bacterial species via nanotubes.

    • Amit K. Baidya
    • , Ilan Rosenshine
    •  & Sigal Ben-Yehuda

  • Article
    | Open Access

    The mechanisms behind the high invasiveness of Streptococcus pneumoniae serotype 1 are unclear. Here, Jacques et al. show that this feature is due to overproduction and rapid release of pneumolysin, which induces cytotoxicity and breakdown of tight junctions, allowing rapid bacterial dissemination from the respiratory tract into the blood.

    • Laura C. Jacques
    • , Stavros Panagiotou
    •  & Aras Kadioglu

  • Article
    | Open Access

    Chakraborty et al. show that phagocyte NADPH oxidase (NOX2) collapses the ΔpH of intracellular Salmonella Typhimurium, leading to oxidative damage of cell envelope proteins. Salmonella responds by shifting redox balance from respiration to glycolysis and fermentation, thereby facilitating folding of periplasmic functions.

    • Sangeeta Chakraborty
    • , Lin Liu
    •  & Andres Vazquez-Torres

  • Article
    | Open Access

    Lipoprotein Lpp provides a covalent crosslink between the outer membrane and the peptidoglycan in E. coli. Here, the authors use atomic force microscopy to show that Lpp contributes to cell envelope stiffness by covalently connecting the two layers and by controlling the width of the periplasmic space.

    • Marion Mathelié-Guinlet
    • , Abir T. Asmar
    •  & Yves F. Dufrêne

  • Article
    | Open Access

    Mfd recognizes stalled transcriptional complexes at sites of lesions and recruits the nucleotide excision repair proteins (UvrAB) to the site. Here the authors use live cell imaging in E. coli to demonstrate that coordinated ATP hydrolysis by UvrA and loading of UvrB on DNA facilitate the dissociation of Mfd from the handoff complex.

    • Han Ngoc Ho
    • , Antoine M. van Oijen
    •  & Harshad Ghodke

  • Article
    | Open Access

    Gram-negative bacteria deliver effectors via the type VI secretion system (T6SS) to outcompete their rivals. Here, Fridman et al. present an approach to identify T6SS effectors encoded in bacterial genomes without prior knowledge of their domain content or genetic neighbourhood, and identify a new family of membrane-disrupting effectors.

    • Chaya M. Fridman
    • , Kinga Keppel
    •  & Dor Salomon

  • Article
    | Open Access

    Bacteria adapt their growth rate to their metabolic status and environmental conditions by modulating the length of their G1 period. Here the authors show that an increase in c-di-GMP concentration modulates the activity of kinase ShkA and transcription factor TacA, thus enabling G1/S transition in Caulobacter.

    • Andreas Kaczmarczyk
    • , Antje M. Hempel
    •  & Urs Jenal

  • Article
    | Open Access

    Pseudomonas aeruginosa bacteremia is presumed to be a ‘dead-end’ for the pathogen and to have no impact on transmission. Here the authors show, in mice, that the bacteria can spread from the bloodstream via the gallbladder to the intestines and feces, leading to transmission to uninfected animals.

    • Kelly E. R. Bachta
    • , Jonathan P. Allen
    •  & Alan R. Hauser

  • Article
    | Open Access

    Bacterial biofilms rely on shared extracellular polymeric substances (EPS) and are often highly tolerant to antibiotics. Here, the authors show in in vitro experiments that Salmonella does not evolve resistance to EPS inhibition because such strains are outcompeted by a susceptible strain under inhibitor treatment.

    • Lise Dieltjens
    • , Kenny Appermans
    •  & Hans P. Steenackers

  • Article
    | Open Access

    The enzyme SpoT is important for accumulation of the alarmone (p)ppGpp, which triggers the stringent response in E. coli. Here, Germain et al. show that the protein YtfK promotes SpoT-dependent accumulation of (p)ppGpp and is required for activation of the stringent response during phosphate and fatty acid starvation.

    • Elsa Germain
    • , Paul Guiraud
    •  & Etienne Maisonneuve

  • Article
    | Open Access

    Type VI secretion systems (T6SSs) are used by bacteria to inject toxic effector proteins into neighbouring cells. Here, Mariano et al. show that an antibacterial effector from Serratia marcescens forms cation-selective pores that lead to inner-membrane depolarisation and increased outer-membrane permeability.

    • Giuseppina Mariano
    • , Katharina Trunk
    •  & Sarah J. Coulthurst

  • Article
    | Open Access

    Bacterial type II secretion systems (T2SSs) translocate virulence factors, toxins and enzymes across the cell outer membrane. Here, Chernyatina and Low use negative stain and cryo-electron microscopy to reveal the core architecture of an assembled T2SS from the pathogen Klebsiella pneumoniae.

    • Anastasia A. Chernyatina
    •  & Harry H. Low

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