351
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Metabolic flux analyses of Pseudomonas aeruginosa cystic fibrosis isolates. Metab Eng 2016; 38:251-263. [PMID: 27637318 DOI: 10.1016/j.ymben.2016.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/07/2016] [Accepted: 09/11/2016] [Indexed: 01/22/2023]
Abstract
Pseudomonas aeruginosa is a metabolically versatile wide-ranging opportunistic pathogen. In humans P. aeruginosa causes infections of the skin, urinary tract, blood, and the lungs of Cystic Fibrosis patients. In addition, P. aeruginosa's broad environmental distribution, relatedness to biotechnologically useful species, and ability to form biofilms have made it the focus of considerable interest. We used 13C metabolic flux analysis (MFA) and flux balance analysis to understand energy and redox production and consumption and to explore the metabolic phenotypes of one reference strain and five strains isolated from the lungs of cystic fibrosis patients. Our results highlight the importance of the oxidative pentose phosphate and Entner-Doudoroff pathways in P. aeruginosa growth. Among clinical strains we report two divergent metabolic strategies and identify changes between genetically related strains that have emerged during a chronic infection of the same patient. MFA revealed that the magnitude of fluxes through the glyoxylate cycle correlates with growth rates.
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352
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Abstract
Microbial adaptation is conspicuous in essentially every environment, but the mechanisms of adaptive evolution are poorly understood. Studying evolution in the laboratory under controlled conditions can be a tractable approach, particularly when new, discernible phenotypes evolve rapidly. This is especially the case in the spatially structured environments of biofilms, which promote the occurrence and stability of new, heritable phenotypes. Further, diversity in biofilms can give rise to nascent social interactions among coexisting mutants and enable the study of the emerging field of sociomicrobiology. Here, we review findings from laboratory evolution experiments with either Pseudomonas fluorescens or Burkholderia cenocepacia in spatially structured environments that promote biofilm formation. In both systems, ecotypes with overlapping niches evolve and produce competitive or facilitative interactions that lead to novel community attributes, demonstrating the parallelism of adaptive processes captured in the lab.
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353
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Abstract
The advent of microscale technologies, such as microfluidics, has revolutionized many areas of biology yet has only recently begun to impact the field of bacterial biofilms. By enabling accurate control and manipulation of physical and chemical conditions, these new microscale approaches afford the ability to combine important features of natural and artificial microbial habitats, such as fluid flow and ephemeral nutrient sources, with an unprecedented level of flexibility and quantification. Here, we review selected case studies to exemplify this potential, discuss limitations, and suggest that this approach opens new vistas into biofilm research over traditional setups, allowing us to expand our understanding of the formation and consequences of biofilms in a broad range of environments and applications.
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354
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Abstract
Nitric oxide (NO) is a freely diffusible, radical gas that has now been established as an integral signaling molecule in eukaryotes and bacteria. It has been demonstrated that NO signaling is initiated upon ligation to the heme iron of an H-NOX domain in mammals and in some bacteria. Bacterial H-NOX proteins have been found to interact with enzymes that participate in signaling pathways and regulate bacterial processes such as quorum sensing, biofilm formation, and symbiosis. Here, we review the biochemical characterization of these signaling pathways and, where available, describe how ligation of NO to H-NOX specifically regulates the activity of these pathways and their associated bacterial phenotypes.
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Affiliation(s)
- Lisa-Marie Nisbett
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, NY, 11794-3400
| | - Elizabeth M. Boon
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400
- Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, NY, 11794-3400
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, NY, 11794-3400
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355
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Liu S, Gunawan C, Barraud N, Rice SA, Harry EJ, Amal R. Understanding, Monitoring, and Controlling Biofilm Growth in Drinking Water Distribution Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:8954-8976. [PMID: 27479445 DOI: 10.1021/acs.est.6b00835] [Citation(s) in RCA: 192] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In drinking water distribution systems (DWDS), biofilms are the predominant mode of microbial growth, with the presence of extracellular polymeric substance (EPS) protecting the biomass from environmental and shear stresses. Biofilm formation poses a significant problem to the drinking water industry as a potential source of bacterial contamination, including pathogens, and, in many cases, also affecting the taste and odor of drinking water and promoting the corrosion of pipes. This article critically reviews important research findings on biofilm growth in DWDS, examining the factors affecting their formation and characteristics as well as the various technologies to characterize and monitor and, ultimately, to control their growth. Research indicates that temperature fluctuations potentially affect not only the initial bacteria-to-surface attachment but also the growth rates of biofilms. For the latter, the effect is unique for each type of biofilm-forming bacteria; ammonia-oxidizing bacteria, for example, grow more-developed biofilms at a typical summer temperature of 22 °C compared to 12 °C in fall, and the opposite occurs for the pathogenic Vibrio cholerae. Recent investigations have found the formation of thinner yet denser biofilms under high and turbulent flow regimes of drinking water, in comparison to the more porous and loosely attached biofilms at low flow rates. Furthermore, in addition to the rather well-known tendency of significant biofilm growth on corrosion-prone metal pipes, research efforts also found leaching of growth-promoting organic compounds from the increasingly popular use of polymer-based pipes. Knowledge of the unique microbial members of drinking water biofilms and, importantly, the influence of water characteristics and operational conditions on their growth can be applied to optimize various operational parameters to minimize biofilm accumulation. More-detailed characterizations of the biofilm population size and structure are now feasible with fluorescence microscopy (epifluorescence and CLSM imaging with DNA, RNA, EPS, and protein and lipid stains) and electron microscopy imaging (ESEM). Importantly, thorough identification of microbial fingerprints in drinking water biofilms is achievable with DNA sequencing techniques (the 16S rRNA gene-based identification), which have revealed a prevalence of previously undetected bacterial members. Technologies are now moving toward in situ monitoring of biomass growth in distribution networks, including the development of optical fibers capable of differentiating biomass from chemical deposits. Taken together, management of biofilm growth in water distribution systems requires an integrated approach, starting from the treatment of water prior to entering the networks to the potential implementation of "biofilm-limiting" operational conditions and, finally, ending with the careful selection of available technologies for biofilm monitoring and control. For the latter, conventional practices, including chlorine-chloramine disinfection, flushing of DWDS, nutrient removal, and emerging technologies are discussed with their associated challenges.
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Affiliation(s)
| | - Cindy Gunawan
- ithree institute, University of Technology Sydney , Sydney, NSW 2007, Australia
| | - Nicolas Barraud
- Department of Microbiology, Genetics of Biofilms Unit, Institut Pasteur , Paris 75015, France
| | - Scott A Rice
- The Singapore Centre for Environmental Life Sciences Engineering and School of Biological Sciences, Nanyang Technological University , 639798, Singapore
| | - Elizabeth J Harry
- ithree institute, University of Technology Sydney , Sydney, NSW 2007, Australia
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356
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Parnasa R, Nagar E, Sendersky E, Reich Z, Simkovsky R, Golden S, Schwarz R. Small secreted proteins enable biofilm development in the cyanobacterium Synechococcus elongatus. Sci Rep 2016; 6:32209. [PMID: 27558743 PMCID: PMC4997328 DOI: 10.1038/srep32209] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 08/03/2016] [Indexed: 11/18/2022] Open
Abstract
Small proteins characterized by a double-glycine (GG) secretion motif, typical of secreted bacterial antibiotics, are encoded by the genomes of diverse cyanobacteria, but their functions have not been investigated to date. Using a biofilm-forming mutant of Synechococcus elongatus PCC 7942 and a mutational approach, we demonstrate the involvement of four small secreted proteins and their GG-secretion motifs in biofilm development. These proteins are denoted EbfG1-4 (enable biofilm formation with a GG-motif). Furthermore, the conserved cysteine of the peptidase domain of the Synpcc7942_1133 gene product (dubbed PteB for peptidase transporter essential for biofilm) is crucial for biofilm development and is required for efficient secretion of the GG-motif containing proteins. Transcriptional profiling of ebfG1-4 indicated elevated transcript levels in the biofilm-forming mutant compared to wild type (WT). However, these transcripts decreased, acutely but transiently, when the mutant was cultured in extracellular fluids from a WT culture, and biofilm formation was inhibited. We propose that WT cells secrete inhibitor(s) that suppress transcription of ebfG1-4, whereas secretion of the inhibitor(s) is impaired in the biofilm-forming mutant, leading to synthesis and secretion of EbfG1-4 and supporting the formation of biofilms.
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Affiliation(s)
- Rami Parnasa
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Elad Nagar
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Eleonora Sendersky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Ziv Reich
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ryan Simkovsky
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan Golden
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
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357
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Freidman BL, Gras SL, Snape I, Stevens GW, Mumford KA. The performance of ammonium exchanged zeolite for the biodegradation of petroleum hydrocarbons migrating in soil water. JOURNAL OF HAZARDOUS MATERIALS 2016; 313:272-282. [PMID: 27132074 DOI: 10.1016/j.jhazmat.2016.03.095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/30/2016] [Accepted: 03/31/2016] [Indexed: 06/05/2023]
Abstract
Nitrogen deficiency has been identified as the main inhibiting factor for biodegradation of petroleum hydrocarbons in low nutrient environments. This study examines the performance of ammonium exchanged zeolite to enhance biodegradation of petroleum hydrocarbons migrating in soil water within laboratory scale flow cells. Biofilm formation and biodegradation were accelerated by the exchange of cations in soil water with ammonium in the pores of the exchanged zeolite when compared with natural zeolite flow cells. These results have implications for sequenced permeable reactive barrier design and the longevity of media performance within such barriers at petroleum hydrocarbon contaminated sites deficient in essential soil nutrients.
