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Yan J, Xie J. Comparative Proteome Analysis of Shewanella putrefaciens WS13 Mature Biofilm Under Cold Stress. Front Microbiol 2020; 11:1225. [PMID: 32582122 PMCID: PMC7296144 DOI: 10.3389/fmicb.2020.01225] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 05/14/2020] [Indexed: 12/19/2022] Open
Abstract
Worldwide, Shewanella putrefaciens is the predominant seafood spoilage microorganism during cold storage. This bacterium can attach to biotic/abiotic surfaces to form biofilms which contribute to seafood quality degradation and shelf-life reduction. The mechanism of S. putrefaciens biofilm formation is not yet described. Crystal violet staining in combination with confocal laser scanning microscopy (CLSM) was used to study the sequence of events leading to the establishment of a mature biofilm at 4, 15, and 30°C. In addition, the main chemical constituents of the mature biofilm were determined by Raman spectroscopy (RM), whereas, comparative proteomic analysis was used to quantify changes in metabolic pathways and to find out underlying protein determinants. The physical dimensions of the mature biofilm, i.e., biomass, biovolume, and mean thickness, were higher at 4°C when compared to 15 and 30°C. The variations of proteins measured by RM confirmed the importance of proteins during the formation of a mature biofilm. Comparative proteomic analysis showed that siderophore and iron chelate transport proteins were down-regulated during mature biofilm formation. The down-regulated aforementioned proteins are involved in promoting iron storage in response to a higher demand for metabolic energy, whereas, the upregulated proteins of the sulfur relay system, pyrimidine metabolism, and purine metabolism are related to bacterial adaptability. Synthesis of proteins related to cold stress was increased and proteins involved in aminoacyl-tRNA biosynthesis were up-regulated, whereas, proteins involved in aminopeptidase activity were down-regulated. Proteolysis to scavenge energy was reduced as proteins involved in pyrophosphatase activity were up-regulated. Also extracellular eDNA was found which may play an important role in maintaining the stability of mature S. putrefaciens biofilm structures under cold stress. This work provides a better understanding of the role of proteins in mature biofilms. In addition, the biofilm formation mechanism of a psychrotrophic spoilage bacterial species at low temperature is explored, which may contribute to generating biofilm controlling strategies during seafood preservation and processing.
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Affiliation(s)
- Jun Yan
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
- Laboratory for Quality and Safety Risk Assessment of Aquatic Products in Storage and Preservation of Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
| | - Jing Xie
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
- Laboratory for Quality and Safety Risk Assessment of Aquatic Products in Storage and Preservation of Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China
- Shanghai Professional Technology Service Platform on Cold Chain Equipment Performance and Energy Saving Evaluation, Shanghai Ocean University, Shanghai, China
- National Experimental Teaching Demonstration Center for Food Science and Engineering, Shanghai Ocean University, Shanghai, China
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Sarkar S. Release mechanisms and molecular interactions of Pseudomonas aeruginosa extracellular DNA. Appl Microbiol Biotechnol 2020; 104:6549-6564. [PMID: 32500267 DOI: 10.1007/s00253-020-10687-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/10/2020] [Accepted: 05/17/2020] [Indexed: 12/18/2022]
Abstract
Pseudomonas aeruginosa infection is a significant threat for clinicians. Increasing incidents of resistant biofilm infection result in high mortality rates worldwide. There is a considerable current interest in the field of extracellular DNA (eDNA)-mediated P. aeruginosa biofilm formation. eDNA acts as a glue to make biofilm more stable. This review focuses on the diverse mechanisms and factors, which enhance the eDNA release into the extracellular milieu. Furthermore, eDNA-mediated molecular interactions within the biofilm are emphasized. In addition, drug resistance mechanisms due to the versatility of eDNA are discussed. Spatial physiological diversity is expected due to different metabolic activity of bacterial subpopulation present in P. aeruginosa biofilm layers. In P. aeruginosa, eDNA release is accomplished by cell lysis and OMVs (outer membrane vesicles). eDNA release is a spontaneous and multifactorial process, which may be accomplished by PQS, pyocyanin, and lambda prophage induction. Hydrogen peroxide and pyocin trigger cell death, which may facilitate eDNA release. Lung mucosa of cystic fibrosis patients is enriched with eDNA, which acidifies biofilm and develops P. aeruginosa resistance to aminoglycosides. Further studies on spatial and molecular characterization of bacterial subpopulation in biofilm will shed light on eDNA-biofilm interaction more precisely.Key Points• Extracellular DNA (eDNA) is a key component of Pseudomonas aeruginosa biofilm.• P. aeruginosa eDNA acts as a glue to make biofilm more stronger.• Bacterial cell death or lysis may be the potential way to release P. aeruginosa eDNA into extracellular milieu.• P. aeruginosa eDNA contributes to develop resistance to antimicrobials.
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Affiliation(s)
- Subendu Sarkar
- Department of Surgery, University School of Medicine, Indiana University, Indianapolis, IN, 46202, USA. .,Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA.
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Nelson MT, Pope CE, Marsh RL, Wolter DJ, Weiss EJ, Hager KR, Vo AT, Brittnacher MJ, Radey MC, Hayden HS, Eng A, Miller SI, Borenstein E, Hoffman LR. Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles. Cell Rep 2020; 26:2227-2240.e5. [PMID: 30784601 PMCID: PMC6435281 DOI: 10.1016/j.celrep.2019.01.091] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/20/2018] [Accepted: 01/25/2019] [Indexed: 01/27/2023] Open
Abstract
Metagenomic sequencing is a promising approach for identifying and characterizing organisms and their functional characteristics in complex, polymicrobial infections, such as airway infections in people with cystic fibrosis. These analyses are often hampered, however, by overwhelming quantities of human DNA, yielding only a small proportion of microbial reads for analysis. In addition, many abundant microbes in respiratory samples can produce large quantities of extracellular bacterial DNA originating either from biofilms or dead cells. We describe a method for simultaneously depleting DNA from intact human cells and extracellular DNA (human and bacterial) in sputum, using selective lysis of eukaryotic cells and endonuclease digestion. We show that this method increases microbial sequencing depth and, consequently, both the number of taxa detected and coverage of individual genes such as those involved in antibiotic resistance. This finding underscores the substantial impact of DNA from sources other than live bacteria in micro-biological analyses of complex, chronic infection specimens. Nelson et al. describe a method for reducing both human cellular DNA and extracellular DNA (human and bacterial) in a complex respiratory sample using hypotonic lysis and endonuclease digestion. This method increases effective microbial sequencing depth and minimizes bias introduced into subsequent phylogenetic analysis by bacterial extracellular DNA.
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Affiliation(s)
- Maria T Nelson
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA; Medical Scientist Training Program, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Christopher E Pope
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Robyn L Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Casuarina, NT 0811, Australia
| | - Daniel J Wolter
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA; Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Eli J Weiss
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Kyle R Hager
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Anh T Vo
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Mitchell J Brittnacher
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Matthew C Radey
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Hillary S Hayden
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Alexander Eng
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Samuel I Miller
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA; Department of Medicine, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98105, USA; Department of Computer Science and Engineering, University of Washington School of Medicine, Seattle, WA 98105, USA; Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel; Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Lucas R Hoffman
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA; Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA.
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54
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Lewenza S, Johnson L, Charron-Mazenod L, Hong M, Mulcahy-O'Grady H. Extracellular DNA controls expression of Pseudomonas aeruginosa genes involved in nutrient utilization, metal homeostasis, acid pH tolerance and virulence. J Med Microbiol 2020; 69:895-905. [PMID: 32242794 DOI: 10.1099/jmm.0.001184] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Introduction. Pseudomonas aeruginosa grows in extracellular DNA (eDNA)-enriched biofilms and infection sites. eDNA is generally considered to be a structural biofilm polymer required for aggregation and biofilm maturation. In addition, eDNA can sequester divalent metal cations, acidify growth media and serve as a nutrient source.Aim. We wanted to determine the genome-wide influence on the transcriptome of planktonic P. aeruginosa PAO1 grown in the presence of eDNA.Methodology. RNA-seq analysis was performed to determine the genome-wide effects on gene expression of PAO1 grown with eDNA. Transcriptional lux fusions were used to confirm eDNA regulation and to validate phenotypes associated with growth in eDNA.Results. The transcriptome of eDNA-regulated genes included 89 induced and 76 repressed genes (FDR<0.05). A large number of eDNA-induced genes appear to be involved in utilizing DNA as a nutrient. Several eDNA-induced genes are also induced by acidic pH 5.5, and eDNA/acidic pH promoted an acid tolerance response in P. aeruginosa. The cyoABCDE terminal oxidase is induced by both eDNA and pH 5.5, and contributed to the acid tolerance phenotype. Quantitative metal analysis confirmed that DNA binds to diverse metals, which helps explain why many genes involved in a general uptake of metals were controlled by eDNA. Growth in the presence of eDNA also promoted intracellular bacterial survival and influenced virulence in the acute infection model of fruit flies.Conclusion. The diverse functions of the eDNA-regulated genes underscore the important role of this extracellular polymer in promoting antibiotic resistance, virulence, acid tolerance and nutrient utilization; phenotypes that contribute to long-term survival.
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Affiliation(s)
- Shawn Lewenza
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Cummings School of Medicine, Snyder Institute of Chronic Diseases, Calgary, Alberta, Canada.,Athabasca University, Faculty of Science and Technology, Athabasca, Alberta, Canada
| | - Lori Johnson
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Cummings School of Medicine, Snyder Institute of Chronic Diseases, Calgary, Alberta, Canada
| | - Laetitia Charron-Mazenod
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Cummings School of Medicine, Snyder Institute of Chronic Diseases, Calgary, Alberta, Canada
| | - Mia Hong
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Cummings School of Medicine, Snyder Institute of Chronic Diseases, Calgary, Alberta, Canada
| | - Heidi Mulcahy-O'Grady
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Cummings School of Medicine, Snyder Institute of Chronic Diseases, Calgary, Alberta, Canada
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Kovach KN, Fleming D, Wells MJ, Rumbaugh KP, Gordon VD. Specific Disruption of Established Pseudomonas aeruginosa Biofilms Using Polymer-Attacking Enzymes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:1585-1595. [PMID: 31990563 PMCID: PMC7063831 DOI: 10.1021/acs.langmuir.9b02188] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Biofilms are communities of bacteria embedded in a polymeric matrix which are found in infections and in environments outside the body. Breaking down the matrix renders biofilms more susceptible to physical disruption and to treatments such as antibiotics. Different species of bacteria, and different strains within the same species, produce different types of matrix polymers. This suggests that targeting specific polymers for disruption may be more effective than nonspecific approaches to disrupting biofilm matrixes. In this study, we treated Pseudomonas aeruginosa biofilms with enzymes that are specific to different matrix polymers. We measured the resulting alteration in biofilm mechanics using bulk rheology and changes in structure using electron microscopy. We find that, for biofilms grown in vitro, the effect of enzymatic treatment is greatest when the enzyme is specific to a dominant matrix polymer. Specifically matched enzymatic treatment tends to reduce yield strain and yield stress and increase the rate of biofilm drying, due to increased diffusivity as a result of network compromise. Electron micrographs qualitatively suggest that well-matched enzymatic treatments reduce long-range structure and shorten connecting network fibers. Previous work has shown that generic glycoside hydrolases can cause dispersal of bacteria from in vivo and ex vivo biofilms into a free-swimming state, and thereby make antibiotic treatment more effective. For biofilms grown in wounded mice, we find that well-matched treatments that result in the greatest mechanical compromise in vitro induce the least dispersal ex vivo. Moreover, we find that generic glycoside hydrolases have no measurable effect on the mechanics of biofilms grown in vitro, while previous work has shown them to be highly effective at inducing dispersal in vivo and ex vivo. This highlights the possibility that effective approaches to eradicating biofilms may depend strongly on the growth environment.
