1
|
Nastouli A, Moschona A, Bizirtsakis PA, Sweeney J, Angelidaki I, Harasek M, Karabelas AJ, Patsios SI. A Novel Bio-Purification Process Employing an Engineered E. coli Strain for Downstream Processing of Lactic Acid Solutions from the Fermentation of Agro-Industrial by-Products. Bioengineering (Basel) 2024; 11:412. [PMID: 38790280 PMCID: PMC11118208 DOI: 10.3390/bioengineering11050412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
This study aims to integrate a novel bio-purification process employing an engineered E. coli strain in the downstream processing of lactic acid (LA) fermentation broths from low-cost renewable biological feedstocks. Fermentation broth of candy waste and digestate mixture was used as a real biological feedstock. An engineered E. coli strain that selectively catabolize impurities without catabolizing LA was initially adapted on the biological feedstock, followed by shake flask experiments to prove the bio-purification concept. Scale-up and validation in a bench-scale bioreactor followed, before developing a semi-continuous membrane bioreactor (MBR) bio-purification process. The MBR bio-purification was assessed with biological feedstocks which simulated ultrafiltration or nanofiltration permeates. Incomplete removal of impurities and increased fouling was observed in the case of the ultrafiltration permeate. Contrarily, the nanofiltration permeate was successfully treated with MBR bio-purification, since low membrane fouling, 100% maltose and acetic acid removal, and no LA catabolism was achieved. MBR bio-purification as a post-treatment step in the downstream processing of LA was demonstrated as a promising technology for increasing the purity of LA solutions.
Collapse
Affiliation(s)
- Alexandra Nastouli
- Laboratory of Natural Resources and Renewable Energies, Chemical Process & Energy Resources Institute (CPERI), Centre for Research and Technology-Hellas (CERTH), GR 57001 Thessaloniki, Greece; (A.N.); (A.M.); (P.A.B.); (A.J.K.)
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, AT 1060 Vienna, Austria;
| | - Alexandra Moschona
- Laboratory of Natural Resources and Renewable Energies, Chemical Process & Energy Resources Institute (CPERI), Centre for Research and Technology-Hellas (CERTH), GR 57001 Thessaloniki, Greece; (A.N.); (A.M.); (P.A.B.); (A.J.K.)
| | - Panagiotis A. Bizirtsakis
- Laboratory of Natural Resources and Renewable Energies, Chemical Process & Energy Resources Institute (CPERI), Centre for Research and Technology-Hellas (CERTH), GR 57001 Thessaloniki, Greece; (A.N.); (A.M.); (P.A.B.); (A.J.K.)
| | - Joseph Sweeney
- School of Biosystems and Food Engineering, University College Dublin (UCD), D04 V1W8 Dublin, Ireland;
| | - Irini Angelidaki
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark;
| | - Michael Harasek
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, AT 1060 Vienna, Austria;
| | - Anastasios J. Karabelas
- Laboratory of Natural Resources and Renewable Energies, Chemical Process & Energy Resources Institute (CPERI), Centre for Research and Technology-Hellas (CERTH), GR 57001 Thessaloniki, Greece; (A.N.); (A.M.); (P.A.B.); (A.J.K.)
| | - Sotiris I. Patsios
- Laboratory of Natural Resources and Renewable Energies, Chemical Process & Energy Resources Institute (CPERI), Centre for Research and Technology-Hellas (CERTH), GR 57001 Thessaloniki, Greece; (A.N.); (A.M.); (P.A.B.); (A.J.K.)
| |
Collapse
|
2
|
Ngom SI, Maski S, Rached B, Chouati T, Oliveira Correia L, Juste C, Meylheuc T, Henrissat B, El Fahime E, Amar M, Béra-Maillet C. Exploring the hemicellulolytic properties and safety of Bacillus paralicheniformis as stepping stone in the use of new fibrolytic beneficial microbes. Sci Rep 2023; 13:22785. [PMID: 38129471 PMCID: PMC10740013 DOI: 10.1038/s41598-023-49724-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Bacillus strains from the Moroccan Coordinated Collections of Microorganisms (CCMM) were characterised and tested for fibrolytic function and safety properties that would be beneficial for maintaining intestinal homeostasis, and recommend beneficial microbes in the field of health promotion research. Forty strains were investigated for their fibrolytic activities towards complex purified polysaccharides and natural fibres representative of dietary fibres (DFs) entering the colon for digestion. We demonstrated hemicellulolytic activities for nine strains of Bacillus aerius, re-identified as Bacillus paralicheniformis and Bacillus licheniformis, using xylan, xyloglucan or lichenan as purified polysaccharides, and orange, apple and carrot natural fibres, with strain- and substrate-dependent production of glycoside hydrolases (GHs). Our combined methods, based on enzymatic assays, secretome, and genome analyses, highlighted the hemicellulolytic activities of B. paralicheniformis and the secretion of specific glycoside hydrolases, in particular xylanases, compared to B. licheniformis. Genomic features of these strains revealed a complete set of GH genes dedicated to the degradation of various polysaccharides from DFs, including cellulose, hemicellulose and pectin, which may confer on the strains the ability to digest a variety of DFs. Preliminary experiments on the safety and immunomodulatory properties of B. paralicheniformis fibrolytic strains were evaluated in light of applications as beneficial microbes' candidates for health improvement. B. paralicheniformis CCMM B969 was therefore proposed as a new fibrolytic beneficial microbe candidate.