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Affiliation(s)
- Benjamin L Freidman
- Particulate Fluids Processing Centre, Department of Chemical and Biomolecular Engineering, The University of Melbourne, VIC 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, VIC 3010, Australia
| | - Sally L Gras
- Particulate Fluids Processing Centre, Department of Chemical and Biomolecular Engineering, The University of Melbourne, VIC 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, VIC 3010, Australia; The ARC Dairy Innovation Hub, The University of Melbourne, VIC 3010, Australia
| | - Ian Snape
- Australian Antarctic Division, Channel Highway, Kingston, Tasmania 7050, Australia
| | - Geoff W Stevens
- Particulate Fluids Processing Centre, Department of Chemical and Biomolecular Engineering, The University of Melbourne, VIC 3010, Australia
| | - Kathryn A Mumford
- Particulate Fluids Processing Centre, Department of Chemical and Biomolecular Engineering, The University of Melbourne, VIC 3010, Australia.
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358
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Minh Tran T, MacIntyre A, Khokhani D, Hawes M, Allen C. Extracellular DNases of Ralstonia solanacearum modulate biofilms and facilitate bacterial wilt virulence. Environ Microbiol 2016; 18:4103-4117. [PMID: 27387368 DOI: 10.1111/1462-2920.13446] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/01/2016] [Indexed: 12/21/2022]
Abstract
Ralstonia solanacearum is a soil-borne vascular pathogen that colonizes plant xylem vessels, a flowing, low-nutrient habitat where biofilms could be adaptive. Ralstonia solanacearum forms biofilm in vitro, but it was not known if the pathogen benefits from biofilms during infection. Scanning electron microscopy revealed that during tomato infection, R. solanacearum forms biofilm-like masses in xylem vessels. These aggregates contain bacteria embedded in a matrix including chromatin-like fibres commonly observed in other bacterial biofilms. Chemical and enzymatic assays demonstrated that the bacterium releases extracellular DNA in culture and that DNA is an integral component of the biofilm matrix. An R. solanacearum mutant lacking the pathogen's two extracellular nucleases (exDNases) formed non-spreading colonies and abnormally thick biofilms in vitro. The biofilms formed by the exDNase mutant in planta contained more and thicker fibres. This mutant was also reduced in virulence on tomato plants and did not spread in tomato stems as well as the wild-type strain, suggesting that these exDNases facilitate biofilm maturation and bacterial dispersal. To our knowledge, this is the first demonstration that R. solanacearum forms biofilms in plant xylem vessels, and the first documentation that plant pathogens use DNases to modulate their biofilm structure for systemic spread and virulence.
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Affiliation(s)
- Tuan Minh Tran
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - April MacIntyre
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Devanshi Khokhani
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Martha Hawes
- Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ, 85721, USA
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, 53706, USA
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359
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Gu H, Chen A, Song X, Brasch ME, Henderson JH, Ren D. How Escherichia coli lands and forms cell clusters on a surface: a new role of surface topography. Sci Rep 2016; 6:29516. [PMID: 27412365 PMCID: PMC4944170 DOI: 10.1038/srep29516] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 06/20/2016] [Indexed: 12/21/2022] Open
Abstract
Bacterial response to surface topography during biofilm formation was studied using 5 μm tall line patterns of poly (dimethylsiloxane) (PDMS). Escherichia coli cells attached on top of protruding line patterns were found to align more perpendicularly to the orientation of line patterns when the pattern narrowed. Consistently, cell cluster formation per unit area on 5 μm wide line patterns was reduced by 14-fold compared to flat PDMS. Contrasting the reduced colony formation, cells attached on narrow patterns were longer and had higher transcriptional activities, suggesting that such unfavorable topography may present a stress to attached cells. Results of mutant studies indicate that flagellar motility is involved in the observed preference in cell orientation on narrow patterns, which was corroborated by the changes in cell rotation pattern before settling on different surface topographies. These findings led to a set of new design principles for creating antifouling topographies, which was validated using 10 μm tall hexagonal patterns.
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Affiliation(s)
- Huan Gu
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA.,Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Aaron Chen
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA.,Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Xinran Song
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA.,Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Megan E Brasch
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA.,Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, USA
| | - James H Henderson
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA.,Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Dacheng Ren
- Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY 13244, USA.,Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, USA.,Department of Civil and Environmental Engineering, Syracuse University, Syracuse, NY 13244, USA.,Department of Biology, Syracuse University, Syracuse, NY 13244, United States
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360
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Synthesis and Evaluation of Ciprofloxacin-Nitroxide Conjugates as Anti-Biofilm Agents. Molecules 2016; 21:molecules21070841. [PMID: 27355936 PMCID: PMC6273952 DOI: 10.3390/molecules21070841] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/17/2016] [Accepted: 06/21/2016] [Indexed: 12/14/2022] Open
Abstract
As bacterial biofilms are often refractory to conventional antimicrobials, the need for alternative and/or novel strategies for the treatment of biofilm related infections has become of paramount importance. Herein, we report the synthesis of novel hybrid molecules comprised of two different hindered nitroxides linked to the piperazinyl secondary amine of ciprofloxacin via a tertiary amine linker achieved utilising reductive amination. The corresponding methoxyamine derivatives were prepared alongside their radical-containing counterparts as controls. Subsequent biological evaluation of the hybrid compounds on preformed P. aeruginosa flow cell biofilms divulged significant dispersal and eradication abilities for ciprofloxacin-nitroxide hybrid compound 10 (up to 95% eradication of mature biofilms at 40 μM). Importantly, these hybrids represent the first dual-action antimicrobial-nitroxide agents, which harness the dispersal properties of the nitroxide moiety to circumvent the well-known resistance of biofilms to treatment with antimicrobial agents.
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361
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Kimyon Ö, Das T, Ibugo AI, Kutty SK, Ho KK, Tebben J, Kumar N, Manefield M. Serratia Secondary Metabolite Prodigiosin Inhibits Pseudomonas aeruginosa Biofilm Development by Producing Reactive Oxygen Species that Damage Biological Molecules. Front Microbiol 2016; 7:972. [PMID: 27446013 PMCID: PMC4922266 DOI: 10.3389/fmicb.2016.00972] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/06/2016] [Indexed: 11/13/2022] Open
Abstract
Prodigiosin is a heterocyclic bacterial secondary metabolite belonging to the class of tripyrrole compounds, synthesized by various types of bacteria including Serratia species. Prodigiosin has been the subject of intense research over the last decade for its ability to induce apoptosis in several cancer cell lines. Reports suggest that prodigiosin promotes oxidative damage to double-stranded DNA (dsDNA) in the presence of copper ions and consequently leads to inhibition of cell-cycle progression and cell death. However, prodigiosin has not been previously implicated in biofilm inhibition. In this study, the link between prodigiosin and biofilm inhibition through the production of redox active metabolites is presented. Our study showed that prodigiosin (500 μM) (extracted from Serratia marcescens culture) and a prodigiosin/copper(II) (100 μM each) complex have strong RNA and dsDNA cleaving properties while they have no pronounced effect on protein. Results support a role for oxidative damage to biomolecules by H2O2 and hydroxyl radical generation. Further, it was demonstrated that reactive oxygen species scavengers significantly reduced the DNA and RNA cleaving property of prodigiosin. P. aeruginosa cell surface hydrophobicity and biofilm integrity were significantly altered due to the cleavage of nucleic acids by prodigiosin or the prodigiosin/copper(II) complex. In addition, prodigiosin also facilitated the bactericidal activity. The ability of prodigiosinto cause nucleic acid degradation offers novel opportunities to interfere with extracellular DNA dependent bacterial biofilms.
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Affiliation(s)
- Önder Kimyon
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Theerthankar Das
- School of Biotechnology and Biomolecular Sciences, The University of New South WalesSydney, NSW, Australia; Department of Infectious Diseases and Immunology, Sydney Medical School, The University of SydneySydney, NSW, Australia
| | - Amaye I Ibugo
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales Sydney, NSW, Australia
| | - Samuel K Kutty
- School of Chemistry, The University of New South Wales Sydney, NSW, Australia
| | - Kitty K Ho
- School of Chemistry, The University of New South Wales Sydney, NSW, Australia
| | - Jan Tebben
- Ecological Chemistry, Alfred Wegener Institute for Polar and Marine Research Institute Bremerhaven, Germany
| | - Naresh Kumar
- School of Chemistry, The University of New South Wales Sydney, NSW, Australia
| | - Mike Manefield
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales Sydney, NSW, Australia
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362
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Combating chronic bacterial infections by manipulating cyclic nucleotide-regulated biofilm formation. Future Med Chem 2016; 8:949-61. [PMID: 27304227 DOI: 10.4155/fmc-2015-0002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Many pathogenic bacteria can form biofilms in clinical settings with major consequences for the progression of infections. Bacterial biofilm communities are typically much more resistant to both antibiotic treatment and clearance by the immune system in comparison to free-living cells. Therefore, drugs that specifically target the formation or maintenance of biofilms would be very valuable additions to current clinical options. Cyclic nucleotide second messengers, in particular cyclic-diguanosine-GMP (c-di-GMP), are now known to play a major role in biofilm formation, and maintenance, in many bacterial species. In this special report, we will review recent progress toward the development of drugs that interfere with c-di-GMP signaling as a route to control biofilm infections. We will focus on the chronic infections associated with the notorious opportunistic pathogen Pseudomonas aeruginosa, although the principles outlined here are also relevant to most bacterial pathogens.
