Bacteria articles within Nature Communications

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  • Article
    | Open Access

    The interconnected network of cellular metabolism is potentially prone to generating oscillatory behaviour. Here, the authors use single-cell FRET measurements of pyruvate levels to reveal large periodic fluctuations in bacterial glycolysis.

    • Shuangyu Bi
    • , Manika Kargeti
    •  & Victor Sourjik

  • Article
    | Open Access

    Legionella pneumophilia is known to secrete more than 300 effectors via a type IV secretion system. Here, Schator et al. characterise how the chromatin modifying effectors RomA and LphD work synergistically to hijack host responses and facilitate bacterial replication.

    • Daniel Schator
    • , Sonia Mondino
    •  & Monica Rolando

  • Article
    | Open Access

    Rapid antibiotic resistance in bacteria is putting pressure on both existing therapies as well as the development pipeline. Here, the authors present a dual-acting anti-virulence treatment that evades antibiotic resistance mechanisms and remains effective against Top Priority pathogens.

    • Christopher Jonkergouw
    • , Ngong Kodiah Beyeh
    •  & Markus B. Linder

  • Article
    | Open Access

    Dudek et al. describe rectangular bacterial structures in the mouths of dolphins. Using various genomic and microscopy techniques, they show that the structures consist of bacterial cells that appear to divide along the longitudinal axis and display other unusual features.

    • Natasha K. Dudek
    • , Jesus G. Galaz-Montoya
    •  & David A. Relman

  • Article
    | Open Access

    Bacteria often express multiple adhesive proteins (adhesins) for biofilm formation, but it is often unclear whether adhesins have specialized or redundant roles. Here, the authors show that Vibrio cholerae uses two adhesins with overlapping but distinct functions to achieve robust adhesion to diverse surfaces.

    • Xin Huang
    • , Thomas Nero
    •  & Jing Yan

  • Article
    | Open Access

    Phage-plasmids are bacterial extrachromosomal elements that act both as plasmids and as viruses. Here, Shan et al. show that segregational drift and loss-of-function mutations play key roles in the infection dynamics of a cosmopolitan phage-plasmid, allowing it to create continuous productive infections in marine bacteria.

    • Xiaoyu Shan
    • , Rachel E. Szabo
    •  & Otto X. Cordero

  • Comment
    | Open Access

    The type three secretion system (T3SS) is a membrane-anchored nano-machine utilized by many pathogenic bacteria to inject effector proteins and thus take control of host cells. In a recent article, Kaval et al. reveal a striking colocalization of a T3SS-encoding locus, its transcriptional activators, protein products, and the complete structure at the cell membrane, which they claim provides evidence for a mechanism known as ‘transertion’.

    • Itzhak Fishov
    •  & Sharanya Namboodiri

  • Article
    | Open Access

    Geographical hotspots with high frequency of multi-drug resistant tuberculosis (MDR-TB) have been observed in several locations, such as the country of Georgia. Here, the authors analyse genomic sequences from tuberculosis bacteria isolated from Georgia to show that the transmission fitness of MDR-TB strains is heterogeneous, and highly drug-resistant and transmissible isolates contribute to the emergence and maintenance of MDR-TB hotspots.

    • Chloé Loiseau
    • , Etthel M. Windels
    •  & Sebastien Gagneux

  • Article
    | Open Access

    An increase in shigellosis cases among men who have sex with men in the United Kingdom has been linked to an extensively drug-resistant strain of Shigella sonnei. In this genomic epidemiology study, the authors investigate the genetic basis, evolutionary history, and international dissemination of the outbreak strain.

    • Lewis C. E. Mason
    • , David R. Greig
    •  & Kate S. Baker

  • Article
    | Open Access

    Enteropathogenic bacteria use extracellular appendages, known as F-pili, to share plasmids carrying antibiotic resistance genes. Here, the authors show that F-pili are highly flexible but robust at the same time, and this is important for plasmid transfer and formation of biofilms that protect against the action of antibiotics.

    • Jonasz B. Patkowski
    • , Tobias Dahlberg
    •  & Tiago R. D. Costa

  • Article
    | Open Access

    People with the rare Bombay-type Oh blood group can only be transfused with Oh blood. Here, the authors characterize a bacterial α−1,2-fucosidase that can convert universal O type into rare Bombay type blood.

    • Itxaso Anso
    • , Andreas Naegeli
    •  & Marcelo E. Guerin

  • Article
    | Open Access

    Escherichia albertii is an emerging gastrointestinal pathogen that causes disease in humans and animals, notably birds. In this genomic epidemiology study, the authors investigate characteristics of isolates sampled from humans and birds in Great Britain and find that they tend to cluster separately.

    • Rebecca J. Bengtsson
    • , Kate S. Baker
    •  & Becki Lawson

  • Article
    | Open Access

    Disentangling how evolutionary history and environmental adaptation shape metabolic phenotypes is an open problem, especially for microbes whose phenotypes cannot be determined directly and are inferred from genomic information. Here, Ramon & Stelling propose sensitivity correlations to quantify similarity of predicted metabolic network responses to perturbations, and link genotype and environment to phenotype for 245 bacterial species.