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Affiliation(s)
- Kristin N Kovach
- Department of Physics and Center for Nonlinear Dynamics , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Derek Fleming
- Department of Surgery , Texas Tech University Health Sciences Center , Lubbock , Texas 79430 , United States
| | - Marilyn J Wells
- Department of Physics and Center for Nonlinear Dynamics , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Kendra P Rumbaugh
- Department of Surgery , Texas Tech University Health Sciences Center , Lubbock , Texas 79430 , United States
| | - Vernita Diane Gordon
- Department of Physics and Center for Nonlinear Dynamics , The University of Texas at Austin , Austin , Texas 78712 , United States
- Institute for Cellular and Molecular Biology , The University of Texas at Austin , Austin , Texas 78712 , United States
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Yuan G, Li P, Xu X, Li P, Zhong Q, He S, Yi H, Yi W, Guan Y, Wen ZT. Azalomycin F 5a Eradicates Staphylococcus aureus Biofilm by Rapidly Penetrating and Subsequently Inducing Cell Lysis. Int J Mol Sci 2020; 21:ijms21030862. [PMID: 32013221 PMCID: PMC7036916 DOI: 10.3390/ijms21030862] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 12/14/2022] Open
Abstract
Antimicrobial resistance has emerged as a serious threat to public health. Bacterial biofilm, as a natural lifestyle, is a major contributor to resistance to antimicrobials. Azalomycin F5a, a natural guanidine-containing polyhydroxy macrolide, has remarkable activities against Gram-positive bacteria, including Staphylococcus aureus, a major causative agent of hospital-acquired infections. To further evaluate its potential to be developed as a new antimicrobial agent, its influence on S. aureus biofilm formation was evaluated using the crystal violet method, and then its eradication effect against mature biofilms was determined by confocal laser scanning microscopy, the drop plate method, and regrowth experiments. The results showed that azalomycin F5a could significantly inhibit S. aureus biofilm formation, and such effects were concentration dependent. In addition, it can also eradicate S. aureus mature biofilms with the minimum biofilm eradication concentration of 32.0 μg/mL. As extracellular deoxyribonucleic acid (eDNA) plays important roles in the structural integrity of bacterial biofilm, its influence on the eDNA release in S. aureus biofilm was further analyzed using gel electrophoresis. Combined with our previous works, these results indicate that azalomycin F5a could rapidly penetrate biofilm and causes damages to the cell membrane, leading to an increase in DNase release and eventually eradicating S. aureus biofilm.
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Affiliation(s)
- Ganjun Yuan
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (P.L.); (Q.Z.)
- Department of Oral and Craniofacial Biology, Louisiana State University Health Sciences Center, New Orleans, LA 70119, USA
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70119, USA
- Correspondence: (G.Y.); (Z.T.W.); Tel.: +86-791-83813459 (G.Y.); +1-504-9418465 (Z.T.W.)
| | - Pingyi Li
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (P.L.); (Q.Z.)
| | - Xuejie Xu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (P.L.); (Q.Z.)
| | - Peibo Li
- School of Life Sciences, Sun Yat-sen University, 135 Xingang Road, Guangzhou 510275, China
| | - Qiwang Zhong
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (P.L.); (Q.Z.)
| | - Su He
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (P.L.); (Q.Z.)
| | - Houqin Yi
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (P.L.); (Q.Z.)
| | - Wenfang Yi
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (P.L.); (Q.Z.)
| | - Yingying Guan
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang 330045, China; (P.L.); (Q.Z.)
| | - Zezhang Tom Wen
- Department of Oral and Craniofacial Biology, Louisiana State University Health Sciences Center, New Orleans, LA 70119, USA
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA 70119, USA
- Correspondence: (G.Y.); (Z.T.W.); Tel.: +86-791-83813459 (G.Y.); +1-504-9418465 (Z.T.W.)
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Desai S, Sanghrajka K, Gajjar D. High Adhesion and Increased Cell Death Contribute to Strong Biofilm Formation in Klebsiella pneumoniae. Pathogens 2019; 8:pathogens8040277. [PMID: 31805671 PMCID: PMC6963951 DOI: 10.3390/pathogens8040277] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/14/2019] [Accepted: 11/28/2019] [Indexed: 01/29/2023] Open
Abstract
Klebsiella pneumoniae (Kp), is a frequent cause of hospital and community-acquired infections and WHO had declared it as a "priority pathogen". Biofilm is a major virulence factor of Kp and yet the mechanism of strong biofilm formation in Kp is unclear. A key objective of the present study is to investigate the differences between strong and weak biofilms formed by clinical isolates of Kp on various catheters and in different media conditions and to identify constituents contributing to strong biofilm formation. Quantification of matrix components (extracellular DNA (eDNA), protein, exopolysaccharides (EPS), and bacterial cells), confocal laser scanning microscopy (CLSM), field emission gun scanning electron microscopy (FEG-SEM) and flow-cytometry analysis were performed to compare strong and weak biofilm matrix. Our results suggest increased biofilm formation on latex catheters compared to silicone and silicone-coated latex catheters. Higher amounts of eDNA, protein, EPS, and dead cells were observed in the strong biofilm of Kp. High adhesion capacity and cell death seem to play a major role in formation of strong Kp biofilms. The enhanced eDNA, EPS, and protein in the biofilm matrix appear as a consequence of increased cell death.
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Silva MOD, Pernthaler J. Priming of microcystin degradation in carbon-amended membrane biofilm communities is promoted by oxygen-limited conditions. FEMS Microbiol Ecol 2019; 95:5582606. [PMID: 31589311 PMCID: PMC6804753 DOI: 10.1093/femsec/fiz157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/04/2019] [Indexed: 01/09/2023] Open
Abstract
Microbial biofilms are an important element of gravity-driven membrane (GDM) filtration systems for decentralized drinking water production. Mature biofilms fed with biomass from the toxic cyanobacterium Microcystis aeruginosa efficiently remove the cyanotoxin microcystin (MC). MC degradation can be ‘primed’ by prior addition of biomass from a non-toxic M. aeruginosa strain. Increased proportions of bacteria with an anaerobic metabolism in M. aeruginosa-fed biofilms suggest that this ‘priming’ could be due to higher productivity and the resulting changes in habitat conditions. We, therefore, investigated GDM systems amended with the biomass of toxic (WT) or non-toxic (MUT) M. aeruginosa strains, of diatoms (DT), or with starch solution (ST). After 25 days, these treatments were changed to receiving toxic cyanobacterial biomass. MC degradation established significantly more rapidly in MUT and ST than in DT. Oxygen measurements suggested that this was due to oxygen-limited conditions in MUT and ST already prevailing before addition of MC-containing biomass. Moreover, the microbial communities in the initial ST biofilms featured high proportions of facultative anaerobic taxa, whereas aerobes dominated in DT biofilms. Thus, the ‘priming’ of MC degradation in mature GDM biofilms seems to be related to the prior establishment of oxygen-limited conditions mediated by higher productivity.
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Affiliation(s)
- Marisa O D Silva
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Seestrasse 187, CH-8802 Kilchberg, Switzerland
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Seestrasse 187, CH-8802 Kilchberg, Switzerland
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Zulkefli NS, Kim KH, Hwang SJ. Effects of Microbial Activity and Environmental Parameters on the Degradation of Extracellular Environmental DNA from a Eutrophic Lake. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16183339. [PMID: 31510040 PMCID: PMC6765872 DOI: 10.3390/ijerph16183339] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/21/2019] [Accepted: 09/05/2019] [Indexed: 12/26/2022]
Abstract
Extracellular DNA (exDNA) pool in aquatic environments is a valuable source for biomonitoring and bioassessment. However, degradation under particular environmental conditions can hamper exDNA detectability over time. In this study, we analyzed how different biotic and abiotic factors affect the degradation rate of extracellular environmental DNA using 16S rDNA sequences extracted from the sediment of a eutrophic lake and Anabaena variabilis cultured in the laboratory. We exposed the extracted exDNA to different levels of temperature, light, pH, and bacterial activity, and quantitatively analyzed the concentration of exDNA during 4 days. The solution containing bacteria for microbial activity treatment was obtained from the lake sediment using four consecutive steps of filtration; two mesh filters (100 μm and 60 μm mesh) and two glass fiber filters (2.7 μm and 1.2 μm pore-sized). We found that temperature individually and in combination with bacterial abundance had significant positive effects on the degradation of exDNA. The highest degradation rate was observed in samples exposed to high microbial activity, where exDNA was completely degraded within 1 day at a rate of 3.27 day−1. Light intensity and pH had no significant effects on degradation rate of exDNA. Our results indicate that degradation of exDNA in freshwater ecosystems is driven by the combination of both biotic and abiotic factors and it may occur very fast under particular conditions.
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Affiliation(s)
| | - Keon-Hee Kim
- Human & Eco-Care Center, Department of Environmental Health Science, Konkuk University, Seoul 05029, Korea.
| | - Soon-Jin Hwang
- Department of Environmental Health Science, Konkuk University, Seoul 05029, Korea.
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Lachica MRCT, Anutrakunchai C, Prajaneh S, Nazmi K, Bolscher JGM, Taweechaisupapong S. Synergistic effects of LFchimera and antibiotic against planktonic and biofilm form of Aggregatibacter actinomycetemcomitans. PLoS One 2019; 14:e0217205. [PMID: 31329599 PMCID: PMC6645458 DOI: 10.1371/journal.pone.0217205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/07/2019] [Indexed: 12/02/2022] Open
Abstract
Adjunctive use of antibiotics in periodontal treatment have limitations and disadvantages including bacterial resistance. Antimicrobial peptides (AMPs) are potential new agents that can combat bacterial infection. In this study, antimicrobial activity of different concentrations of conventional antibiotics minocycline (MH), doxycycline (DOX), and antimicrobial peptides LL-37, LL-31, Lactoferrin chimera (LFchimera) and Innate Defense Regulator Peptide 1018 (IDR-1018) against Aggregatibacter actinomycetemcomitans ATCC 43718 were determined using colony culturing assay. Subsequently, in vitro activity of the most effective drug and peptide combination was evaluated by checkerboard technique. Impact of the drug and peptide co-administration on biofilm at different stages, i.e., during adhesion and 1-day old biofilm was compared to each of the agents used alone. Results revealed that the killing effects of all AMPs range from 13–100%. In contrast, MH and DOX at 1 and 5 μM showed no killing activity and instead stimulated growth of bacteria. DOX has better killing activity than MH. LFchimera displayed the strongest killing amongst the peptides. Checkerboard technique revealed that combining DOX and LFchimera yielded synergism. Confocal laser scanning microscopy further showed that the combination of DOX and LFchimera caused significant reduction of bacterial adhesion and reduction of biomass, average biofilm thickness and substratum biofilm coverage of 1-day old biofilm compared to DOX and LFchimera alone. In conclusion, LFchimera alone and in combination with DOX exhibited strong antibacterial and anti-biofilm property against A. actinomycetemcomitans. The findings suggest that LFchimera should be considered for development as a new potential therapeutic agent that may be used as an adjunctive treatment for periodontitis.