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363
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Surface-attached and suspended bacterial community structure as affected by C/N ratios: relationship between bacteria and fish production. World J Microbiol Biotechnol 2016; 32:116. [DOI: 10.1007/s11274-016-2065-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 04/02/2016] [Indexed: 12/21/2022]
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364
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Qayyum S, Sharma D, Bisht D, Khan AU. Protein translation machinery holds a key for transition of planktonic cells to biofilm state in Enterococcus faecalis : A proteomic approach. Biochem Biophys Res Commun 2016; 474:652-659. [DOI: 10.1016/j.bbrc.2016.04.145] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 04/30/2016] [Indexed: 11/26/2022]
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365
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Recent Advances in the Study of Marine Microbial Biofilm: From the Involvement of Quorum Sensing in Its Production up to Biotechnological Application of the Polysaccharide Fractions. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2016. [DOI: 10.3390/jmse4020034] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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366
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Kim HS, Cha E, Kim Y, Jeon YH, Olson BH, Byun Y, Park HD. Raffinose, a plant galactoside, inhibits Pseudomonas aeruginosa biofilm formation via binding to LecA and decreasing cellular cyclic diguanylate levels. Sci Rep 2016; 6:25318. [PMID: 27141909 PMCID: PMC4855137 DOI: 10.1038/srep25318] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/15/2016] [Indexed: 12/16/2022] Open
Abstract
Biofilm formation on biotic or abiotic surfaces has unwanted consequences in medical, clinical, and industrial settings. Treatments with antibiotics or biocides are often ineffective in eradicating biofilms. Promising alternatives to conventional agents are biofilm-inhibiting compounds regulating biofilm development without toxicity to growth. Here, we screened a biofilm inhibitor, raffinose, derived from ginger. Raffinose, a galactotrisaccharide, showed efficient biofilm inhibition of Pseudomonas aeruginosa without impairing its growth. Raffinose also affected various phenotypes such as colony morphology, matrix formation, and swarming motility. Binding of raffinose to a carbohydrate-binding protein called LecA was the cause of biofilm inhibition and altered phenotypes. Furthermore, raffinose reduced the concentration of the second messenger, cyclic diguanylate (c-di-GMP), by increased activity of a c-di-GMP specific phosphodiesterase. The ability of raffinose to inhibit P. aeruginosa biofilm formation and its molecular mechanism opens new possibilities for pharmacological and industrial applications.
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Affiliation(s)
- Han-Shin Kim
- School of Civil, Environmental and Architectural Engineering, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 136-713, South Korea
| | - Eunji Cha
- School of Civil, Environmental and Architectural Engineering, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 136-713, South Korea
| | - YunHye Kim
- College of Pharmacy, Korea University, Sejong-ro 2511, Jochiwon-eup, Sejong, 339-700, South Korea
| | - Young Ho Jeon
- College of Pharmacy, Korea University, Sejong-ro 2511, Jochiwon-eup, Sejong, 339-700, South Korea
| | - Betty H. Olson
- Department of Civil and Environmental Engineering, University of California, Irvine, CA 92697, USA
| | - Youngjoo Byun
- College of Pharmacy, Korea University, Sejong-ro 2511, Jochiwon-eup, Sejong, 339-700, South Korea
| | - Hee-Deung Park
- School of Civil, Environmental and Architectural Engineering, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 136-713, South Korea
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367
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Lebeaux D, Lucet JC, Barbier FS. Nouvelles recommandations pour les infections associées au biofilm : implications en réanimation. MEDECINE INTENSIVE REANIMATION 2016. [DOI: 10.1007/s13546-016-1182-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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368
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Kirsebom LA, Dasgupta S, Fredrik Pettersson BM. Pleiomorphism in Mycobacterium. ADVANCES IN APPLIED MICROBIOLOGY 2016; 80:81-112. [PMID: 22794145 DOI: 10.1016/b978-0-12-394381-1.00004-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Morphological variants in mycobacterial cultures under different growth conditions, including aging of the culture, have been shown to include fibrous aggregates, biofilms, coccoids, and spores. Here we discuss the diversity in shape and size changes demonstrated by bacterial cells with special reference to pleiomorphism observed in Mycobacterium spp. in response to nutritional and other environmental stresses. Inherent asymmetry in cell division and compartmentalization of cell interior under different growth conditions might contribute toward the observed pleiomorphism in mycobacteria. The regulatory genes comprising the bacterial signaling pathway responsible for initiating morphogenesis are speculated upon from bioinformatic identifications of genes for known sensors, kinases, and phosphatases existing in mycobacterial genomes as well as on the basis of what is known in other bacteria.
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369
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O'May C, Amzallag O, Bechir K, Tufenkji N. Cranberry derivatives enhance biofilm formation and transiently impair swarming motility of the uropathogen Proteus mirabilis HI4320. Can J Microbiol 2016; 62:464-74. [PMID: 27090825 DOI: 10.1139/cjm-2015-0715] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Proteus mirabilis is a major cause of catheter-associated urinary tract infection (CAUTI), emphasizing that novel strategies for targeting this bacterium are needed. Potential targets are P. mirabilis surface-associated swarming motility and the propensity of these bacteria to form biofilms that may lead to catheter blockage. We previously showed that the addition of cranberry powder (CP) to lysogeny broth (LB) medium resulted in impaired P. mirabilis swarming motility over short time periods (up to 16 h). Herein, we significantly expanded on those findings by exploring (i) the effects of cranberry derivatives on biofilm formation of P. mirabilis, (ii) whether swarming inhibition occurred transiently or over longer periods more relevant to real infections (∼3 days), (iii) whether swarming was also blocked by commercially available cranberry juices, (iv) whether CP or cranberry juices exhibited effects under natural urine conditions, and (v) the effects of cranberry on medium pH, which is an indirect indicator of urease activity. At short time scales (24 h), CP and commercially available pure cranberry juice impaired swarming motility and repelled actively swarming bacteria in LB medium. Over longer time periods more representative of infections (∼3 days), the capacity of the cranberry material to impair swarming diminished and bacteria would start to migrate across the surface, albeit by exhibiting a different motility phenotype to the regular "bull's-eye" swarming phenotype of P. mirabilis. This bacterium did not swarm on urine agar or LB agar supplemented with urea, suggesting that any potential application of anti-swarming compounds may be better suited to settings external to the urine environment. Anti-swarming effects were confounded by the ability of cranberry products to enhance biofilm formation in both LB and urine conditions. These findings provide key insights into the long-term strategy of targeting P. mirabilis CAUTIs.
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Affiliation(s)
- Che O'May
- Department of Chemical Engineering, McGill University, 3610 University Street, Montréal, QC H3A 0C5, Canada.,Department of Chemical Engineering, McGill University, 3610 University Street, Montréal, QC H3A 0C5, Canada
| | - Olivier Amzallag
- Department of Chemical Engineering, McGill University, 3610 University Street, Montréal, QC H3A 0C5, Canada.,Department of Chemical Engineering, McGill University, 3610 University Street, Montréal, QC H3A 0C5, Canada
| | - Karim Bechir
- Department of Chemical Engineering, McGill University, 3610 University Street, Montréal, QC H3A 0C5, Canada.,Department of Chemical Engineering, McGill University, 3610 University Street, Montréal, QC H3A 0C5, Canada
| | - Nathalie Tufenkji
- Department of Chemical Engineering, McGill University, 3610 University Street, Montréal, QC H3A 0C5, Canada.,Department of Chemical Engineering, McGill University, 3610 University Street, Montréal, QC H3A 0C5, Canada
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370
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Abstract
Bacterial biofilms are dense and often mixed-species surface-attached communities in which bacteria coexist and compete for limited space and nutrients. Here we present the different antagonistic interactions described in biofilm environments and their underlying molecular mechanisms, along with ecological and evolutionary insights as to how competitive interactions arise and are maintained within biofilms.
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371
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Abstract
The formation of the organized bacterial community called biofilm is a crucial event in bacterial physiology. Given that biofilms are often refractory to antibiotics and disinfectants to which planktonic bacteria are susceptible, their formation is also an industrially and medically relevant issue. Pseudomonas aeruginosa, a well-known human pathogen causing acute and chronic infections, is considered a model organism to study biofilms. A large number of environmental cues control biofilm dynamics in bacterial cells. In particular, the dispersal of individual cells from the biofilm requires metabolic and morphological reprogramming in which the second messenger bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) plays a central role. The diatomic gas nitric oxide (NO), a well-known signaling molecule in both prokaryotes and eukaryotes, is able to induce the dispersal of P. aeruginosa and other bacterial biofilms by lowering c-di-GMP levels. In this review, we summarize the current knowledge on the molecular mechanisms connecting NO sensing to the activation of c-di-GMP-specific phosphodiesterases in P. aeruginosa, ultimately leading to c-di-GMP decrease and biofilm dispersal.
