Biofilms articles within Nature Communications

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  • Article
    | Open Access

    Bacteria form matrix-encapsulated communities, called biofilms, which protect resident cells from environmental challenges. Here, the authors show that Vibrio cholerae cells detect environmental threats by sensing a cellular component released through kin cell lysis, which induces formation of biofilms by surviving cells.

    • Jojo A. Prentice
    • , Robert van de Weerd
    •  & Andrew A. Bridges

  • Article
    | Open Access

    The second messenger c-di-GMP regulates various processes in bacteria, including biofilm formation and motility. Here, the authors show that iron regulates c-di-GMP levels in Pseudomonas aeruginosa by modulating the interaction between an iron-sensing protein and a diguanylate cyclase.

    • Xueliang Zhan
    • , Kuo Zhang
    •  & Haihua Liang

  • Article
    | Open Access

    Anaerobic methanotrophic (ANME) archaea are uncultivated microbes that oxidize the greenhouse gas methane and engage in extracellular electron transfer with other microbes, metal oxides, and electrodes. Here, Ouboter et al. observe strong methane-dependent current associated with high enrichment of ANME archaea on the anode, and provide insights into the mechanisms underlying extracellular electron transfer.

    • Heleen T. Ouboter
    • , Rob Mesman
    •  & Cornelia U. Welte

  • Article
    | Open Access

    Cyclic di-GMP (c-di-GMP) is a second messenger that promotes biofilm formation through unclear mechanisms in several bacterial species. Here, Ling et al. report that c-di-GMP promotes biofilm formation in mycobacteria by binding to protein Lsr2, which upregulates the synthesis of keto-mycolic acid and thus biofilm formation.

    • Xiaocui Ling
    • , Xiao Liu
    •  & Weihui Li

  • Article
    | Open Access

    The bacterium Bacillus subtilis can form various types of surface-associated communities, such as colonies, pellicles and submerged biofilms. Here, Dergham et al. provide a direct comparison of spatial transcriptional heterogeneity across the three types of surface-associated communities, revealing mosaic expression patterns for genes involved in various pathways.

    • Yasmine Dergham
    • , Dominique Le Coq
    •  & Romain Briandet

  • Article
    | Open Access

    Ferumoxytol (Fer) is an FDA-approved iron oxide formulation that disrupts caries-causing biofilms with high specificity but cannot interfere with enamel acid demineralization. Here, Fer is combined with stannous fluoride (SnF2), resulting in enhanced stability of SnF2 and inhibition of both biofilm accumulation and enamel damage more effectively than either alone.

    • Yue Huang
    • , Yuan Liu
    •  & Hyun Koo

  • Article
    | Open Access

    Cooperative interactions might be important in spatially structured microbial habitats. Here, the authors show that cooperative interactions between planktonic and biofilm-forming bacteria drive spatial segregation, and thereby enable species’ coexistence, in a microfluidic chip environment.

    • Yichao Wu
    • , Chengxia Fu
    •  & Peng Cai

  • Article
    | Open Access

    Plasmids are the main vector by which antibiotic resistance is transferred between bacterial cells within surface-associated communities. Here, Ma et al. show that plasmid spread peaks at intermediate antibiotic administration times, when the intermixing of plasmid donors and potential recipients is maximal.

    • Yinyin Ma
    • , Josep Ramoneda
    •  & David R. Johnson

  • Article
    | Open Access

    Streptococcus mutans (S. mutans) has been implicated as a major pathogen in childhood caries. Here, the authors show that Selenomonas sputigena, a flagellated anaerobe, interacts with S. mutans in the supragingival biofilm, builds a honeycomb-like multicellular-superstructure that encapsulates it, and promotes the development of childhood dental caries.

    • Hunyong Cho
    • , Zhi Ren
    •  & Hyun Koo

  • Article
    | Open Access

    Bacteria produce several high molecular weight polysaccharides with ill-defined anti-adhesion properties. Here, the authors identified key molecular and biophysical determinants of active antibiofilm polysaccharides, opening new perspectives to identify or engineer new compounds able to control bacterial adhesion and biofilm formation.

    • Joaquín Bernal-Bayard
    • , Jérôme Thiebaud
    •  & Jean-Marc Ghigo

  • 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

    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

    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

    Bacteria can form organized multicellular communities through regulation of cell growth, motility, shape and differentiation. Here, Ellison et al. show that bacterial multicellular development can also be driven by specific patterns of localization of appendages known as type IV pili.