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Affiliation(s)
- Marie Rossini Carmela T. Lachica
- Biofilm Research Group, Faculty of Dentistry, Khon Kaen University, Khon Kaen, Thailand
- Department of Periodontology, Faculty of Dentistry, Khon Kaen University, Khon Kaen, Thailand
| | | | - Saengsome Prajaneh
- Department of Periodontology, Faculty of Dentistry, Khon Kaen University, Khon Kaen, Thailand
| | - Kamran Nazmi
- Department of Oral Biochemistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
| | - Jan G. M. Bolscher
- Department of Oral Biochemistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
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Abstract
We developed a new approach that couples Southwestern blotting and mass spectrometry to discover proteins that bind extracellular DNA (eDNA) in bacterial biofilms. Using Staphylococcus aureus as a model pathogen, we identified proteins with known DNA-binding activity and uncovered a series of lipoproteins with previously unrecognized DNA-binding activity. We demonstrated that expression of these lipoproteins results in an eDNA-dependent biofilm enhancement. Additionally, we found that while deletion of lipoproteins had a minimal impact on biofilm accumulation, these lipoprotein mutations increased biofilm porosity, suggesting that lipoproteins and their associated interactions contribute to biofilm structure. For one of the lipoproteins, SaeP, we showed that the biofilm phenotype requires the lipoprotein to be anchored to the outside of the cellular membrane, and we further showed that increased SaeP expression correlates with more retention of high-molecular-weight DNA on the bacterial cell surface. SaeP is a known auxiliary protein of the SaeRS system, and we also demonstrated that the levels of SaeP correlate with nuclease production, which can further impact biofilm development. It has been reported that S. aureus biofilms are stabilized by positively charged cytoplasmic proteins that are released into the extracellular environment, where they make favorable electrostatic interactions with the negatively charged cell surface and eDNA. In this work we extend this electrostatic net model to include secreted eDNA-binding proteins and membrane-attached lipoproteins that can function as anchor points between eDNA in the biofilm matrix and the bacterial cell surface.IMPORTANCE Many bacteria are capable of forming biofilms encased in a matrix of self-produced extracellular polymeric substances (EPS) that protects them from chemotherapies and the host defenses. As a result of these inherent resistance mechanisms, bacterial biofilms are extremely difficult to eradicate and are associated with chronic wounds, orthopedic and surgical wound infections, and invasive infections, such as infective endocarditis and osteomyelitis. It is therefore important to understand the nature of the interactions between the bacterial cell surface and EPS that stabilize biofilms. Extracellular DNA (eDNA) has been recognized as an EPS constituent for many bacterial species and has been shown to be important in promoting biofilm formation. Using Staphylococcus aureus biofilms, we show that membrane-attached lipoproteins can interact with the eDNA in the biofilm matrix and promote biofilm formation, which suggests that lipoproteins are potential targets for novel therapies aimed at disrupting bacterial biofilms.
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Neves SO, Magalhães LMD, Corrêa JD, Dutra WO, Gollob KJ, Silva TA, Horta MCR, Souza PEA. Composite-derived monomers affect cell viability and cytokine expression in human leukocytes stimulated with Porphyromonas gingivalis. J Appl Oral Sci 2019; 27:e20180529. [PMID: 31166413 PMCID: PMC6546269 DOI: 10.1590/1678-7757-2018-0529] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/09/2018] [Accepted: 12/30/2018] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES Dental composites release unreacted resin monomers into the oral environment, even after polymerization. Periodontal cells are, therefore, exposed to substances that potentially elicit the immune inflammatory response. The underlying molecular mechanisms associated with the interaction between resin monomers and human immune cells found in the gingival crevicular fluid are not fully understood yet. This study investigated the ability of bisphenol A-glycidyl methacrylate (BISGMA), urethane dimethacrylate (UDMA) and triethylene glycol dimethacrylate (TEGDMA) to induce apoptosis and cytokine release by human leukocytes stimulated with a periodontal pathogen. METHODOLOGY Peripheral blood mononuclear cells (PBMC) from 16 healthy individuals were included in this study. To determine the toxicity, the PBMC were incubated for 20 hours, with monomers, for the analysis of cell viability using MTT assay. To evaluate cell death in the populations of monocytes and lymphocytes, they were exposed to sub-lethal doses of each monomer and of heat-inactivated Porphyromonas gingivalis (P. gingivalis) for 5 hours. Secretions of IL-1β, IL-6, IL-10 and TNF-α were determined by ELISA after 20 hours. RESULTS UDMA and TEGDMA induced apoptosis after a short-time exposure. Bacterial challenge induced significant production of IL-1β and TNF-α (p<0.05). TEGDMA reduced the bacterial-induced release of IL-1β and TNF-α, whereas UDMA reduced IL-1β release (p<0.05). These monomers did not affect IL-10 and IL-6 secretion. BISGMA did not significantly interfere in cytokine release. CONCLUSIONS These results show that resin monomers are toxic to PBMC in a dose-dependent manner, and may influence the local immune inflammatory response and tissue damage mechanisms via regulation of bacterial-induced IL-1β and TNF-α secretion by PBMC.
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Affiliation(s)
- Sheyla Omonte Neves
- Pontifícia Universidade Católica de Minas Gerais, Departamento de Odontologia, Programa de Pós-graduação em Odontologia, Belo Horizonte, Minas Gerais, Brasil
| | - Luísa Mourão Dias Magalhães
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departmento de Morfologia, Belo Horizonte, Minas Gerais, Brasil
| | - Jôice Dias Corrêa
- Pontifícia Universidade Católica de Minas Gerais, Departamento de Odontologia, Programa de Pós-graduação em Odontologia, Belo Horizonte, Minas Gerais, Brasil
- Universidade Federal de Minas Gerais, Faculdade de Odontologia, Belo Horizonte, Minas Gerais, Brasil
| | - Walderez Ornelas Dutra
- Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Departmento de Morfologia, Belo Horizonte, Minas Gerais, Brasil
- Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais – INCT-DT, Belo Horizonte, Minas Gerais, Brasil
| | - Kenneth John Gollob
- International Research Center, A.C.Camargo Cancer Center, São Paulo, SP, Brasil
- Instituto Nacional de Ciência e Tecnologia em Doenças Tropicais – INCT-DT, Belo Horizonte, Minas Gerais, Brasil
| | - Tarcília Aparecida Silva
- Universidade Federal de Minas Gerais, Faculdade de Odontologia, Belo Horizonte, Minas Gerais, Brasil
| | - Martinho Campolina Rebello Horta
- Pontifícia Universidade Católica de Minas Gerais, Departamento de Odontologia, Programa de Pós-graduação em Odontologia, Belo Horizonte, Minas Gerais, Brasil
| | - Paulo Eduardo Alencar Souza
- Pontifícia Universidade Católica de Minas Gerais, Departamento de Odontologia, Programa de Pós-graduação em Odontologia, Belo Horizonte, Minas Gerais, Brasil
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Al-Wahaibi ASM, Lapinska E, Rajarajan N, Dobretsov S, Upstill-Goddard R, Burgess JG. Secretion of DNases by Marine Bacteria: A Culture Based and Bioinformatics Approach. Front Microbiol 2019; 10:969. [PMID: 31134017 PMCID: PMC6514286 DOI: 10.3389/fmicb.2019.00969] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/16/2019] [Indexed: 01/23/2023] Open
Abstract
The vast majority of bacteria present in the natural environment are present in the form of aggregates and/or biofilms. Microbial aggregates are ubiquitous in the marine environment and are inhabited by diverse microbial communities which often express intense extracellular enzymatic activities. However, the secretion of an important group of enzymes, DNases, by bacteria from marine aggregates has not been studied, despite the importance of these aggregates in biogeochemical cycling of nutrients in the oceans. In this work, we therefore, employed both culture-based and bioinformatics approaches to understand the diversity of bacterial DNases in marine bacterioplankton. We found that 34% of 345 strains of attached and non-attached marine bacteria showed extracellular DNase activity. Most of these isolates belong to Proteobacteria (53%) and Firmicutes (34%). Secretion of DNases by bacteria isolated from marine gel particles (MGP) is reported here for the first time. Then, to further understand the wider diversity of the potential to produce DNases, sequences were compared using 2316 whole genome and 42 metagenome datasets. Thirty-nine different taxonomic groups corresponding to 10 bacterial phyla were found to encode genes responsible for DNase secretion. This study highlights the unexpected and widespread presence of DNase secretion in bacteria in general and in MGP more specifically. This has important implications for understanding the dynamics and fate of marine microbial aggregates in the oceans.
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Affiliation(s)
- Aisha S. M. Al-Wahaibi
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, Al Khoud, Oman
| | - Emilia Lapinska
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Nithyalakshmy Rajarajan
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sergey Dobretsov
- Centre of Excellence in Marine Biotechnology, Sultan Qaboos University, Al Khoud, Oman
- Department of Marine Science and Fisheries, Sultan Qaboos University, Al Khoud, Oman
| | - Robert Upstill-Goddard
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - J. Grant Burgess
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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Zheng J, Xia Y, Liu Q, He X, Yu J, Feng Y. Extracellular DNA enhances the formation and stability of symplasmata in Pantoea agglomerans YS19. J GEN APPL MICROBIOL 2019; 65:11-17. [PMID: 30185735 DOI: 10.2323/jgam.2018.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Extracellular DNA (eDNA) is an important polymeric substance that plays essential roles in cell aggregation and nutrient provision for the sessile bacteria. eDNA in bacterial biofilms was extensively studied. Here we found that eDNA also exists in symplasmata, a bacterial cell aggregate, which is different to a biofilm, in the rice enophyte Pantoea agglomerans YS19. We found that exogenous eDNA enhanced the formation and stability of symplasmata significantly, and that, exogenous eDNA also improved the stress resistance and colonization ability of the bacterium on host rice. These results strongly indicate novel roles of the eDNA in Pantoea agglomerans YS19, showing its special relation to the stress-resistance and endophyte-host association of the strain.
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Affiliation(s)
- Jing Zheng
- School of Life Science, Beijing Institute of Technology
| | - Yifan Xia
- School of Life Science, Beijing Institute of Technology
| | - Qi Liu
- School of Life Science, Beijing Institute of Technology
| | - Xinyu He
- School of Life Science, Beijing Institute of Technology
| | - Jiajia Yu
- School of Life Science, Beijing Institute of Technology
| | - Yongjun Feng
- School of Life Science, Beijing Institute of Technology
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Tan A, Li WS, Verderosa AD, Blakeway LV, D Mubaiwa T, Totsika M, Seib KL. Moraxella catarrhalis NucM is an entry nuclease involved in extracellular DNA and RNA degradation, cell competence and biofilm scaffolding. Sci Rep 2019; 9:2579. [PMID: 30796312 PMCID: PMC6384898 DOI: 10.1038/s41598-019-39374-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/18/2019] [Indexed: 11/10/2022] Open
Abstract
Moraxella catarrhalis is a host-adapted bacterial pathogen that causes otitis media and exacerbations of chronic obstructive pulmonary disease. This study characterises the conserved M. catarrhalis extracellular nuclease, a member of the ββα metal finger family of nucleases, that we have named NucM. NucM shares conserved sequence motifs from the ββα nuclease family, including the DRGH catalytic core and Mg2+ co-ordination site, but otherwise shares little primary sequence identity with other family members, such as the Serratia Nuc and pneumococcal EndA nucleases. NucM is secreted from the cell and digests linear and circular nucleic acid. However, it appears that a proportion of NucM is also associated with the cell membrane and acts as an entry nuclease, facilitating transformation of M. catarrhalis cells. This is the first example of a ββα nuclease in a Gram negative bacteria that acts as an entry nuclease. In addition to its role in competence, NucM affects cell aggregation and biofilm formation by M. catarrhalis, with ΔnucM mutants having increased biofilm biomass. NucM is likely to increase the ability of cells to survive and persist in vivo, increasing the virulence of M. catarrhalis and potentially affecting the behaviour of other pathogens that co-colonise the otorhinolaryngological niche.
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Affiliation(s)
- Aimee Tan
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Wing-Sze Li
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Anthony D Verderosa
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4006, Australia
| | - Luke V Blakeway
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Tsitsi D Mubaiwa
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia
| | - Makrina Totsika
- Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, 4006, Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, 4215, Australia.