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372
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Qi L, Li H, Zhang C, Liang B, Li J, Wang L, Du X, Liu X, Qiu S, Song H. Relationship between Antibiotic Resistance, Biofilm Formation, and Biofilm-Specific Resistance in Acinetobacter baumannii. Front Microbiol 2016; 7:483. [PMID: 27148178 PMCID: PMC4828443 DOI: 10.3389/fmicb.2016.00483] [Citation(s) in RCA: 202] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 03/22/2016] [Indexed: 01/09/2023] Open
Abstract
In this study, we aimed to examine the relationships between antibiotic resistance, biofilm formation, and biofilm-specific resistance in clinical isolates of Acinetobacter baumannii. The tested 272 isolates were collected from several hospitals in China during 2010–2013. Biofilm-forming capacities were evaluated using the crystal violet staining method. Antibiotic resistance/susceptibility profiles to 21 antibiotics were assessed using VITEK 2 system, broth microdilution method or the Kirby-Bauer disc diffusion method. The minimum inhibitory concentration (MIC) and minimum biofilm eradication concentration (MBEC) to cefotaxime, imipenem, and ciprofloxacin were evaluated using micro dilution assays. Genetic relatedness of the isolates was also analyzed by pulsed-field gel electrophoresis (PFGE) and plasmid profile. Among all the 272 isolates, 31 were multidrug-resistant (MDR), and 166 were extensively drug-resistant (XDR). PFGE typing revealed 167 pattern types and 103 clusters with a similarity of 80%. MDR and XDR isolates built up the main prevalent genotypes. Most of the non-MDR isolates were distributed in a scattered pattern. Additionally, 249 isolates exhibited biofilm formation, among which 63 were stronger biofilm formers than type strain ATCC19606. Population that exhibited more robust biofilm formation likely contained larger proportion of non-MDR isolates. Isolates with higher level of resistance tended to form weaker biofilms. The MBECs for cefotaxime, imipenem, and ciprofloxacin showed a positive correlation with corresponding MICs, while the enhancement in resistance occurred independent of the quantity of biofilm biomass produced. Results from this study imply that biofilm acts as a mechanism for bacteria to get a better survival, especially in isolates with resistance level not high enough. Moreover, even though biofilms formed by isolates with high level of resistance are always weak, they could still provide similar level of protection for the isolates. Further explorations genetically would improve our understanding of these processes and provide novel insights in the therapeutics and prevention against A. baumannii biofilm-related infections.
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Affiliation(s)
- Lihua Qi
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Hao Li
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Chuanfu Zhang
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Beibei Liang
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Jie Li
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Ligui Wang
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Xinying Du
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Xuelin Liu
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Shaofu Qiu
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
| | - Hongbin Song
- Department of Infectious Disease Control, Institute of Disease Control and Prevention, Academy of Military Medical Sciences Beijing, China
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373
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Ribeiro SM, Cardoso MH, Cândido EDS, Franco OL. Understanding, preventing and eradicating Klebsiella pneumoniae biofilms. Future Microbiol 2016; 11:527-38. [PMID: 27064296 DOI: 10.2217/fmb.16.7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The ability of pathogenic bacteria to aggregate and form biofilm represents a great problem for public health, since they present extracellular components that encase these micro-organisms, making them more resistant to antibiotics and host immune attack. This may become worse when antibiotic-resistant bacterial strains form biofilms. However, antibiofilm screens with different compounds may reveal potential therapies to prevent/treat biofilm infections. Here, we focused on Klebsiella pneumoniae, an opportunistic bacterium that causes different types of infections, including in the bloodstream, meninges, lungs, urinary system and at surgical sites. We also highlight aspects involved in the formation and maintenance of K. pneumoniae biofilms, as well as resistance and the emergence of new trends to combat this health challenge.
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Affiliation(s)
- Suzana Meira Ribeiro
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil.,S-Inova, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande- MS, Brazil
| | - Marlon Henrique Cardoso
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil.,S-Inova, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande- MS, Brazil.,Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília-DF, Brazil
| | - Elizabete de Souza Cândido
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil.,S-Inova, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande- MS, Brazil
| | - Octávio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil.,S-Inova, Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande- MS, Brazil.,Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Brasília-DF, Brazil
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374
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Low Concentrations of Nitric Oxide Modulate Streptococcus pneumoniae Biofilm Metabolism and Antibiotic Tolerance. Antimicrob Agents Chemother 2016; 60:2456-66. [PMID: 26856845 DOI: 10.1128/aac.02432-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/05/2016] [Indexed: 12/24/2022] Open
Abstract
Streptococcus pneumoniaeis one of the key pathogens responsible for otitis media (OM), the most common infection in children and the largest cause of childhood antibiotic prescription. Novel therapeutic strategies that reduce the overall antibiotic consumption due to OM are required because, although widespread pneumococcal conjugate immunization has controlled invasive pneumococcal disease, overall OM incidence has not decreased. Biofilm formation represents an important phenotype contributing to the antibiotic tolerance and persistence ofS. pneumoniaein chronic or recurrent OM. We investigated the treatment of pneumococcal biofilms with nitric oxide (NO), an endogenous signaling molecule and therapeutic agent that has been demonstrated to trigger biofilm dispersal in other bacterial species. We hypothesized that addition of low concentrations of NO to pneumococcal biofilms would improve antibiotic efficacy and that higher concentrations exert direct antibacterial effects. Unlike in many other bacterial species, low concentrations of NO did not result inS. pneumoniaebiofilm dispersal. Instead, treatment of bothin vitrobiofilms andex vivoadenoid tissue samples (a reservoir forS. pneumoniaebiofilms) with low concentrations of NO enhanced pneumococcal killing when combined with amoxicillin-clavulanic acid, an antibiotic commonly used to treat chronic OM. Quantitative proteomic analysis using iTRAQ (isobaric tag for relative and absolute quantitation) identified 13 proteins that were differentially expressed following low-concentration NO treatment, 85% of which function in metabolism or translation. Treatment with low-concentration NO, therefore, appears to modulate pneumococcal metabolism and may represent a novel therapeutic approach to reduce antibiotic tolerance in pneumococcal biofilms.
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375
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Kragh KN, Hutchison JB, Melaugh G, Rodesney C, Roberts AEL, Irie Y, Jensen PØ, Diggle SP, Allen RJ, Gordon V, Bjarnsholt T. Role of Multicellular Aggregates in Biofilm Formation. mBio 2016; 7:e00237. [PMID: 27006463 PMCID: PMC4807362 DOI: 10.1128/mbio.00237-16] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 02/22/2016] [Indexed: 11/25/2022] Open
Abstract
UNLABELLED In traditional models ofin vitrobiofilm development, individual bacterial cells seed a surface, multiply, and mature into multicellular, three-dimensional structures. Much research has been devoted to elucidating the mechanisms governing the initial attachment of single cells to surfaces. However, in natural environments and during infection, bacterial cells tend to clump as multicellular aggregates, and biofilms can also slough off aggregates as a part of the dispersal process. This makes it likely that biofilms are often seeded by aggregates and single cells, yet how these aggregates impact biofilm initiation and development is not known. Here we use a combination of experimental and computational approaches to determine the relative fitness of single cells and preformed aggregates during early development ofPseudomonas aeruginosabiofilms. We find that the relative fitness of aggregates depends markedly on the density of surrounding single cells, i.e., the level of competition for growth resources. When competition between aggregates and single cells is low, an aggregate has a growth disadvantage because the aggregate interior has poor access to growth resources. However, if competition is high, aggregates exhibit higher fitness, because extending vertically above the surface gives cells at the top of aggregates better access to growth resources. Other advantages of seeding by aggregates, such as earlier switching to a biofilm-like phenotype and enhanced resilience toward antibiotics and immune response, may add to this ecological benefit. Our findings suggest that current models of biofilm formation should be reconsidered to incorporate the role of aggregates in biofilm initiation. IMPORTANCE During the past decades, there has been a consensus around the model of development of a biofilm, involving attachment of single planktonic bacterial cells to a surface and the subsequent development of a mature biofilm. This study presents results that call for a modification of this rigorous model. We show how free floating biofilm aggregates can have a profound local effect on biofilm development when attaching to a surface. Our findings show that an aggregate landing on a surface will eventually outcompete the biofilm population arising from single cells attached around the aggregate and dominate the local biofilm development. These results point to a regime where preformed biofilm aggregates may have a fitness advantage over planktonic cells when it comes to accessing nutrients. Our findings add to the increasingly prominent comprehension that biofilm lifestyle is the default for bacteria and that planktonic single cells may be only a transition state at the most.
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Affiliation(s)
- Kasper N Kragh
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Jaime B Hutchison
- Center for Nonlinear Dynamics and Department of Physics, The University of Texas at Austin, Austin, Texas, USA
| | - Gavin Melaugh
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Chris Rodesney
- Center for Nonlinear Dynamics and Department of Physics, The University of Texas at Austin, Austin, Texas, USA
| | - Aled E L Roberts
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Yasuhiko Irie
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Peter Ø Jensen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Stephen P Diggle
- Centre for Biomolecular Sciences, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Rosalind J Allen
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Vernita Gordon
- Center for Nonlinear Dynamics and Department of Physics, The University of Texas at Austin, Austin, Texas, USA Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Thomas Bjarnsholt
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
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376
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Abstract
The dense aggregation of cells on a surface, as seen in biofilms, inevitably results in both environmental and cellular heterogeneity. For example, nutrient gradients can trigger cells to differentiate into various phenotypic states. Not only do cells adapt physiologically to the local environmental conditions, but they also differentiate into cell types that interact with each other. This allows for task differentiation and, hence, the division of labor. In this article, we focus on cell differentiation and the division of labor in three bacterial species: Myxococcus xanthus, Bacillus subtilis, and Pseudomonas aeruginosa. During biofilm formation each of these species differentiates into distinct cell types, in some cases leading to cooperative interactions. The division of labor and the cooperative interactions between cell types are assumed to yield an emergent ecological benefit. Yet in most cases the ecological benefits have yet to be elucidated. A notable exception is M. xanthus, in which cell differentiation within fruiting bodies facilitates the dispersal of spores. We argue that the ecological benefits of the division of labor might best be understood when we consider the dynamic nature of both biofilm formation and degradation.