Collapse
Affiliation(s)
- Serigne Inssa Ngom
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Soufiane Maski
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Département de Biologie, Faculté des Sciences, Université Mohammed V, Rabat, Morocco
| | - Bahia Rached
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Laboratoire de Chimie-Physique et Biotechnologies des Biomolécules et Matériaux/Equipe Microbiologie Biomolécules et Biotechnologies, Faculté des Sciences et Techniques, Mohammedia, Morocco
| | - Taha Chouati
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Biologie médicale, Pathologie humaine et Expérimentale et Environnement, Faculté de Médecine et de pharmacie de Rabat, Rabat, Morocco
| | - Lydie Oliveira Correia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, PAPPSO, 78350, Jouy-en-Josas, France
| | - Catherine Juste
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Thierry Meylheuc
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, MIMA2, 78350, Jouy en Josas, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique, Aix-Marseille Université, 13288, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Elmostafa El Fahime
- Plateforme Génomique Fonctionnelle, Unité d'Appui Technique à la Recherche Scientifique, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Biologie médicale, Pathologie humaine et Expérimentale et Environnement, Faculté de Médecine et de pharmacie de Rabat, Rabat, Morocco
| | - Mohamed Amar
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
- Collections Coordonnées Marocaines de Microorganismes, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco
| | - Christel Béra-Maillet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
- Laboratoire de Microbiologie et Biologie Moléculaire, Centre National pour la Recherche Scientifique et Technique, Rabat, Morocco.
| |
Collapse
|
3
|
Dergham Y, Le Coq D, Bridier A, Sanchez-Vizuete P, Jbara H, Deschamps J, Hamze K, Yoshida KI, Noirot-Gros MF, Briandet R. Bacillus subtilis NDmed, a model strain for biofilm genetic studies. Biofilm 2023; 6:100152. [PMID: 37694162 PMCID: PMC10485040 DOI: 10.1016/j.bioflm.2023.100152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/20/2023] [Accepted: 08/27/2023] [Indexed: 09/12/2023] Open
Abstract
The Bacillus subtilis strain NDmed was isolated from an endoscope washer-disinfector in a medical environment. NDmed can form complex macrocolonies with highly wrinkled architectural structures on solid medium. In static liquid culture, it produces thick pellicles at the interface with air as well as remarkable highly protruding ''beanstalk-like'' submerged biofilm structures at the solid surface. Since these mucoid submerged structures are hyper-resistant to biocides, NDmed has the ability to protect pathogens embedded in mixed-species biofilms by sheltering them from the action of these agents. Additionally, this non-domesticated and highly biofilm forming strain has the propensity of being genetically manipulated. Due to all these properties, the NDmed strain becomes a valuable model for the study of B. subtilis biofilms. This review focuses on several studies performed with NDmed that have highlighted the sophisticated genetic dynamics at play during B. subtilis biofilm formation. Further studies in project using modern molecular tools of advanced technologies with this strain, will allow to deepen our knowledge on the emerging properties of multicellular bacterial life.
Collapse
Affiliation(s)
- Yasmine Dergham
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Lebanese University, Faculty of Science, 1003 Beirut, Lebanon
| | - Dominique Le Coq
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Arnaud Bridier
- Fougères Laboratory, Antibiotics, Biocides, Residues and Resistance Unit, Anses, 35300, Fougères, France
| | - Pilar Sanchez-Vizuete
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Hadi Jbara
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Julien Deschamps
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Kassem Hamze
- Lebanese University, Faculty of Science, 1003 Beirut, Lebanon
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | | | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| |
Collapse
|
4
|
Geisel S, Secchi E, Vermant J. Experimental challenges in determining the rheological properties of bacterial biofilms. Interface Focus 2022; 12:20220032. [PMID: 36330324 PMCID: PMC9560794 DOI: 10.1098/rsfs.2022.0032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/03/2022] [Indexed: 08/01/2023] Open
Abstract
Bacterial biofilms are communities living in a matrix consisting of self-produced, hydrated extracellular polymeric substances. Most microorganisms adopt the biofilm lifestyle since it protects by conferring resistance to antibiotics and physico-chemical stress factors. Consequently, mechanical removal is often necessary but rendered difficult by the biofilm's complex, viscoelastic response, and adhesive properties. Overall, the mechanical behaviour of biofilms also plays a role in the spreading, dispersal and subsequent colonization of new surfaces. Therefore, the characterization of the mechanical properties of biofilms plays a crucial role in controlling and combating biofilms in industrial and medical environments. We performed in situ shear rheological measurements of Bacillus subtilis biofilms grown between the plates of a rotational rheometer under well-controlled conditions relevant to many biofilm habitats. We investigated how the mechanical history preceding rheological measurements influenced biofilm mechanics and compared these results to the techniques commonly used in the literature. We also compare our results to measurements using interfacial rheology on bacterial pellicles formed at the air-water interface. This work aims to help understand how different growth and measurement conditions contribute to the large variability of mechanical properties reported in the literature and provide a new tool for the rigorous characterization of matrix components and biofilms.