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Alves-Barroco C, Roma-Rodrigues C, Balasubramanian N, Guimarães MA, Ferreira-Carvalho BT, Muthukumaran J, Nunes D, Fortunato E, Martins R, Santos-Silva T, Figueiredo AMS, Fernandes AR, Santos-Sanches I. Biofilm development and computational screening for new putative inhibitors of a homolog of the regulatory protein BrpA in Streptococcus dysgalactiae subsp. dysgalactiae. Int J Med Microbiol 2019; 309:169-181. [PMID: 30799091 DOI: 10.1016/j.ijmm.2019.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 02/14/2019] [Accepted: 02/17/2019] [Indexed: 01/15/2023] Open
Abstract
Streptococcus dysgalactiae subsp. dysgalactiae (SDSD), a Lancefield group C streptococci (GCS), is a frequent cause of bovine mastitis. This highly prevalent disease is the costliest in dairy industry. Adherence and biofilm production are important factors in streptoccocal pathogenesis. We have previously described the adhesion and internalization of SDSD isolates in human cells and now we describe the biofilm production capability of this bacterium. In this work we integrated microbiology, imaging and computational methods to evaluate the biofilm production capability of SDSD isolates; to assess the presence of biofilm regulatory protein BrpA homolog in the biofilm producers; and to predict a structural model of BrpA-like protein and its binding to putative inhibitors. Our results show that SDSD isolates form biofilms on abiotic surface such as glass (hydrophilic) and polystyrene (hydrophobic), with the strongest biofilm formation observed in glass. This ability was mainly associated with a proteinaceous extracellular matrix, confirmed by the dispersion of the biofilms after proteinase K and trypsin treatment. The biofilm formation in SDSD isolates was also confirmed by confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM). Under SEM observation, VSD16 isolate formed cell aggregates during biofilm growth while VSD9 and VSD10 formed smooth and filmy layers. We show that brpA-like gene is present and expressed in SDSD biofilm-producing isolates and its expression levels correlated with the biofilm production capability, being more expressed in the late exponential phase of planktonic growth compared to biofilm growth. Fisetin, a known biofilm inhibitor and a putative BrpA binding molecule, dramatically inhibited biofilm formation by the SDSD isolates but did not affect planktonic growth, at the tested concentrations. Homology modeling was used to predict the 3D structure of BrpA-like protein. Using high throughput virtual screening and molecular docking, we selected five ligand molecules with strong binding affinity to the hydrophobic cleft of the protein, making them potential inhibitor candidates of the SDSD BrpA-like protein. These results warrant further investigations for developing novel strategies for SDSD anti-biofilm therapy.
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Affiliation(s)
- Cinthia Alves-Barroco
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Catarina Roma-Rodrigues
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Natesan Balasubramanian
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal; Department of Immunology, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India
| | | | | | - Jayaraman Muthukumaran
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Daniela Nunes
- i3N/CENIMAT, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, Caparica, Portugal
| | - Elvira Fortunato
- i3N/CENIMAT, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, Caparica, Portugal
| | - Rodrigo Martins
- i3N/CENIMAT, Departamento de Ciência dos Materiais, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Campus de Caparica, Caparica, Portugal
| | - Teresa Santos-Silva
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.
| | - Agnes M S Figueiredo
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, RJ, Brazil.
| | - Alexandra R Fernandes
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.
| | - Ilda Santos-Sanches
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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Sadiq FA, Flint S, Sakandar HA, He G. Molecular regulation of adhesion and biofilm formation in high and low biofilm producers of Bacillus licheniformis using RNA-Seq. BIOFOULING 2019; 35:143-158. [PMID: 30884970 DOI: 10.1080/08927014.2019.1575960] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 01/14/2019] [Accepted: 01/22/2019] [Indexed: 06/09/2023]
Abstract
RNA sequencing was used to reveal transcriptional changes during the motile-to-sessile switch in high and low biofilm-forming dairy strains of B. licheniformis isolated from Chinese milk powders. A significant part of the whole gene content was affected during this transition in both strains. In terms of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, seven metabolic pathways were significantly downregulated in the planktonic state compared to the biofilm state in both strains. Lipid and sugar metabolism seemed to play an important role in matrix production. Several genes involved in adhesion, matrix production and the matrix coating were either absent or less expressed in the biofilm state of the low biofilm producer compared to the high biofilm producer. Genes related to sporulation and the production of extracellular polymeric substances were concomitantly expressed in the biofilm state of both strains. These comprehensive insights will be helpful for future research into mechanisms and targets.
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Affiliation(s)
- Faizan Ahmed Sadiq
- a School of Food Science and Technology , Jiangnan University , Wuxi , PR China
- b College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou , PR China
| | - Steve Flint
- c School of Food and Nutrition , Massey University , Private Bag 11 222 , Palmerston North , New Zealand
| | - Hafiz Arbab Sakandar
- a School of Food Science and Technology , Jiangnan University , Wuxi , PR China
- d Faculty of Biological Sciences , Quaid-i-Azam University , Islamabad , Pakistan
| | - GuoQing He
- b College of Biosystems Engineering and Food Science , Zhejiang University , Hangzhou , PR China
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Ebner P, Götz F. Bacterial Excretion of Cytoplasmic Proteins (ECP): Occurrence, Mechanism, and Function. Trends Microbiol 2019; 27:176-187. [DOI: 10.1016/j.tim.2018.10.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 09/11/2018] [Accepted: 10/16/2018] [Indexed: 12/28/2022]
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69
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Boháčová M, Pazlarová J, Fuchsová V, Švehláková T, Demnerová K. Quantitative evaluation of biofilm extracellular DNA by fluorescence-based techniques. Folia Microbiol (Praha) 2019; 64:567-577. [DOI: 10.1007/s12223-019-00681-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/10/2019] [Indexed: 10/27/2022]
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YU MK, KIM MA, ROSA V, HWANG YC, DEL FABBRO M, SOHN WJ, MIN KS. Role of extracellular DNA in Enterococcus faecalis biofilm formation and its susceptibility to sodium hypochlorite. J Appl Oral Sci 2019; 27:e20180699. [PMID: 31411265 PMCID: PMC9648955 DOI: 10.1590/1678-7757-2018-0699] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/25/2019] [Indexed: 12/04/2022] Open
Abstract
Objective This study investigated the role of extracellular deoxyribonucleic acid (eDNA) on Enterococcus faecalis ( E. faecalis ) biofilm and the susceptibility of E. faecalis to sodium hypochlorite (NaOCl). Methodology E. faecalis biofilm was formed in bovine tooth specimens and the biofilm was cultured with or without deoxyribonuclease (DNase), an inhibitor of eDNA. Then, the role of eDNA in E. faecalis growth and biofilm formation was investigated using colony forming unit (CFUs) counting, eDNA level assay, crystal violet staining, confocal laser scanning microscopy, and scanning electron microscopy. The susceptibility of E. faecalis biofilm to low (0.5%) or high (5%) NaOCl concentrations was also analyzed by CFU counting. Results CFUs and biofilm formation decreased significantly with DNase treatment (p<0.05). The microstructure of DNase-treated biofilms exhibited less structured features when compared to the control. The volume of exopolysaccharides in the DNase-treated biofilm was significantly lower than that of control (p<0.05). Moreover, the CFUs, eDNA level, biofilm formation, and exopolysaccharides volume were lower when the biofilm was treated with DNase de novo when compared to when DNase was applied to matured biofilm (p<0.05). E. faecalis in the biofilm was more susceptible to NaOCl when it was cultured with DNase (p<0.05). Furthermore, 0.5% NaOCl combined with DNase treatment was as efficient as 5% NaOCl alone regarding susceptibility (p>0.05). Conclusions Inhibition of eDNA leads to decrease of E. faecalis biofilm formation and increase of susceptibility of E. faecalis to NaOCl even at low concentrations. Therefore, our results suggest that inhibition of eDNA would be beneficial in facilitating the efficacy of NaOCl and reducing its concentration.
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Affiliation(s)
- Mi-Kyung YU
- Chonbuk National University, Korea; Chonbuk National University, Korea; Chonbuk National University Hospital, Korea
| | | | | | | | - Massimo DEL FABBRO
- Università degli Studi di Milano, Italy; IRCCS Istituto Ortopedico Galeazzi, Italy
| | | | - Kyung-San MIN
- Chonbuk National University, Korea; Chonbuk National University, Korea; Chonbuk National University Hospital, Korea
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71
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Marsh PD. In Sickness and in Health-What Does the Oral Microbiome Mean to Us? An Ecological Perspective. Adv Dent Res 2018; 29:60-65. [PMID: 29355410 DOI: 10.1177/0022034517735295] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The oral microbiome is natural and has a symbiotic relationship with the host by delivering important benefits. In oral health, a dynamic balance is reached between the host, the environment, and the microbiome. However, the frequent intake of sugar and/or reductions in saliva flow results in extended periods of low pH in the biofilm, which disrupts this symbiotic relationship. Such conditions inhibit the growth of beneficial species and drive the selection of bacteria with an acid-producing/acid-tolerating phenotype, thereby increasing the risk of caries (dysbiosis). A more detailed understanding of the interdependencies and interactions that exist among the resident microbiota in dental biofilms, and an increased awareness of the relationship between the host and the oral microbiome, is providing new insights and fresh opportunities to promote symbiosis and prevent dysbiosis. These include modifying the oral microbiome (e.g., with prebiotics and probiotics), manipulating the oral environment to selectively favor the growth of beneficial species, and moderating the growth and metabolism of the biofilm to reduce the likelihood of dysbiosis. Evidence is provided to suggest that the regular provision of interventions that deliver small but relevant benefits, consistently over a prolonged period, can support the maintenance of a symbiotic oral microbiome.
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Affiliation(s)
- P D Marsh
- 1 Department of Oral Biology, School of Dentistry, University of Leeds, Leeds, UK
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Gaylarde C, Baptista-Neto JA, Tabasco-Novelo C, Ortega-Morales O. Weathering of granitic gneiss: A geochemical and microbiological study in the polluted sub-tropical city of Rio de Janeiro. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 644:1641-1647. [PMID: 30743877 DOI: 10.1016/j.scitotenv.2018.07.303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 07/21/2018] [Accepted: 07/21/2018] [Indexed: 06/09/2023]
Abstract
Chemical and biological weathering were studied on two historic churches in the city of Rio de Janeiro, Brazil. The churches exhibited contour scaling, granular disintegration and black crust development. High levels of SO4 were found in façade stones of one church, São José, with significant levels of lead and copper. This suggests that vehicle emissions were important in stonework decay. Both gypsum and halite were detected, typical of buildings influenced by marine atmosphere and fuel-polluted environment. There was little bioweathering on this church, although the filamentous cyanobacterium Scytonema detected could be involved in black crust production. The other church (Nossa Senhora da Gloria) showed strong granular disintegration, with a green coloration on internal surfaces of some flakes removed for study. This church showed lower levels of geochemically important weathering compounds but was more colonized by fungi and cyanobacteria. The latter were shown by scanning electron microscopy to grow within the granitic gneiss stone and were probably involved in dissolution and redeposition of minerals. This church is rather far from the intense traffic of the centre of Rio de Janeiro and from Guanabara Bay, source of marine aerosols; it is located upon a green hill, where plant-associated fungi and cyanobacteria can readily gain access to the façade. The results of this study show the importance of local environment on the relative proportions of chemical and biological weathering of stone.
