1
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Wu X, Wu D, Cui G, Lee KH, Yang T, Zhang Z, Liu Q, Zhang J, Chua EG, Chen Z. Association Between Biofilm Formation and Structure and Antibiotic Resistance in H. pylori. Infect Drug Resist 2024; 17:2501-2512. [PMID: 38933776 PMCID: PMC11199321 DOI: 10.2147/idr.s468126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Background Persistent infections caused by Helicobacter pylori (H. pylori), which are resistant to antibiotic treatment, pose a growing global public health concern. Biofilm formation is known to be associated with persistent infections due to its role in enhancing antimicrobial resistance and the tolerance of many pathogenic bacteria. Objective This study aims to evaluate the biofilm formation of clinical isolates of H. pylori and its impact on antibiotic eradication. Methods The thickness, morphology, and structure of biofilms derived from nine H. pylori strains were examined using confocal laser scanning microscopy, scanning electron microscopy, and transmission electron microscopy. Subsequently, the susceptibility of both planktonic and biofilm bacteria was assessed through the determination of minimum inhibitory concentration and minimum biofilm eradication concentration for amoxicillin, clarithromycin, levofloxacin, and tetracycline. Results The results revealed varying biofilm thicknesses and densities among the strains, characterised by the presence of numerous filaments intertwining and connecting bacterial cells. Additionally, several cases exhibited susceptibility based on MIC measurements but resistance according to MBEC measurements, with MBEC indicating a higher resistance rate. Pearson Correlation analysis demonstrated a positive correlation between biofilm thickness and MBEC results (0 < r < 1), notably significant for amoxicillin (r = 0.801, P = 0.009) and tetracycline (r = 0.696, P = 0.037). Conclusion Different strains of H. pylori exhibit variations in their capacity to release outer membrane vesicles (OMVs) and form biofilms. Biofilm formation can influence the effectiveness of amoxicillin and tetracycline in eradicating susceptible bacterial strains.
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Affiliation(s)
- Xiaojuan Wu
- Key Laboratory of Microbiology and Parasitology of Education Department of Guizhou & Joint Laboratory of Helicobacter Pylori and Intestinal Microecology of Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Guiyang, People’s Republic of China
- Key Laboratory of Endemic and Ethnic Diseases of Ministry of Education, Guizhou Medical University, Guiyang, People’s Republic of China
| | - Daoyan Wu
- Key Laboratory of Microbiology and Parasitology of Education Department of Guizhou & Joint Laboratory of Helicobacter Pylori and Intestinal Microecology of Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Guiyang, People’s Republic of China
- Key Laboratory of Endemic and Ethnic Diseases of Ministry of Education, Guizhou Medical University, Guiyang, People’s Republic of China
| | - Guzhen Cui
- Key Laboratory of Microbiology and Parasitology of Education Department of Guizhou & Joint Laboratory of Helicobacter Pylori and Intestinal Microecology of Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Guiyang, People’s Republic of China
| | - Khui Hung Lee
- Helicobacter Research Laboratory, the Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Tingxiu Yang
- Key Laboratory of Microbiology and Parasitology of Education Department of Guizhou & Joint Laboratory of Helicobacter Pylori and Intestinal Microecology of Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Guiyang, People’s Republic of China
- Key Laboratory of Endemic and Ethnic Diseases of Ministry of Education, Guizhou Medical University, Guiyang, People’s Republic of China
| | - Zhengrong Zhang
- Key Laboratory of Microbiology and Parasitology of Education Department of Guizhou & Joint Laboratory of Helicobacter Pylori and Intestinal Microecology of Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Guiyang, People’s Republic of China
- Key Laboratory of Endemic and Ethnic Diseases of Ministry of Education, Guizhou Medical University, Guiyang, People’s Republic of China
| | - Qi Liu
- Department of Gastroenterology, Affiliated Hospital of Guizhou Medical University, Guiyang, People’s Republic of China
| | - Jinbao Zhang
- Key Laboratory of Microbiology and Parasitology of Education Department of Guizhou & Joint Laboratory of Helicobacter Pylori and Intestinal Microecology of Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Guiyang, People’s Republic of China
| | - Eng Guan Chua
- Helicobacter Research Laboratory, the Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Zhenghong Chen
- Key Laboratory of Microbiology and Parasitology of Education Department of Guizhou & Joint Laboratory of Helicobacter Pylori and Intestinal Microecology of Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Guiyang, People’s Republic of China
- Key Laboratory of Endemic and Ethnic Diseases of Ministry of Education, Guizhou Medical University, Guiyang, People’s Republic of China
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2
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Puri D, Allison KR. Escherichia coli self-organizes developmental rosettes. Proc Natl Acad Sci U S A 2024; 121:e2315850121. [PMID: 38814871 PMCID: PMC11161754 DOI: 10.1073/pnas.2315850121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 05/01/2024] [Indexed: 06/01/2024] Open
Abstract
Rosettes are self-organizing, circular multicellular communities that initiate developmental processes, like organogenesis and embryogenesis, in complex organisms. Their formation results from the active repositioning of adhered sister cells and is thought to distinguish multicellular organisms from unicellular ones. Though common in eukaryotes, this multicellular behavior has not been reported in bacteria. In this study, we found that Escherichia coli forms rosettes by active sister-cell repositioning. After division, sister cells "fold" to actively align at the 2- and 4-cell stages of clonal division, thereby producing rosettes with characteristic quatrefoil configuration. Analysis revealed that folding follows an angular random walk, composed of ~1 µm strokes and directional randomization. We further showed that this motion was produced by the flagellum, the extracellular tail whose rotation generates swimming motility. Rosette formation was found to require de novo flagella synthesis suggesting it must balance the opposing forces of Ag43 adhesion and flagellar propulsion. We went on to show that proper rosette formation was required for subsequent morphogenesis of multicellular chains, rpoS gene expression, and formation of hydrostatic clonal-chain biofilms. Moreover, we found self-folding rosette-like communities in the standard motility assay, indicating that this behavior may be a general response to hydrostatic environments in E. coli. These findings establish self-organization of clonal rosettes by a prokaryote and have implications for evolutionary biology, synthetic biology, and medical microbiology.
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Affiliation(s)
- Devina Puri
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA30322
| | - Kyle R. Allison
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA30322
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA30322
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3
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Long J, Yang C, Liu J, Ma C, Jiao M, Hu H, Xiong J, Zhang Y, Wei W, Yang H, He Y, Zhu M, Yu Y, Fu L, Chen H. Tannic acid inhibits Escherichia coli biofilm formation and underlying molecular mechanisms: Biofilm regulator CsgD. Biomed Pharmacother 2024; 175:116716. [PMID: 38735084 DOI: 10.1016/j.biopha.2024.116716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/27/2024] [Accepted: 05/06/2024] [Indexed: 05/14/2024] Open
Abstract
Biofilms often engender persistent infections, heightened antibiotic resistance, and the recurrence of infections. Therefor, infections related to bacterial biofilms are often chronic and pose challenges in terms of treatment. The main transcription regulatory factor, CsgD, activates csgABC-encoded curli to participate in the composition of extracellular matrix, which is an important skeleton for biofilm development in enterobacteriaceae. In our previous study, a wide range of natural bioactive compounds that exhibit strong affinity to CsgD were screened and identified via molecular docking. Tannic acid (TA) was subsequently chosen, based on its potent biofilm inhibition effect as observed in crystal violet staining. Therefore, the aim of this study was to investigate the specific effects of TA on the biofilm formation of clinically isolated Escherichia coli (E. coli). Results demonstrated a significant inhibition of E. coli Ec032 biofilm formation by TA, while not substantially affecting the biofilm of the ΔcsgD strain. Moreover, deletion of the csgD gene led to a reduction in Ec032 biofilm formation, alongside diminished bacterial motility and curli synthesis inhibition. Transcriptomic analysis and RT-qPCR revealed that TA repressed genes associated with the csg operon and other biofilm-related genes. In conclusion, our results suggest that CsgD is one of the key targets for TA to inhibit E. coli biofilm formation. This work preliminarily elucidates the molecular mechanisms of TA inhibiting E. coli biofilm formation, which could provide a lead structure for the development of future antibiofilm drugs.
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Affiliation(s)
- Jinying Long
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; National Center of Technology Innovation for Pigs, Chongqing 402460, China; Immunology Research Center, Medical Research Institute, Southwest University, Chongqing 402460, China
| | - Can Yang
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; National Center of Technology Innovation for Pigs, Chongqing 402460, China; Immunology Research Center, Medical Research Institute, Southwest University, Chongqing 402460, China
| | - JingJing Liu
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Chengjun Ma
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Min Jiao
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Huiming Hu
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China
| | - Jing Xiong
- National Center of Technology Innovation for Pigs, Chongqing 402460, China; Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Yang Zhang
- National Center of Technology Innovation for Pigs, Chongqing 402460, China; Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Wei Wei
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; National Center of Technology Innovation for Pigs, Chongqing 402460, China; Traditional Chinese Veterinary Research Institute, Southwest University, Chongqing 402460, China
| | - Hongzao Yang
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; National Center of Technology Innovation for Pigs, Chongqing 402460, China; Traditional Chinese Veterinary Research Institute, Southwest University, Chongqing 402460, China
| | - Yuzhang He
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; Immunology Research Center, Medical Research Institute, Southwest University, Chongqing 402460, China
| | - Maixun Zhu
- National Center of Technology Innovation for Pigs, Chongqing 402460, China; Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Yuandi Yu
- National Center of Technology Innovation for Pigs, Chongqing 402460, China; Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Lizhi Fu
- National Center of Technology Innovation for Pigs, Chongqing 402460, China; Chongqing Academy of Animal Sciences, Chongqing 402460, China.
| | - Hongwei Chen
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; National Center of Technology Innovation for Pigs, Chongqing 402460, China; Immunology Research Center, Medical Research Institute, Southwest University, Chongqing 402460, China; Traditional Chinese Veterinary Research Institute, Southwest University, Chongqing 402460, China.
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4
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Sousa AM, Ferreira D, Rodrigues LR, Pereira MO. Aptamer-based therapy for fighting biofilm-associated infections. J Control Release 2024; 367:522-539. [PMID: 38295992 DOI: 10.1016/j.jconrel.2024.01.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/06/2024] [Accepted: 01/27/2024] [Indexed: 02/06/2024]
Abstract
Biofilms are key players in the pathogenesis of most of chronic infections associated with host tissue or fluids and indwelling medical devices. These chronic infections are hard to be treated due to the increased biofilms tolerance towards antibiotics in comparison to planktonic (or free living) cells. Despite the advanced understanding of their formation and physiology, biofilms continue to be a challenge and there is no standardized therapeutic approach in clinical practice to eradicate them. Aptamers offer distinctive properties, including excellent affinity, selectivity, stability, making them valuable tools for therapeutic purposes. This review explores the flexibility and designability of aptamers as antibiofilm drugs but, importantly, as targeting tools for diverse drug and delivery systems. It highlights specific examples of application of aptamers in biofilms of diverse species according to different modes of action including inhibition of motility and adhesion, blocking of quorum sensing molecules, and dispersal of biofilm-cells to planktonic state. Moreover, it discusses the limitations and challenges that impaired an increased success of the use of aptamers on biofilm management, as well as the opportunities related to aptamers modifications that can significantly expand their applicability on the biofilm field.
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Affiliation(s)
- Ana Margarida Sousa
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga, Guimarães, Portugal.
| | - Débora Ferreira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga, Guimarães, Portugal
| | - Lígia Raquel Rodrigues
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga, Guimarães, Portugal
| | - Maria Olívia Pereira
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; LABBELS - Associate Laboratory, Braga, Guimarães, Portugal.
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5
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Dayton H, Kiss J, Wei M, Chauhan S, LaMarre E, Cornell WC, Morgan CJ, Janakiraman A, Min W, Tomer R, Price-Whelan A, Nirody JA, Dietrich LEP. Cellular arrangement impacts metabolic activity and antibiotic tolerance in Pseudomonas aeruginosa biofilms. PLoS Biol 2024; 22:e3002205. [PMID: 38300958 PMCID: PMC10833521 DOI: 10.1371/journal.pbio.3002205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 12/19/2023] [Indexed: 02/03/2024] Open
Abstract
Cells must access resources to survive, and the anatomy of multicellular structures influences this access. In diverse multicellular eukaryotes, resources are provided by internal conduits that allow substances to travel more readily through tissue than they would via diffusion. Microbes growing in multicellular structures, called biofilms, are also affected by differential access to resources and we hypothesized that this is influenced by the physical arrangement of the cells. In this study, we examined the microanatomy of biofilms formed by the pathogenic bacterium Pseudomonas aeruginosa and discovered that clonal cells form striations that are packed lengthwise across most of a mature biofilm's depth. We identified mutants, including those defective in pilus function and in O-antigen attachment, that show alterations to this lengthwise packing phenotype. Consistent with the notion that cellular arrangement affects access to resources within the biofilm, we found that while the wild type shows even distribution of tested substrates across depth, the mutants show accumulation of substrates at the biofilm boundaries. Furthermore, we found that altered cellular arrangement within biofilms affects the localization of metabolic activity, the survival of resident cells, and the susceptibility of subpopulations to antibiotic treatment. Our observations provide insight into cellular features that determine biofilm microanatomy, with consequences for physiological differentiation and drug sensitivity.