Collapse
Affiliation(s)
- Steffen Geisel
- Laboratory for Soft Materials, Department of Materials, ETH Zurich, Zurich, Switzerland
| | - Eleonora Secchi
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Jan Vermant
- Laboratory for Soft Materials, Department of Materials, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
5
|
Gierl L, Horn H, Wagner M. Impact of Fe 2+ and Shear Stress on the Development and Mesoscopic Structure of Biofilms-A Bacillus subtilis Case Study. Microorganisms 2022; 10:2234. [PMID: 36422304 PMCID: PMC9699539 DOI: 10.3390/microorganisms10112234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 07/25/2023] Open
Abstract
Bivalent cations are known to affect the structural and mechanical properties of biofilms. In order to reveal the impact of Fe2+ ions within the cultivation medium on biofilm development, structure and stability, Bacillus subtilis biofilms were cultivated in mini-fluidic flow cells. Two different Fe2+ inflow concentrations (0.25 and 2.5 mg/L, respectively) and wall shear stress levels (0.05 and 0.27 Pa, respectively) were tested. Mesoscopic biofilm structure was determined daily in situ and non-invasively by means of optical coherence tomography. A set of ten structural parameters was used to quantify biofilm structure, its development and change. The study focused on characterizing biofilm structure and development at the mesoscale (mm-range). Therefore, biofilm replicates (n = 10) were cultivated and analyzed. Three hypotheses were defined in order to estimate the effect of Fe2+ inflow concentration and/or wall shear stress on biofilm development and structure, respectively. It was not the intention to investigate and describe the underlying mechanisms of iron incorporation as this would require a different set of tools applied at microscopic levels as well as the use of, i.e., omic approaches. Fe2+ addition influenced biofilm development (e.g., biofilm accumulation) and structure markedly. Experiments revealed the accumulation of FeO(OH) within the biofilm matrix and a positive correlation of Fe2+ inflow concentration and biofilm accumulation. In more detail, independent of the wall shear stress applied during cultivation, biofilms grew approximately four times thicker at 2.5 mg Fe2+/L (44.8 µmol/L; high inflow concentration) compared to the low Fe2+ inflow concentration of 0.25 mg Fe2+/L (4.48 µmol/L). This finding was statistically verified (Scheirer-Ray-Hare test, ANOVA) and hints at a higher stability of Bacillus subtilis biofilms (e.g., elevated cohesive and adhesive strength) when grown at elevated Fe2+ inflow concentrations.
Collapse
Affiliation(s)
- Luisa Gierl
- Water Chemistry and Water Technology, Engler-Bunte-Institut, Karlsruhe Institute of Technology, Engler-Bunte-Ring 9a, 76131 Karlsruhe, Germany
| | - Harald Horn
- Water Chemistry and Water Technology, Engler-Bunte-Institut, Karlsruhe Institute of Technology, Engler-Bunte-Ring 9a, 76131 Karlsruhe, Germany
- German Technical and Scientific Association for Gas and Water (DVGW) Research Site at Karlsruhe Institute of Technology, Water Chemistry and Water Technology, Engler-Bunte-Ring 9a, 76131 Karlsruhe, Germany
| | - Michael Wagner
- Water Chemistry and Water Technology, Engler-Bunte-Institut, Karlsruhe Institute of Technology, Engler-Bunte-Ring 9a, 76131 Karlsruhe, Germany
- Institute of Biological Interfaces (IBG-1), Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| |
Collapse
|
6
|
Lamba S, Mundanda Muthappa D, Fanning S, Scannell AGM. Sporulation and Biofilms as Survival Mechanisms of Bacillus Species in Low-Moisture Food Production Environments. Foodborne Pathog Dis 2022; 19:448-462. [PMID: 35819266 DOI: 10.1089/fpd.2022.0006] [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: 11/13/2022] Open
Abstract
Low-moisture foods (LMF) have clear advantages with respect to limiting the growth of foodborne pathogens. However, the incidences of Bacillus species in LMF reported in recent years raise concerns about food quality and safety, particularly when these foods are used as ingredients in more complex higher moisture products. This literature review describes the interlinked pathways of sporulation and biofilm formation by Bacillus species and their underlying molecular mechanisms that contribute to the bacteriums' persistence in LMF production environments. The long-standing challenges of food safety and quality in the LMF industry are also discussed with a focus on the bakery industry.
Collapse
Affiliation(s)
- Sakshi Lamba
- UCD Institute of Food and Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD Centre for Food Safety, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD School of Agriculture and Food Science, and Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Dechamma Mundanda Muthappa
- UCD Centre for Food Safety, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD School of Agriculture and Food Science, and Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Séamus Fanning
- UCD Institute of Food and Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD Centre for Food Safety, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD School of Public Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| | - Amalia G M Scannell
- UCD Institute of Food and Health, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD Centre for Food Safety, Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland.,UCD School of Agriculture and Food Science, and Physiotherapy and Sports Science, University College Dublin, Dublin, Ireland
| |
Collapse
|
7
|
Systems view of Bacillus subtilis pellicle development. NPJ Biofilms Microbiomes 2022; 8:25. [PMID: 35414070 PMCID: PMC9005697 DOI: 10.1038/s41522-022-00293-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/19/2022] [Indexed: 11/08/2022] Open
Abstract
In this study, we link pellicle development at the water-air interface with the vertical distribution and viability of the individual B. subtilis PS-216 cells throughout the water column. Real-time interfacial rheology and time-lapse confocal laser scanning microscopy were combined to correlate mechanical properties with morphological changes (aggregation status, filament formation, pellicle thickness, spore formation) of the growing pellicle. Six key events were identified in B. subtilis pellicle formation that are accompanied by a major change in viscoelastic and morphology behaviour of the pellicle. The results imply that pellicle development is a multifaceted response to a changing environment induced by bacterial growth that causes population redistribution within the model system, reduction of the viable habitat to the water-air interface, cell development, and morphogenesis. The outcome is a build-up of mechanical stress supporting structure that eventually, due to nutrient deprivation, reaches the finite thickness. After prolonged incubation, the formed pellicle collapses, which correlates with the spore releasing process. The pellicle loses the ability to support mechanical stress, which marks the end of the pellicle life cycle and entry of the system into the dormant state.