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Affiliation(s)
- Christine Gaylarde
- Department of Microbiology and Plant Biology, Oklahoma University, 770 Van Vleet Oval, Norman, OK 73019, USA.
| | | | - Carolina Tabasco-Novelo
- Department of Applied Physics, CINVESTAV-Unidad Mérida, Carretera Antigua a Progreso, Km. 6, 97310 Mérida, Yucatán, Mexico
| | - Otto Ortega-Morales
- Departamento de Microbiología Ambiental y Biotecnología, Universidad Autónoma de Campeche, Av. Agustín Melgar s/n, Col. Buenavista, C.P. 24039, Campeche, Campeche, Mexico
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Rodríguez-Melcón C, Riesco-Peláez F, Carballo J, García-Fernández C, Capita R, Alonso-Calleja C. Structure and viability of 24- and 72-h-old biofilms formed by four pathogenic bacteria on polystyrene and glass contact surfaces. Food Microbiol 2018; 76:513-517. [DOI: 10.1016/j.fm.2018.06.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/25/2018] [Accepted: 06/24/2018] [Indexed: 01/07/2023]
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Curli-Containing Enteric Biofilms Inside and Out: Matrix Composition, Immune Recognition, and Disease Implications. Microbiol Mol Biol Rev 2018; 82:82/4/e00028-18. [PMID: 30305312 DOI: 10.1128/mmbr.00028-18] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Biofilms of enteric bacteria are highly complex, with multiple components that interact to fortify the biofilm matrix. Within biofilms of enteric bacteria such as Escherichia coli and Salmonella species, the main component of the biofilm is amyloid curli. Other constituents include cellulose, extracellular DNA, O antigen, and various surface proteins, including BapA. Only recently, the roles of these components in the formation of the enteric biofilm individually and in consortium have been evaluated. In addition to enhancing the stability and strength of the matrix, the components of the enteric biofilm influence bacterial virulence and transmission. Most notably, certain components of the matrix are recognized as pathogen-associated molecular patterns. Systemic recognition of enteric biofilms leads to the activation of several proinflammatory innate immune receptors, including the Toll-like receptor 2 (TLR2)/TLR1/CD14 heterocomplex, TLR9, and NLRP3. In the model of Salmonella enterica serovar Typhimurium, the immune response to curli is site specific. Although a proinflammatory response is generated upon systemic presentation of curli, oral administration of curli ameliorates the damaged intestinal epithelial barrier and reduces the severity of colitis. Furthermore, curli (and extracellular DNA) of enteric biofilms potentiate the autoimmune disease systemic lupus erythematosus (SLE) and promote the fibrillization of the pathogenic amyloid α-synuclein, which is implicated in Parkinson's disease. Homologues of curli-encoding genes are found in four additional bacterial phyla, suggesting that the biomedical implications involved with enteric biofilms are applicable to numerous bacterial species.
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Kim M, Jeon J, Kim J. Streptococcus mutans extracellular DNA levels depend on the number of bacteria in a biofilm. Sci Rep 2018; 8:13313. [PMID: 30190485 PMCID: PMC6127218 DOI: 10.1038/s41598-018-31275-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/14/2018] [Indexed: 01/01/2023] Open
Abstract
Streptococcus mutans is a component of oral plaque biofilm that accumulates on the surface of teeth. The biofilm consists of extracellular components including extracellular DNA (eDNA). This study was conducted to investigate the factors that may affect the eDNA levels of S. mutans in biofilms. For the study, S. mutans UA159 biofilms were formed for 52 h on hydroxyapatite (HA) discs in 0% (w/v) sucrose +0% glucose, 0.5% sucrose, 1% sucrose, 0.5% glucose, 1% glucose, or 0.5% sucrose +0.5% glucose. Acidogenicity of S. mutans in the biofilms was measured after biofilm formation (22 h) up to 52 h. eDNA was collected after 52 h biofilm formation and measured using DNA binding fluorescent dye, SYBR Green I. Biofilms cultured in 0.5% sucrose or glucose had more eDNA and colony forming units (CFUs) and less exopolysaccharides (EPSs) than the biofilms cultured in 1% sucrose or glucose at 52 h, respectively. The biofilms formed in 0% sucrose +0% glucose maintained pH around 7, while the biofilms grown in 0.5% sucrose had more acidogenicity than those grown in 1% sucrose, and the same pattern was shown in glucose. In conclusion, the results of this study show that the number of S. mutans in biofilms affects the concentrations of eDNA as well as the acidogenicity of S. mutans in the biofilms. In addition, the thickness of EPS is irrelevant to eDNA aggregation within biofilms.
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Affiliation(s)
- Miah Kim
- Department of Conservative Dentistry, Chonbuk National University, 567 Baekjaedaero, Jeonju-city Jeonbuk, 54896, South Korea
| | - Jaegyu Jeon
- Department of Preventive Dentistry, School of Dentistry, Chonbuk National University, 567 Baekjaedaero, Jeonju-city Jeonbuk, 54896, South Korea
| | - Jaegon Kim
- Department of Pediatric Dentistry, School of Dentistry, Chonbuk National University, 567 Baekjaedaero, Jeonju-city Jeonbuk, 54896, South Korea.
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Lin H, Wang C, Zhao H, Chen G, Chen X. Interaction between copper and extracellular nucleic acids in the EPS of unsaturated Pseudomonas putida CZ1 biofilm. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:24172-24180. [PMID: 29948696 DOI: 10.1007/s11356-018-2473-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/01/2018] [Indexed: 06/08/2023]
Abstract
The role of extracellular DNA (eDNA) in biofilm in heavy metal complexation has been little reported. In this study, the interaction between the extracellular fraction of unsaturated biofilms and Cu2+ was studied using random amplified polymorphic DNA (RAPD) and synchrotron-based X-ray absorption spectroscopy (XAS) analyses. Under Cu2+ stress, the amount of eDNA was about 10-fold higher than the treatment without Cu2+ stress, which was substantially more than the amount of intracellular DNA (iDNA) present in the biofilm. The eDNA content increased significantly under Cu2+ stress and higher eDNA contents were found in colloidal extracellular polymeric substances (EPS) than in capsular EPS in Luria-Bertani medium. It was found that the composition of eDNA was distinctly changed under conditions of Cu2+ stress compared with the treatments without Cu2+ treatments, with specific eDNA bands appearing under Cu2+ treatments as revealed by RAPD analyses. X-ray absorption fine structure (XAFS) analysis assessing the molecular speciation of copper showed that copper in the secreted eDNA mainly existed as species resembling Cu3(PO4)2, followed by Cu-citrate species. This study investigated the interaction between copper and eDNA in unsaturated Pseudomonas putida CZ1 biofilms. Potential function of eDNA in biofilms under Cu2+ stress was found.
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Affiliation(s)
- Huirong Lin
- Department of Environmental Science and Engineering, College of Chemical Engineering, Huaqiao University, Xiamen, 361021, Fujian, China
| | - Chengyun Wang
- The First Affiliated Hospital of Xiamen University, Xiamen, 361003, People's Republic of China
| | - Hongmei Zhao
- Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, 398 Ruoshui Road, SEID, Suzhou Industrial Park, Suzhou, Jiangsu Province, 215123, People's Republic of China
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Guangcun Chen
- Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, 398 Ruoshui Road, SEID, Suzhou Industrial Park, Suzhou, Jiangsu Province, 215123, People's Republic of China.
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China.
| | - Xincai Chen
- Department of Environmental Engineering, Zhejiang University, Hangzhou, 310058, People's Republic of China
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Effect of DNase Treatment on Adhesion and Early Biofilm Formation of Enterococcus Faecalis. Eur Endod J 2018; 3:82-86. [PMID: 32161861 PMCID: PMC7006568 DOI: 10.14744/eej.2018.55264] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/20/2018] [Accepted: 05/22/2018] [Indexed: 11/20/2022] Open
Abstract
Objective Extracellular DNA (eDNA) has been shown to be important for biofilm stability of the endodontic pathogen Enterococcus faecalis. In this study, we hypothesized that treatment with DNase prevents adhesion and disperses young E. faecalis biofilms in 96-well plates and root canals of extracted teeth. Methods E. faecalis eDNA in 96-well plates was visualized with TOTO-1®. The effect of DNase treatment was assessed in 96-well plates and in extracted single-rooted premolars (n=37) using a two-phase crossover design. E. faecalis was treated with DNase (50 Kunitz/mL) or heat-inactivated DNase for 1 h during adhesion or after 24 h of biofilm formation. In 96-well plates, adhering cells were quantified using confocal microscopy and digital image analysis. In root canals, the number of adhering cells was determined in dentine samples based on colony forming unit counts. Data from the 96-well plate were analyzed using one-tailed t-tests, and data from extracted teeth were analyzed using mixed-effect Poisson regressions. Results eDNA was present in wells colonized by E. faecalis after 1 h of adhesion and 24 h of biofilm formation; it was removed by DNase treatment, as evidenced by TOTO®-1 staining. DNase treatment reduced the area covered by cells in 96-well plates after 1 h (P<0.05), but not after 24 h (P=0.96). No significant differences in the number of adhering cells were observed in extracted teeth after 1 (P=0.14) and 24 h (P=0.98). Conclusion DNase treatment does not disperse endodontic E. faecalis biofilms. The sole use of DNase as an anti-biofilm agent in root canal treatments is not recommendable.
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78
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Bakshani CR, Morales-Garcia AL, Althaus M, Wilcox MD, Pearson JP, Bythell JC, Burgess JG. Evolutionary conservation of the antimicrobial function of mucus: a first defence against infection. NPJ Biofilms Microbiomes 2018; 4:14. [PMID: 30002868 PMCID: PMC6031612 DOI: 10.1038/s41522-018-0057-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/05/2018] [Accepted: 06/06/2018] [Indexed: 02/07/2023] Open
Abstract
Mucus layers often provide a unique and multi-functional hydrogel interface between the epithelial cells of organisms and their external environment. Mucus has exceptional properties including elasticity, changeable rheology and an ability to self-repair by re-annealing, and is therefore an ideal medium for trapping and immobilising pathogens and serving as a barrier to microbial infection. The ability to produce a functional surface mucosa was an important evolutionary step, which evolved first in the Cnidaria, which includes corals, and the Ctenophora. This allowed the exclusion of non-commensal microbes and the subsequent development of the mucus-lined digestive cavity seen in higher metazoans. The fundamental architecture of the constituent glycoprotein mucins is also evolutionarily conserved. Although an understanding of the biochemical interactions between bacteria and the mucus layer are important to the goal of developing new antimicrobial strategies, they remain relatively poorly understood. This review summarises the physicochemical properties and evolutionary importance of mucus, which make it so successful in the prevention of bacterial infection. In addition, the strategies developed by bacteria to counteract the mucus layer are also explored.
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Affiliation(s)
- Cassie R Bakshani
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Ana L Morales-Garcia
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Mike Althaus
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew D Wilcox
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Jeffrey P Pearson
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - John C Bythell
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - J Grant Burgess
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
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79
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Dragoš A, Kiesewalter H, Martin M, Hsu CY, Hartmann R, Wechsler T, Eriksen C, Brix S, Drescher K, Stanley-Wall N, Kümmerli R, Kovács ÁT. Division of Labor during Biofilm Matrix Production. Curr Biol 2018; 28:1903-1913.e5. [PMID: 29887307 DOI: 10.1016/j.cub.2018.04.046] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/13/2018] [Accepted: 04/13/2018] [Indexed: 01/06/2023]
Abstract
Organisms as simple as bacteria can engage in complex collective actions, such as group motility and fruiting body formation. Some of these actions involve a division of labor, where phenotypically specialized clonal subpopulations or genetically distinct lineages cooperate with each other by performing complementary tasks. Here, we combine experimental and computational approaches to investigate potential benefits arising from division of labor during biofilm matrix production. We show that both phenotypic and genetic strategies for a division of labor can promote collective biofilm formation in the soil bacterium Bacillus subtilis. In this species, biofilm matrix consists of two major components, exopolysaccharides (EPSs) and TasA. We observed that clonal groups of B. subtilis phenotypically segregate into three subpopulations composed of matrix non-producers, EPS producers, and generalists, which produce both EPSs and TasA. This incomplete phenotypic specialization was outperformed by a genetic division of labor, where two mutants, engineered as specialists, complemented each other by exchanging EPSs and TasA. The relative fitness of the two mutants displayed a negative frequency dependence both in vitro and on plant roots, with strain frequency reaching a stable equilibrium at 30% TasA producers, corresponding exactly to the population composition where group productivity is maximized. Using individual-based modeling, we show that asymmetries in strain ratio can arise due to differences in the relative benefits that matrix compounds generate for the collective and that genetic division of labor can be favored when it breaks metabolic constraints associated with the simultaneous production of two matrix components.