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Affiliation(s)
- Hannah Dayton
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Julie Kiss
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Mian Wei
- Department of Chemistry, Columbia University, New York, New York, United States of America
| | - Shradha Chauhan
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Emily LaMarre
- Program in Biology, The Graduate Center, City University of New York, New York, New York, United States of America
| | - William Cole Cornell
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Chase J. Morgan
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Anuradha Janakiraman
- Program in Biology, The Graduate Center, City University of New York, New York, New York, United States of America
| | - Wei Min
- Department of Chemistry, Columbia University, New York, New York, United States of America
| | - Raju Tomer
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Jasmine A. Nirody
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, Illinois, United States of America
| | - Lars E. P. Dietrich
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
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6
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Teteneva N, Sanches-Medeiros A, Sourjik V. Genome-wide screen of genetic determinants that govern Escherichia coli growth and persistence in lake water. THE ISME JOURNAL 2024; 18:wrae096. [PMID: 38874171 PMCID: PMC11188689 DOI: 10.1093/ismejo/wrae096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 06/15/2024]
Abstract
Although enteric bacteria normally reside within the animal intestine, the ability to persist extraintestinally is an essential part of their overall lifestyle, and it might contribute to transmission between hosts. Despite this potential importance, few genetic determinants of extraintestinal growth and survival have been identified, even for the best-studied model, Escherichia coli. In this work, we thus used a genome-wide library of barcoded transposon insertions to systematically identify functional clusters of genes that are crucial for E. coli fitness in lake water. Our results revealed that inactivation of pathways involved in maintaining outer membrane integrity, nucleotide biosynthesis, and chemotaxis negatively affected E. coli growth or survival in this extraintestinal environment. In contrast, inactivation of another group of genes apparently benefited E. coli growth or persistence in filtered lake water, resulting in higher abundance of these mutants. This group included rpoS, which encodes the general stress response sigma factor, as well as genes encoding several other global transcriptional regulators and RNA chaperones, along with several poorly annotated genes. Based on this co-enrichment, we identified these gene products as novel positive regulators of RpoS activity. We further observed that, despite their enhanced growth, E. coli mutants with inactive RpoS had reduced viability in lake water, and they were not enriched in the presence of the autochthonous microbiota. This highlights the duality of the general stress response pathway for E. coli growth outside the host.
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Affiliation(s)
- Nataliya Teteneva
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), D-35043 Marburg, Germany
| | - Ananda Sanches-Medeiros
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), D-35043 Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), D-35043 Marburg, Germany
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7
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Cordisco E, Zanor MI, Moreno DM, Serra DO. Selective inhibition of the amyloid matrix of Escherichia coli biofilms by a bifunctional microbial metabolite. NPJ Biofilms Microbiomes 2023; 9:81. [PMID: 37857690 PMCID: PMC10587114 DOI: 10.1038/s41522-023-00449-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023] Open
Abstract
The propensity of bacteria to grow collectively in communities known as biofilms and their ability to overcome clinical treatments in this condition has become a major medical problem, emphasizing the need for anti-biofilm strategies. Antagonistic microbial interactions have extensively served as searching platforms for antibiotics, but their potential as sources for anti-biofilm compounds has barely been exploited. By screening for microorganisms that in agar-set pairwise interactions could antagonize Escherichia coli's ability to form macrocolony biofilms, we found that the soil bacterium Bacillus subtilis strongly inhibits the synthesis of amyloid fibers -known as curli-, which are the primary extracellular matrix (ECM) components of E. coli biofilms. We identified bacillaene, a B. subtilis hybrid non-ribosomal peptide/polyketide metabolite, previously described as a bacteriostatic antibiotic, as the effector molecule. We found that bacillaene combines both antibiotic and anti-curli functions in a concentration-dependent order that potentiates the ecological competitiveness of B. subtilis, highlighting bacillaene as a metabolite naturally optimized for microbial inhibition. Our studies revealed that bacillaene inhibits curli by directly impeding the assembly of the CsgB and CsgA curli subunits into amyloid fibers. Moreover, we found that curli inhibition occurs despite E. coli attempts to reinforce its protective ECM by inducing curli genes via a RpoS-mediated competition sensing response trigged by the threatening presence of B. subtilis. Overall, our findings illustrate the relevance of exploring microbial interactions not only for finding compounds with unknown and unique activities, but for uncovering additional functions of compounds previously categorized as antibiotics.
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Affiliation(s)
- Estefanía Cordisco
- Laboratorio de Estructura y Fisiología de Biofilms Microbianos, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, Ocampo y Esmeralda, (2000), Rosario, Argentina
| | - María Inés Zanor
- Laboratorio de Metabolismo y Señalización en Plantas, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, Ocampo y Esmeralda, (2000), Rosario, Argentina
| | - Diego Martín Moreno
- Instituto de Química Rosario (IQUIR, CONICET-UNR), Predio CONICET Rosario, Ocampo y Esmeralda, (2000) Rosario, Argentina. Facultad de Ciencias Bioquímicas y Farmacéuticas, Suipacha 531, (2000), Rosario, Argentina
| | - Diego Omar Serra
- Laboratorio de Estructura y Fisiología de Biofilms Microbianos, Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Predio CONICET Rosario, Ocampo y Esmeralda, (2000), Rosario, Argentina.
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8
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van Gestel J, Wagner A, Ackermann M. Pleiotropic hubs drive bacterial surface competition through parallel changes in colony composition and expansion. PLoS Biol 2023; 21:e3002338. [PMID: 37844064 PMCID: PMC10578586 DOI: 10.1371/journal.pbio.3002338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/18/2023] [Indexed: 10/18/2023] Open
Abstract
Bacteria commonly adhere to surfaces where they compete for both space and resources. Despite the importance of surface growth, it remains largely elusive how bacteria evolve on surfaces. We previously performed an evolution experiment where we evolved distinct Bacilli populations under a selective regime that favored colony spreading. In just a few weeks, colonies of Bacillus subtilis showed strongly advanced expansion rates, increasing their radius 2.5-fold relative to that of the ancestor. Here, we investigate what drives their rapid evolution by performing a uniquely detailed analysis of the evolutionary changes in colony development. We find mutations in diverse global regulators, RicT, RNAse Y, and LexA, with strikingly similar pleiotropic effects: They lower the rate of sporulation and simultaneously facilitate colony expansion by either reducing extracellular polysaccharide production or by promoting filamentous growth. Combining both high-throughput flow cytometry and gene expression profiling, we show that regulatory mutations lead to highly reproducible and parallel changes in global gene expression, affecting approximately 45% of all genes. This parallelism results from the coordinated manner by which regulators change activity both during colony development-in the transition from vegetative growth to dormancy-and over evolutionary time. This coordinated activity can however also break down, leading to evolutionary divergence. Altogether, we show how global regulators function as major pleiotropic hubs that drive rapid surface adaptation by mediating parallel changes in both colony composition and expansion, thereby massively reshaping gene expression.
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Affiliation(s)
- Jordi van Gestel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
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Visser JA, Yager D, Chambers SA, Lim JY, Cao X, Cegelski L. Nordihydroguaiaretic Acid (NDGA) Inhibits CsgA Polymerization, Bacterial Amyloid Biogenesis, and Biofilm Formation. Chembiochem 2023; 24:e202300266. [PMID: 37195016 DOI: 10.1002/cbic.202300266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 05/18/2023]
Abstract
Escherichia coli and other Enterobacteriaceae thrive in robust biofilm communities through the coproduction of curli amyloid fibers and phosphoethanolamine cellulose. Curli promote adhesion to abiotic surfaces and plant and human host tissues and are associated with pathogenesis in urinary tract infection and food-borne illness. The production of curli in the host has also been implicated in the pathogenesis of neurodegenerative diseases. We report that the natural product nordihydroguaiaretic acid (NDGA) is effective as a curlicide in E. coli. NDGA prevents CsgA polymerization in vitro in a dose-dependent manner. NDGA selectively inhibits cell-associated curli assembly and inhibits uropathogenic E. coli biofilm formation. More broadly, this work emphasizes the ability to evaluate and identify bioactive amyloid assembly inhibitors by using the powerful gene-directed amyloid biogenesis machinery in E. coli.
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Affiliation(s)
- Joshua A Visser
- Department of Chemistry, Stanford University, 380 Roth Way, Keck Building, Stanford, CA, 94305, USA
| | - Deborah Yager
- Department of Chemistry, Stanford University, 380 Roth Way, Keck Building, Stanford, CA, 94305, USA
| | - Schuyler A Chambers
- Department of Chemistry, Stanford University, 380 Roth Way, Keck Building, Stanford, CA, 94305, USA
| | - Ji Youn Lim
- Department of Chemistry, Stanford University, 380 Roth Way, Keck Building, Stanford, CA, 94305, USA
| | - Xujun Cao
- Department of Chemistry, Stanford University, 380 Roth Way, Keck Building, Stanford, CA, 94305, USA
| | - Lynette Cegelski
- Department of Chemistry, Stanford University, 380 Roth Way, Keck Building, Stanford, CA, 94305, USA
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10
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Bai M, Dai J, Li C, Cui H, Lin L. Antibacterial and antibiofilm performance of low-frequency ultrasound against Escherichia coli O157:H7 and its application in fresh produce. Int J Food Microbiol 2023; 400:110266. [PMID: 37263173 DOI: 10.1016/j.ijfoodmicro.2023.110266] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 05/02/2023] [Accepted: 05/25/2023] [Indexed: 06/03/2023]
Abstract
Ultrasound technology has been focused on due to its unique advantages in biofilm removal compared with traditional antibacterial methods. Herein, the anti-biofilm properties of low-frequency ultrasound (LFUS) were studied against Enterohemorrhagic Escherichia coli O157: H7 (E. coli O157:H7). After ultrasonication (20 kHz, 300 W) for 5 min, the removal rate of biofilm from polystyrene sheets reached up to 99.999 %. However, the bacterial cells could not be inactivated completely even extending the duration of ultrasonic irradiation to 30 min. Fortunately, this study indicated that LFUS could efficiently weaken the metabolic capacity and biofilm-forming ability of bacterial cells separated from biofilm. It could be associated with the removal of cell surface appendages and damage to cell membrane induced by mechanical vibration and acoustic cavitation. Besides, the genetic analysis proved that the transcription level of genes involved in curli formation was significantly down-regulated during ultrasonic irradiation, thus impeding the process of irreversible adhesion and cells aggregation. Finally, the actual application effect of LFUS was also evaluated in different fresh produces model. The results of this study would provide a theoretical basis for the further application of ultrasound in the food preservation.
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Affiliation(s)
- Mei Bai
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jinming Dai
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410007, China
| | - Haiying Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Lin Lin
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China; State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410007, China.
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11
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Ratheesh NK, Zdimal AM, Calderon CA, Shrivastava A. Bacterial Swarm-Mediated Phage Transportation Disrupts a Biofilm Inherently Protected from Phage Penetration. Microbiol Spectr 2023; 11:e0093723. [PMID: 37358420 PMCID: PMC10434198 DOI: 10.1128/spectrum.00937-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/05/2023] [Indexed: 06/27/2023] Open
Abstract
Physical forces that arise due to bacterial motility and growth play a significant role in shaping the biogeography of the human oral microbiota. Bacteria of the genus Capnocytophaga are abundant in the human oral microbiota and yet very little is known about their physiology. The human oral isolate Capnocytophaga gingivalis exhibits robust gilding motility that is driven by the rotary type 9 secretion system (T9SS), and cells of C. gingivalis transport nonmotile oral microbes as cargo. Phages, i.e., viruses that infect bacteria, are found in abundance within the microbiota. By tracking fluorescently labeled lambda phages that do not infect C. gingivalis, we report active phage transportation by C. gingivalis swarms. Lambda phage-carrying C. gingivalis swarms were propagated near an Escherichia coli colony. The rate of disruption of the E. coli colony increased 10 times compared with a control where phages simply diffused to the E. coli colony. This finding suggests a mechanism where fluid flows produced by motile bacteria increase the rate of transport of phages to their host bacterium. Additionally, C. gingivalis swarms formed tunnel-like structures within a curli fiber-containing E. coli biofilm that increased the efficiency of phage penetration. Our data suggest that invasion by a C. gingivalis swarm changes the spatial structure of the prey biofilm and further increases the penetration of phages. IMPORTANCE Dysbiosis of the human oral microbiota is associated with several diseases, but the factors that shape the biogeography of the oral microbiota are mostly opaque. Biofilms that form in the human supragingival and subgingival regions have a diverse microbial community where some microbes form well-defined polymicrobial structures. C. gingivalis, a bacterium abundant in human gingival regions, has robust gliding motility that is powered by the type 9 secretion system. We demonstrate that swarms of C. gingivalis can transport phages through a complex biofilm which increases the death rate of the prey biofilm. These findings suggest that C. gingivalis could be used as a vehicle for the transportation of antimicrobials and that active phage transportation could shape the spatial structure of a microbial community.