Collapse
|
8
|
Understanding photosynthetic biofilm productivity and structure through 2D simulation. PLoS Comput Biol 2022; 18:e1009904. [PMID: 35377868 PMCID: PMC9037940 DOI: 10.1371/journal.pcbi.1009904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/25/2022] [Accepted: 02/09/2022] [Indexed: 11/30/2022] Open
Abstract
We present a spatial model describing the growth of a photosynthetic microalgae biofilm. In this 2D-model we consider photosynthesis, cell carbon accumulation, extracellular matrix excretion, and mortality. The rate of each of these mechanisms is given by kinetic laws regulated by light, nitrate, oxygen and inorganic carbon. The model is based on mixture theory and the behaviour of each component is defined on one hand by mass conservation, which takes into account biological features of the system, and on the other hand by conservation of momentum, which expresses the physical properties of the components. The model simulates the biofilm structural dynamics following an initial colonization phase. It shows that a 75 μm thick active region drives the biofilm development. We then determine the optimal harvesting period and biofilm height which maximize productivity. Finally, different harvesting patterns are tested and their effect on biofilm structure are discussed. The optimal strategy differs whether the objective is to recover the total biofilm or just the algal biomass. Microalgae have many industrial applications, ranging from aquaculture, pharmaceutics, food industry to green energy. Planktonic cultivation of microalgae is energy-consuming. Growing them under a biofilm form is a new trend with attracting promises. Biofilms are complex heterogeneous ecosystems composed of microorganisms embedded within a self-produced extracellular matrix and stuck to a surface. Most of the studies have focused on bacterial biofilms and knowledge about microalgae biofilms is still very limited. In this paper, we propose a mathematical model describing microalgae biofilm development. We simulate in 1D and 2D the impact of harvesting conditions on biofilm productivity. In agreement with available experimental observations, we find that there exist optimal frequencies and patterns that optimize the productivity. We also show that the optimal conditions differ whether for maximizing the productivity of microalgae or of the whole biofilm.
Collapse
|
9
|
OUIDIR T, GABRIEL B, CHABANE YNAIT. Overview of multi-species biofilms in different ecosystems: wastewater treatment, soil and oral cavity. J Biotechnol 2022; 350:67-74. [DOI: 10.1016/j.jbiotec.2022.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 01/27/2023]
|
10
|
Zhurina MV, Bogdanov KI, Gannesen AV, Mart’yanov SV, Plakunov VK. Microplastics as a New Ecological Niche For Multispecies Microbial Biofilms within the Plastisphere. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722020126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
|
11
|
Bridier A, Briandet R. Microbial Biofilms: Structural Plasticity and Emerging Properties. Microorganisms 2022; 10:138. [PMID: 35056587 PMCID: PMC8778831 DOI: 10.3390/microorganisms10010138] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 02/01/2023] Open
Abstract
Microbial biofilms are found everywhere and can be either beneficial or detrimental, as they are involved in crucial ecological processes and in severe chronic infections. The functional properties of biofilms are closely related to their three-dimensional (3D) structure, and the ability of microorganisms to collectively and dynamically shape the community spatial organization in response to stresses in such biological edifices. A large number of works have shown a relationship between the modulation of the spatial organization and ecological interactions in biofilms in response to environmental fluctuations, as well as their emerging properties essential for nutrient cycling and bioremediation processes in natural environments. On the contrary, numerous studies have emphasized the role of structural rearrangements and matrix production in the increased tolerance of bacteria in biofilms toward antimicrobials. In these last few years, the development of innovative approaches, relying on recent technological advances in imaging, computing capacity, and other analytical tools, has led to the production of original data that have improved our understanding of this close relationship. However, it has also highlighted the need to delve deeper into the study of cell behavior in such complex communities during 3D structure development and maturation- from a single-cell to a multicellular scale- to better control or harness positive and negative impacts of biofilms. For this Special Issue, the interplay between biofilm emerging properties and their 3D spatial organization considering different models, from single bacteria to complex environmental communities, and various environments, from natural ecosystems to industrial and medical settings are addressed.
Collapse
Affiliation(s)
- Arnaud Bridier
- Antibiotics, Biocides, Residues and Resistance Unit, Fougères Laboratory, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 35300 Fougères, France
| | - Romain Briandet
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| |
Collapse
|
12
|
Ronin D, Boyer J, Alban N, Natoli RM, Johnson A, Kjellerup BV. Current and novel diagnostics for orthopedic implant biofilm infections: a review. APMIS 2021; 130:59-81. [PMID: 34862649 DOI: 10.1111/apm.13197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/25/2021] [Indexed: 12/12/2022]
Abstract
Biofilm infections involving orthopedic implants are a global problem. They contribute to severe complications and mortality, as well as increased use of antibiotic treatments and development of antibiotic-resistant microorganisms. More than 1 million hip and knee arthroplasties are performed each year in the United States. These hard-to-treat infections lead to patient distress, increased morbidity, and high financial costs to both patients and healthcare systems. There is a need to improve the diagnosis of such biofilm infections to allow for earlier detection and treatment. Current diagnostics rely on clinical signs for infections such as loss of function, fever, rubor, patient history of the predisposing condition, persisting infection, failure of antibiotic treatment, and documentation of antibiotic failure. Below, we present a framework which outlines the data gaps in the conventional laboratory techniques used in clinical diagnostics; we also discuss promising novel diagnostic methods which are currently used solely in research. It is critical to assess these novel infection diagnostic techniques and address the data gaps and clinical hesitance preventing application in a clinical setting. Additionally, the combination of conventional and novel diagnostic technologies would streamline the diagnostic process of biofilm infections associated with orthopedic implants.