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Affiliation(s)
- Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs Lyngby 2800, Denmark; Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Heiko Kiesewalter
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Marivic Martin
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs Lyngby 2800, Denmark; Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena 07743, Germany
| | - Chih-Yu Hsu
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Raimo Hartmann
- Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany
| | - Tobias Wechsler
- Department of Plant and Microbial Biology, University of Zürich, Zürich 8057, Switzerland
| | - Carsten Eriksen
- Disease Systems Immunology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Susanne Brix
- Disease Systems Immunology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Marburg 35043, Germany; Department of Physics, Philipps University, Marburg 35037, Germany
| | | | - Rolf Kümmerli
- Department of Plant and Microbial Biology, University of Zürich, Zürich 8057, Switzerland
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs Lyngby 2800, Denmark; Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena 07743, Germany.
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80
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Boháčová M, Zdeňková K, Tomáštíková Z, Fuchsová V, Demnerová K, Karpíšková R, Pazlarová J. Monitoring of resistance genes in Listeria monocytogenes isolates and their presence in the extracellular DNA of biofilms: a case study from the Czech Republic. Folia Microbiol (Praha) 2018; 63:653-664. [DOI: 10.1007/s12223-018-0603-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/28/2018] [Indexed: 11/29/2022]
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81
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Sałamaszyńska-Guz A, Stefańska I, Bącal P, Binek M. Evaluation of selected phenotypic features among Campylobacter sp. strains of animal origin. Vet Microbiol 2018. [PMID: 29519521 DOI: 10.1016/j.vetmic.2018.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A total of 43 Campylobacter isolates from poultry, cattle and pigs were investigated for their ability to form biofilm. The studied strains were also screened for motility, adhesion and invasion of Caco-2 cells as well as extracellular DNase activity. The relation between biofilm formation and selected phenotypes was examined. Biofilm formation by the tested strains was found as irrespective from their motility and not associated with colonization abilities of human Caco-2 cells. Results of our study show that Campylobacter isolates from various animal sources are able to form biofilm and invade human Caco-2 cells in vitro.
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Affiliation(s)
- Agnieszka Sałamaszyńska-Guz
- Division of Microbiology, Department of Pre-Clinical Sciences, Faculty of Veterinary Medicine, Warsaw University of Live Sciences - SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland.
| | - Ilona Stefańska
- Division of Microbiology, Department of Pre-Clinical Sciences, Faculty of Veterinary Medicine, Warsaw University of Live Sciences - SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Paweł Bącal
- Nałęcz Institute of Biocybernetics and Biomedical Engineering Polish Academy of Sciences, Trojdena 4, Warsaw 02-109, Poland
| | - Marian Binek
- Division of Microbiology, Department of Pre-Clinical Sciences, Faculty of Veterinary Medicine, Warsaw University of Live Sciences - SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland
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82
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Role of cell surface composition and lysis in static biofilm formation by Lactobacillus plantarum WCFS1. Int J Food Microbiol 2018; 271:15-23. [PMID: 29477805 DOI: 10.1016/j.ijfoodmicro.2018.02.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/26/2018] [Accepted: 02/11/2018] [Indexed: 01/20/2023]
Abstract
Next to applications in fermentations, Lactobacillus plantarum is recognized as a food spoilage organism, and its dispersal from biofilms in food processing environments might be implicated in contamination or recontamination of food products. This study provides new insights into biofilm development by L. plantarum WCFS1 through comparative analysis of wild type and mutants affected in cell surface composition, including mutants deficient in the production of Sortase A involved in the covalent attachment of 27 predicted surface proteins to the cell wall peptidoglycan (ΔsrtA) and mutants deficient in the production of capsular polysaccharides (CPS1-4, Δcps1-4). Surface adhesion and biofilm formation studies revealed none of the imposed cell surface modifications to affect the initial attachment of cells to polystyrene while biofilm formation based on Crystal Violet (CV) staining was severely reduced in the ΔsrtA mutant and significantly increased in mutants lacking the cps1 cluster, compared to the wild-type strain. Fluorescence microscopy analysis of biofilm samples pointed to a higher presence of extracellular DNA (eDNA) in cps1 mutants and this corresponded with increased autolysis activity. Subsequent studies using Δacm2 and ΔlytA derivatives affected in lytic behaviour revealed reduced biofilm formation measured by CV staining, confirming the relevance of lysis for the build-up of the biofilm matrix with eDNA.
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83
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Hall CW, Mah TF. Molecular mechanisms of biofilm-based antibiotic resistance and tolerance in pathogenic bacteria. FEMS Microbiol Rev 2018; 41:276-301. [PMID: 28369412 DOI: 10.1093/femsre/fux010] [Citation(s) in RCA: 887] [Impact Index Per Article: 147.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 02/22/2017] [Indexed: 02/06/2023] Open
Abstract
Biofilms are surface-attached groups of microbial cells encased in an extracellular matrix that are significantly less susceptible to antimicrobial agents than non-adherent, planktonic cells. Biofilm-based infections are, as a result, extremely difficult to cure. A wide range of molecular mechanisms contribute to the high degree of recalcitrance that is characteristic of biofilm communities. These mechanisms include, among others, interaction of antimicrobials with biofilm matrix components, reduced growth rates and the various actions of specific genetic determinants of antibiotic resistance and tolerance. Alone, each of these mechanisms only partially accounts for the increased antimicrobial recalcitrance observed in biofilms. Acting in concert, however, these defences help to ensure the survival of biofilm cells in the face of even the most aggressive antimicrobial treatment regimens. This review summarises both historical and recent scientific data in support of the known biofilm resistance and tolerance mechanisms. Additionally, suggestions for future work in the field are provided.
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84
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Baslé A, Hewitt L, Koh A, Lamb HK, Thompson P, Burgess JG, Hall MJ, Hawkins AR, Murray H, Lewis RJ. Crystal structure of NucB, a biofilm-degrading endonuclease. Nucleic Acids Res 2018; 46:473-484. [PMID: 29165717 PMCID: PMC5758888 DOI: 10.1093/nar/gkx1170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/13/2017] [Indexed: 01/23/2023] Open
Abstract
Bacterial biofilms are a complex architecture of cells that grow on moist interfaces, and are held together by a molecular glue of extracellular proteins, sugars and nucleic acids. Biofilms are particularly problematic in human healthcare as they can coat medical implants and are thus a potential source of disease. The enzymatic dispersal of biofilms is increasingly being developed as a new strategy to treat this problem. Here, we have characterized NucB, a biofilm-dispersing nuclease from a marine strain of Bacillus licheniformis, and present its crystal structure together with the biochemistry and a mutational analysis required to confirm its active site. Taken together, these data support the categorization of NucB into a unique subfamily of the ββα metal-dependent non-specific endonucleases. Understanding the structure and function of NucB will facilitate its future development into an anti-biofilm therapeutic agent.
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Affiliation(s)
- Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Lorraine Hewitt
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Alan Koh
- Centre for Bacterial Cell Biology, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Heather K Lamb
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Paul Thompson
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - J Grant Burgess
- Marine Biology, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Michael J Hall
- Chemistry, School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Alastair R Hawkins
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Heath Murray
- Centre for Bacterial Cell Biology, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK,To whom correspondence should be addressed. Tel: +44 191 208 5482;
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85
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Interplay between Antibiotic Efficacy and Drug-Induced Lysis Underlies Enhanced Biofilm Formation at Subinhibitory Drug Concentrations. Antimicrob Agents Chemother 2017; 62:AAC.01603-17. [PMID: 29061740 PMCID: PMC5740344 DOI: 10.1128/aac.01603-17] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/13/2017] [Indexed: 12/29/2022] Open
Abstract
Subinhibitory concentrations of antibiotics have been shown to enhance biofilm formation in multiple bacterial species. While antibiotic exposure has been associated with modulated expression of many biofilm-related genes, the mechanisms of drug-induced biofilm formation remain a focus of ongoing research efforts and may vary significantly across species. In this work, we investigate antibiotic-induced biofilm formation in Enterococcus faecalis, a leading cause of nosocomial infections. We show that biofilm formation is enhanced by subinhibitory concentrations of cell wall synthesis inhibitors but not by inhibitors of protein, DNA, folic acid, or RNA synthesis. Furthermore, enhanced biofilm is associated with increased cell lysis, increases in extracellular DNA (eDNA) levels, and increases in the density of living cells in the biofilm. In addition, we observe similar enhancement of biofilm formation when cells are treated with nonantibiotic surfactants that induce cell lysis. These findings suggest that antibiotic-induced biofilm formation is governed by a trade-off between drug toxicity and the beneficial effects of cell lysis. To understand this trade-off, we developed a simple mathematical model that predicts changes in antibiotic-induced biofilm formation due to external perturbations, and we verified these predictions experimentally. Specifically, we demonstrate that perturbations that reduce eDNA (DNase treatment) or decrease the number of living cells in the planktonic phase (a second antibiotic) decrease biofilm induction, while chemical inhibitors of cell lysis increase relative biofilm induction and shift the peak to higher antibiotic concentrations. Overall, our results offer experimental evidence linking cell wall synthesis inhibitors, cell lysis, increased eDNA levels, and biofilm formation in E. faecalis while also providing a predictive quantitative model that sheds light on the interplay between cell lysis and antibiotic efficacy in developing biofilms.
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86
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Rath H, Feng D, Neuweiler I, Stumpp NS, Nackenhorst U, Stiesch M. Biofilm formation by the oral pioneer colonizer Streptococcus gordonii: an experimental and numerical study. FEMS Microbiol Ecol 2017; 93:2966864. [PMID: 28158402 DOI: 10.1093/femsec/fix010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/30/2017] [Indexed: 11/14/2022] Open
Abstract
For decades, extensive research efforts have been conducted to improve the functionality and stability of implants. Especially in dentistry, implant treatment has become a standard medical practice. The treatment restores full dental functionality, helping patients to maintain high quality of life. However, about 10% of the patients suffer from early and late device failure due to peri-implantitis, an inflammatory disease of the tissues surrounding the implant. Peri-implantitis is caused by progressive microbial colonization of the device surface and the formation of microbial communities, so-called biofilms. This infection can ultimately lead to implant failure. The causative agents for the inflammatory disease, periodontal pathogenic biofilms, have already been extensively studied, but are still not completely understood. As numerical simulations will have the potential to predict oral biofilm formation precisely in the future, for the first time, this study aimed to analyze Streptococcus gordonii biofilms by combining experimental studies and numerical simulation. The study demonstrated that numerical simulation was able to precisely model the influence of different nutrient concentration and spatial distribution of active and inactive biomass of the biofilm in comparison with the experimental data. This model may provide a less time-consuming method for the future investigation of any bacterial biofilm.
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Affiliation(s)
- Henryke Rath
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hanover Medical School, Hannover 30625, Germany
| | - Dianlei Feng
- Institute of Fluid Mechanics and Environmental Physics in Civil Engineering, Leibniz Universität Hannover, Hannover 30167, Germany
| | - Insa Neuweiler
- Institute of Fluid Mechanics and Environmental Physics in Civil Engineering, Leibniz Universität Hannover, Hannover 30167, Germany
| | - Nico S Stumpp
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hanover Medical School, Hannover 30625, Germany
| | - Udo Nackenhorst
- Institute of Mechanics and Computational Mechanics, Leibniz Universität Hannover, Hannover 30167, Germany
| | - Meike Stiesch
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hanover Medical School, Hannover 30625, Germany
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87
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Mamou G, Fiyaksel O, Sinai L, Ben-Yehuda S. Deficiency in Lipoteichoic Acid Synthesis Causes a Failure in Executing the Colony Developmental Program in Bacillus subtilis. Front Microbiol 2017; 8:1991. [PMID: 29114240 PMCID: PMC5660684 DOI: 10.3389/fmicb.2017.01991] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 09/27/2017] [Indexed: 01/18/2023] Open
Abstract
Colonies are an abundant form of bacterial multicellularity; however, relatively little is known about the initial stages of their construction. We have previously described that colony development of the soil bacterium Bacillus subtilis is a highly ordered process, typically initiating with the formation of extending cell chains arranged in a Y shape structure. Furthermore, we demonstrated that Y arm extension is a key for defining the size of the future colony. Here we conducted a genetic screen surveying for mutants deficient in these early developmental stages, and revealed LtaS, the major lipoteichoic acid (LTA) synthase, to be crucial for execution of these events. We found that the ltaS mutant fails to produce proper Y shape structures, forming extremely elongated chains of cells with no evidence of chain breakage, necessary for Y shape formation. Furthermore, we show that frequent cell death at the tips of the cell chains is a major cause in limiting arm extension. Collectively, these perturbations lead to the production of a small sized colony by the mutant. Thus, deficiency in LTA synthesis causes a mechanical failure in executing the colony developmental program.