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Affiliation(s)
- Nichith K. Ratheesh
- Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
| | - Amanda M. Zdimal
- Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
| | - Cole A. Calderon
- Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
| | - Abhishek Shrivastava
- Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
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12
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Quendera AP, Pinto SN, Pobre V, Antunes W, Bonifácio VDB, Arraiano CM, Andrade JM. The ribonuclease PNPase is a key regulator of biofilm formation in Listeria monocytogenes and affects invasion of host cells. NPJ Biofilms Microbiomes 2023; 9:34. [PMID: 37286543 DOI: 10.1038/s41522-023-00397-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/18/2023] [Indexed: 06/09/2023] Open
Abstract
Biofilms provide an environment that protects microorganisms from external stresses such as nutrient deprivation, antibiotic treatments, and immune defences, thereby creating favorable conditions for bacterial survival and pathogenesis. Here we show that the RNA-binding protein and ribonuclease polynucleotide phosphorylase (PNPase) is a positive regulator of biofilm formation in the human pathogen Listeria monocytogenes, a major responsible for food contamination in food-processing environments. The PNPase mutant strain produces less biofilm biomass and exhibits an altered biofilm morphology that is more susceptible to antibiotic treatment. Through biochemical assays and microscopical analysis, we demonstrate that PNPase is a previously unrecognized regulator of the composition of the biofilm extracellular matrix, greatly affecting the levels of proteins, extracellular DNA, and sugars. Noteworthy, we have adapted the use of the fluorescent complex ruthenium red-phenanthroline for the detection of polysaccharides in Listeria biofilms. Transcriptomic analysis of wild-type and PNPase mutant biofilms reveals that PNPase impacts many regulatory pathways associated with biofilm formation, particularly by affecting the expression of genes involved in the metabolism of carbohydrates (e.g., lmo0096 and lmo0783, encoding PTS components), of amino acids (e.g., lmo1984 and lmo2006, encoding biosynthetic enzymes) and in the Agr quorum sensing-like system (lmo0048-49). Moreover, we show that PNPase affects mRNA levels of the master regulator of virulence PrfA and PrfA-regulated genes, and these results could help to explain the reduced bacterial internalization in human cells of the ΔpnpA mutant. Overall, this work demonstrates that PNPase is an important post-transcriptional regulator for virulence and adaptation to the biofilm lifestyle of Gram-positive bacteria and highlights the expanding role of ribonucleases as critical players in pathogenicity.
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Affiliation(s)
- Ana Patrícia Quendera
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-901, Oeiras, Portugal
| | - Sandra Nunes Pinto
- Institute for Bioengineering and Biosciences (IBB) and Associate Laboratory-Institute for Health and Bioeconomy (i4HB), Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | - Vânia Pobre
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-901, Oeiras, Portugal
| | - Wilson Antunes
- Laboratório de Imagem, Nanomorfologia e Espectroscopia de Raios-X (Linx) da Unidade Militar Laboratorial de Defesa Biológica e Química (UMLDBQ), Instituto Universitário Militar, Centro de Investigação, Inovação e Desenvolvimento da Academia Militar, Av. Dr Alfredo Bensaúde, 1100-471, Lisboa, Portugal
| | - Vasco D B Bonifácio
- Institute for Bioengineering and Biosciences (IBB) and Associate Laboratory-Institute for Health and Bioeconomy (i4HB), Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
- Bioengineering Department, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | - Cecília Maria Arraiano
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-901, Oeiras, Portugal
| | - José Marques Andrade
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Avenida da República, 2780-901, Oeiras, Portugal.
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13
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Hammarén MM, Luukinen H, Sillanpää A, Remans K, Lapouge K, Custódio T, Löw C, Myllymäki H, Montonen T, Seeger M, Robertson J, Nyman TA, Savijoki K, Parikka M. In vitro and ex vivo proteomics of Mycobacterium marinum biofilms and the development of biofilm-binding synthetic nanobodies. mSystems 2023:e0107322. [PMID: 37184670 DOI: 10.1128/msystems.01073-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
The antibiotic-tolerant biofilms present in tuberculous granulomas add an additional layer of complexity when treating mycobacterial infections, including tuberculosis (TB). For a more efficient treatment of TB, the biofilm forms of mycobacteria warrant specific attention. Here, we used Mycobacterium marinum (Mmr) as a biofilm-forming model to identify the abundant proteins covering the biofilm surface. We used biotinylation/streptavidin-based proteomics on the proteins exposed at the Mmr biofilm matrices in vitro to identify 448 proteins and ex vivo proteomics to detect 91 Mmr proteins from the mycobacterial granulomas isolated from adult zebrafish. In vitro and ex vivo proteomics data are available via ProteomeXchange with identifier PXD033425 and PXD039416, respectively. Data comparisons pinpointed the molecular chaperone GroEL2 as the most abundant Mmr protein within the in vitro and ex vivo proteomes, while its paralog, GroEL1, with a known role in biofilm formation, was detected with slightly lower intensity values. To validate the surface exposure of these targets, we created in-house synthetic nanobodies (sybodies) against the two chaperones and identified sybodies that bind the mycobacterial biofilms in vitro and those present in ex vivo granulomas. Taken together, the present study reports a proof-of-concept showing that surface proteomics in vitro and ex vivo proteomics combined are a valuable strategy to identify surface-exposed proteins on the mycobacterial biofilm. Biofilm-surface-binding nanobodies could be eventually used as homing agents to deliver biofilm-targeting treatments to the sites of persistent biofilm infection.
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Affiliation(s)
- Milka Marjut Hammarén
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Hanna Luukinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Alina Sillanpää
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Kim Remans
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Karine Lapouge
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tânia Custódio
- Centre for Structural Systems Biology, Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Christian Löw
- Centre for Structural Systems Biology, Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
- European Molecular Biology Laboratory, Hamburg, Germany
| | - Henna Myllymäki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Toni Montonen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Markus Seeger
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Joseph Robertson
- Department of Immunology, University of Oslo, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | - Tuula A Nyman
- Department of Immunology, University of Oslo, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | - Kirsi Savijoki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland
| | - Mataleena Parikka
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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14
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Lamprecht O, Ratnikava M, Jacek P, Kaganovitch E, Buettner N, Fritz K, Biazruchka I, Köhler R, Pietsch J, Sourjik V. Regulation by cyclic di-GMP attenuates dynamics and enhances robustness of bimodal curli gene activation in Escherichia coli. PLoS Genet 2023; 19:e1010750. [PMID: 37186613 DOI: 10.1371/journal.pgen.1010750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 05/25/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Curli amyloid fibers are a major constituent of the extracellular biofilm matrix formed by bacteria of the Enterobacteriaceae family. Within Escherichia coli biofilms, curli gene expression is limited to a subpopulation of bacteria, leading to heterogeneity of extracellular matrix synthesis. Here we show that bimodal activation of curli gene expression also occurs in well-mixed planktonic cultures of E. coli, resulting in all-or-none stochastic differentiation into distinct subpopulations of curli-positive and curli-negative cells at the entry into the stationary phase of growth. Stochastic curli activation in individual E. coli cells could further be observed during continuous growth in a conditioned medium in a microfluidic device, which further revealed that the curli-positive state is only metastable. In agreement with previous reports, regulation of curli gene expression by the second messenger c-di-GMP via two pairs of diguanylate cyclase and phosphodiesterase enzymes, DgcE/PdeH and DgcM/PdeR, modulates the fraction of curli-positive cells. Unexpectedly, removal of this regulatory network does not abolish the bimodality of curli gene expression, although it affects dynamics of activation and increases heterogeneity of expression levels among individual cells. Moreover, the fraction of curli-positive cells within an E. coli population shows stronger dependence on growth conditions in the absence of regulation by DgcE/PdeH and DgcM/PdeR pairs. We thus conclude that, while not required for the emergence of bimodal curli gene expression in E. coli, this c-di-GMP regulatory network attenuates the frequency and dynamics of gene activation and increases its robustness to cellular heterogeneity and environmental variation.
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Affiliation(s)
- Olga Lamprecht
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Maryia Ratnikava
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Paulina Jacek
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Eugen Kaganovitch
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Nina Buettner
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Kirstin Fritz
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ina Biazruchka
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Robin Köhler
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Julian Pietsch
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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15
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Khani M, Hansen MF, Knøchel S, Rasekh B, Ghasemipanah K, Zamir SM, Nosrati M, Burmølle M. Antifouling potential of enzymes applied to Reverse Osmosis Membranes. Biofilm 2023; 5:100119. [PMID: 37131492 PMCID: PMC10149195 DOI: 10.1016/j.bioflm.2023.100119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 04/03/2023] Open
Abstract
Many companies in the food industry apply reverse osmosis (RO) membranes to ensure high-quality reuse of water. Biofouling is however, a common, recalcitrant and recurring problem that blocks transport over membranes and decreases the water recovery. Microorganisms adhering to membranes may form biofilm and produce an extracellular matrix, which protects against external stress and ensures continuous attachment. Thus, various agents are tested for their ability to degrade and disperse biofilms. Here, we identified industrially relevant bacterial model communities that form biofilms on RO membranes used for treating process water before reuse. There was a marked difference in the biofilm forming capabilities of bacteria isolated from contaminated RO membranes. One species, Raoultella ornithinolytica, was particularly capable of forming biofilm and was included in most communities. The potential of different enzymes (Trypsin-EDTA, Proteinase K, α-Amylase, β-Mannosidase and Alginate lyase) as biofouling dispersing agents was evaluated at different concentrations (0.05 U/ml and 1.28 U/ml). Among the tested enzymes, β-Mannosidase was the only enzyme able to reduce biofilm formation significantly within 4 h of exposure at 25 °C (0.284 log reduction), and only at the high concentration. Longer exposure duration, however, resulted in significant biofilm reduction by all enzymes tested (0.459-0.717 log reduction) at both low and high concentrations. Using confocal laser scanning microscopy, we quantified the biovolume on RO membranes after treatment with two different enzyme mixtures. The application of proteinase K and β-Mannosidase significantly reduced the amount of attached biomass (43% reduction), and the combination of all five enzymes showed even stronger reducing effect (71% reduction). Overall, this study demonstrates a potential treatment strategy, using matrix-degrading enzymes for biofouled RO membranes in food processing water treatment streams. Future studies on optimization of buffer systems, temperature and other factors could facilitate cleaning operations based on enzymatic treatment extending the lifespan of membranes with a continuous flux.
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16
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Sugimoto S, Kinjo Y. Instantaneous Clearing of Biofilm (iCBiofilm): an optical approach to revisit bacterial and fungal biofilm imaging. Commun Biol 2023; 6:38. [PMID: 36690667 PMCID: PMC9870912 DOI: 10.1038/s42003-022-04396-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 12/21/2022] [Indexed: 01/24/2023] Open
Abstract
Whole-biofilm imaging at single-cell resolution is necessary for system-level analysis of cellular heterogeneity, identification of key matrix component functions and response to immune cells and antimicrobials. To this end, we developed a whole-biofilm clearing and imaging method, termed instantaneous clearing of biofilm (iCBiofilm). iCBiofilm is a simple, rapid, and efficient method involving the immersion of biofilm samples in a refractive index-matching medium, enabling instant whole-biofilm imaging with confocal laser scanning microscopy. We also developed non-fixing iCBiofilm, enabling live and dynamic imaging of biofilm development and actions of antimicrobials. iCBiofilm is applicable for multicolor imaging of fluorescent proteins, immunostained matrix components, and fluorescence labeled cells in biofilms with a thickness of several hundred micrometers. iCBiofilm is scalable from bacterial to fungal biofilms and can be used to observe biofilm-neutrophil interactions. iCBiofilm therefore represents an important advance for examining the dynamics and functions of biofilms and revisiting bacterial and fungal biofilm formation.
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Affiliation(s)
- Shinya Sugimoto
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan.
- Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan.
| | - Yuki Kinjo
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
- Jikei Center for Biofilm Science and Technology, The Jikei University School of Medicine, 3-25-8 Nishi-Shimbashi, Minato-ku, Tokyo, 105-8461, Japan
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17
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Morris RJ, Stevenson D, Sukhodub T, Stanley-Wall NR, MacPhee CE. Density and temperature controlled fluid extraction in a bacterial biofilm is determined by poly-γ-glutamic acid production. NPJ Biofilms Microbiomes 2022; 8:98. [PMID: 36528619 PMCID: PMC9759580 DOI: 10.1038/s41522-022-00361-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
A hallmark of microbial biofilms is the self-production of an extracellular molecular matrix that encases the resident cells. The matrix provides protection from the environment, while spatial heterogeneity of gene expression influences the structural morphology and colony spreading dynamics. Bacillus subtilis is a model bacterial system used to uncover the regulatory pathways and key building blocks required for biofilm growth and development. In this work, we report on the emergence of a highly active population of bacteria during the early stages of biofilm formation, facilitated by the extraction of fluid from the underlying agar substrate. We trace the origin of this fluid extraction to the production of poly-γ-glutamic acid (PGA). The flagella-dependent activity develops behind a moving front of fluid that propagates from the boundary of the biofilm towards the interior. The extent of fluid proliferation is controlled by the presence of extracellular polysaccharides (EPS). We also find that PGA production is positively correlated with higher temperatures, resulting in high-temperature mature biofilm morphologies that are distinct from the rugose colony biofilm architecture typically associated with B. subtilis. Although previous reports have suggested that PGA production does not play a major role in biofilm morphology in the undomesticated isolate NCIB 3610, our results suggest that this strain produces distinct biofilm matrices in response to environmental conditions.