Collapse
Affiliation(s)
- Dana Ronin
- Department of Civil and Environmental Engineering, University of Maryland, College Park, Maryland, USA.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, USA
| | - Jessica Boyer
- Department of Civil and Environmental Engineering, University of Maryland, College Park, Maryland, USA.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, USA
| | - Nathan Alban
- Department of Civil and Environmental Engineering, University of Maryland, College Park, Maryland, USA.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, USA
| | - Roman M Natoli
- Department of Orthopaedic Surgery, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Aaron Johnson
- Department of Orthopaedics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Birthe Veno Kjellerup
- Department of Civil and Environmental Engineering, University of Maryland, College Park, Maryland, USA.,Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, USA
| |
Collapse
|
13
|
Kamyshinsky RA, Patsaev TD, Tenchurin TK, Zagoskin YD, Grigoriev TE, Darienko KA, Panteleyev AA, Chvalun SN, Vasiliev AL. Environmental Scanning Electron Microscopy of Dermal Fibroblasts on Various Types of Polymer Scaffolds. CRYSTALLOGR REP+ 2020. [DOI: 10.1134/s1063774520050107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
14
|
Cattò C, Cappitelli F. Testing Anti-Biofilm Polymeric Surfaces: Where to Start? Int J Mol Sci 2019; 20:E3794. [PMID: 31382580 PMCID: PMC6696330 DOI: 10.3390/ijms20153794] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/02/2019] [Indexed: 12/11/2022] Open
Abstract
Present day awareness of biofilm colonization on polymeric surfaces has prompted the scientific community to develop an ever-increasing number of new materials with anti-biofilm features. However, compared to the large amount of work put into discovering potent biofilm inhibitors, only a small number of papers deal with their validation, a critical step in the translation of research into practical applications. This is due to the lack of standardized testing methods and/or of well-controlled in vivo studies that show biofilm prevention on polymeric surfaces; furthermore, there has been little correlation with the reduced incidence of material deterioration. Here an overview of the most common methods for studying biofilms and for testing the anti-biofilm properties of new surfaces is provided.
Collapse
Affiliation(s)
- Cristina Cattò
- Department of Food Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Francesca Cappitelli
- Department of Food Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy.
| |
Collapse
|
15
|
Horvat M, Pannuri A, Romeo T, Dogsa I, Stopar D. Viscoelastic response of Escherichia coli biofilms to genetically altered expression of extracellular matrix components. SOFT MATTER 2019; 15:5042-5051. [PMID: 31179461 DOI: 10.1039/c9sm00297a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
How the viscoelastic properties of the extracellular matrix affect the various biological functions conferred by biofilms is an important question in microbiology. In this study, the viscoelastic response of Escherichia coli biofilms to the genetically altered expression of extracellular matrix components was studied. Biofilms of the wild type E. coli MG1655 and its mutant strains producing different amounts of extracellular matrix components (curli, colanic acid, and poly-β-1,6-N-acetyl-d-glucosamine) were used to examine the viscoelastic behavior of biofilms grown at the solid-atmosphere interface. The results suggest that the presence of curli proteins dominates biofilm mechanical behavior. The rheological data indicate that the cohesive energy of the biofilm was the highest in the wild type strain. The results demonstrate the importance of extracellular matrix composition for biofilm mechanical properties. We propose that by genetically altering the expression of extracellular matrix polymers, bacteria are able to modulate the mechanical properties of their local environment in accordance with bulk environmental conditions.
Collapse
Affiliation(s)
- Maruša Horvat
- University of Ljubljana, Biotechnical Faculty, Chair of Microbiology, Department of Food Science and Technology, Večna pot 111, 1000 Ljubljana, Slovenia.
| | | | | | | | | |
Collapse
|
16
|
Luo TL, Hayashi M, Zsiska M, Circello B, Eisenberg M, Gonzalez-Cabezas C, Foxman B, Marrs CF, Rickard AH. Introducing BAIT (Biofilm Architecture Inference Tool): a software program to evaluate the architecture of oral multi-species biofilms. MICROBIOLOGY (READING, ENGLAND) 2019; 165:527-537. [PMID: 30882296 DOI: 10.1099/mic.0.000761] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Biofilm model systems are used to study biofilm growth and predict the effects of anti-biofilm interventions within the human oral cavity. Many in vitro biofilm model systems use a confocal laser scanning microscope (CLSM) in conjunction with image analysis tools to study biofilms. The aim of this study was to evaluate an in-house developed image analysis software program that we call BAIT (Biofilm Architecture Inference Tool) to quantify the architecture of oral multi-species biofilms following anti-biofilm interventions using a microfluidic biofilm system. Differences in architecture were compared between untreated biofilms and those treated with water (negative control), sodium gluconate ('placebo') or stannous fluoride (SnF2). The microfluidic system was inoculated with pooled human saliva and biofilms were developed over 22 h in filter-sterilized 25 % pooled human saliva. During this period, biofilms were treated with water, sodium gluconate, or SnF2 (1000, 3439 or 10 000 p.p.m. Sn2+) 8 and 18 h post-inoculation. After 22 h of growth, biofilms were stained with LIVE/DEAD stain, and imaged by CLSM. BAIT was used to calculate biofilm biovolume, total number of objects, surface area, fluffiness, connectivity, convex hull porosity and viability. Image analysis showed oral biofilm architecture was significantly altered by 3439 and 10 000 p.p.m. Sn2+ treatment regimens, resulting in decreased biovolume, surface area, number of objects and connectivity, while fluffiness increased (P<0.01). In conclusion, BAIT was shown to be able to measure the changes in biofilm architecture and detects possible antimicrobial and anti-biofilm effects of candidate agents.