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377
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Guilhen C, Charbonnel N, Parisot N, Gueguen N, Iltis A, Forestier C, Balestrino D. Transcriptional profiling of Klebsiella pneumoniae defines signatures for planktonic, sessile and biofilm-dispersed cells. BMC Genomics 2016; 17:237. [PMID: 26979871 PMCID: PMC4791964 DOI: 10.1186/s12864-016-2557-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/29/2016] [Indexed: 12/22/2022] Open
Abstract
Background Surface-associated communities of bacteria, known as biofilms, play a critical role in the persistence and dissemination of bacteria in various environments. Biofilm development is a sequential dynamic process from an initial bacterial adhesion to a three-dimensional structure formation, and a subsequent bacterial dispersion. Transitions between these different modes of growth are governed by complex and partially known molecular pathways. Results Using RNA-seq technology, our work provided an exhaustive overview of the transcriptomic behavior of the opportunistic pathogen Klebsiella pneumoniae derived from free-living, biofilm and biofilm-dispersed states. For each of these conditions, the combined use of Z-scores and principal component analysis provided a clear illustration of distinct expression profiles. In particular, biofilm-dispersed cells appeared as a unique stage in the bacteria lifecycle, different from both planktonic and sessile states. The K-means cluster analysis showed clusters of Coding DNA Sequences (CDS) and non-coding RNA (ncRNA) genes differentially transcribed between conditions. Most of them included dominant functional classes, emphasizing the transcriptional changes occurring in the course of K. pneumoniae lifestyle transitions. Furthermore, analysis of the whole transcriptome allowed the selection of an overall of 40 transcriptional signature genes for the five bacterial physiological states. Conclusions This transcriptional study provides additional clues to understand the key molecular mechanisms involved in the transition between biofilm and the free-living lifestyles, which represents an important challenge to control both beneficial and harmful biofilm. Moreover, this exhaustive study identified physiological state specific transcriptomic reference dataset useful for the research community. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2557-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cyril Guilhen
- Laboratoire Microorganismes: Génome Environnement, UMR CNRS 6023, Université d'Auvergne, Clermont Ferrand, F-63001, France
| | - Nicolas Charbonnel
- Laboratoire Microorganismes: Génome Environnement, UMR CNRS 6023, Université d'Auvergne, Clermont Ferrand, F-63001, France
| | - Nicolas Parisot
- UMR 203 BF2I, Biologie Fonctionnelle Insectes et Interactions, INRA, INSA de Lyon, Université de Lyon, F-69621, Villeurbanne, France
| | - Nathalie Gueguen
- Laboratoire Microorganismes: Génome Environnement, UMR CNRS 6023, Université d'Auvergne, Clermont Ferrand, F-63001, France
| | - Agnès Iltis
- Genostar, Montbonnot Saint Martin, F-38330, France
| | - Christiane Forestier
- Laboratoire Microorganismes: Génome Environnement, UMR CNRS 6023, Université d'Auvergne, Clermont Ferrand, F-63001, France
| | - Damien Balestrino
- Laboratoire Microorganismes: Génome Environnement, UMR CNRS 6023, Université d'Auvergne, Clermont Ferrand, F-63001, France.
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378
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Biofilm plasmids with a rhamnose operon are widely distributed determinants of the 'swim-or-stick' lifestyle in roseobacters. ISME JOURNAL 2016; 10:2498-513. [PMID: 26953602 PMCID: PMC5030684 DOI: 10.1038/ismej.2016.30] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 01/12/2016] [Accepted: 01/24/2016] [Indexed: 12/17/2022]
Abstract
Alphaproteobacteria of the metabolically versatile Roseobacter group (Rhodobacteraceae) are abundant in marine ecosystems and represent dominant primary colonizers of submerged surfaces. Motility and attachment are the prerequisite for the characteristic 'swim-or-stick' lifestyle of many representatives such as Phaeobacter inhibens DSM 17395. It has recently been shown that plasmid curing of its 65-kb RepA-I-type replicon with >20 genes for exopolysaccharide biosynthesis including a rhamnose operon results in nearly complete loss of motility and biofilm formation. The current study is based on the assumption that homologous biofilm plasmids are widely distributed. We analyzed 33 roseobacters that represent the phylogenetic diversity of this lineage and documented attachment as well as swimming motility for 60% of the strains. All strong biofilm formers were also motile, which is in agreement with the proposed mechanism of surface attachment. We established transposon mutants for the four genes of the rhamnose operon from P. inhibens and proved its crucial role in biofilm formation. In the Roseobacter group, two-thirds of the predicted biofilm plasmids represent the RepA-I type and their physiological role was experimentally validated via plasmid curing for four additional strains. Horizontal transfer of these replicons was documented by a comparison of the RepA-I phylogeny with the species tree. A gene content analysis of 35 RepA-I plasmids revealed a core set of genes, including the rhamnose operon and a specific ABC transporter for polysaccharide export. Taken together, our data show that RepA-I-type biofilm plasmids are essential for the sessile mode of life in the majority of cultivated roseobacters.
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379
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Hong NTX, Baruah K, Vanrompay D, Bossier P. Characterization of phenotype variations of luminescent and non-luminescent variants of Vibrio harveyi wild type and quorum sensing mutants. JOURNAL OF FISH DISEASES 2016; 39:317-327. [PMID: 25865123 DOI: 10.1111/jfd.12365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/05/2015] [Accepted: 02/05/2015] [Indexed: 06/04/2023]
Abstract
Vibrio harveyi, a luminescent Gram-negative motile marine bacterium, is an important pathogen responsible for causing severe diseases in shrimp, finfish and molluscs leading to severe economic losses. Non-luminescent V. harveyi obtained by culturing luminescent strains under static and dark condition were reported to alter the levels of virulence factors and metalloprotease gene and luxR expression when compared to their luminescent variants. Presently, we conducted an in vitro study aiming at the characterization of virulence-related phenotypic traits of the wild-type V. harveyi BB120 strain and its isogenic quorum sensing mutants before and after switching to the non-luminescent status. We measured the production of caseinase, haemolysin and elastase and examined swimming motility and biofilm formation. Our results showed that switching from the bioluminescent to the non-luminescent state changed the phenotypic physiology or behaviour of V. harveyi resulting in alterations in caseinase and haemolytic activities, swimming motility and biofilm formation. The switching capacity was to a large extent independent from the quorum sensing status, in that quorum sensing mutants were equally capable of making the phenotypic switch.
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Affiliation(s)
- N T X Hong
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Production, Faculty of Bioscience Engineering, Rozier 44, Ghent 9000, Belgium
- Faculty of Aquaculture, Hue University of Agriculture and Forestry, Hue City, Vietnam
| | - K Baruah
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Production, Faculty of Bioscience Engineering, Rozier 44, Ghent 9000, Belgium
| | - D Vanrompay
- Laboratory of Immunology and Animal Biotechnology, Department of Molecular Biotechnology, Ghent University, Coupure links 653, Ghent 9000, Belgium
| | - P Bossier
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Production, Faculty of Bioscience Engineering, Rozier 44, Ghent 9000, Belgium
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380
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Architectural transitions in Vibrio cholerae biofilms at single-cell resolution. Proc Natl Acad Sci U S A 2016; 113:E2066-72. [PMID: 26933214 DOI: 10.1073/pnas.1601702113] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many bacterial species colonize surfaces and form dense 3D structures, known as biofilms, which are highly tolerant to antibiotics and constitute one of the major forms of bacterial biomass on Earth. Bacterial biofilms display remarkable changes during their development from initial attachment to maturity, yet the cellular architecture that gives rise to collective biofilm morphology during growth is largely unknown. Here, we use high-resolution optical microscopy to image all individual cells in Vibrio cholerae biofilms at different stages of development, including colonies that range in size from 2 to 4,500 cells. From these data, we extracted the precise 3D cellular arrangements, cell shapes, sizes, and global morphological features during biofilm growth on submerged glass substrates under flow. We discovered several critical transitions of the internal and external biofilm architectures that separate the major phases of V. cholerae biofilm growth. Optical imaging of biofilms with single-cell resolution provides a new window into biofilm formation that will prove invaluable to understanding the mechanics underlying biofilm development.
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381
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Craven M, Kasper S, Canfield M, Diaz-Morales R, Hrabie J, Cady N, Strickland A. Nitric oxide-releasing polyacrylonitrile disperses biofilms formed by wound-relevant pathogenic bacteria. J Appl Microbiol 2016; 120:1085-99. [DOI: 10.1111/jam.13059] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 01/01/2016] [Accepted: 01/04/2016] [Indexed: 12/13/2022]
Affiliation(s)
| | - S.H. Kasper
- College of Nanoscale Science & Engineering; SUNY Polytechnic Institute; Albany NY USA
| | | | | | - J.A. Hrabie
- Frederick National Laboratory for Cancer Research; National Cancer Institute; Frederick MD USA
| | - N.C. Cady
- College of Nanoscale Science & Engineering; SUNY Polytechnic Institute; Albany NY USA
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382
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França A, Carvalhais V, Vilanova M, Pier GB, Cerca N. Characterization of an in vitro fed-batch model to obtain cells released from S. epidermidis biofilms. AMB Express 2016; 6:23. [PMID: 27001438 PMCID: PMC4801823 DOI: 10.1186/s13568-016-0197-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 03/14/2016] [Indexed: 12/22/2022] Open
Abstract
Both dynamic and fed-batch systems have been used for the study of biofilms. Dynamic systems, whose hallmark is the presence of continuous flow, have been considered the most appropriate for the study of the last stage of the biofilm lifecycle: biofilm disassembly. However, fed-batch is still the most used system in the biofilm research field. Hence, we have used a fed-batch system to collect cells released from Staphylococcus epidermidis biofilms, one of the most important etiological agents of medical device-associated biofilm infections. Herein, we showed that using this model it was possible to collect cells released from biofilms formed by 12 different S. epidermidis clinical and commensal isolates. In addition, our data indicated that biofilm disassembly occurred by both passive and active mechanisms, although the last occurred to a lesser extent. Moreover, it was observed that S. epidermidis biofilm-released cells presented higher tolerance to vancomycin and tetracycline, as well as a particular gene expression phenotype when compared with either biofilm or planktonic cells. Using this model, biofilm-released cells phenotype and their interaction with the host immune system could be studied in more detail, which could help providing significant insights into the pathophysiology of biofilm-related infections.