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Affiliation(s)
- Gideon Mamou
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Osher Fiyaksel
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lior Sinai
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sigal Ben-Yehuda
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, The Hebrew University Hadassah Medical School, Hebrew University of Jerusalem, Jerusalem, Israel
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88
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Randrianjatovo-Gbalou I, Rouquette P, Lefebvre D, Girbal-Neuhauser E, Marcato-Romain CE. In situ analysis of Bacillus licheniformis biofilms: amyloid-like polymers and eDNA are involved in the adherence and aggregation of the extracellular matrix. J Appl Microbiol 2017; 122:1262-1274. [PMID: 28214364 DOI: 10.1111/jam.13423] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 12/14/2016] [Accepted: 02/09/2017] [Indexed: 12/11/2022]
Abstract
AIMS This study attempts to determine which of the exopolymeric substances are involved in the adherence and aggregation of a Bacillus licheniformis biofilm. METHODS AND RESULTS The involvement of extracellular proteins and eDNA were particularly investigated using DNase and proteinase K treatment. The permeability of the biofilms increased fivefold after DNase I treatment. The quantification of the matrix components showed that, irrespective to the enzyme tested, eDNA and amyloid-like polymers were removed simultaneously. Size-exclusion chromatography analyses supported these observations and revealed the presence of associated nucleic acid and protein complexes in the biofilm lysates. These data suggest that some extracellular DNA and amyloid-like proteins were closely interlaced within the matrix. Finally, confocal laser scanning microscopy imaging gave supplementary clues about the 3D organization of the biofilms, confirming that eDNA and exoproteins were essentially layered under and around the bacterial cells, whereas the amyloid-like fractions were homogeneously distributed within the matrix. CONCLUSION These results confirm that some DNA-amyloid complexes play a key role in the modulation of the mechanical resistance of B. licheniformis biofilms. SIGNIFICANCE AND IMPACT OF THE STUDY The study highlights the need to consider the whole structure of biofilms and to target the interactions between matrix components. A better understanding of B. licheniformis biofilm physiology and the structural organization of the matrix will strengthen strategies of biofilm control.
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Affiliation(s)
- I Randrianjatovo-Gbalou
- LBAE, Laboratoire de Biotechnologies Agroalimentaire et Environnementale, Institut Universitaire de Technologie, Université de Toulouse, UPS, Auch, France
| | - P Rouquette
- LBAE, Laboratoire de Biotechnologies Agroalimentaire et Environnementale, Institut Universitaire de Technologie, Université de Toulouse, UPS, Auch, France
| | - D Lefebvre
- LBAE, Laboratoire de Biotechnologies Agroalimentaire et Environnementale, Institut Universitaire de Technologie, Université de Toulouse, UPS, Auch, France
| | - E Girbal-Neuhauser
- LBAE, Laboratoire de Biotechnologies Agroalimentaire et Environnementale, Institut Universitaire de Technologie, Université de Toulouse, UPS, Auch, France
| | - C-E Marcato-Romain
- LBAE, Laboratoire de Biotechnologies Agroalimentaire et Environnementale, Institut Universitaire de Technologie, Université de Toulouse, UPS, Auch, France
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89
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Approaches to Dispersing Medical Biofilms. Microorganisms 2017; 5:microorganisms5020015. [PMID: 28368320 PMCID: PMC5488086 DOI: 10.3390/microorganisms5020015] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 03/22/2017] [Accepted: 03/31/2017] [Indexed: 02/07/2023] Open
Abstract
Biofilm-associated infections pose a complex problem to the medical community, in that residence within the protection of a biofilm affords pathogens greatly increased tolerances to antibiotics and antimicrobials, as well as protection from the host immune response. This results in highly recalcitrant, chronic infections and high rates of morbidity and mortality. Since as much as 80% of human bacterial infections are biofilm-associated, many researchers have begun investigating therapies that specifically target the biofilm architecture, thereby dispersing the microbial cells into their more vulnerable, planktonic mode of life. This review addresses the current state of research into medical biofilm dispersal. We focus on three major classes of dispersal agents: enzymes (including proteases, deoxyribonucleases, and glycoside hydrolases), antibiofilm peptides, and dispersal molecules (including dispersal signals, anti-matrix molecules, and sequestration molecules). Throughout our discussion, we provide detailed lists and summaries of some of the most prominent and extensively researched dispersal agents that have shown promise against the biofilms of clinically relevant pathogens, and we catalog which specific microorganisms they have been shown to be effective against. Lastly, we discuss some of the main hurdles to development of biofilm dispersal agents, and contemplate what needs to be done to overcome them.
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90
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Rostami N, Shields RC, Yassin SA, Hawkins AR, Bowen L, Luo TL, Rickard AH, Holliday R, Preshaw PM, Jakubovics NS. A Critical Role for Extracellular DNA in Dental Plaque Formation. J Dent Res 2016; 96:208-216. [PMID: 27770039 DOI: 10.1177/0022034516675849] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Extracellular DNA (eDNA) has been identified in the matrix of many different monospecies biofilms in vitro, including some of those produced by oral bacteria. In many cases, eDNA stabilizes the structure of monospecies biofilms. Here, the authors aimed to determine whether eDNA is an important component of natural, mixed-species oral biofilms, such as plaque on natural teeth or dental implants. To visualize eDNA in oral biofilms, approaches for fluorescently stained eDNA with either anti-DNA antibodies or an ultrasensitive cell-impermeant dye, YOYO-1, were first developed using Enterococcus faecalis, an organism that has previously been shown to produce extensive eDNA structures within biofilms. Oral biofilms were modelled as in vitro "microcosms" on glass coverslips inoculated with the natural microbial population of human saliva and cultured statically in artificial saliva medium. Using antibodies and YOYO-1, eDNA was found to be distributed throughout microcosm biofilms, and was particularly abundant in the immediate vicinity of cells. Similar arrangements of eDNA were detected in biofilms on crowns and overdenture abutments of dental implants that had been recovered from patients during the restorative phase of treatment, and in subgingival dental plaque of periodontitis patients, indicating that eDNA is a common component of natural oral biofilms. In model oral biofilms, treatment with a DNA-degrading enzyme, NucB from Bacillus licheniformis, strongly inhibited the accumulation of biofilms. The bacterial species diversity was significantly reduced by treatment with NucB and particularly strong reductions were observed in the abundance of anaerobic, proteolytic bacteria such as Peptostreptococcus, Porphyromonas and Prevotella. Preformed biofilms were not significantly reduced by NucB treatment, indicating that eDNA is more important or more exposed during the early stages of biofilm formation. Overall, these data demonstrate that dental plaque eDNA is potentially an important target for oral biofilm control.
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Affiliation(s)
- N Rostami
- 1 School of Dental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - R C Shields
- 1 School of Dental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - S A Yassin
- 1 School of Dental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - A R Hawkins
- 2 Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - L Bowen
- 3 Department of Physics, Durham University, Durham, UK
| | - T L Luo
- 4 Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - A H Rickard
- 4 Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - R Holliday
- 1 School of Dental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - P M Preshaw
- 1 School of Dental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - N S Jakubovics
- 1 School of Dental Sciences, Newcastle University, Newcastle upon Tyne, UK
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91
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Watters C, Fleming D, Bishop D, Rumbaugh KP. Host Responses to Biofilm. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 142:193-239. [PMID: 27571696 DOI: 10.1016/bs.pmbts.2016.05.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
From birth to death the human host immune system interacts with bacterial cells. Biofilms are communities of microbes embedded in matrices composed of extracellular polymeric substance (EPS), and have been implicated in both the healthy microbiome and disease states. The immune system recognizes many different bacterial patterns, molecules, and antigens, but these components can be camouflaged in the biofilm mode of growth. Instead, immune cells come into contact with components of the EPS matrix, a diverse, hydrated mixture of extracellular DNA (bacterial and host), proteins, polysaccharides, and lipids. As bacterial cells transition from planktonic to biofilm-associated they produce small molecules, which can increase inflammation, induce cell death, and even cause necrosis. To survive, invading bacteria must overcome the epithelial barrier, host microbiome, complement, and a variety of leukocytes. If bacteria can evade these initial cell populations they have an increased chance at surviving and causing ongoing disease in the host. Planktonic cells are readily cleared, but biofilms reduce the effectiveness of both polymorphonuclear neutrophils and macrophages. In addition, in the presence of these cells, biofilm formation is actively enhanced, and components of host immune cells are assimilated into the EPS matrix. While pathogenic biofilms contribute to states of chronic inflammation, probiotic Lactobacillus biofilms cause a negligible immune response and, in states of inflammation, exhibit robust antiinflammatory properties. These probiotic biofilms colonize and protect the gut and vagina, and have been implicated in improved healing of damaged skin. Overall, biofilms stimulate a unique immune response that we are only beginning to understand.
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Affiliation(s)
- C Watters
- Wound Infections Department, Naval Medical Research Center, Silver Spring, MD, United States
| | - D Fleming
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, United States; Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States
| | - D Bishop
- Wound Infections Department, Naval Medical Research Center, Silver Spring, MD, United States
| | - K P Rumbaugh
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, United States; Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, United States.
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92
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Puga C, SanJose C, Orgaz B. Biofilm development at low temperatures enhances Listeria monocytogenes resistance to chitosan. Food Control 2016. [DOI: 10.1016/j.foodcont.2016.01.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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93
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Loera-Muro A, Jacques M, Avelar-González FJ, Labrie J, Tremblay YDN, Oropeza-Navarro R, Guerrero-Barrera AL. Auxotrophic Actinobacillus pleurpneumoniae grows in multispecies biofilms without the need for nicotinamide-adenine dinucleotide (NAD) supplementation. BMC Microbiol 2016; 16:128. [PMID: 27349384 PMCID: PMC4924255 DOI: 10.1186/s12866-016-0742-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 06/15/2016] [Indexed: 12/22/2022] Open
Abstract
Background Actinobacillus pleuropneumoniae is the etiologic agent of porcine contagious pleuropneumonia, which causes important worldwide economic losses in the swine industry. Several respiratory tract infections are associated with biofilm formation, and A. pleuropneumoniae has the ability to form biofilms in vitro. Biofilms are structured communities of bacterial cells enclosed in a self-produced polymer matrix that are attached to an abiotic or biotic surface. Virtually all bacteria can grow as a biofilm, and multi-species biofilms are the most common form of microbial growth in nature. The goal of this study was to determine the ability of A. pleuropneumoniae to form multi-species biofilms with other bacteria frequently founded in pig farms, in the absence of pyridine compounds (nicotinamide mononucleotide [NMN], nicotinamide riboside [NR] or nicotinamide adenine dinucleotide [NAD]) that are essential for the growth of A. pleuropneumoniae. Results For the biofilm assay, strain 719, a field isolate of A. pleuropneumoniae serovar 1, was mixed with swine isolates of Streptococcus suis, Bordetella bronchiseptica, Pasteurella multocida, Staphylococcus aureus or Escherichia coli, and deposited in 96-well microtiter plates. Based on the CFU results, A. pleuropneumoniae was able to grow with every species tested in the absence of pyridine compounds in the culture media. Interestingly, A. pleuropneumoniae was also able to form strong biofilms when mixed with S. suis, B. bronchiseptica or S. aureus. In the presence of E. coli, A. pleuropneumoniae only formed a weak biofilm. The live and dead populations, and the matrix composition of multi-species biofilms were also characterized using fluorescent markers and enzyme treatments. The results indicated that poly-N-acetyl-glucosamine remains the primary component responsible for the biofilm structure. Conclusions In conclusion, A. pleuropneumoniae apparently is able to satisfy the requirement of pyridine compounds through of other swine pathogens by cross-feeding, which enables A. pleuropneumoniae to grow and form multi-species biofilms. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0742-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Abraham Loera-Muro
- Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Ags., Mexico, 20131
| | - Mario Jacques
- Groupe de recherche sur la maladies infectieuses du porc, Faculté de médecine vétérinaire, Université de Montréal, St-Hyacinthe, Québec, J2S 7C6, Canada
| | | | - Josée Labrie
- Groupe de recherche sur la maladies infectieuses du porc, Faculté de médecine vétérinaire, Université de Montréal, St-Hyacinthe, Québec, J2S 7C6, Canada
| | - Yannick D N Tremblay
- Groupe de recherche sur la maladies infectieuses du porc, Faculté de médecine vétérinaire, Université de Montréal, St-Hyacinthe, Québec, J2S 7C6, Canada
| | - Ricardo Oropeza-Navarro
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico, 62260
| | - Alma L Guerrero-Barrera
- Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Ags., Mexico, 20131. .,Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Ags., Mexico, 20131.