Collapse
Affiliation(s)
- Ting L Luo
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Michael Hayashi
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | | | | | - Marisa Eisenberg
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Carlos Gonzalez-Cabezas
- Department of Cariology, Restorative Sciences and Endodontics, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - Betsy Foxman
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Carl F Marrs
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Alexander H Rickard
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| |
Collapse
|
17
|
Romero CM, Martorell PV, López AG, Peñalver CGN, Chaves S, Mechetti M. Architecture and physicochemical characterization of Bacillus biofilm as a potential enzyme immobilization factory. Colloids Surf B Biointerfaces 2017; 162:246-255. [PMID: 29216511 DOI: 10.1016/j.colsurfb.2017.11.057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/09/2017] [Accepted: 11/22/2017] [Indexed: 11/18/2022]
Abstract
Biocatalysis for industrial application is based on the use of enzymes to perform complex transformations. However, these systems have some disadvantage related to the costs of the biocatalyst. In this work, an alternative strategy for producing green immobilized biocatalysts based on biofilm was developed.A study of the rheological behavior of the biofilm from Bacillus sp. Mcn4, as well as the determination of its composition, was carried out. The dynamic rheological measurements, viscosity (G") and elasticity (G') module, showed that the biofilm presents appreciable elastic components, which is a recognized property for enzymes immobilization. After the partial purification, the exopolysaccharidewas identified as a levan with a non-Newtonian behavior. Extracellular DNA with fragments between 10,000 and 1000bp was detected also in the biofilm, and amyloid protein in the extracellular matrix using a fluorescence technique was identified. Bacillus sp. Mcn4 biofilms were developed on different surfaces, being the most stable those developed on hydrophilic supports. The biofilm showed lipase activity suggesting the presence of constitutive lipases entrapped into the biofilm. Indeed, two enzymes with lipase activity were identified in native PAGE. These were used as biocatalysts, whose reuse showed a residual lipase activity after more than one cycle of catalysis. The components identified in the biofilm could be the main contributors of the rheological characteristic of this material, giving an exceptional environment to the lipase enzyme. Based on these findings, the current study proposes green and natural biopolymers matrix as support for the enzyme immobilization for industrial applications.
Collapse
Affiliation(s)
- C M Romero
- PROIMI, PROIMI-CONICET, Av. Belgrano y Pasaje Caseros, T4001 MVB, Tucumán Fac. Bioq., Qca. y Farmacia (UNT), Ayacucho 471, 4000, Tucumán, Argentina.
| | - P V Martorell
- PROIMI, PROIMI-CONICET, Av. Belgrano y Pasaje Caseros, T4001 MVB, Tucumán Fac. Bioq., Qca. y Farmacia (UNT), Ayacucho 471, 4000, Tucumán, Argentina
| | - A Gómez López
- Laboratorio de Física de Fluidos y Electrorreología, Instituto de Física del Noroeste Argentino-INFINOA (CONICET-UNT), Facultad de Ciencias Exactas y Tecnología, Universidad Nacional de Tucumán, Av. Independencia 1800, San Miguel de Tucumán, 4000, Argentina
| | - C G Nieto Peñalver
- PROIMI, PROIMI-CONICET, Av. Belgrano y Pasaje Caseros, T4001 MVB, Tucumán Fac. Bioq., Qca. y Farmacia (UNT), Ayacucho 471, 4000, Tucumán, Argentina
| | - S Chaves
- Instituto Superior de Investigaciones Biológicas (INSIBIO), CONICET-UNT, Instituto de Química Biológica "Dr. Bernabé Bloj", Facultad de Bioquímica, Química y Farmacia, UNT. Chacabuco 461, T4000ILI, San Miguel de Tucumán, Argentina
| | - M Mechetti
- Laboratorio de Física de Fluidos y Electrorreología, Instituto de Física del Noroeste Argentino-INFINOA (CONICET-UNT), Facultad de Ciencias Exactas y Tecnología, Universidad Nacional de Tucumán, Av. Independencia 1800, San Miguel de Tucumán, 4000, Argentina
| |
Collapse
|
18
|
Gingichashvili S, Duanis-Assaf D, Shemesh M, Featherstone JDB, Feuerstein O, Steinberg D. Bacillus subtilis Biofilm Development - A Computerized Study of Morphology and Kinetics. Front Microbiol 2017; 8:2072. [PMID: 29163384 PMCID: PMC5674941 DOI: 10.3389/fmicb.2017.02072] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 10/10/2017] [Indexed: 11/24/2022] Open
Abstract
Biofilm is commonly defined as accumulation of microbes, embedded in a self-secreted extra-cellular matrix, on solid surfaces or liquid interfaces. In this study, we analyze several aspects of Bacillus subtilis biofilm formation using tools from the field of image processing. Specifically, we characterize the growth kinetics and morphological features of B. subtilis colony type biofilm formation and compare these in colonies grown on two different types of solid media. Additionally, we propose a model for assessing B. subtilis biofilm complexity across different growth conditions. GFP-labeled B. subtilis cells were cultured on agar surfaces over a 4-day period during which microscopic images of developing colonies were taken at equal time intervals. The images were used to perform a computerized analysis of few aspects of biofilm development, based on features that characterize