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383
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Bacteria differently deploy type-IV pili on surfaces to adapt to nutrient availability. NPJ Biofilms Microbiomes 2016; 2:15029. [PMID: 28721239 PMCID: PMC5515259 DOI: 10.1038/npjbiofilms.2015.29] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 11/12/2015] [Accepted: 11/18/2015] [Indexed: 12/27/2022] Open
Abstract
The structure of bacterial biofilms depends on environmental conditions, such as availability of nutrients, during biofilm formation. In turn, variations in biofilm structure in part reflect differences in bacterial motility during early biofilm formation. Pseudomonas aeruginosa deprived of nutrients remain dispersed on a surface, whereas cells supplemented with additional nutrients cluster and form microcolonies. At the single-cell scale, how bacteria modify their motility to favour distinct life cycle outcomes remains poorly understood. High-throughput algorithms were used to track thousands of P. aeruginosa moving using type-IV pili (TFP) on surfaces in varying nutrient conditions and hence identify four distinct motility types. A minimal stochastic model was used to reproduce the TFP-driven motility types. We report that P. aeruginosa cells differently deploy TFP to alter the distribution of motility types under different nutrient conditions. Bacteria preferentially crawl unidirectionally under nutrient-limited conditions, but preferentially stall under nutrient-supplemented conditions. Motility types correlate with subcellular localisation of FimX, a protein required for TFP assembly and implicated in environmental response. The subcellular distribution of FimX is asymmetric for unidirectional crawling, consistent with TFP assembled primarily at the leading pole, whereas for non-translational types FimX expression is symmetric or non-existent. These results are consistent with a minimal stochastic model that reproduces the motility types from the subcellular average concentration and asymmetry of FimX. These findings reveal that P. aeruginosa deploy TFP symmetrically or asymmetrically to modulate motility behaviours in different nutrient conditions and thereby form biofilms only where nutrients are sufficient, which greatly enhances their competitive capacity in diverse environments.
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384
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van Gestel J, Nowak MA. Phenotypic Heterogeneity and the Evolution of Bacterial Life Cycles. PLoS Comput Biol 2016; 12:e1004764. [PMID: 26894881 PMCID: PMC4760940 DOI: 10.1371/journal.pcbi.1004764] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/20/2016] [Indexed: 11/21/2022] Open
Abstract
Most bacteria live in colonies, where they often express different cell types. The ecological significance of these cell types and their evolutionary origin are often unknown. Here, we study the evolution of cell differentiation in the context of surface colonization. We particularly focus on the evolution of a ‘sticky’ cell type that is required for surface attachment, but is costly to express. The sticky cells not only facilitate their own attachment, but also that of non-sticky cells. Using individual-based simulations, we show that surface colonization rapidly evolves and in most cases leads to phenotypic heterogeneity, in which sticky and non-sticky cells occur side by side on the surface. In the presence of regulation, cell differentiation leads to a remarkable set of bacterial life cycles, in which cells alternate between living in the liquid and living on the surface. The dominant life stage is formed by the surface-attached colony that shows many complex features: colonies reproduce via fission and by producing migratory propagules; cells inside the colony divide labour; and colonies can produce filaments to facilitate expansion. Overall, our model illustrates how the evolution of an adhesive cell type goes hand in hand with the evolution of complex bacterial life cycles. In nature, most bacteria occur in surface-attached colonies. Inside these colonies, cells often express many different phenotypes. The significance of these phenotypes often remains unknown. We study the evolution of cell differentiation in the context of surface colonization. We particularly focus on the evolution of a ‘sticky’ cell type that is needed for surface attachment. We show that the sticky cell type readily evolves and escapes from competition in the liquid by attaching to the surface. In most cases, surface colonization is accompanied by phenotypic heterogeneity, in which sticky and non-sticky cell co-occupy the surface. The non-sticky cells hitchhike with the sticky cells, thereby profiting from surface attachment without paying the cost of being sticky. In the presence of regulation, cell differentiation leads to the evolution of intricate bacterial life cycles in which cells alternate between living in surface-attached colonies and living in the liquid. The bacterial life cycles are orchestrated by temporal and spatial pattern formation of cell types. Our model illustrates how cell differentiation can be of key importance for the evolution of bacterial life cycles.
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Affiliation(s)
- Jordi van Gestel
- Program for Evolutionary Dynamics, Departments of Organismic and Evolutionary Biology and Mathematics, Harvard University, Boston, Massachusetts, United States of America
- Theoretical Research in Evolutionary Life Sciences, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands
- * E-mail:
| | - Martin A. Nowak
- Program for Evolutionary Dynamics, Departments of Organismic and Evolutionary Biology and Mathematics, Harvard University, Boston, Massachusetts, United States of America
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385
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Abstract
Bacteria have a natural propensity to grow as sessile, matrix-encapsulated, multicellular communities called biofilms. Formation of biofilms proceeds through genetically programmed, distinct developmental stages signaled by intricate networks of communication among the constituent population and their environment. Growing in the complex and heterogeneous microenvironments of biofilms, the resident bacteria acquire unique phenotypes that are generally not associated with their planktonic counterparts. Most notable among these is an extraordinary level of tolerance to a variety of environmental stresses, including antibiotics. Although mycobacteria have long been observed to spontaneously form complex multicellular structures in vitro, it has only recently become apparent that these structures are not only formed through dedicated genetic pathways but are also tolerant to antibiotics. In this article, we review the recent advances in the understanding of mycobacterial biofilms in vitro. We further consider the possible linkage between biofilm-like lifestyles and characteristic persistence of mycobacterial infections against host-defense mechanisms as well as antibiotics.
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386
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Percival SL, Suleman L. Slough and biofilm: removal of barriers to wound healing by desloughing. J Wound Care 2016; 24:498, 500-3, 506-10. [PMID: 26551642 DOI: 10.12968/jowc.2015.24.11.498] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The presence of non-viable tissue in a chronic wound presents a barrier against effective wound healing, hence removal facilitates healing and reduces areas where microorganisms can attach and form biofilms, effectively reducing the risk of infection. Wound debridement is a necessary process in those wounds that have evidence of cellular debris and non-viable tissue. As slough is a form of non-viable tissue we hypothesise that it will support the attachment and development of biofilms. Biofilms are entities that have serious implications in raising the risk of infection and delaying wound healing. In those wounds that contain only slough, high-risk debridement methods are not considered necessary for its removal. The use of mechanical techniques for removing the slough is regarded as posing a much lower risk to the patient and the wound bed. The process of removing slough from a wound is referred to as 'desloughing'. We propose that mechanical desloughing is a low-risk method of debridement to aid the specific removal of slough. Slough in a wound is a recurrent issue for a large majority of patients. Consequently, desloughing should not be deemed a one-off process but an on-going procedure referred to as 'maintenance desloughing'. Maintenance desloughing will help to achieve and maintain a healthy wound bed and aid the removal of wound biofilms, facilitating wound healing.
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Affiliation(s)
- S L Percival
- 5D Health Protection Group Ltd, Biohub, Alderley Park, Alderley Edge, Cheshire, SK10 4TG, UK.,Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - L Suleman
- 5D Health Protection Group Ltd, Biohub, Alderley Park, Alderley Edge, Cheshire, SK10 4TG, UK.,Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
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387
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Kim SK, Lee JH. Biofilm dispersion in Pseudomonas aeruginosa. J Microbiol 2016; 54:71-85. [PMID: 26832663 DOI: 10.1007/s12275-016-5528-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/22/2015] [Accepted: 12/22/2015] [Indexed: 02/07/2023]
Abstract
In recent decades, many researchers have written numerous articles about microbial biofilms. Biofilm is a complex community of microorganisms and an example of bacterial group behavior. Biofilm is usually considered a sessile mode of life derived from the attached growth of microbes to surfaces, and most biofilms are embedded in self-produced extracellular matrix composed of extracellular polymeric substances (EPSs), such as polysaccharides, extracellular DNAs (eDNA), and proteins. Dispersal, a mode of biofilm detachment indicates active mechanisms that cause individual cells to separate from the biofilm and return to planktonic life. Since biofilm cells are cemented and surrounded by EPSs, dispersal is not simple to do and many researchers are now paying more attention to this active detachment process. Unlike other modes of biofilm detachment such as erosion or sloughing, which are generally considered passive processes, dispersal occurs as a result of complex spatial differentiation and molecular events in biofilm cells in response to various environmental cues, and there are many biological reasons that force bacterial cells to disperse from the biofilms. In this review, we mainly focus on the spatial differentiation of biofilm that is a prerequisite for dispersal, as well as environmental cues and molecular events related to the biofilm dispersal. More specifically, we discuss the dispersal-related phenomena and mechanisms observed in Pseudomonas aeruginosa, an important opportunistic human pathogen and representative model organism for biofilm study.