    • Courtney K. Ellison
    • , Chenyi Fei
    •  & Zemer Gitai

  • Article
    | Open Access

    Bacterial cells at fluid interfaces can self-assemble into soft living materials, called pellicles. Here, Qin and Bassler use the bacterium Vibrio cholerae as a model system to identify regulatory and structural components that drive sequential mechanical instabilities underlying pellicle morphogenesis, culminating in fractal patterning.

    • Boyang Qin
    •  & Bonnie L. Bassler

  • Article
    | Open Access

    Despite enormous potential of solar-driven biocatalysis, most living systems lack photoactive proteins and require toxic and expensive synthetic materials limiting the performance. Here, a class of natural photoconductors is demonstrated through sub-picosecond heme-to-heme electron transfer in bacteria-produced protein nanowires.

    • Jens Neu
    • , Catharine C. Shipps
    •  & Nikhil S. Malvankar

  • Article
    | Open Access

    SCCmec is a large mobile genetic element that confers resistance to β-lactam antibiotics in methicillin-resistant Staphylococcus aureus. Here, the authors show that biofilm growth conditions enhance the efficiency of natural transformation in S. aureus and allow the transfer of SCCmec to methicillin-sensitive strains.

    • Mais Maree
    • , Le Thuy Thi Nguyen
    •  & Kazuya Morikawa

  • Article
    | Open Access

    Nucleotide second messengers, such as cAMP and c-di-GMP, regulate many physiological processes in bacteria, including biofilm formation. Here, the authors provide evidence of cross-talk between cAMP and c-di-GMP pathways through direct interaction of their effectors, showing that the cAMP receptor protein (CRP) can play regulatory roles at the post-translational level.

    • Cong Liu
    • , Di Sun
    •  & Weijie Liu

  • 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

    The fungal pathogen Candida albicans can release extracellular vesicles that promote biofilm formation and antifungal resistance. Here, Zarnowski et al. define functions for numerous vesicle cargo proteins in biofilm matrix assembly and drug resistance, as well as in fungal cell adhesion and dissemination.

    • Robert Zarnowski
    • , Andrea Noll
    •  & David R. Andes

  • 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

    Little is known about viral-host interactions in the continental subsurface. Here, the authors use a combination of metagenomics, fluorescence in situ hybridization, and electron microscopy to show infections of abundant C-fixing subsurface archaea by lytic viruses.

    • Janina Rahlff
    • , Victoria Turzynski
    •  & Alexander J. Probst

  • Article
    | Open Access

    Adherent-invasive E. coli (AIEC) are frequently isolated from Crohn’s disease (CD) patients. Here, Elhenawy et al. conduct a genome-wide screen to identify AIEC genes required for in vivo intestinal colonization, and show that a type IV secretion system contributes to AIEC persistence in the gut and is enriched in CD patients’ isolates.

    • Wael Elhenawy
    • , Sarah Hordienko
    •  & Brian K. Coombes

  • Article
    | Open Access

    Many bacteria use the second messenger cyclic diguanylate (c-di-GMP) to control motility, biofilm production and virulence. Here, the authors identify a thermosensitive enzyme that synthesizes c-di-GMP and modulates temperature-dependent motility, biofilm development and virulence in the opportunistic pathogen Pseudomonas aeruginosa.

    • Henrik Almblad
    • , Trevor E. Randall
    •  & Joe Jonathan Harrison

  • Article
    | Open Access

    Mycobacterium tuberculosis forms biofilms in vitro, but it is unclear whether biofilms are also formed during infection in vivo. Here, Chakraborty et al. demonstrate the formation of biofilms in animal models of infection and in patients with tuberculosis, and that biofilm formation can contribute to drug tolerance.

    • Poushali Chakraborty
    • , Sapna Bajeli
    •  & Ashwani Kumar

  • Article
    | Open Access

    The authors show that the pathogen Staphylococcus aureus induces a distinct airway immunometabolic response, dominated by release of itaconate. This metabolite, in turn, potentiates extracellular polysaccharide synthesis and biofilm formation in S. aureus, which may facilitate chronic infection.

    • Kira L. Tomlinson
    • , Tania Wong Fok Lung
    •  & Sebastián A. Riquelme

  • Article
    | Open Access

    Nanozymes have been used for antibacterial applications but have potential toxicity to mammalian cells. Here the authors suggest that nanozymes that generate surface bound reactive oxygen species disrupt bacterial cell walls but not mammalian cells walls due to the different particle uptake mechanisms.