    • Charlotte Ramon
    •  & Jörg Stelling

  • Article
    | Open Access

    Here, the authors present an expanded version of the Cultivated Genome Reference (CGR), termed CGR2, a catalog that includes 3324 high-quality draft genomes based on gut bacterial isolates from Chinese individuals, and classifies 527 species from 8 phyla, including 179 previously unidentified species, and provides information of secondary metabolite biosynthetic gene clusters and gut phage-bacteria interactions.

    • Xiaoqian Lin
    • , Tongyuan Hu
    •  & Yuanqiang Zou

  • Article
    | Open Access

    Several strategies have been employed to enhance the tumor-targeting and anti-cancer properties of engineered bacteria. Here the authors describe the design of alternating magnetic field-manipulated bacteria engineered to release an anti-CD47 nanobody, promoting anti-tumor immune response in preclinical cancer models.

    • Xiaotu Ma
    • , Xiaolong Liang
    •  & Guangjun Nie

  • Article
    | Open Access

    Cable bacteria are centimeter-long filamentous microbes that conduct electrons via internal wires, thus coupling sulfide oxidation between sediment layers. Here, Bjerg et al. show that the anoxic part of oxygen-respiring cable bacteria attracts swarms of other bacteria, which appear to transfer electrons to cable bacteria via soluble metabolites.

    • Jesper J. Bjerg
    • , Jamie J. M. Lustermans
    •  & Andreas Schramm

  • Comment
    | Open Access

    A recent study from Nature Communications reveals that Mycobacterium tuberculosis can hijack epigenetic machinery in host cells and induce host cell ferroptosis, which promotes pathogen pathogenicity and spread. These findings also suggest new therapeutic strategies to treat tuberculosis.

    • Boyi Gan

  • Article
    | Open Access

    Escherichia coli is a human pathogen and a member of the healthy microbiota. Here, using samples from children of low and middle-income living in sub-Saharan Africa and south Asia countries, the authors characterize the genomic landscape of non-diarrheagenic fecal E. coli, finding similarities to diarrheagenic pathotype E. coli.

    • Tracy H. Hazen
    • , Jane M. Michalski
    •  & David. A. Rasko

  • Article
    | Open Access

    Bacteria and archaea use tripartite ATP-independent periplasmic (TRAP) transporters to import essential nutrients. Davies et al. report a high resolution structure of a TRAP and show that it uses an ‘elevator-with-an operator’ mechanism.

    • James S. Davies
    • , Michael J. Currie
    •  & Renwick C. J. Dobson

  • Article
    | Open Access

    Pathogenic Brucella abortus, containing a mix of lipopolysaccharides with or without O-antigen, grows its envelope in a unipolar manner. Here, Servais et al, localize the LPS translocation machinery and identify the main O-antigen ligase in Brucella species, shedding light on the basic biology of this organism.

    • Caroline Servais
    • , Victoria Vassen
    •  & Xavier De Bolle

  • Article
    | Open Access

    Bacteria can affect cellular processes in other bacteria and in eukaryotic cells by injecting effectors using a type VI secretion system (T6SS). Here, Sá-Pessoa et al. describe how a T6SS effector from the bacterial pathogen Klebsiella pneumoniae triggers the fragmentation of the mitochondrial network in eukaryotic cells.

    • Joana Sá-Pessoa
    • , Sara López-Montesino
    •  & José A. Bengoechea

  • Article
    | Open Access

    Bacteria can exchange DNA through extracellular appendages (‘mating pili’) in a process known as conjugation. Here, Beltran et al. determine atomic structures by cryo-electron microscopy of a bacterial conjugative pilus and two archaeal pili, showing that the archaeal pili are homologous to bacterial mating pili.

    • Leticia C. Beltran
    • , Virginija Cvirkaite-Krupovic
    •  & Mart Krupovic

  • Article
    | Open Access

    Dietary glycans are a major driver of the human gut microbiota composition. Here, the authors apply next-generation metabolic labeling coupled with fluorescence-activated cell sorting to identify and isolate gut bacteria consumers of dietary glycans in human stool samples, linking bacteria to the glycans they consume.

    • Lharbi Dridi
    • , Fernando Altamura
    •  & Bastien Castagner

  • Article
    | Open Access

    Bacteria undergo nutrient fluctuations during repeated feast and famine cycles and need to metabolically adapt to these changes. Using quantitative proteomics, Zhu & Dai show that the stringent response of (p)ppGpp is crucial for the timely adaption of bacterial growth to both amino acid and carbon downshift.

    • Manlu Zhu
    •  & Xiongfeng Dai

  • Article
    | Open Access

    There have been increasing reports of extensively drug-resistant (XDR) Shigella sonnei infections in recent years. In this laboratory surveillance study from France, the authors document the rise of XDR isolates from 2005 to 2021 and perform whole genome sequencing to investigate their genomic diversity and evolutionary history.