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Affiliation(s)
- Soo-Kyoung Kim
- Department of Pharmacy, College of Pharmacy, Pusan National University, Busan, 609-735, Republic of Korea
| | - Joon-Hee Lee
- Department of Pharmacy, College of Pharmacy, Pusan National University, Busan, 609-735, Republic of Korea.
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388
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Nguyen TK, Selvanayagam R, Ho KKK, Chen R, Kutty SK, Rice SA, Kumar N, Barraud N, Duong HTT, Boyer C. Co-delivery of nitric oxide and antibiotic using polymeric nanoparticles. Chem Sci 2016; 7:1016-1027. [PMID: 28808526 PMCID: PMC5531038 DOI: 10.1039/c5sc02769a] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/24/2015] [Indexed: 12/22/2022] Open
Abstract
The rise of hospital-acquired infections, also known as nosocomial infections, is a growing concern in intensive healthcare, causing the death of hundreds of thousands of patients and costing billions of dollars worldwide every year. In addition, a decrease in the effectiveness of antibiotics caused by the emergence of drug resistance in pathogens living in biofilm communities poses a significant threat to our health system. The development of new therapeutic agents is urgently needed to overcome this challenge. We have developed new dual action polymeric nanoparticles capable of storing nitric oxide, which can provoke dispersal of biofilms into an antibiotic susceptible planktonic form, together with the aminoglycoside gentamicin, capable of killing the bacteria. The novelty of this work lies in the attachment of NO-releasing moiety to an existing clinically used drug, gentamicin. The nanoparticles were found to release both agents simultaneously and demonstrated synergistic effects, reducing the viability of Pseudomonas aeruginosa biofilm and planktonic cultures by more than 90% and 95%, respectively, while treatments with antibiotic or nitric oxide alone resulted in less than 20% decrease in biofilm viability.
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Affiliation(s)
- Thuy-Khanh Nguyen
- Centre for Advanced Macromolecular Design (CAMD) and Australian Centre for NanoMedicine (ACN) , School of Chemical Engineering , UNSW Australia , Sydney , NSW 2052 , Australia . ;
| | - Ramona Selvanayagam
- Centre for Advanced Macromolecular Design (CAMD) and Australian Centre for NanoMedicine (ACN) , School of Chemical Engineering , UNSW Australia , Sydney , NSW 2052 , Australia . ;
| | - Kitty K K Ho
- School of Chemistry , UNSW Australia , Sydney , NSW 2052 , Australia
| | - Renxun Chen
- School of Chemistry , UNSW Australia , Sydney , NSW 2052 , Australia
| | - Samuel K Kutty
- School of Chemistry , UNSW Australia , Sydney , NSW 2052 , Australia
| | - Scott A Rice
- Centre for Marine-Innovation , School of Biological , Earth and Environmental Sciences , University of New South Wales , Sydney , Australia 2052 .
- The Singapore Centre for Environmental Life Sciences Engineering and The School of Biological Sciences , Nanyang Technological University , Singapore
| | - Naresh Kumar
- School of Chemistry , UNSW Australia , Sydney , NSW 2052 , Australia
| | - Nicolas Barraud
- Centre for Marine-Innovation , School of Biological , Earth and Environmental Sciences , University of New South Wales , Sydney , Australia 2052 .
- Department of Microbiology , Genetics of Biofilms Unit , Institute Pasteur , Paris , France
| | - Hien T T Duong
- Centre for Advanced Macromolecular Design (CAMD) and Australian Centre for NanoMedicine (ACN) , School of Chemical Engineering , UNSW Australia , Sydney , NSW 2052 , Australia . ;
| | - Cyrille Boyer
- Centre for Advanced Macromolecular Design (CAMD) and Australian Centre for NanoMedicine (ACN) , School of Chemical Engineering , UNSW Australia , Sydney , NSW 2052 , Australia . ;
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389
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Petrova OE, Sauer K. Escaping the biofilm in more than one way: desorption, detachment or dispersion. Curr Opin Microbiol 2016; 30:67-78. [PMID: 26826978 DOI: 10.1016/j.mib.2016.01.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 12/15/2022]
Abstract
Biofilm bacteria have developed escape strategies to avoid stresses associated with biofilm growth, respond to changing environmental conditions, and disseminate to new locations. An ever-expanding body of research suggests that cellular release from biofilms is distinct from a simple reversal of attachment and reversion to a planktonic mode of growth, with biofilm dispersion involving sensing of specific cues, regulatory signal transduction, and consequent physiological alterations. However, dispersion is only one of many ways to escape the biofilm mode of growth. The present review is aimed at distinguishing this active and regulated process of dispersion from the passive processes of desorption and detachment by highlighting the regulatory processes and distinct phenotypes specific to dispersed cells.
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Affiliation(s)
- Olga E Petrova
- Department of Biological Sciences, Binghamton Biofilm Research Center, Binghamton University, Binghamton, NY 13902, United States
| | - Karin Sauer
- Department of Biological Sciences, Binghamton Biofilm Research Center, Binghamton University, Binghamton, NY 13902, United States.
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390
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Hidalgo-Cantabrana C, López P, Gueimonde M, de Los Reyes-Gavilán CG, Suárez A, Margolles A, Ruas-Madiedo P. Immune Modulation Capability of Exopolysaccharides Synthesised by Lactic Acid Bacteria and Bifidobacteria. Probiotics Antimicrob Proteins 2016; 4:227-37. [PMID: 26782182 DOI: 10.1007/s12602-012-9110-2] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
During recent years, the exopolysaccharides (EPS) produced by some strains of lactic acid bacteria and bifidobacteria have attracted the attention of researchers, mainly due to their potential technological applications. However, more recently, it has been observed that some of these EPS present immunomodulatory properties, which suggest a potential effect on human health. Whereas EPS from lactic acid bacteria have been studied in some detail, those of bifidobacteria largely remain uncharacterized in spite of the ubiquity of EPS genes in Bifidobacterium genomes. In this review, we have analysed the data collected in the literature about the potential immune-modulating capability of EPS produced by lactic acid bacteria and bifidobacteria. From this data analysis, as well as from results obtained in our group, a hypothesis relating the physicochemical characteristics of EPS with their immune modulation capability was highlighted. We propose that EPS having negative charge and/or small size (molecular weight) are able to act as mild stimulators of immune cells, whereas those polymers non-charged and with a large size present a suppressive profile.
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Affiliation(s)
- Claudio Hidalgo-Cantabrana
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Patricia López
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
- Department of Functional Biology, University of Oviedo, Immunology Area, Oviedo, Asturias, Spain
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Clara G de Los Reyes-Gavilán
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Ana Suárez
- Department of Functional Biology, University of Oviedo, Immunology Area, Oviedo, Asturias, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias-Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Río Linares s/n, 33300, Villaviciosa, Asturias, Spain.
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391
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Using Molecular Networking for Microbial Secondary Metabolite Bioprospecting. Metabolites 2016; 6:metabo6010002. [PMID: 26761036 PMCID: PMC4812331 DOI: 10.3390/metabo6010002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 12/23/2015] [Accepted: 12/30/2015] [Indexed: 01/02/2023] Open
Abstract
The oceans represent an understudied resource for the isolation of bacteria with the potential to produce novel secondary metabolites. In particular, actinomyces are well known to produce chemically diverse metabolites with a wide range of biological activities. This study characterised spore-forming bacteria from both Scottish and Antarctic sediments to assess the influence of isolation location on secondary metabolite production. Due to the selective isolation method used, all 85 isolates belonged to the phyla Firmicutes and Actinobacteria, with the majority of isolates belonging to the genera Bacillus and Streptomyces. Based on morphology, thirty-eight isolates were chosen for chemical investigation. Molecular networking based on chemical profiles (HR-MS/MS) of fermentation extracts was used to compare complex metabolite extracts. The results revealed 40% and 42% of parent ions were produced by Antarctic and Scottish isolated bacteria, respectively, and only 8% of networked metabolites were shared between these locations, implying a high degree of biogeographic influence upon secondary metabolite production. The resulting molecular network contained over 3500 parent ions with a mass range of m/z 149–2558 illustrating the wealth of metabolites produced. Furthermore, seven fermentation extracts showed bioactivity against epithelial colon adenocarcinoma cells, demonstrating the potential for the discovery of novel bioactive compounds from these understudied locations.
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392
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Biomechanical Analysis of Infectious Biofilms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 915:99-114. [PMID: 27193540 DOI: 10.1007/978-3-319-32189-9_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The removal of infectious biofilms from tissues or implanted devices and their transmission through fluid transport systems depends in part of the mechanical properties of their polymeric matrix. Linking the various physical and chemical microscopic interactions to macroscopic deformation and failure modes promises to unveil design principles for novel therapeutic strategies targeting biofilm eradication, and provide a predictive capability to accelerate the development of devices, water lines, etc, that minimise microbial dispersal. Here, our current understanding of biofilm mechanics is appraised from the perspective of biophysics , with an emphasis on constitutive modelling that has been highly successful in soft matter. Fitting rheometric data to viscoelastic models has quantified linear and nonlinear stress relaxation mechanisms, how they vary between species and environments, and how candidate chemical treatments alter the mechanical response. The rich interplay between growth, mechanics and hydrodynamics is just becoming amenable to computational modelling and promises to provide unprecedented characterisation of infectious biofilms in their native state.