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Affiliation(s)
- Ryan J. Morris
- grid.4305.20000 0004 1936 7988National Biofilms Innovation Centre, School of Physics and Astronomy, The University of Edinburgh, Edinburgh, EH9 3FD UK
| | - David Stevenson
- grid.8241.f0000 0004 0397 2876Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH UK
| | - Tetyana Sukhodub
- grid.8241.f0000 0004 0397 2876Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH UK
| | - Nicola R. Stanley-Wall
- grid.8241.f0000 0004 0397 2876Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH UK
| | - Cait E. MacPhee
- grid.4305.20000 0004 1936 7988National Biofilms Innovation Centre, School of Physics and Astronomy, The University of Edinburgh, Edinburgh, EH9 3FD UK
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18
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Eckert JA, Rosenberg M, Rhen M, Choong FX, Richter-Dahlfors A. An optotracer-based antibiotic susceptibility test specifically targeting the biofilm lifestyle of Salmonella. Biofilm 2022; 4:100083. [PMID: 36117547 PMCID: PMC9474290 DOI: 10.1016/j.bioflm.2022.100083] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022] Open
Abstract
Antimicrobial resistance is a medical threat of global dimensions. Proper antimicrobial susceptibility testing (AST) for drug development, patient diagnosis and treatment is crucial to counteract ineffective drug use and resistance development. Despite the important role of bacterial biofilms in chronic and device-associated infections, the efficacy of antibiotics is determined using planktonic cultures. To address the need for antibiotics targeting bacteria in the biofilm lifestyle, we here present an optotracing-based biofilm-AST using Salmonella as model. Our non-disruptive method enables real-time recording of the extracellular matrix (ECM) components, providing specific detection of the biofilm lifestyle. Biofilm formation prior to antibiotic challenge can thus be confirmed and pre-treatment data collected. By introducing Kirby-Bauer discs, we performed a broad screen of the effects of antibiotics representing multiple classes, and identified compounds with ECM inhibitory as well as promoting effects. These compounds were further tested in agar-based dose-response biofilm-AST assays. By quantifying the ECM based on the amount of curli, and by visualizing the biofilm size and morphology, we achieved new information directly reflecting the treated biofilm. This verified the efficacy of several antibiotics that were effective in eradicating pre-formed biofilms, and it uncovered intriguing possible resistance mechanisms initiated in response to treatments. By providing deeper insights into the resistances and susceptibilities of microbes, expanded use of the biofilm-AST will contribute to more effective treatments of infections and reduced resistance development.
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Affiliation(s)
- Johannes A Eckert
- AIMES - Center for the Advancement of Integrated Medical and Engineering Sciences, Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, Solnavägen 9, SE-171 77, Stockholm, Sweden
| | - Ming Rosenberg
- AIMES - Center for the Advancement of Integrated Medical and Engineering Sciences, Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, Solnavägen 9, SE-171 77, Stockholm, Sweden
| | - Mikael Rhen
- AIMES - Center for the Advancement of Integrated Medical and Engineering Sciences, Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, SE-171 77, Stockholm, Sweden
| | - Ferdinand X Choong
- AIMES - Center for the Advancement of Integrated Medical and Engineering Sciences, Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, Solnavägen 9, SE-171 77, Stockholm, Sweden
| | - Agneta Richter-Dahlfors
- AIMES - Center for the Advancement of Integrated Medical and Engineering Sciences, Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, Solnavägen 9, SE-171 77, Stockholm, Sweden
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19
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Park H, Schwartzman AF, Tang TC, Wang L, Lu TK. Ultra-lightweight living structural material for enhanced stiffness and environmental sensing. Mater Today Bio 2022; 18:100504. [PMID: 36504543 PMCID: PMC9729073 DOI: 10.1016/j.mtbio.2022.100504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
Natural materials such as bone, wood, and bamboo can inspire the fabrication of stiff, lightweight structural materials. Biofilms are one of the most dominant forms of life in nature. However, little is known about their physical properties as a structural material. Here we report an Escherichia coli biofilm having a Young's modulus close to 10 GPa with ultra-low density, indicating a high-performance structural material. The mechanical and structural characterization of the biofilm and its components illuminates its adaptable bottom-up design, consisting of lightweight microscale cells covered by a dense network of amyloid nanofibrils on the surface. We engineered E. coli such that 1) carbon nanotubes assembled on the biofilm, enhancing its stiffness to over 30 GPa, or that 2) the biofilm sensitively detected heavy metal as an example of an environmental toxin. These demonstrations offer new opportunities for developing responsive living structural materials to serve many real-world applications.
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Affiliation(s)
- Heechul Park
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alan F. Schwartzman
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tzu-Chieh Tang
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Lei Wang
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Timothy K. Lu
- Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA,Corresponding author. Synthetic Biology Group, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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20
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Raad N, Tandon D, Hapfelmeier S, Polacek N. The stationary phase-specific sRNA FimR2 is a multifunctional regulator of bacterial motility, biofilm formation and virulence. Nucleic Acids Res 2022; 50:11858-11875. [PMID: 36354005 PMCID: PMC9723502 DOI: 10.1093/nar/gkac1025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 10/06/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022] Open
Abstract
Bacterial pathogens employ a plethora of virulence factors for host invasion, and their use is tightly regulated to maximize infection efficiency and manage resources in a nutrient-limited environment. Here we show that during Escherichia coli stationary phase the 3' UTR-derived small non-coding RNA FimR2 regulates fimbrial and flagellar biosynthesis at the post-transcriptional level, leading to biofilm formation as the dominant mode of survival under conditions of nutrient depletion. FimR2 interacts with the translational regulator CsrA, antagonizing its functions and firmly tightening control over motility and biofilm formation. Generated through RNase E cleavage, FimR2 regulates stationary phase biology by fine-tuning target mRNA levels independently of the chaperones Hfq and ProQ. The Salmonella enterica orthologue of FimR2 induces effector protein secretion by the type III secretion system and stimulates infection, thus linking the sRNA to virulence. This work reveals the importance of bacterial sRNAs in modulating various aspects of bacterial physiology including stationary phase and virulence.
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Affiliation(s)
- Nicole Raad
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, Bern, Switzerland,Graduate School for Cellular and Biomedical Sciences, Bern, Switzerland
| | - Disha Tandon
- Graduate School for Cellular and Biomedical Sciences, Bern, Switzerland,Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Norbert Polacek
- To whom correspondence should be addressed. Tel: +41 31 684 43 20;
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21
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Shared biophysical mechanisms determine early biofilm architecture development across different bacterial species. PLoS Biol 2022; 20:e3001846. [PMID: 36288405 PMCID: PMC9605341 DOI: 10.1371/journal.pbio.3001846] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022] Open
Abstract
Bacterial biofilms are among the most abundant multicellular structures on Earth and play essential roles in a wide range of ecological, medical, and industrial processes. However, general principles that govern the emergence of biofilm architecture across different species remain unknown. Here, we combine experiments, simulations, and statistical analysis to identify shared biophysical mechanisms that determine early biofilm architecture development at the single-cell level, for the species Vibrio cholerae, Escherichia coli, Salmonella enterica, and Pseudomonas aeruginosa grown as microcolonies in flow chambers. Our data-driven analysis reveals that despite the many molecular differences between these species, the biofilm architecture differences can be described by only 2 control parameters: cellular aspect ratio and cell density. Further experiments using single-species mutants for which the cell aspect ratio and the cell density are systematically varied, and mechanistic simulations show that tuning these 2 control parameters reproduces biofilm architectures of different species. Altogether, our results show that biofilm microcolony architecture is determined by mechanical cell-cell interactions, which are conserved across different species.
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22
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Halsted MC, Bible AN, Morrell-Falvey JL, Retterer ST. Quantifying biofilm propagation on chemically modified surfaces. Biofilm 2022; 4:100088. [PMID: 36303845 PMCID: PMC9594113 DOI: 10.1016/j.bioflm.2022.100088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/26/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022] Open
Abstract
Conditions affecting biofilm formation differ among bacterial species and this presents a challenge to studying biofilms in the lab. This work leverages functionalized silanes to control surface chemistry in the study of early biofilm propagation, quantified with a semi-automated image processing algorithm. These methods support the study of Pantoea sp. YR343, a gram-negative bacterium isolated from the poplar rhizosphere. We found that Pantoea sp. YR343 does not readily attach to hydrophilic surfaces but will form biofilms with a “honeycomb” morphology on hydrophobic surfaces. Our image processing algorithm described here quantified the evolution of the honeycomb morphology over time, and found the propagation to display a logarithmic behavior. This methodology was repeated with a flagella-deficient fliR mutant of Pantoea sp. YR343 which resulted in reduced surface attachment. Quantifiable differences between Pantoea WT and ΔfliR biofilm morphologies were captured by the image processing algorithm, further demonstrating the insight gained from these methods.
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Affiliation(s)
| | - Amber N. Bible
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Scott T. Retterer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA,Center for Nanophase Materials Sciences, Oak Ridge, TN, USA,Corresponding author. Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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23
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Spatial Structure Formation by RsmE-Regulated Extracellular Secretions in Pseudomonas fluorescens Pf0-1. J Bacteriol 2022; 204:e0028522. [PMID: 36165622 PMCID: PMC9578434 DOI: 10.1128/jb.00285-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cells in microbial communities on surfaces live and divide in close proximity, which greatly enhances the potential for social interactions. Spatiogenetic structures are manifested through competitive and cooperative interactions among the same and different genotypes within a shared space, and extracellular secretions appear to function dynamically at the forefront. A previous experimental evolution study utilizing Pseudomonas fluorescens Pf0-1 colonies demonstrated that diverse mutations in the rsmE gene were repeatedly and exclusively selected through the formation of a dominant spatial structure. RsmE's primary molecular function is translation repression, and its homologs regulate various social and virulence phenotypes. Pseudomonas spp. possess multiple paralogs of Rsm proteins, and RsmA, RsmE, and RsmI are the most prevalent. Here, we demonstrate that the production of a mucoid polymer and a biosurfactant are exclusively regulated through RsmE, contradicting the generalized notion of functional redundancy among the Rsm paralogs. Furthermore, we identified the biosurfactant as the cyclic lipopeptide gacamide A. Competition and microscopy analyses showed that the mucoid polymer is solely responsible for creating a space of low cellular density, which is shared exclusively by the same genotype. Gacamide A and other RsmE-regulated products appear to establish a physical boundary that prevents the encroachment of the competing genotype into the newly created space. Although cyclic lipopeptides and other biosurfactants are best known for their antimicrobial properties and reducing surface tension to promote the spreading of cells on various surfaces, they also appear to help define spatial structure formation within a dense community. IMPORTANCE In densely populated colonies of the bacterium Pseudomonas fluorescens Pf0-1, diverse mutations in the rsmE gene are naturally selected by solving the problem of overcrowding. Here, we show that RsmE-regulated secretions function together to create and protect space of low cell density. A biosurfactant generally promotes the spreading of bacterial cells on abiotic surfaces; however, it appears to function atypically within a crowded population by physically defining genotypic boundaries. Another significant finding is that these secretions are not regulated by RsmE's paralogs that share high sequence similarity. The experimental pipeline described in this study is highly tractable and should facilitate future studies to explore additional RsmE-regulated products and address why RsmE is functionally unique from its paralogs.
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24
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Pérez-Mendoza D, Romero-Jiménez L, Rodríguez-Carvajal MÁ, Lorite MJ, Muñoz S, Olmedilla A, Sanjuán J. The Role of Two Linear β-Glucans Activated by c-di-GMP in Rhizobium etli CFN42. BIOLOGY 2022; 11:biology11091364. [PMID: 36138843 PMCID: PMC9495663 DOI: 10.3390/biology11091364] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/06/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Bacterial exopolysaccharides (EPS) are secreted biopolymers with often critical roles in bacterial physiology and ecology. In addition to their biological role, there is increasing interest for EPS in various industrial sectors. β-glucans are among the most important ones including cellulose as the most abundant organic polymer on earth, but also newcomers, such as the bacterial Mixed Linkage β-Glucan (MLG), displaying a unique repeating unit suggestive of biotechnological potential. In this work we describe Rhizobium etli as the first bacterium reported to be able to produce these two linear β-glucans cellulose and MLG. Rhizobium etli is an agronomic relevant rhizobacteria able to perform Biological Nitrogen Fixation (BNF) in a symbiotic association with common bean plants. The production and regulation of cellulose and MLG by Rhizobium etli CFN42 is discussed and their impact on its free-living and symbiotic lifestyles evaluated. Abstract Bacterial exopolysaccharides (EPS) have been implicated in a variety of functions that assist in bacterial survival, colonization, and host–microbe interactions. Among them, bacterial linear β-glucans are polysaccharides formed by D-glucose units linked by β-glycosidic bonds, which include curdlan, cellulose, and the new described Mixed Linkage β-Glucan (MLG). Bis-(3′,5′)-cyclic dimeric guanosine monophosphate (c-di-GMP) is a universal bacterial second messenger that usually promote EPS production. Here, we report Rhizobium etli as the first bacterium capable of producing cellulose and MLG. Significant amounts of these two β-glucans are not produced under free-living laboratory conditions, but their production is triggered upon elevation of intracellular c-di-GMP levels, both contributing to Congo red (CR+) and Calcofluor (CF+) phenotypes. Cellulose turned out to be more relevant for free-living phenotypes promoting flocculation and biofilm formation under high c-di-GMP conditions. None of these two EPS are essential for attachment to roots of Phaseolus vulgaris, neither for nodulation nor for symbiotic nitrogen fixation. However, both β-glucans separately contribute to the fitness of interaction between R. etli and its host. Overproduction of these β-glucans, particularly cellulose, appears detrimental for symbiosis. This indicates that their activation by c-di-GMP must be strictly regulated in time and space and should be controlled by different, yet unknown, regulatory pathways.