the different phenotypes of B. subtilis colonies. Specifically, the analysis focused on the segmented structure of the colonies, consisting of two different regions of sub-populations that comprise the biofilm – a central “core” region and an “expanding” region surrounding it. Our results demonstrate that complex biofilm of B. subtillis grown on biofilm-promoting medium [standard lysogeny broth (LB) supplemented with manganese and glycerol] is characterized by rapidly developing three-dimensional complex structure observed at its core compared to biofilm grown on standard LB. As the biofilm develops, the core size remains largely unchanged during development and colony expansion is mostly attributed to the expansion in area of outer cell sub-populations. Moreover, when comparing the bacterial growth on biofilm-promoting agar to that of colonies grown on LB, we found a significant decrease in the GFP production of colonies that formed a more complex biofilm. This suggests that complex biofilm formation has a diminishing effect on cell populations at the biofilm core, likely due to a combination of reduced metabolic rate and increased levels of cell death within this region.
Collapse
Affiliation(s)
- Sarah Gingichashvili
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University-Hadassah, Jerusalem, Israel.,Department of Prosthodontics, Faculty of Dental Medicine, Hebrew University-Hadassah, Jerusalem, Israel
| | - Danielle Duanis-Assaf
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University-Hadassah, Jerusalem, Israel.,Department of Food Quality and Safety, Institute for Postharvest Technology and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, Israel
| | - Moshe Shemesh
- Department of Food Quality and Safety, Institute for Postharvest Technology and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, Bet Dagan, Israel
| | - John D B Featherstone
- School of Dentistry, University of California, San Francisco, San Francisco, CA, United States
| | - Osnat Feuerstein
- Department of Prosthodontics, Faculty of Dental Medicine, Hebrew University-Hadassah, Jerusalem, Israel
| | - Doron Steinberg
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University-Hadassah, Jerusalem, Israel
| |
Collapse
|
19
|
Tasaki S, Nakayama M, Shoji W. Morphologies of Bacillus subtilis communities responding to environmental variation. Dev Growth Differ 2017; 59:369-378. [PMID: 28675458 DOI: 10.1111/dgd.12383] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/24/2017] [Accepted: 06/06/2017] [Indexed: 12/20/2022]
Abstract
Bacterial communities exhibit a variety of growth morphologies in constructing robust systems under different environmental conditions. We review the diverse morphologies of Bacillus subtilis communities and their mechanisms of self-organization. B. subtilis uses different cell types to suit environmental conditions and cell density. The subpopulation of each cell type exhibits various environment-sensitive properties. Furthermore, division of labor among the subpopulations results in flexible development for the community as a whole. We review how B. subtilis community morphologies and growth strategies respond to environmental perturbations.
Collapse
Affiliation(s)
- Sohei Tasaki
- Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, 6-3 Aramaki-aza-Aoba, Aoba-ku, Japan.,Graduate School of Science, Tohoku University, 6-3 Aramaki-aza-Aoba, Aoba-ku, Japan
| | - Madoka Nakayama
- Sendai National College of Technology, 48 Nodayama, Medeshima-Shiote, Natori, Miyagi, 981-1239, Japan
| | - Wataru Shoji
- Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, 6-3 Aramaki-aza-Aoba, Aoba-ku, Japan.,Institute of Development, Aging and Cancer, Tohoku University, 1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Yi J, Cheng J. Effects of water chemistry and surface contact on the toxicity of silver nanoparticles to Bacillus subtilis. ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:639-647. [PMID: 28378128 DOI: 10.1007/s10646-017-1796-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/22/2017] [Indexed: 06/07/2023]
Abstract
The growing use of silver nanoparticles (AgNPs) has created concerns about its potential impacts on natural microbial communities. In this study, the physicochemical properties of AgNPs and its toxicity on natural bacteria Bacillus subtilis (B. subtilis) were investigated in aqueous conditions. The characterization data showed that AgNPs highly aggregated in aqueous conditions, and the hydrodynamic diameter of AgNPs in aqueous conditions was larger than its primary size. The studied AgNPs was less toxic to B. subtilis in estuarine water as compared to that in Milli-Q water and artificial seawater, which might be due to the observed enhanced aggregation of AgNPs in estuarine water. The toxicity of AgNPs to B. subtilis was greatly reduced when their surface contact was blocked by a dialysis membrane. Scanning electron microscope images showed that exposure contact to AgNPs resulted in damage of the microbial cell wall and enhanced formation of fibrillar structures. These results suggest that particle-cell contact is largely responsible for the observed toxicity of AgNPs in B. subtilis. This study can help to understand the potential impacts of AgNPs to natural microbes, especially in the complex aquatic environments.