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393
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Ganjali Dashti M, Abdeshahian P, Sudesh K, Phua KK. Optimization of Salmonella Typhi biofilm assay on polypropylene microtiter plates using response surface methodology. BIOFOULING 2016; 32:477-487. [PMID: 26963754 DOI: 10.1080/08927014.2015.1135328] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The objective of this study was to develop an optimized assay for Salmonella Typhi biofilm that mimics the environment of the gallbladder as an experimental model for chronic typhoid fever. Multi-factorial assays are difficult to optimize using traditional one-factor-at-a-time optimization methods. Response surface methodology (RSM) was used to optimize six key variables involved in S. Typhi biofilm formation on cholesterol-coated polypropylene 96-well microtiter plates. The results showed that bile (1.22%), glucose (2%), cholesterol (0.05%) and potassium chloride (0.25%) were critical factors affecting the amount of biofilm produced, but agitation (275 rpm) and sodium chloride (0.5%) had antagonistic effects on each other. Under these optimum conditions the maximum OD reading for biofilm formation was 3.4 (λ600 nm), and the coefficients of variation for intra-plate and inter-plate assays were 3% (n = 20) and 5% (n = 8), respectively. These results showed that RSM is an effective approach for biofilm assay optimization.
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Affiliation(s)
- M Ganjali Dashti
- a Ecobiomaterial Research Laboratory, School of Biological Sciences , Universiti Sains Malaysia , Penang , Malaysia
- b Enteric Diseases Research Cluster, Institute for Research in Molecular Medicine (INFORMM) , Universiti Sains Malaysia , Penang , Malaysia
| | - P Abdeshahian
- c Department of Bioprocess Engineering, Faculty of Chemical Engineering , Universiti Teknologi Malaysia, UTM , Skudai , Johor , Malaysia
| | - K Sudesh
- a Ecobiomaterial Research Laboratory, School of Biological Sciences , Universiti Sains Malaysia , Penang , Malaysia
| | - K K Phua
- b Enteric Diseases Research Cluster, Institute for Research in Molecular Medicine (INFORMM) , Universiti Sains Malaysia , Penang , Malaysia
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394
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Barzegar Amiri Olia M, Zavras A, Schiesser CH, Alexander SA. Blue ‘turn-on’ fluorescent probes for the direct detection of free radicals and nitric oxide in Pseudomonas aeruginosa biofilms. Org Biomol Chem 2016; 14:2272-81. [DOI: 10.1039/c5ob02441b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Novel blue cell-permeable ‘turn-on’ fluorescent probes have been developed to visualize and quantify nitric oxide and free radical formation and reaction within aPseudomonas aeruginosabiofilm.
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Affiliation(s)
- Mina Barzegar Amiri Olia
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
- Australia
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute
- The University of Melbourne
- Victoria
| | - Athanasios Zavras
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
- Australia
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute
- The University of Melbourne
- Victoria
| | - Carl H. Schiesser
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
- Australia
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute
- The University of Melbourne
- Victoria
| | - Stefanie-Ann Alexander
- ARC Centre of Excellence for Free Radical Chemistry and Biotechnology
- Australia
- School of Chemistry and Bio21 Molecular Science and Biotechnology Institute
- The University of Melbourne
- Victoria
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395
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Gambino M, Cappitelli F. Mini-review: Biofilm responses to oxidative stress. BIOFOULING 2016; 32:167-178. [PMID: 26901587 DOI: 10.1080/08927014.2015.1134515] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 12/14/2015] [Indexed: 06/05/2023]
Abstract
Biofilms constitute the predominant microbial style of life in natural and engineered ecosystems. Facing harsh environmental conditions, microorganisms accumulate reactive oxygen species (ROS), potentially encountering a dangerous condition called oxidative stress. While high levels of oxidative stress are toxic, low levels act as a cue, triggering bacteria to activate effective scavenging mechanisms or to shift metabolic pathways. Although a complex and fragmentary picture results from current knowledge of the pathways activated in response to oxidative stress, three main responses are shown to be central: the existence of common regulators, the production of extracellular polymeric substances, and biofilm heterogeneity. An investigation into the mechanisms activated by biofilms in response to different oxidative stress levels could have important consequences from ecological and economic points of view, and could be exploited to propose alternative strategies to control microbial virulence and deterioration.
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Affiliation(s)
- Michela Gambino
- a Department of Food, Environmental and Nutrition Sciences , Università degli Studi di Milano , Milan , Italy
| | - Francesca Cappitelli
- a Department of Food, Environmental and Nutrition Sciences , Università degli Studi di Milano , Milan , Italy
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396
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Pointing SB. Hypolithic Communities. BIOLOGICAL SOIL CRUSTS: AN ORGANIZING PRINCIPLE IN DRYLANDS 2016. [DOI: 10.1007/978-3-319-30214-0_11] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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397
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Wolinsky E, Libby E. Evolution of regulated phenotypic expression during a transition to multicellularity. Evol Ecol 2015. [DOI: 10.1007/s10682-015-9814-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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398
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Iron oxide nanoparticle-mediated hyperthermia stimulates dispersal in bacterial biofilms and enhances antibiotic efficacy. Sci Rep 2015; 5:18385. [PMID: 26681339 PMCID: PMC4683393 DOI: 10.1038/srep18385] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/17/2015] [Indexed: 11/08/2022] Open
Abstract
The dispersal phase that completes the biofilm lifecycle is of particular interest for its potential to remove recalcitrant, antimicrobial tolerant biofilm infections. Here we found that temperature is a cue for biofilm dispersal and a rise by 5 °C or more can induce the detachment of Pseudomonas aeruginosa biofilms. Temperature upshifts were found to decrease biofilm biomass and increase the number of viable freely suspended cells. The dispersal response appeared to involve the secondary messenger cyclic di-GMP, which is central to a genetic network governing motile to sessile transitions in bacteria. Furthermore, we used poly((oligo(ethylene glycol) methyl ether acrylate)-block-poly(monoacryloxy ethyl phosphate)-stabilized iron oxide nanoparticles (POEGA-b-PMAEP@IONPs) to induce local hyperthermia in established biofilms upon exposure to a magnetic field. POEGA-b-PMAEP@IONPs were non-toxic to bacteria and when heated induced the detachment of biofilm cells. Finally, combined treatments of POEGA-b-PMAEP@IONPs and the antibiotic gentamicin reduced by 2-log the number of colony-forming units in both biofilm and planktonic phases after 20 min, which represent a 3.2- and 4.1-fold increase in the efficacy against planktonic and biofilm cells, respectively, compared to gentamicin alone. The use of iron oxide nanoparticles to disperse biofilms may find broad applications across a range of clinical and industrial settings.
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399
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Abstract
In recent years, remarkable progress has been made in the field of virus environmental ecology. In marine ecosystems, for example, viruses are now thought to play pivotal roles in the biogeochemical cycling of nutrients and to be mediators of microbial evolution through horizontal gene transfer. The diversity and ecology of viruses in soils are poorly understood, but evidence supports the view that the diversity and ecology of viruses in soils differ substantially from those in aquatic systems. Desert biomes cover ∼ 33% of global land masses, and yet the diversity and roles of viruses in these dominant ecosystems remain poorly understood. There is evidence that hot hyperarid desert soils are characterized by high levels of bacterial lysogens and low extracellular virus counts. In contrast, cold desert soils contain high extracellular virus titers. We suggest that the prevalence of microbial biofilms in hyperarid soils, combined with extreme thermal regimens, exerts strong selection pressures on both temperate and virulent viruses. Many desert soil virus sequences show low values of identity to virus genomes in public databases, suggesting the existence of distinct and as-yet-uncharacterized soil phylogenetic lineages (e.g., cyanophages). We strongly advocate for amplification-free metavirome analyses while encouraging the classical isolation of phages from dominant and culturable microbial isolates in order to populate sequence databases. This review provides an overview of recent advances in the study of viruses in hyperarid soils and of the factors that contribute to viral abundance and diversity in hot and cold deserts and offers technical recommendations for future studies.
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Yu SH, Hu J, Ercole F, Truong NP, Davis TP, Whittaker MR, Quinn JF. Transformation of RAFT Polymer End Groups into Nitric Oxide Donor Moieties: En Route to Biochemically Active Nanostructures. ACS Macro Lett 2015; 4:1278-1282. [PMID: 35614828 DOI: 10.1021/acsmacrolett.5b00733] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Polymers with a terminal S-nitrosothiol moiety were synthesized by modifying the thiocarbonylthio end group formed by reversible addition-fragmentation chain transfer polymerization. Specifically, benzodithioate-terminated poly[oligo(ethylene glycol) methyl ether methacrylate] (POEGMA) was first synthesized by polymerizing OEGMA in the presence of 4-cyano-4-(phenylcarbonothioylthio)pentanoic acid. Sequential treatment with hydrazine hydrate and a stoichiometric amount of nitrous acid resulted in the formation of S-nitrosothiol-terminated polymers. A similar approach was applied to block copolymers of POEGMA incorporating a domain of poly[(N,N-diisopropylamino)ethyl methacrylate], thus, enabling the preparation of pH responsive nitric oxide (NO)-releasing micelles. The micelles possessed substantially modified S-nitrosothiol loss kinetics compared to the hydrophilic homopolymer analogue. Moreover, thiol-triggered degradation of the S-nitrosothiol was significantly slower when the S-nitrosothiol was embedded in a micellar structure. These results demonstrate that it is possible to incorporate nitric oxide donor moieties directly onto a polymer chain end, enabling simple synthesis of biochemically active nanostructures.
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Affiliation(s)
- Sul Hwa Yu
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Jinming Hu
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Francesca Ercole
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Nghia P. Truong
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Thomas P. Davis
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
- Department
of Chemistry, University of Warwick, Coventry, ULCV4 7AL, United Kingdom
| | - Michael R. Whittaker
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - John F. Quinn
- ARC
Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
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