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Affiliation(s)
- Daniel Pérez-Mendoza
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
- Correspondence: (D.P.-M.); (J.S.); Tel.: +34-958-526-522 (D.P.-M.); +34-958-526-552 (J.S.)
| | - Lorena Romero-Jiménez
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | | | - María J. Lorite
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - Socorro Muñoz
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - Adela Olmedilla
- Department of Stress, Development and Signaling in Plants, CSIC, 18008 Granada, Spain
| | - Juan Sanjuán
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
- Correspondence: (D.P.-M.); (J.S.); Tel.: +34-958-526-522 (D.P.-M.); +34-958-526-552 (J.S.)
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25
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Guo J, Deng X, Zhang Y, Song S, Zhao T, Zhu D, Cao S, Baryshnikov PI, Cao G, Blair HT, Chen C, Gu X, Liu L, Zhang H. The Flagellar Transcriptional Regulator FtcR Controls Brucella melitensis 16M Biofilm Formation via a betI-Mediated Pathway in Response to Hyperosmotic Stress. Int J Mol Sci 2022; 23:ijms23179905. [PMID: 36077302 PMCID: PMC9456535 DOI: 10.3390/ijms23179905] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
The expression of flagellar proteins in Brucella species likely evolved through genetic transference from other microorganisms, and contributed to virulence, adaptability, and biofilm formation. Despite significant progress in defining the molecular mechanisms behind flagellar gene expression, the genetic program controlling biofilm formation remains unclear. The flagellar transcriptional factor (FtcR) is a master regulator of the flagellar system’s expression, and is critical for B. melitensis 16M’s flagellar biogenesis and virulence. Here, we demonstrate that FtcR mediates biofilm formation under hyperosmotic stress. Chromatin immunoprecipitation with next-generation sequencing for FtcR and RNA sequencing of ftcR-mutant and wild-type strains revealed a core set of FtcR target genes. We identified a novel FtcR-binding site in the promoter region of the osmotic-stress-response regulator gene betI, which is important for the survival of B. melitensis 16M under hyperosmotic stress. Strikingly, this site autoregulates its expression to benefit biofilm bacteria’s survival under hyperosmotic stress. Moreover, biofilm reduction in ftcR mutants is independent of the flagellar target gene fliF. Collectively, our study provides new insights into the extent and functionality of flagellar-related transcriptional networks in biofilm formation, and presents phenotypic and evolutionary adaptations that alter the regulation of B. melitensis 16M to confer increased tolerance to hyperosmotic stress.
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Affiliation(s)
- Jia Guo
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
| | - Xingmei Deng
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
| | - Yu Zhang
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
| | - Shengnan Song
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
| | - Tianyi Zhao
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
| | - Dexin Zhu
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
| | - Shuzhu Cao
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
| | - Peter Ivanovic Baryshnikov
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
- College of Veterinary, Altai State Agricultural University, 656000 Barnaul, Russia
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430000, China
| | - Hugh T. Blair
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
- International Sheep Research Center, School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand
| | - Chuangfu Chen
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
| | - Xinli Gu
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
| | - Liangbo Liu
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
- Correspondence: (L.L.); (H.Z.); Tel.: +86-0993-2057971 (L.L. & H.Z.)
| | - Hui Zhang
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi 832003, China
- Correspondence: (L.L.); (H.Z.); Tel.: +86-0993-2057971 (L.L. & H.Z.)
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26
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Guo J, Zhu J, Zhao T, Sun Z, Song S, Zhang Y, Zhu D, Cao S, Deng X, Chai Y, Sun Y, Maratbek S, Chen C, Liu L, Zhang H. Survival characteristics and transcriptome profiling reveal the adaptive response of the Brucella melitensis 16M biofilm to osmotic stress. Front Microbiol 2022; 13:968592. [PMID: 36060772 PMCID: PMC9428795 DOI: 10.3389/fmicb.2022.968592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Brucella can inhabit hostile environments, including osmotic stress. How Brucella responds collectively to osmotic stress is largely unexplored, particularly in spatially structured communities such as a biofilm. To gain insight into this growth mode, we set out to characterize the Brucella melitensis 16M biofilm, describe its phenotype, and carry out a comparative transcriptomic analysis between biofilms under osmotic stress and control conditions. We determined that the bacteria challenged with 1.5 M NaCl had a reduced ability to aggregate and form clumps and develop a biofilm; however, the salt stress promoted the release of the outer membrane vesicles from the biofilm. Together with the genotypical response to osmotic stress, we identified 279 differentially expressed genes in B. melitensis 16M grown under osmotic conditions compared with control conditions; 69 genes were upregulated and 210 downregulated. Under osmotic stress, the main changed genes of biofilm were predicted to be involved in flagellar assembly, cell envelope, translation, small RNA regulation, transport and binding proteins, and energy metabolism. In addition, the ABC transporter was enriched in the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. We highlight 12 essential ABC transporter genes associated with a bacterial response to osmotic stress at the biofilm stage, including one specific locus, BME_RS12880, mediating betaine accumulation in biofilms to eliminate osmotic stress. The current study results can help researchers gain insights into B. melitensis 16M biofilm adaptation to osmotic stress and provide information for developing intervention strategies to control Brucella.
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Affiliation(s)
- Jia Guo
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Jiale Zhu
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Tianyi Zhao
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Zhihua Sun
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Shengnan Song
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Yu Zhang
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Dexin Zhu
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Shuzhu Cao
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Xingmei Deng
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Yingjin Chai
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Yongxue Sun
- Collaborative Innovation Center for Sheep Healthy Farming and Zoonotic Disease Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Suleimenov Maratbek
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi, China
- College of Veterinary, National Agricultural University of Kazakhstan, Nur-Sultan, Kazakhstan
| | - Chuangfu Chen
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Liangbo Liu
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi, China
- *Correspondence: Liangbo Liu,
| | - Hui Zhang
- State International Joint Research Center for Animal Health Breeding, College of Animal Science and Technology, Shihezi University, Shihezi, China
- Hui Zhang,
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27
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Rhythmic Spatial Self-Organization of Bacterial Colonies. mBio 2022; 13:e0170322. [PMID: 35938723 PMCID: PMC9426452 DOI: 10.1128/mbio.01703-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bacteria display a remarkable capacity to organize themselves in space and time within biofilms. Traditionally, the spatial organization of biofilms has been dissected vertically; however, biofilms can exhibit complex, temporally structured, two-dimensional radial patterns while spreading on a surface. Kahl and colleagues report a ring pattern that indicates the alternating redox metabolism of P. aeruginosa biofilms under light/dark cycles. Does the presence of a rhythmic, daily phenotype imply a circadian rhythm? Here, we highlight several examples of rhythmic patterns reported in the literature for surface-colonizing multicellular assemblies and discuss the conceptual requirements for proving the presence of a prokaryotic circadian clock behind pattern formation.
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28
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Tarsitano J, Ramis LY, Alonso LG, Russo DM, Zorreguieta A. RapD Is a Multimeric Calcium-Binding Protein That Interacts With the Rhizobium leguminosarum Biofilm Exopolysaccharide, Influencing the Polymer Lengths. Front Microbiol 2022; 13:895526. [PMID: 35875570 PMCID: PMC9298526 DOI: 10.3389/fmicb.2022.895526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/12/2022] [Indexed: 11/15/2022] Open
Abstract
Rhizobium leguminosarum synthesizes an acidic polysaccharide mostly secreted to the extracellular medium, known as exopolysaccharide (EPS) and partially retained on the bacterial surface as a capsular polysaccharide (CPS). Rap proteins, extracellular protein substrates of the PrsDE type I secretion system (TISS), share at least one Ra/CHDL (cadherin-like) domain and are involved in biofilm matrix development either through cleaving the polysaccharide by Ply glycanases or by altering the bacterial adhesive properties. It was shown that the absence or excess of extracellular RapA2 (a monomeric CPS calcium-binding lectin) alters the biofilm matrix’s properties. Here, we show evidence of the role of a new Rap protein, RapD, which comprises an N-terminal Ra/CHDL domain and a C-terminal region of unknown function. RapD was completely released to the extracellular medium and co-secreted with the other Rap proteins in a PrsDE-dependent manner. Furthermore, high levels of RapD secretion were found in biofilms under conditions that favor EPS production. Interestingly, size exclusion chromatography of the EPS produced by the ΔrapA2ΔrapD double mutant showed a profile of EPS molecules of smaller sizes than those of the single mutants and the wild type strain, suggesting that both RapA2 and RapD proteins influence EPS processing on the cell surface. Biophysical studies showed that calcium triggers proper folding and multimerization of recombinant RapD. Besides, further conformational changes were observed in the presence of EPS. Enzyme-Linked ImmunoSorbent Assay (ELISA) and Binding Inhibition Assays (BIA) indicated that RapD specifically binds the EPS and that galactose residues would be involved in this interaction. Taken together, these observations indicate that RapD is a biofilm matrix-associated multimeric protein that influences the properties of the EPS, the main structural component of the rhizobial biofilm.
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Affiliation(s)
- Julián Tarsitano
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Lila Y. Ramis
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Leonardo G. Alonso
- Instituto de Nanobiotecnología (NANOBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Daniela M. Russo
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- *Correspondence: Daniela M. Russo,
| | - Angeles Zorreguieta
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- Angeles Zorreguieta,
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29
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Elpers L, Deiwick J, Hensel M. Effect of Environmental Temperatures on Proteome Composition of Salmonella enterica Serovar Typhimurium. Mol Cell Proteomics 2022; 21:100265. [PMID: 35788066 PMCID: PMC9396072 DOI: 10.1016/j.mcpro.2022.100265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 06/17/2022] [Accepted: 06/30/2022] [Indexed: 12/29/2022] Open
Abstract
Salmonella enterica serovar Typhimurium (STM) is a major cause of gastroenteritis and transmitted by consumption of contaminated food. STM is associated to food originating from animals (pork, chicken, eggs) or plants (vegetables, fruits, nuts, and herbs). Infection of warm-blooded mammalian hosts by STM and the underlying complex regulatory network of virulence gene expression depend on various environmental conditions encountered in hosts. However, less is known about the proteome and possible regulatory networks for gene expression of STM outside the preferred host. Nutritional limitations and changes in temperature are the most obvious stresses outside the native host. Thus, we analyzed the proteome profile of STM grown in rich medium (LB medium) or minimal medium (PCN medium) at temperatures ranging from 8 °C to 37 °C. LB medium mimics the nutritional rich environment inside the host, whereas minimal PCN medium represents nutritional limitations outside the host, found during growth of fresh produce (field conditions). Further, the range of temperatures analyzed reflects conditions within natural hosts (37 °C), room temperature (20 °C), during growth under agricultural conditions (16 °C and 12 °C), and during food storage (8 °C). Implications of altered nutrient availability and growth temperature on STM proteomes were analyzed by HPLC/MS-MS and label-free quantification. Our study provides first insights into the complex adaptation of STM to various environmental temperatures, which allows STM not only to infect mammalian hosts but also to enter new infection routes that have been poorly studied so far. With the present dataset, global virulence factors, their impact on infection routes, and potential anti-infective strategies can now be investigated in detail. Especially, we were able to demonstrate functional flagella at 12 °C growth temperature for STM with an altered motility behavior.
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Affiliation(s)
- Laura Elpers
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Jörg Deiwick
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Michael Hensel
- Abt. Mikrobiologie, Universität Osnabrück, Osnabrück, Germany,CellNanOs – Center of Cellular Nanoanalytics Osnabrück, School of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany,For correspondence: Michael Hensel
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30
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Guo M, Tan S, Zhu J, Sun A, Du P, Liu X. Genes Involved in Biofilm Matrix Formation of the Food Spoiler Pseudomonas fluorescens PF07. Front Microbiol 2022; 13:881043. [PMID: 35733961 PMCID: PMC9207406 DOI: 10.3389/fmicb.2022.881043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
The extracellular matrix is essential for the biofilm formation of food spoilers. Pseudomonas fluorescens PF07 is a previous isolate from spoiled marine fish; however, the genes involved in the extracellular matrix formation of PF07 biofilms remain poorly defined. In this study, PF07 formed a wrinkled macrocolony biofilm through the high production of extracellular matrix. The genes involved in biofilm matrix formation and regulation were screened and identified by RNA-seq-dependent transcriptomic analysis and gene knock-out analysis. The macrocolony biofilms of PF07 grown for 5 days (PF07_5d) were compared with those grown for 1 day (PF07_1d). A total of 1,403 genes were significantly differentially expressed during biofilm formation. These mainly include the genes related to biofilm matrix proteins, polysaccharides, rhamnolipids, secretion system, biofilm regulation, and metabolism. Among them, functional amyloid genes fapABCDE were highly upregulated in the mature biofilm, and the operon fapA-E had a –24/–12 promoter dependent on the sigma factor RpoN. Moreover, the RNA-seq analyses of the rpoN mutant, compared with PF07, revealed 159 genes were differentially expressed in the macrocolony biofilms, and fapA-E genes were positively regulated by RpoN. In addition, the deletion mutants of fapC, rpoN, and brfA (a novel gene coding for an RpoN-dependent transcriptional regulator) were defective in forming mature macrocolony biofilms, solid surface-associated (SSA) biofilms, and pellicles, and they showed significantly reduced biofilm matrices. The fap genes were significantly downregulated in ΔbrfA, as in ΔrpoN. These findings suggest that the functional amyloid Fap is the main component of PF07 biofilm matrices, and RpoN may directly regulate the transcription of fap genes, in conjunction with BrfA. These genes may serve as potential molecular targets for screening new anti-biofilm agents or for biofilm detection in food environments.