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94
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Sub-Optimal Treatment of Bacterial Biofilms. Antibiotics (Basel) 2016; 5:antibiotics5020023. [PMID: 27338489 PMCID: PMC4929437 DOI: 10.3390/antibiotics5020023] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 05/08/2016] [Accepted: 06/13/2016] [Indexed: 01/22/2023] Open
Abstract
Bacterial biofilm is an emerging clinical problem recognized in the treatment of infectious diseases within the last two decades. The appearance of microbial biofilm in clinical settings is steadily increasing due to several reasons including the increased use of quality of life-improving artificial devices. In contrast to infections caused by planktonic bacteria that respond relatively well to standard antibiotic therapy, biofilm-forming bacteria tend to cause chronic infections whereby infections persist despite seemingly adequate antibiotic therapy. This review briefly describes the responses of biofilm matrix components and biofilm-associated bacteria towards sub-lethal concentrations of antimicrobial agents, which may include the generation of genetic and phenotypic variabilities. Clinical implications of bacterial biofilms in relation to antibiotic treatments are also discussed.
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95
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Sena-Vélez M, Redondo C, Graham JH, Cubero J. Presence of Extracellular DNA during Biofilm Formation by Xanthomonas citri subsp. citri Strains with Different Host Range. PLoS One 2016; 11:e0156695. [PMID: 27248687 PMCID: PMC4889101 DOI: 10.1371/journal.pone.0156695] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/18/2016] [Indexed: 12/23/2022] Open
Abstract
Xanthomonas citri subsp. citri (Xcc) A strain causes citrus bacterial canker, a serious leaf, fruit and stem spotting disease of several Citrus species. X. alfalfae subsp. citrumelonis (Xac) is the cause of citrus bacterial spot, a minor disease of citrus nursery plants and X. campestris pv. campestris (Xc) is a systemic pathogen that causes black rot of cabbage. Xanthomonas spp. form biofilms in planta that facilitate the host infection process. Herein, the role of extracellular DNA (eDNA) was evaluated in the formation and stabilization of the biofilm matrix at different stages of biofilm development. Fluorescence and light microscopy, as well as DNAse treatments, were used to determine the presence of eDNA in biofilms and bacterial cultures. DNAse treatments of Xcc strains and Xac reduced biofilm formation at the initial stage of development, as well as disrupted preformed biofilm. By comparison, no significant effect of the DNAse was detected for biofilm formation by Xc. DNAse effects on biofilm formation or disruption varied among Xcc strains and Xanthomonas species which suggest different roles for eDNA. Variation in the structure of fibers containing eDNA in biofilms, bacterial cultures, and in twitching motility was also visualized by microscopy. The proposed roles for eDNA are as an adhesin in the early stages of biofilm formation, as an structural component of mature bacterial aggregates, and twitching motility structures.
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Affiliation(s)
- Marta Sena-Vélez
- Department of Plant Protection, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Cristina Redondo
- Department of Plant Protection, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - James H. Graham
- Citrus Research and Education Center (CREC), University of Florida, Lake Alfred, Florida, United States of America
| | - Jaime Cubero
- Department of Plant Protection, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
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Hayrapetyan H, Abee T, Nierop Groot M. Sporulation dynamics and spore heat resistance in wet and dry biofilms of Bacillus cereus. Food Control 2016. [DOI: 10.1016/j.foodcont.2015.08.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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97
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Schwartz K, Ganesan M, Payne DE, Solomon MJ, Boles BR. Extracellular DNA facilitates the formation of functional amyloids in Staphylococcus aureus biofilms. Mol Microbiol 2015; 99:123-34. [PMID: 26365835 DOI: 10.1111/mmi.13219] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2015] [Indexed: 11/27/2022]
Abstract
Persistent staphylococcal infections often involve surface-associated communities called biofilms. Staphylococcus aureus biofilm development is mediated by the co-ordinated production of the biofilm matrix, which can be composed of polysaccharides, extracellular DNA (eDNA) and proteins including amyloid fibers. The nature of the interactions between matrix components, and how these interactions contribute to the formation of matrix, remain unclear. Here we show that the presence of eDNA in S. aureus biofilms promotes the formation of amyloid fibers. Conditions or mutants that do not generate eDNA result in lack of amyloids during biofilm growth despite the amyloidogeneic subunits, phenol soluble modulin peptides, being produced. In vitro studies revealed that the presence of DNA promotes amyloid formation by PSM peptides. Thus, this work exposes a previously unacknowledged interaction between biofilm matrix components that furthers our understanding of functional amyloid formation and S. aureus biofilm biology.
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Affiliation(s)
- Kelly Schwartz
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Mahesh Ganesan
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - David E Payne
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.,Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Michael J Solomon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Blaise R Boles
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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98
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An Electrostatic Net Model for the Role of Extracellular DNA in Biofilm Formation by Staphylococcus aureus. J Bacteriol 2015; 197:3779-87. [PMID: 26416831 DOI: 10.1128/jb.00726-15] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/20/2015] [Indexed: 01/22/2023] Open
Abstract
UNLABELLED Staphylococcus aureus is an important human pathogen that can form biofilms on various surfaces. These cell communities are protected from the environment by a self-produced extracellular matrix composed of proteins, DNA, and polysaccharide. The exact compositions and roles of the different components are not fully understood. In this study, we investigated the role of extracellular DNA (eDNA) and its interaction with the recently identified cytoplasmic proteins that have a moonlighting role in the biofilm matrix. These matrix proteins associate with the cell surface upon the drop in pH that naturally occurs during biofilm formation, and we found here that this association is independent of eDNA. Conversely, the association of eDNA with the matrix was dependent on matrix proteins. Both proteinase and DNase treatments severely reduced clumping of resuspended biofilms; highlighting the importance of both proteins and eDNA in connecting cells together. By adding an excess of exogenous DNA to DNase-treated biofilm, clumping was partially restored, confirming the crucial role of eDNA in the interconnection of cells. On the basis of our results, we propose that eDNA acts as an electrostatic net, interconnecting cells surrounded by positively charged matrix proteins at a low pH. IMPORTANCE Extracellular DNA (eDNA) is an important component of the biofilm matrix of diverse bacteria, but its role in biofilm formation is not well understood. Here we report that in Staphylococcus aureus, eDNA associates with cells in a manner that depends on matrix proteins and that eDNA is required to link cells together in the biofilm. These results confirm previous studies that showed that eDNA is an important component of the S. aureus biofilm matrix and also suggest that eDNA acts as an electrostatic net that tethers cells together via the proteinaceous layer of the biofilm matrix.
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Jachlewski S, Jachlewski WD, Linne U, Bräsen C, Wingender J, Siebers B. Isolation of Extracellular Polymeric Substances from Biofilms of the Thermoacidophilic Archaeon Sulfolobus acidocaldarius. Front Bioeng Biotechnol 2015; 3:123. [PMID: 26380258 PMCID: PMC4550784 DOI: 10.3389/fbioe.2015.00123] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 08/10/2015] [Indexed: 11/13/2022] Open
Abstract
Extracellular polymeric substances (EPS) are the major structural and functional components of microbial biofilms. The aim of this study was to establish a method for EPS isolation from biofilms of the thermoacidophilic archaeon, Sulfolobus acidocaldarius, as a basis for EPS analysis. Biofilms of S. acidocaldarius were cultivated on the surface of gellan gum-solidified Brock medium at 78°C for 4 days. Five EPS extraction methods were compared, including shaking of biofilm suspensions in phosphate buffer, cation-exchange resin (CER) extraction, and stirring with addition of EDTA, crown ether, or NaOH. With respect to EPS yield, impact on cell viability, and compatibility with subsequent biochemical analysis, the CER extraction method was found to be the best suited isolation procedure resulting in the detection of carbohydrates and proteins as the major constituents and DNA as a minor component of the EPS. Culturability of CER-treated cells was not impaired. Analysis of the extracellular proteome using two-dimensional gel electrophoresis resulted in the detection of several hundreds of protein spots, mainly with molecular masses of 25–116 kDa and pI values of 5–8. Identification of proteins suggested a cytoplasmic origin for many of these proteins, possibly released via membrane vesicles or biofilm-inherent cell lysis during biofilm maturation. Functional analysis of EPS proteins, using fluorogenic substrates as well as zymography, demonstrated the activity of diverse enzyme classes, such as proteases, lipases, esterases, phosphatases, and glucosidases. In conclusion, the CER extraction method, as previously applied to bacterial biofilms, also represents a suitable method for isolation of water soluble EPS from the archaeal biofilms of S. acidocaldarius, allowing the investigation of composition and function of EPS components in these types of biofilms.
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Affiliation(s)
- Silke Jachlewski
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University Duisburg-Essen , Essen , Germany
| | - Witold D Jachlewski
- Aquatic Microbiology, Biofilm Centre, Centre for Water and Environmental Research (CWE), University Duisburg-Essen , Essen , Germany
| | - Uwe Linne
- Core Facility for Mass Spectrometry and Elemental Analysis, Department of Chemistry and SYNMIKRO, Philipps-University of Marburg , Marburg , Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University Duisburg-Essen , Essen , Germany
| | - Jost Wingender
- Aquatic Microbiology, Biofilm Centre, Centre for Water and Environmental Research (CWE), University Duisburg-Essen , Essen , Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Biofilm Centre, Centre for Water and Environmental Research (CWE), University Duisburg-Essen , Essen , Germany
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100
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Biofilms in chronic rhinosinusitis: what is new and where next? The Journal of Laryngology & Otology 2015; 129:744-51. [DOI: 10.1017/s0022215115001620] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
AbstractBackground:Chronic rhinosinusitis is a common, heterogeneous condition. An effective means of mitigating disease in chronic rhinosinusitis patients remains elusive. A variety of causes have been implicated, with the biofilm theory gaining increasing prominence.Objective:This article reviews the literature on the role of biofilms in chronic rhinosinusitis, in terms of pathophysiology and with regard to avenues for future treatment.Methods:A systematic review of case series was performed using databases with independently developed search strategies, including Medline, Embase, Cumulative Index to Nursing and Allied Health Literature, Cochrane library, and Zetoc, in addition to conference proceedings and a manual search of literature, with the last search conducted on 18 January 2014. The search terms included the following, used in various combinations to maximise the yield of articles identified: ‘biofilms’, ‘chronic rhinosinusitis’, ‘DNase’, ‘extracellular DNA’ and ‘biofilm dispersal’.Results:The existing evidence lends further support for the role of biofilms (particularly the Staphylococcus aureus phenotype) in more severe, recalcitrant disease and poorer surgical outcomes.Conclusion:Multimodality treatment, with a shift in paradigm to incorporate anti-biofilm strategies, is likely to form the mainstay of future recalcitrant chronic rhinosinusitis management.
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