    • Feng Gao
    • , Tianyi Shao
    •  & Lihua Yang

  • Article
    | Open Access

    Accurate cell detection in dense bacterial biofilms is challenging. Here, the authors report an image analysis pipeline that is able to accurately segment and classify single bacterial cells in 3D fluorescence images: Bacterial Cell Morphometry 3D (BCM3D).

    • Mingxing Zhang
    • , Ji Zhang
    •  & Andreas Gahlmann

  • Article
    | Open Access

    Small regulatory RNAs (sRNAs) in Vibrio cholerae have been shown to modulate several biological processess including virulence, biofilm formation, quorum sensing, colony morphology and stress resistance. Here, the authors show that VadR sRNA acts as a posttranscriptional inhibitor of the crvA mRNA and that mutation of vadR increases cell curvature, whereas overexpression has the inverse effect.

    • Nikolai Peschek
    • , Roman Herzog
    •  & Kai Papenfort

  • Article
    | Open Access

    The small molecule AI-2 acts as a quorum sensing signal, mediating communication within and between many bacterial species. Here, the authors identify a new type of AI-2 receptor, consisting of a dCACHE domain that is present in many bacterial and archaeal proteins.

    • Lei Zhang
    • , Shuyu Li
    •  & Xihui Shen

  • Article
    | Open Access

    The exopolysaccharide galactosaminogalactan (GAG) is an important virulence factor of the fungal pathogen Aspergillus fumigatus. Here, the authors study an A. fumigatus enzyme that deacetylates GAG in a metal-dependent manner and constitutes a founding member of a new carbohydrate esterase family.

    • Natalie C. Bamford
    • , François Le Mauff
    •  & P. Lynne Howell

  • Article
    | Open Access

    The amyloid protein TasA is a main component of the extracellular matrix in Bacillus subtilis biofilms. Here the authors show that, in addition to a structural function during biofilm assembly and interactions with plants, TasA contributes to the stabilization of membrane dynamics during stationary phase.

    • Jesús Cámara-Almirón
    • , Yurena Navarro
    •  & Diego Romero

  • Article
    | Open Access

    Biofilm formation by Vibrio cholerae is regulated by c-di-GMP and requires the type IV MSHA pilus. Here, Floyd et al. show that the MSHA pilus is a dynamic system, and that both extension and retraction are directly controlled by c-di-GMP via regulation of activity of the extension ATPase MshE.

    • Kyle A. Floyd
    • , Calvin K. Lee
    •  & Fitnat H. Yildiz

  • Article
    | Open Access

    Stochastic pulsing of gene expression can generate phenotypic diversity in a genetically identical population of cells. Here, the authors show that stochastic pulsing in the expression of a sigma factor enables the formation of spatial patterns in a multicellular system, Bacillus subtilis bacterial biofilms.

    • Eugene Nadezhdin
    • , Niall Murphy
    •  & James C. W. Locke

  • Article
    | Open Access

    Yersinia pestis, the causative agent of plague, can change its biofilm production to influence the dynamics of flea-borne transmission. Here, the authors sequence Y. pestis isolates sampled over 40 years in China and show evidence for climate-associated selection on rpoZ to increase biofilm production.

    • Yujun Cui
    • , Boris V. Schmid
    •  & Ruifu Yang

  • Article
    | Open Access

    A major component of bacterial biofilms is curli amyloid fibrils secreted by the curli biogenesis system. Here authors use cryo-EM to visualize the secretion channel complexes (CsgF-CsgG) with and without the curli substrate and provide insights into curli biogenesis.

    • Zhaofeng Yan
    • , Meng Yin
    •  & Xueming Li

  • 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

    Membrane use as a cathode is a common measure to retard fouling in anaerobic electrochemical membrane bioreactors, but this cannot avoid the fouling growth. Here the authors report on using membranes as anodes to create equilibrium between fouling and oxidation to maintain stable operation.

    • Qilin Yu
    •  & Yaobin Zhang

  • 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

    Surface association and quorum sensing regulate bacterial community behaviours such as biofilm formation and motility. Here, Chuang et al. show that surface association promotes stronger quorum-sensing responses in Pseudomonas aeruginosa by upregulating the master regulator LasR.

    • Sara K. Chuang
    • , Geoffrey D. Vrla
    •  & Zemer Gitai

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