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Affiliation(s)
- Miao Guo
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
- School of Public Health, Hangzhou Medical College, Hangzhou, China
| | - Siqi Tan
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
- School of Public Health, Hangzhou Medical College, Hangzhou, China
| | - Junli Zhu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Aihua Sun
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Peng Du
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Xiaoxiang Liu
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Xiaoxiang Liu,
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Cohen-Cymberknoh M, Kolodkin-Gal D, Keren-Paz A, Peretz S, Brumfeld V, Kapishnikov S, Suissa R, Shteinberg M, McLeod D, Maan H, Patrauchan M, Zamir G, Kerem E, Kolodkin-Gal I. Calcium carbonate mineralization is essential for biofilm formation and lung colonization. iScience 2022; 25:104234. [PMID: 35521519 PMCID: PMC9062676 DOI: 10.1016/j.isci.2022.104234] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/18/2021] [Accepted: 04/07/2022] [Indexed: 11/27/2022] Open
Abstract
Biofilms are differentiated microbial communities held together by an extracellular matrix. μCT X-ray revealed structured mineralized areas within biofilms of lung pathogens belonging to two distant phyla - the proteobacteria Pseudomonas aeruginosa and the actinobacteria Mycobacterium abscessus. Furthermore, calcium chelation inhibited the assembly of complex bacterial structures for both organisms with little to no effect on cell growth. The molecular mechanisms promoting calcite scaffold formation were surprisingly conserved between the two pathogens as biofilm development was similarly impaired by genetic and biochemical inhibition of calcium uptake and carbonate accumulation. Moreover, chemical inhibition and mutations targeting mineralization significantly reduced the attachment of P. aeruginosa to the lung, as well as the subsequent damage inflicted by biofilms to lung tissues, and restored their sensitivity to antibiotics. This work offers underexplored druggable targets for antibiotics to combat otherwise untreatable biofilm infections.
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Affiliation(s)
- Malena Cohen-Cymberknoh
- Pediatric Pulmonary Unit and Cystic fibrosis Center, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Dror Kolodkin-Gal
- Department of Experimental Surgery, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Alona Keren-Paz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- National Center for Antibiotic Resistance and Infection Control, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Shani Peretz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Vlad Brumfeld
- Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Kapishnikov
- Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Ronit Suissa
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Shteinberg
- Pulmonology Institute and CF Center, Carmel Medical Center, Haifa, Israel
| | - Daniel McLeod
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Harsh Maan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Marianna Patrauchan
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Gideon Zamir
- Department of Experimental Surgery, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eitan Kerem
- Pediatric Pulmonary Unit and Cystic fibrosis Center, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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32
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Dietler J, Gelfert R, Kaiser J, Borin V, Renzl C, Pilsl S, Ranzani AT, García de Fuentes A, Gleichmann T, Diensthuber RP, Weyand M, Mayer G, Schapiro I, Möglich A. Signal transduction in light-oxygen-voltage receptors lacking the active-site glutamine. Nat Commun 2022; 13:2618. [PMID: 35552382 PMCID: PMC9098866 DOI: 10.1038/s41467-022-30252-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 04/22/2022] [Indexed: 11/12/2022] Open
Abstract
In nature as in biotechnology, light-oxygen-voltage photoreceptors perceive blue light to elicit spatiotemporally defined cellular responses. Photon absorption drives thioadduct formation between a conserved cysteine and the flavin chromophore. An equally conserved, proximal glutamine processes the resultant flavin protonation into downstream hydrogen-bond rearrangements. Here, we report that this glutamine, long deemed essential, is generally dispensable. In its absence, several light-oxygen-voltage receptors invariably retained productive, if often attenuated, signaling responses. Structures of a light-oxygen-voltage paradigm at around 1 Å resolution revealed highly similar light-induced conformational changes, irrespective of whether the glutamine is present. Naturally occurring, glutamine-deficient light-oxygen-voltage receptors likely serve as bona fide photoreceptors, as we showcase for a diguanylate cyclase. We propose that without the glutamine, water molecules transiently approach the chromophore and thus propagate flavin protonation downstream. Signaling without glutamine appears intrinsic to light-oxygen-voltage receptors, which pertains to biotechnological applications and suggests evolutionary descendance from redox-active flavoproteins. Light-oxygen-voltage (LOV) photoreceptors perceive blue light to elicit spatio-temporally defined cellular responses, and their signalling process has been extensively characterized. Here the authors report that the light signal is still transduced in the absence of a conserved Gln residue, thought to be key.
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Affiliation(s)
- Julia Dietler
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Renate Gelfert
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Jennifer Kaiser
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Veniamin Borin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Christian Renzl
- Life and Medical Sciences (LIMES), University of Bonn, 53121, Bonn, Germany
| | - Sebastian Pilsl
- Life and Medical Sciences (LIMES), University of Bonn, 53121, Bonn, Germany
| | | | | | - Tobias Gleichmann
- Biophysical Chemistry, Humboldt-University Berlin, 10115, Berlin, Germany
| | | | - Michael Weyand
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany
| | - Günter Mayer
- Life and Medical Sciences (LIMES), University of Bonn, 53121, Bonn, Germany.,Center of Aptamer Research & Development, University of Bonn, 53121, Bonn, Germany
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, 95447, Bayreuth, Germany. .,Biophysical Chemistry, Humboldt-University Berlin, 10115, Berlin, Germany. .,Bayreuth Center for Biochemistry & Molecular Biology, Universität Bayreuth, 95447, Bayreuth, Germany. .,North-Bavarian NMR Center, Universität Bayreuth, 95447, Bayreuth, Germany.
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33
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Caniglia G, Sportelli MC, Heinzmann A, Picca RA, Valentini A, Barth H, Mizaikoff B, Cioffi N, Kranz C. Silver-fluoropolymer (Ag-CFX) films: Kinetic study of silver release, and spectroscopic-microscopic insight into the inhibition of P. fluorescens biofilm formation. Anal Chim Acta 2022; 1212:339892. [DOI: 10.1016/j.aca.2022.339892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 04/19/2022] [Accepted: 04/28/2022] [Indexed: 11/29/2022]
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Bremer E, Hoffmann T, Dempwolff F, Bedrunka P, Bange G. The many faces of the unusual biofilm activator RemA. Bioessays 2022; 44:e2200009. [PMID: 35289951 DOI: 10.1002/bies.202200009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 11/08/2022]
Abstract
Biofilms can be viewed as tissue-like structures in which microorganisms are organized in a spatial and functional sophisticated manner. Biofilm formation requires the orchestration of a highly integrated network of regulatory proteins to establish cell differentiation and production of a complex extracellular matrix. Here, we discuss the role of the essential Bacillus subtilis biofilm activator RemA. Despite intense research on biofilms, RemA is a largely underappreciated regulatory protein. RemA forms donut-shaped octamers with the potential to assemble into dimeric superstructures. The presumed DNA-binding mode suggests that RemA organizes its target DNA into nucleosome-like structures, which are the basis for its role as transcriptional activator. We discuss how RemA affects gene expression in the context of biofilm formation, and its regulatory interplay with established components of the biofilm regulatory network, such as SinR, SinI, SlrR, and SlrA. We emphasize the additional role of RemA played in nitrogen metabolism and osmotic-stress adjustment.
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Affiliation(s)
- Erhard Bremer
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Tamara Hoffmann
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Felix Dempwolff
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Patricia Bedrunka
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.,Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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35
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An Introduction to Bacterial Biofilms and Their Proteases, and Their Roles in Host Infection and Immune Evasion. Biomolecules 2022; 12:biom12020306. [PMID: 35204806 PMCID: PMC8869686 DOI: 10.3390/biom12020306] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/03/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022] Open
Abstract
Bacterial biofilms represent multicellular communities embedded in a matrix of extracellular polymeric substances, conveying increased resistance against environmental stress factors but also antibiotics. They are shaped by secreted enzymes such as proteases, which can aid pathogenicity by degrading host proteins of the connective tissue or the immune system. Importantly, both secreted proteases and the capability of biofilm formation are considered key virulence factors. In this review, we focus on the basic aspects of proteolysis and protein secretion, and highlight various secreted bacterial proteases involved in biofilm establishment and dispersal, and how they aid bacteria in immune evasion by degrading immunoglobulins and components of the complement system. Thus, secreted proteases represent not only prominent antimicrobial targets but also enzymes that can be used for dedicated applications in biotechnology and biomedicine, including their use as laundry detergents, in mass spectrometry for the glycoprofiling of antibodies, and the desensitization of donor organs intended for positive crossmatch patients.
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36
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Zhang S, Ali A, Su J, Huang T, Li M. Performance and enhancement mechanism of redox mediator for nitrate removal in immobilized bioreactor with preponderant microbes. WATER RESEARCH 2022; 209:117899. [PMID: 34861436 DOI: 10.1016/j.watres.2021.117899] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/22/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
The acceleration of nitrate removal in wastewater treatment by redox mediator (RM) is greatly weakened due to wash-out loss and mass transfer resistance (low hydrophilia) of RM during operation. In this study, an RM reactor with the fixed 1-Amino-4-hydroxyanthraquinone (AHAQ) and three core strains was established and achieved high nitrate removal efficiency (NRE) under low carbon to nitrogen ratio (C/N) and short hydraulic retention time (HRT) conditions, with the maximum efficiency of 99.41% (14.00 mg L-1 h-1) and average improvement by 11.97% (1.41 mg L-1 h-1). This acceleration led to more proportion of carbon consumption by denitrifying bacteria and improved their competitiveness against others in carbon deficiency, although resulting in nitrite accumulation (NIA) in lower C/N. The RM reactor induced the decorrelation tendencies between NRE and active extracellular organics and more sensitive denitrification toward C/N, which favored the stability of effluent organics and biological activities. The increase of oxidative phosphorylation and ubiquinone and other terpenoid-quinone biosynthesis pathway suggested electron transport activity was potentially enhanced by AHAQ. Although the lower C/N deteriorated the reactor NRE, the abundances of amino acids-, fatty acids- and carbohydrate-related metabolisms (45% of the total up-regulating pathways) were enhanced to utilize carbon source effectively. Meanwhile, the enhanced phosphotransferase system facilitated the balance between carbon and nitrogen metabolism. These indicated the changes in biological strategy to grow better and resist the adverse condition. This study highlighted the superior NRE by AHAQ in an immobilized reactor with core strains and more importantly, extended the RM application in wastewater treatment.
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Affiliation(s)
- Shuai Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Amjad Ali
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Junfeng Su
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China.
| | - Tinglin Huang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
| | - Min Li
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China; Shaanxi Key Laboratory of Environmental Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, China
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37
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Multiscale X-ray study of Bacillus subtilis biofilms reveals interlinked structural hierarchy and elemental heterogeneity. Proc Natl Acad Sci U S A 2022; 119:2118107119. [PMID: 35042817 PMCID: PMC8794879 DOI: 10.1073/pnas.2118107119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2021] [Indexed: 11/24/2022] Open
Abstract
Biofilms are multicellular, soft microbial communities that are able to colonize synthetic surfaces as well as living organisms. To survive sudden environmental changes and efficiently share their common resources, cells in a biofilm divide into subgroups with distinct functions, leading to phenotypic heterogeneity. Here, by studying intact biofilms by synchrotron X-ray diffraction and fluorescence, we revealed correlations between biofilm macroscopic, architectural heterogeneity and the spatiotemporal distribution of extracellular matrix, spores, water, and metal ions. Our findings demonstrate that biofilm heterogeneity is not only affected by local genetic expression and cellular differentiation but also by passive effects resulting from the physicochemical properties of the molecules secreted by the cells, leading to differential distribution of nutrients that propagate through macroscopic length scales. Biofilms are multicellular microbial communities that encase themselves in an extracellular matrix (ECM) of secreted biopolymers and attach to surfaces and interfaces. Bacterial biofilms are detrimental in hospital and industrial settings, but they can be beneficial, for example, in agricultural as well as in food technology contexts. An essential property of biofilms that grants them with increased survival relative to planktonic cells is phenotypic heterogeneity, the division of the biofilm population into functionally distinct subgroups of cells. Phenotypic heterogeneity in biofilms can be traced to the cellular level; however, the molecular structures and elemental distribution across whole biofilms, as well as possible linkages between them, remain unexplored. Mapping X-ray diffraction across intact biofilms in time and space, we revealed the dominant structural features in Bacillus subtilis biofilms, stemming from matrix components, spores, and water. By simultaneously following the X-ray fluorescence signal of biofilms and isolated matrix components, we discovered that the ECM preferentially binds calcium ions over other metal ions, specifically, zinc, manganese, and iron. These ions, remaining free to flow below macroscopic wrinkles that act as water channels, eventually accumulate and may possibly lead to sporulation. The possible link between ECM properties, regulation of metal ion distribution, and sporulation across whole, intact biofilms unravels the importance of molecular-level heterogeneity in shaping biofilm physiology and development.