    • Sophie Lefèvre
    • , Elisabeth Njamkepo
    •  & François-Xavier Weill

  • Article
    | Open Access

    Fitness landscapes largely shape the dynamics of evolution, but it is unclear how they shift upon ecological diversification. By engineering genome-wide knockout libraries of a nascent bacterial community, Ascensao et al. show how ecological and epistatic patterns combine to shape adaptive landscapes.

    • Joao A. Ascensao
    • , Kelly M. Wetmore
    •  & Oskar Hallatschek

  • Article
    | Open Access

    Deep mutational scanning can be used to investigate protein function and stability. Here, Dewachter et al. use deep mutational scanning on three essential bacterial proteins to study the mutations’ effects in their original genomic context, providing insight into the proteins’ function and their potential as targets for new antibiotic development.

    • Liselot Dewachter
    • , Aaron N. Brooks
    •  & Jan Michiels

  • Article
    | Open Access

    Taxonomical complexity has muddled the classification of clinically relevant Enterobacter species. Authors carry out a genome-based study on clinical isolates to investigate colistin resistance and heteroresistance in Enterobacter.

    • Swapnil Prakash Doijad
    • , Nicolas Gisch
    •  & Trinad Chakraborty

  • Article
    | Open Access

    The bacterium Brucella abortus is an intracellular pathogen that modulates autophagy in host cells. Here, the authors identify two B. abortus effectors that interact with host protease SENP3, thus promoting cytoplasmic accumulation of nucleolar proteins associated with ribosomal biogenesis and facilitating intracellular replication of the pathogen

    • Arthur Louche
    • , Amandine Blanco
    •  & Suzana P. Salcedo

  • Article
    | Open Access

    Some bacteria use the muropeptide transporter AmpG for uptake and recycling of cell wall fragments that are released during cell growth and division. Here, Gilmore & Cava show that the plant pathogen Agrobacterium tumefaciens, which lacks an AmpG homologue, uses a different type of transporter for the same function, which is essential for normal growth in this organism.

    • Michael C. Gilmore
    •  & Felipe Cava

  • Article
    | Open Access

    The bacterium Salmonella Paratyphi A causes paratyphoid fever. Here, the authors sequence over 800 isolates from South Asia, build a global database representing 37 countries, and develop a genotyping tool that identifies genomic variation and antimicrobial resistance markers for surveillance studies.

    • Arif M. Tanmoy
    • , Yogesh Hooda
    •  & Senjuti Saha

  • Article
    | Open Access

    Bacteria can deliver toxic effector proteins into the cytosol of neighboring cells. Here, the authors show that Yersinia pseudotuberculosis secretes an effector that modulates gene expression in neighboring cells of the same species and inhibits the growth of other competitors.

    • Dandan Wang
    • , Lingfang Zhu
    •  & Xihui Shen

  • Article
    | Open Access

    ComEA is a DNA-binding protein required for DNA uptake during bacterial transformation. Here, Ahmed et al. determine X-ray crystal structures of ComEA from Gram-positive bacteria, identifying a domain that is absent in Gram-negative bacteria and drives ComEA oligomerization, which is required for transformation.

    • Ishtiyaq Ahmed
    • , Jeanette Hahn
    •  & Matthew B. Neiditch

  • Article
    | Open Access

    Antibiotic resistance through multidrug efflux is a major hurdle in antibiotic development. Here, authors experimentally demonstrate that EmrE, a small multidrug resistance efflux pump from E. coli, can confer resistance or susceptibility depending on the small molecule substrate.

    • Peyton J. Spreacker
    • , Nathan E. Thomas
    •  & Katherine A. Henzler-Wildman

  • Article
    | Open Access

    The pathogen Pseudomonas aeruginosa uses a synthase-dependent secretion system for production of the exopolysaccharide alginate, which is associated with lung infection severity. Here, Gheorghita et al. determine the crystal structure of one of the secretion system components (the AlgKX complex) and show that it binds alginate oligosaccharides and is required for polymer production and biofilm attachment.

    • Andreea A. Gheorghita
    • , Yancheng E. Li
    •  & P. Lynne Howell

  • Article
    | Open Access

    Bacteria respond to nutrients and other compounds via chemotaxis, but little is known of their responses to antibiotics. By tracking cells in antibiotic gradients, the authors show that surface-attached Pseudomonas aeruginosa move towards antibiotics in what appears to be a suicidal attack strategy.

    • Nuno M. Oliveira
    • , James H. R. Wheeler
    •  & Kevin R. Foster

  • Article
    | Open Access

    Small regulatory RNAs (sRNAs) often act in concert with the RNA-chaperone Hfq to regulate the expression of multiple target transcripts in bacteria. Here, the authors identify Hfq-interacting sRNAs and their targets in the pathogen Vibrio cholerae, including an RNA sponge that binds and inactivates four sRNAs that modulate the quorum sensing pathway.

    • Michaela Huber
    • , Anne Lippegaus
    •  & Kai Papenfort

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