Bacteriology articles within Nature Communications

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  • 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

  • Article
    | Open Access

    Quorum sensing (QS) regulates production of ‘public goods’ by Pseudomonas aeruginosa, which releases toxic hydrogen cyanide to constrain QS-deficient cheaters. Here, Yan et al. show that QS-proficient strains protect themselves by producing a cyanide-insensitive enzyme in response to reactive oxygen species released by cheaters.

    • Huicong Yan
    • , Kyle L. Asfahl
    •  & Meizhen Wang

  • Article
    | Open Access

    CRISPR nucleases can be programmed to cleave sequences in specific bacteria to induce cell death. Here, Hamilton et al. present an optimized method for conjugative delivery of CRISPR nucleases, consisting of a single plasmid that encodes both the conjugative machinery and the nuclease.

    • Thomas A. Hamilton
    • , Gregory M. Pellegrino
    •  & David R. Edgell

  • Article
    | Open Access

    Antimicrobial peptides (AMPs) are emerging as drug candidates, but the risk of pathogen resistance is not well understood. Here, the authors investigate AMP resistance evolution in E. coli, finding physicochemical features that make AMPs less prone to resistance and no cross- or horizontally-acquired resistance.

    • Réka Spohn
    • , Lejla Daruka
    •  & Csaba Pál

  • Article
    | Open Access

    Amino acid biosynthetic pathways are an attractive alternative to treat chronic infections such as Mycobacterium tuberculosis (Mtb). Here, the authors investigate the metabolic response to disruption of the aspartate pathway in persistent Mtb and identify essential enzymes as potential new targets for drug development.

    • Erik J. Hasenoehrl
    • , Dannah Rae Sajorda
    •  & Michael Berney

  • Article
    | Open Access

    Salmonella Typhi produces the typhoid toxin. Here, Fowler et al. show that S. Typhi produces two forms of typhoid toxin that are differentially regulated and display different trafficking properties and different effects when administered to laboratory animals.

    • Casey C. Fowler
    • , Gabrielle Stack
    •  & Jorge E. Galán

  • Article
    | Open Access

    The mechanisms behind CO2 dependency in non-autotrophic bacterial isolates are unclear. Here the authors show that the Staphylococcus aureus mpsAB operon is crucial for growth at atmospheric CO2 levels, and provide evidence indicating that MpsAB represents a bicarbonate concentrating system.

    • Sook-Ha Fan
    • , Patrick Ebner
    •  & Friedrich Götz

  • Article
    | Open Access

    Bacteria deliver toxic effectors via type VI secretion systems (T6SSs) to dominate competitors. Here, the authors identify a Vibrio antibacterial effector that contains a new DNase toxin domain and a domain of unknown function that can be used as a marker to identify new T6SS effectors.

    • Biswanath Jana
    • , Chaya M. Fridman
    •  & Dor Salomon

  • Article
    | Open Access

    The virulence factor MgtC is essential for intracellular macrophage survival of Salmonella enterica. Here, the authors show that MgtC targets the PhoB/PhoR regulatory system leading to phosphate uptake inside macrophages and that both phoR mutation and phoB deletion renders Salmonella hypervirulent in mice.

    • Soomin Choi
    • , Eunna Choi
    •  & Eun-Jin Lee

  • Article
    | Open Access

    Trehalose metabolism has been linked to Mycobacterium tuberculosis (Mtb) virulence and biofilm formation. Here, using a model of drug-tolerant persisters and metabolomics, the authors dissect the role of trehalose metabolism in Mtb persister formation, linking trehalose-catalytic shift to antibiotic resistance.

    • Jae Jin Lee
    • , Sun-Kyung Lee
    •  & Hyungjin Eoh

  • Article
    | Open Access

    The C2 sulfonates taurine and isethionate are also present in the anaerobic mammalian gut, where they are converted into toxic H2S by sulfate and sulfite-reducing bacteria. Here the authors characterise the O2-sensitive enzyme IseG that catalyzes the C-S bond cleavage of isethionate and show that IseG also plays a key role in converting taurine into H2S in Bilophila wadsworthia.

    • Meining Xing
    • , Yifeng Wei
    •  & Yan Zhang

  • Article
    | Open Access

    Bacteria can become dormant or form spores when starved for nutrients. Here, Gray et al. describe an alternative strategy, or ‘oligotrophic growth state’, showing that non-sporulating Bacillus subtilis cells can survive deep starvation conditions by adopting an almost coccoid shape and extremely low growth rates.

    • Declan A. Gray
    • , Gaurav Dugar
    •  & Leendert W. Hamoen

  • Article
    | Open Access

    Noisy gene expression leading to phenotypic variability can help organisms to survive in changing environments. Here, Patange et al. show that noisy expression of a stress response regulator, RpoS, allows E. coli cells to modulate their growth rates to survive future adverse environments.

    • Om Patange
    • , Christian Schwall
    •  & James C. W. Locke

  • Article
    | Open Access

    Pseudomonas aeruginosa can cause chronic infections on medical devices by forming biofilms, a process regulated by quorum sensing (QS). Here, the authors show that P. aeruginosa is unable to perceive QS signals in the presence of either host urine or urea, and clinical isolates are often defective in QS.

    • Stephanie J. Cole
    • , Cherisse L. Hall
    •  & Vincent T. Lee

  • Article
    | Open Access

    The FtsZ protein assembles into a structure known as ‘Z-ring’ at midcell for bacterial cell division. Here, Söderström et al. show that Z-ring assembly and dynamics in E. coli cells with unnatural shapes, such as squares and hearts, are generally similar to those observed in cells with normal shape.

    • Bill Söderström
    • , Alexander Badrutdinov
    •  & Ulf Skoglund

  • Article
    | Open Access

    Infection of mice with Citrobacter rodentium is a common model of infection with attaching-and-effacing pathogens. Here, Connolly et al. analyse the transcriptome of C. rodentium during mouse infection, showing host-induced coordinated upregulation of virulence factors and 1,2-propanediol metabolism.

    • James P. R. Connolly
    • , Sabrina L. Slater
    •  & Andrew J. Roe

  • Article
    | Open Access

    Persisters are bacterial subpopulations that are not killed by antibiotics even though they lack genetic resistance. Here, the authors show that persisters can manifest as small colony variants in clinical infections, and arise as a result of a long lag time in stress conditions including antibiotic exposure.

    • Clément Vulin
    • , Nadja Leimer
    •  & Annelies S. Zinkernagel

  • Article
    | Open Access

    Resistance to one antibiotic can in some cases increase susceptibility to other antibiotics. Here, Podnecky et al. study these collateral responses in E. coli clinical isolates and show that efflux-related resistance mechanisms and relative fitness of the strains are principal contributors to this phenomenon.

    • Nicole L. Podnecky
    • , Elizabeth G. A. Fredheim
    •  & Pål J. Johnsen

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