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38
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Bellotto N, Agudo-Canalejo J, Colin R, Golestanian R, Malengo G, Sourjik V. Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions, and cell growth. eLife 2022; 11:82654. [PMID: 36468683 PMCID: PMC9810338 DOI: 10.7554/elife.82654] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Inside prokaryotic cells, passive translational diffusion typically limits the rates with which cytoplasmic proteins can reach their locations. Diffusion is thus fundamental to most cellular processes, but the understanding of protein mobility in the highly crowded and non-homogeneous environment of a bacterial cell is still limited. Here, we investigated the mobility of a large set of proteins in the cytoplasm of Escherichia coli, by employing fluorescence correlation spectroscopy (FCS) combined with simulations and theoretical modeling. We conclude that cytoplasmic protein mobility could be well described by Brownian diffusion in the confined geometry of the bacterial cell and at the high viscosity imposed by macromolecular crowding. We observed similar size dependence of protein diffusion for the majority of tested proteins, whether native or foreign to E. coli. For the faster-diffusing proteins, this size dependence is well consistent with the Stokes-Einstein relation once taking into account the specific dumbbell shape of protein fusions. Pronounced subdiffusion and hindered mobility are only observed for proteins with extensive interactions within the cytoplasm. Finally, while protein diffusion becomes markedly faster in actively growing cells, at high temperature, or upon treatment with rifampicin, and slower at high osmolarity, all of these perturbations affect proteins of different sizes in the same proportions, which could thus be described as changes of a well-defined cytoplasmic viscosity.
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Affiliation(s)
- Nicola Bellotto
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | | | - Remy Colin
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-OrganizationGöttingenGermany,Rudolf Peierls Centre for Theoretical Physics, University of OxfordOxfordUnited Kingdom
| | - Gabriele Malengo
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
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Giacomodonato MN, Sarnacki SH, Aya Castañeda MDR, Garófalo AN, Betancourt DM, Cerquetti MC, Noto Llana M. Salmonella enterica serovar Enteritidis biofilm lifestyle induces lower pathogenicity and reduces inflammatory response in a murine model compared to planktonic bacteria. Rev Argent Microbiol 2021; 54:166-174. [PMID: 34961640 DOI: 10.1016/j.ram.2021.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/28/2021] [Accepted: 10/04/2021] [Indexed: 12/23/2022] Open
Abstract
Salmonellaenterica serovar Enteritidis (S. Enteritidis) is the most frequent serovar involved in human salmonellosis. It has been demonstrated that about 80% of infections are related to biofilm formation. There is scant information about the pathogenicity of S. Enteritidis and its relationship to biofilm production. In this regard, this study aimed to investigate the differential host response induced by S. Enteritidis biofilm and planktonic lifestyle. To this purpose, biofilm and planktonic bacteria were inoculated to BALB/c mice and epithelial cell culture. Survival studies revealed that biofilm is less virulent than planktonic cells. Reduced signs of intestinal inflammation and lower bacterial translocation were observed in animals inoculated with Salmonella biofilm compared to the planktonic group. Results showed that Salmonella biofilm was impaired for invasion of non-phagocytic cells and induces a lower inflammatory response in vivo and in vitro compared to that of planktonic bacteria. Taken together, the outcome of Salmonella-host interaction varies depending on the bacterial lifestyle.
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Affiliation(s)
- Mónica N Giacomodonato
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM-UBA-CONICET), Buenos Aires, Argentina; Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sebastián H Sarnacki
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM-UBA-CONICET), Buenos Aires, Argentina; Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Del Rosario Aya Castañeda
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM-UBA-CONICET), Buenos Aires, Argentina; Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ailín N Garófalo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM-UBA-CONICET), Buenos Aires, Argentina; Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Diana M Betancourt
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM-UBA-CONICET), Buenos Aires, Argentina; Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María C Cerquetti
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM-UBA-CONICET), Buenos Aires, Argentina; Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariángeles Noto Llana
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM-UBA-CONICET), Buenos Aires, Argentina; Departamento de Microbiología, Parasitología e Inmunología, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina.
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40
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Lee SS, Laganenka L, Du X, Hardt WD, Ferguson SJ. Silicon Nitride, a Bioceramic for Bone Tissue Engineering: A Reinforced Cryogel System With Antibiofilm and Osteogenic Effects. Front Bioeng Biotechnol 2021; 9:794586. [PMID: 34976982 PMCID: PMC8714913 DOI: 10.3389/fbioe.2021.794586] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/08/2021] [Indexed: 01/05/2023] Open
Abstract
Silicon nitride (SiN [Si3N4]) is a promising bioceramic for use in a wide variety of orthopedic applications. Over the past decades, it has been mainly used in industrial applications, such as space shuttle engines, but not in the medical field due to scarce data on the biological effects of SiN. More recently, it has been increasingly identified as an emerging material for dental and orthopedic implant applications. Although a few reports about the antibacterial properties and osteoconductivity of SiN have been published to date, there have been limited studies of SiN-based scaffolds for bone tissue engineering. Here, we developed a silicon nitride reinforced gelatin/chitosan cryogel system (SiN-GC) by loading silicon nitride microparticles into a gelatin/chitosan cryogel (GC), with the aim of producing a biomimetic scaffold with antibiofilm and osteogenic properties. In this scaffold system, the GC component provides a hydrophilic and macroporous environment for cells, while the SiN component not only provides antibacterial properties and osteoconductivity but also increases the mechanical stiffness of the scaffold. This provides enhanced mechanical support for the defect area and a better osteogenic environment. First, we analyzed the scaffold characteristics of SiN-GC with different SiN concentrations, followed by evaluation of its apatite-forming capacity in simulated body fluid and protein adsorption capacity. We further confirmed an antibiofilm effect of SiN-GC against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) as well as enhanced cell proliferation, mineralization, and osteogenic gene upregulation for MC3T3-E1 pre-osteoblast cells. Finally, we developed a bioreactor to culture cell-laden scaffolds under cyclic compressive loading to mimic physiological conditions and were able to demonstrate improved mineralization and osteogenesis from SiN-GC. Overall, we confirmed the antibiofilm and osteogenic effect of a silicon nitride reinforced cryogel system, and the results indicate that silicon nitride as a biomaterial system component has a promising potential to be developed further for bone tissue engineering applications.
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Affiliation(s)
- Seunghun S. Lee
- Department of Health Sciences and Technology, Institute for Biomechanics, ETH Zurich, Zurich, Switzerland
| | - Leanid Laganenka
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Xiaoyu Du
- Department of Health Sciences and Technology, Institute for Biomechanics, ETH Zurich, Zurich, Switzerland
| | - Wolf-Dietrich Hardt
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Stephen J. Ferguson
- Department of Health Sciences and Technology, Institute for Biomechanics, ETH Zurich, Zurich, Switzerland
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41
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Choong FX, Huzell S, Rosenberg M, Eckert JA, Nagaraj M, Zhang T, Melican K, Otzen DE, Richter-Dahlfors A. A semi high-throughput method for real-time monitoring of curli producing Salmonella biofilms on air-solid interfaces. Biofilm 2021; 3:100060. [PMID: 34841245 PMCID: PMC8605384 DOI: 10.1016/j.bioflm.2021.100060] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 11/24/2022] Open
Abstract
Biofilms enable bacteria to colonize numerous ecological niches. Bacteria within a biofilm are protected by the extracellular matrix (ECM), of which the fibril-forming amyloid protein curli and polysaccharide cellulose are major components in members of Salmonella, Eschericha and Mycobacterium genus. A shortage of real-time detection methods has limited our understanding of how ECM production contributes to biofilm formation and pathogenicity. Here we present optotracing as a new semi-high throughput method for dynamic monitoring of Salmonella biofilm growth on air-solid interfaces. We show how an optotracer with binding-induced fluorescence acts as a dynamic fluorescent reporter of curli expression during biofilm formation on agar. Using spectrophotometry and microscopic imaging of fluorescence, we analyse in real-time the development of the curli architecture in relation to bacterial cells. With exceptional spatial and temporal precision, this revealed a well-structured, non-uniform distribution of curli organised in distally projecting radial channel patterns. Dynamic monitoring of the biofilm also showed defined regions undergoing different growth phases. ECM structures were found to assemble in regions of late exponential growth phase, suggesting that ECM forms on site after bacteria colonize the surface. As the optotracer biofilm method expedites screening of curli production, providing exceptional spatial-temporal understanding of the surface-associated biofilm lifestyle, this method adds a new technique to further our understanding of bacterial biofilms. Design and evaluation of a method for real-time biofilm experimentation. Optotracing enables real-time monitoring of biofilm formation on solid supports. Definitive biofilm monitoring by selective tracking of ECM components. A method reducing the inherent biases of morphotyping. A semi-high throughput method increasing the ease and efficiency of biofilm detection.
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Affiliation(s)
- Ferdinand X Choong
- AIMES - Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Smilla Huzell
- AIMES - Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ming Rosenberg
- AIMES - Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Johannes A Eckert
- AIMES - Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Madhu Nagaraj
- iNANO and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Tianqi Zhang
- AIMES - Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Keira Melican
- AIMES - Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Daniel E Otzen
- iNANO and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Agneta Richter-Dahlfors
- AIMES - Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
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42
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Fang Y, Visvalingam J, Zhang P, Yang X. Biofilm formation by Non-O157 Shiga toxin-producing Escherichia coli in monocultures and co-cultures with meat processing surface bacteria. Food Microbiol 2021; 102:103902. [PMID: 34809934 DOI: 10.1016/j.fm.2021.103902] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 08/10/2021] [Accepted: 09/10/2021] [Indexed: 11/04/2022]
Abstract
This study investigated the impact of meat processing surface bacteria (MPB) on biofilm formation by non-O157 Shiga toxin-producing Escherichia coli (STEC), and potential links between biofilm formation by STEC and biofilm-related genes in their genomes. Biofilm development by 50 MPB and 6 STEC strains in mono- and co-cultures was assessed by the crystal violet staining method, and their expression of curli and cellulose was determined using the Congo red agar method. Genes (n = 141) associated with biofilm formation in the STEC strains were profiled. Biofilm formation in general correlated with cellulose and curli expression in both mono- and co-cultures. Most MPB strains had antagonistic effects on the biofilm formation of the STEC strains. Of the genes investigated, 81% were common among the STEC strains and there seems to be a gene-redundancy in biofilm formation. The inability of the O26 strain to form biofilms could be due to mutations in the rpoS gene. Truncation in the mlrA gene in the O145 strain seems not affecting its biofilm formation alone or with MPB. The O45 strain, despite having the greatest number of biofilm-related genes, did not form measurable biofilms. Overall, biofilm formation of STEC was affected by curli-cellulose expression and companion strains.
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Affiliation(s)
- Yuan Fang
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, Alberta, T4L 1W1, Canada
| | - Jeyachchandran Visvalingam
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, Alberta, T4L 1W1, Canada
| | - Peipei Zhang
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, Alberta, T4L 1W1, Canada
| | - Xianqin Yang
- Agriculture and Agri-Food Canada Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, Alberta, T4L 1W1, Canada.
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43
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Colin R, Ni B, Laganenka L, Sourjik V. Multiple functions of flagellar motility and chemotaxis in bacterial physiology. FEMS Microbiol Rev 2021; 45:fuab038. [PMID: 34227665 PMCID: PMC8632791 DOI: 10.1093/femsre/fuab038] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/02/2021] [Indexed: 12/13/2022] Open
Abstract
Most swimming bacteria are capable of following gradients of nutrients, signaling molecules and other environmental factors that affect bacterial physiology. This tactic behavior became one of the most-studied model systems for signal transduction and quantitative biology, and underlying molecular mechanisms are well characterized in Escherichia coli and several other model bacteria. In this review, we focus primarily on less understood aspect of bacterial chemotaxis, namely its physiological relevance for individual bacterial cells and for bacterial populations. As evident from multiple recent studies, even for the same bacterial species flagellar motility and chemotaxis might serve multiple roles, depending on the physiological and environmental conditions. Among these, finding sources of nutrients and more generally locating niches that are optimal for growth appear to be one of the major functions of bacterial chemotaxis, which could explain many chemoeffector preferences as well as flagellar gene regulation. Chemotaxis might also generally enhance efficiency of environmental colonization by motile bacteria, which involves intricate interplay between individual and collective behaviors and trade-offs between growth and motility. Finally, motility and chemotaxis play multiple roles in collective behaviors of bacteria including swarming, biofilm formation and autoaggregation, as well as in their interactions with animal and plant hosts.
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Affiliation(s)
- Remy Colin
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
| | - Bin Ni
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
- College of Resources and Environmental Science, National Academy of Agriculture Green Development, China Agricultural University, Yuanmingyuan Xilu No. 2, Beijing 100193, China
| | - Leanid Laganenka
- Institute of Microbiology, D-BIOL, ETH Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
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44
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Díaz-Pascual F, Lempp M, Nosho K, Jeckel H, Jo JK, Neuhaus K, Hartmann R, Jelli E, Hansen MF, Price-Whelan A, Dietrich LEP, Link H, Drescher K. Spatial alanine metabolism determines local growth dynamics of Escherichia coli colonies. eLife 2021; 10:e70794. [PMID: 34751128 PMCID: PMC8579308 DOI: 10.7554/elife.70794] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/18/2021] [Indexed: 12/17/2022] Open
Abstract
Bacteria commonly live in spatially structured biofilm assemblages, which are encased by an extracellular matrix. Metabolic activity of the cells inside biofilms causes gradients in local environmental conditions, which leads to the emergence of physiologically differentiated subpopulations. Information about the properties and spatial arrangement of such metabolic subpopulations, as well as their interaction strength and interaction length scales are lacking, even for model systems like Escherichia coli colony biofilms grown on agar-solidified media. Here, we use an unbiased approach, based on temporal and spatial transcriptome and metabolome data acquired during E. coli colony biofilm growth, to study the spatial organization of metabolism. We discovered that alanine displays a unique pattern among amino acids and that alanine metabolism is spatially and temporally heterogeneous. At the anoxic base of the colony, where carbon and nitrogen sources are abundant, cells secrete alanine via the transporter AlaE. In contrast, cells utilize alanine as a carbon and nitrogen source in the oxic nutrient-deprived region at the colony mid-height, via the enzymes DadA and DadX. This spatially structured alanine cross-feeding influences cellular viability and growth in the cross-feeding-dependent region, which shapes the overall colony morphology. More generally, our results on this precisely controllable biofilm model system demonstrate a remarkable spatiotemporal complexity of metabolism in biofilms. A better characterization of the spatiotemporal metabolic heterogeneities and dependencies is essential for understanding the physiology, architecture, and function of biofilms.
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Affiliation(s)
| | - Martin Lempp
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
| | - Kazuki Nosho
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
| | - Hannah Jeckel
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Department of Physics,
Philipps-Universität MarburgMarburgGermany
- Biozentrum, University of
BaselBaselSwitzerland
| | - Jeanyoung K Jo
- Department of Biological Sciences,
Columbia UniversityNew YorkUnited
States
| | - Konstantin Neuhaus
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Department of Physics,
Philipps-Universität MarburgMarburgGermany
- Biozentrum, University of
BaselBaselSwitzerland
| | - Raimo Hartmann
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
| | - Eric Jelli
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Department of Physics,
Philipps-Universität MarburgMarburgGermany
| | | | - Alexa Price-Whelan
- Department of Biological Sciences,
Columbia UniversityNew YorkUnited
States
| | - Lars EP Dietrich
- Department of Biological Sciences,
Columbia UniversityNew YorkUnited
States
| | - Hannes Link
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Interfaculty Institute for Microbiology
and Infection Medicine, Eberhard Karls Universität
TübingenTübingenGermany
| | - Knut Drescher
- Max Planck Institute for Terrestrial
MicrobiologyMarburgGermany
- Department of Physics,
Philipps-Universität MarburgMarburgGermany
- Biozentrum, University of
BaselBaselSwitzerland
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45
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Richter AM, Buchberger G, Stifter D, Duchoslav J, Hertwig A, Bonse J, Heitz J, Schwibbert K. Spatial Period of Laser-Induced Surface Nanoripples on PET Determines Escherichia coli Repellence. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:3000. [PMID: 34835763 PMCID: PMC8624992 DOI: 10.3390/nano11113000] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 12/18/2022]
Abstract
Bacterial adhesion and biofilm formation on surfaces are associated with persistent microbial contamination, biofouling, and the emergence of resistance, thus, calling for new strategies to impede bacterial surface colonization. Using ns-UV laser treatment (wavelength 248 nm and a pulse duration of 20 ns), laser-induced periodic surface structures (LIPSS) featuring different sub-micrometric periods ranging from ~210 to ~610 nm were processed on commercial poly(ethylene terephthalate) (PET) foils. Bacterial adhesion tests revealed that these nanorippled surfaces exhibit a repellence for E. coli that decisively depends on the spatial periods of the LIPSS with the strongest reduction (~91%) in cell adhesion observed for LIPSS periods of 214 nm. Although chemical and structural analyses indicated a moderate laser-induced surface oxidation, a significant influence on the bacterial adhesion was ruled out. Scanning electron microscopy and additional biofilm studies using a pili-deficient E. coli TG1 strain revealed the role of extracellular appendages in the bacterial repellence observed here.
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Affiliation(s)
- Anja M. Richter
- Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 87, 12205 Berlin, Germany; (A.H.); (J.B.); (K.S.)
| | - Gerda Buchberger
- Institute of Applied Physics, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria; (J.H.)
| | - David Stifter
- Center for Surface and Nanoanalytics, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria; (D.S.); (J.D.)
| | - Jiri Duchoslav
- Center for Surface and Nanoanalytics, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria; (D.S.); (J.D.)
| | - Andreas Hertwig
- Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 87, 12205 Berlin, Germany; (A.H.); (J.B.); (K.S.)
| | - Jörn Bonse
- Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 87, 12205 Berlin, Germany; (A.H.); (J.B.); (K.S.)
| | - Johannes Heitz
- Institute of Applied Physics, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria; (J.H.)
| | - Karin Schwibbert
- Bundesanstalt für Materialforschung und -prüfung (BAM), Unter den Eichen 87, 12205 Berlin, Germany; (A.H.); (J.B.); (K.S.)
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46
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Mangioni SE, dell'Erba MG, Combi B. Structure formation in a conserved mass model of a set of individuals interacting with attractive and repulsive forces. Phys Rev E 2021; 104:014212. [PMID: 34412252 DOI: 10.1103/physreve.104.014212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 06/29/2021] [Indexed: 11/07/2022]
Abstract
We study a set of interacting individuals that conserve their total mass. In order to describe its dynamics we resort to mesoscopic equations of reaction diffusion including currents driven by attractive and repulsive forces. For the mass conservation we consider a linear response parameter that maintains the mass in the vicinity of a optimal value which is determined by the set. We use the reach and intensity of repulsive forces as control parameters. When sweeping a wide range of parameter space we find a great diversity of localized structures, stationary as well as other ones with cyclical and chaotic dynamics. We compare our results with real situations.
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Affiliation(s)
- Sergio E Mangioni
- IFIMAR (Universidad Nacional de Mar del Plata and CONICET), Deán Funes 3350, B7602AYL Mar del Plata, Argentina
| | - Matías G dell'Erba
- IFIMAR (Universidad Nacional de Mar del Plata and CONICET), Deán Funes 3350, B7602AYL Mar del Plata, Argentina
| | - Bruno Combi
- IFIMAR (Universidad Nacional de Mar del Plata and CONICET), Deán Funes 3350, B7602AYL Mar del Plata, Argentina
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47
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Samrot AV, Abubakar Mohamed A, Faradjeva E, Si Jie L, Hooi Sze C, Arif A, Chuan Sean T, Norbert Michael E, Yeok Mun C, Xiao Qi N, Ling Mok P, Kumar SS. Mechanisms and Impact of Biofilms and Targeting of Biofilms Using Bioactive Compounds-A Review. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:839. [PMID: 34441045 PMCID: PMC8401077 DOI: 10.3390/medicina57080839] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/10/2021] [Indexed: 12/31/2022]
Abstract
Biofilms comprising aggregates of microorganisms or multicellular communities have been a major issue as they cause resistance against antimicrobial agents and biofouling. To date, numerous biofilm-forming microorganisms have been identified, which have been shown to result in major effects including biofouling and biofilm-related infections. Quorum sensing (which describes the cell communication within biofilms) plays a vital role in the regulation of biofilm formation and its virulence. As such, elucidating the various mechanisms responsible for biofilm resistance (including quorum sensing) will assist in developing strategies to inhibit and control the formation of biofilms in nature. Employing biological control measures (such as the use of bioactive compounds) in targeting biofilms is of great interest since they naturally possess antimicrobial activity among other favorable attributes and can also possibly act as potent antibiofilm agents. As an effort to re-establish the current notion and understanding of biofilms, the present review discuss the stages involved in biofilm formation, the factors contributing to its development, the effects of biofilms in various industries, and the use of various bioactive compounds and their strategies in biofilm inhibition.
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Affiliation(s)
- Antony V. Samrot
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Amira Abubakar Mohamed
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Etel Faradjeva
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Lee Si Jie
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Chin Hooi Sze
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Akasha Arif
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Tan Chuan Sean
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Emmanuel Norbert Michael
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Chua Yeok Mun
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Ng Xiao Qi
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Pooi Ling Mok
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Suresh S. Kumar
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Department of Biotechnology, Bharath Institute of Higher Education and Research, Agharam Road Selaiyur, Chennai 600 073, Tamil Nadu, India
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48
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Serra DO, Hengge R. Bacterial Multicellularity: The Biology of Escherichia coli Building Large-Scale Biofilm Communities. Annu Rev Microbiol 2021; 75:269-290. [PMID: 34343018 DOI: 10.1146/annurev-micro-031921-055801] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biofilms are a widespread multicellular form of bacterial life. The spatial structure and emergent properties of these communities depend on a polymeric extracellular matrix architecture that is orders of magnitude larger than the cells that build it. Using as a model the wrinkly macrocolony biofilms of Escherichia coli, which contain amyloid curli fibers and phosphoethanolamine (pEtN)-modified cellulose as matrix components, we summarize here the structure, building, and function of this large-scale matrix architecture. Based on different sigma and other transcription factors as well as second messengers, the underlying regulatory network reflects the fundamental trade-off between growth and survival. It controls matrix production spatially in response to long-range chemical gradients, but it also generates distinct patterns of short-range matrix heterogeneity that are crucial for tissue-like elasticity and macroscopic morphogenesis. Overall, these biofilms confer protection and a potential for homeostasis, thereby reducing maintenance energy, which makes multicellularity an emergent property of life itself. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Diego O Serra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Rosario (UNR), 2000 Rosario, Argentina
| | - Regine Hengge
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany;
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49
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Xu Q, Hu X, Wang Y. Alternatives to Conventional Antibiotic Therapy: Potential Therapeutic Strategies of Combating Antimicrobial-Resistance and Biofilm-Related Infections. Mol Biotechnol 2021; 63:1103-1124. [PMID: 34309796 DOI: 10.1007/s12033-021-00371-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/08/2021] [Indexed: 12/14/2022]
Abstract
Antibiotics have been denoted as the orthodox therapeutic agents for fighting bacteria-related infections in clinical practices for decades. Nevertheless, overuse of antibiotics has led to the upsurge of species with antimicrobial resistance (AMR) or multi-drug resistance. Bacteria can also grow into the biofilm, which accounts for at least two-thirds of infections. Distinct gene expression and self-produced heterogeneous hydrated extracellular polymeric substance matrix architecture of biofilm contribute to their tolerance and externally manifest as antibiotic resistance. In this review, the difficulties in combating biofilm formation and AMR are introduced, and novel alternatives to antibiotics such as metal nanoparticles and quaternary ammonium compounds, chitosan and its derivatives, antimicrobial peptides, stimuli-responsive materials, phage therapy and other therapeutic strategies, from compounds to hydrogel, from inorganic to biological, are discussed. We expect to provide useful information for the readers who are seeking for solutions to the problem of AMR and biofilm-related infections.
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Affiliation(s)
- Qian Xu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China
| | - Xuefeng Hu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.
| | - Yunbing Wang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610065, Sichuan, People's Republic of China.
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50
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Bond MC, Vidakovic L, Singh PK, Drescher K, Nadell CD. Matrix-trapped viruses can prevent invasion of bacterial biofilms by colonizing cells. eLife 2021; 10:65355. [PMID: 34240700 PMCID: PMC8346279 DOI: 10.7554/elife.65355] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 07/08/2021] [Indexed: 12/19/2022] Open
Abstract
Bacteriophages can be trapped in the matrix of bacterial biofilms, such that the cells inside them are protected. It is not known whether these phages are still infectious and whether they pose a threat to newly arriving bacteria. Here, we address these questions using Escherichia coli and its lytic phage T7. Prior work has demonstrated that T7 phages are bound in the outermost curli polymer layers of the E. coli biofilm matrix. We show that these phages do remain viable and can kill colonizing cells that are T7-susceptible. If cells colonize a resident biofilm before phages do, we find that they can still be killed by phage exposure if it occurs soon thereafter. However, if colonizing cells are present on the biofilm long enough before phage exposure, they gain phage protection via envelopment within curli-producing clusters of the resident biofilm cells.
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Affiliation(s)
- Matthew C Bond
- Department of Biological Sciences, Dartmouth College, Hanover, United States
| | - Lucia Vidakovic
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Praveen K Singh
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.,Department of Physics, Philipps University Marburg, Marburg, Germany.,Biozentrum, University of Basel, Basel, Switzerland
| | - Carey D Nadell
- Department of Biological Sciences, Dartmouth College, Hanover, United States
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