Collapse
Affiliation(s)
- Jun Yi
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China
- Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China
| | - Jinping Cheng
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, 200062, China.
- Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China.
- Environmental Science Programs, School of Science, Hong Kong University of Science and Technology, Clear Water Bay, New Territories, Hong Kong.
| |
Collapse
|
22
|
Costa-Orlandi CB, Sardi JCO, Pitangui NS, de Oliveira HC, Scorzoni L, Galeane MC, Medina-Alarcón KP, Melo WCMA, Marcelino MY, Braz JD, Fusco-Almeida AM, Mendes-Giannini MJS. Fungal Biofilms and Polymicrobial Diseases. J Fungi (Basel) 2017; 3:jof3020022. [PMID: 29371540 PMCID: PMC5715925 DOI: 10.3390/jof3020022] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/19/2017] [Accepted: 05/04/2017] [Indexed: 12/29/2022] Open
Abstract
Biofilm formation is an important virulence factor for pathogenic fungi. Both yeasts and filamentous fungi can adhere to biotic and abiotic surfaces, developing into highly organized communities that are resistant to antimicrobials and environmental conditions. In recent years, new genera of fungi have been correlated with biofilm formation. However, Candida biofilms remain the most widely studied from the morphological and molecular perspectives. Biofilms formed by yeast and filamentous fungi present differences, and studies of polymicrobial communities have become increasingly important. A key feature of resistance is the extracellular matrix, which covers and protects biofilm cells from the surrounding environment. Furthermore, to achieve cell–cell communication, microorganisms secrete quorum-sensing molecules that control their biological activities and behaviors and play a role in fungal resistance and pathogenicity. Several in vitro techniques have been developed to study fungal biofilms, from colorimetric methods to omics approaches that aim to identify new therapeutic strategies by developing new compounds to combat these microbial communities as well as new diagnostic tools to identify these complex formations in vivo. In this review, recent advances related to pathogenic fungal biofilms are addressed.
Collapse
Affiliation(s)
- Caroline B Costa-Orlandi
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Janaina C O Sardi
- Department of Physiological Sciences, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba SP 13414-018, Brazil.
| | - Nayla S Pitangui
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Haroldo C de Oliveira
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Liliana Scorzoni
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Mariana C Galeane
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Kaila P Medina-Alarcón
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Wanessa C M A Melo
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Mônica Y Marcelino
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Jaqueline D Braz
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Ana Marisa Fusco-Almeida
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| | - Maria José S Mendes-Giannini
- Department of Clinical Analysis, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara SP 14800-903, Brazil.
| |
Collapse
|
23
|
Wagner M, Horn H. Optical coherence tomography in biofilm research: A comprehensive review. Biotechnol Bioeng 2017; 114:1386-1402. [DOI: 10.1002/bit.26283] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/10/2017] [Accepted: 03/01/2017] [Indexed: 01/29/2023]
Affiliation(s)
- Michael Wagner
- Karlsruhe Institute of Technology; Engler-Bunte-Institut; Chair of Water Chemistry and Water Technology; Engler-Bunte-Ring 9 76131 Karlsruhe Germany
- Karlsruhe Institute of Technology; Institute of Functional Interfaces; Eggenstein-Leopoldshafen Germany
| | - Harald Horn
- Karlsruhe Institute of Technology; Engler-Bunte-Institut; Chair of Water Chemistry and Water Technology; Engler-Bunte-Ring 9 76131 Karlsruhe Germany
| |
Collapse
|
24
|
Azeredo J, Azevedo NF, Briandet R, Cerca N, Coenye T, Costa AR, Desvaux M, Di Bonaventura G, Hébraud M, Jaglic Z, Kačániová M, Knøchel S, Lourenço A, Mergulhão F, Meyer RL, Nychas G, Simões M, Tresse O, Sternberg C. Critical review on biofilm methods. Crit Rev Microbiol 2016; 43:313-351. [PMID: 27868469 DOI: 10.1080/1040841x.2016.1208146] [Citation(s) in RCA: 536] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Biofilms are widespread in nature and constitute an important strategy implemented by microorganisms to survive in sometimes harsh environmental conditions. They can be beneficial or have a negative impact particularly when formed in industrial settings or on medical devices. As such, research into the formation and elimination of biofilms is important for many disciplines. Several new methodologies have been recently developed for, or adapted to, biofilm studies that have contributed to deeper knowledge on biofilm physiology, structure and composition. In this review, traditional and cutting-edge methods to study biofilm biomass, viability, structure, composition and physiology are addressed. Moreover, as there is a lack of consensus among the diversity of techniques used to grow and study biofilms. This review intends to remedy this, by giving a critical perspective, highlighting the advantages and limitations of several methods. Accordingly, this review aims at helping scientists in finding the most appropriate and up-to-date methods to study their biofilms.
Collapse
Affiliation(s)
- Joana Azeredo
- a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal
| | - Nuno F Azevedo
- b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Romain Briandet
- c Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay , Jouy-en-Josas , France
| | - Nuno Cerca
- a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal
| | - Tom Coenye
- d Laboratory of Pharmaceutical Microbiology , Ghent University , Ghent , Belgium
| | - Ana Rita Costa
- a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal
| | - Mickaël Desvaux
- e INRA Centre Auvergne-Rhône-Alpes , UR454 Microbiologie , Saint-Genès Champanelle , France
| | - Giovanni Di Bonaventura
- f Department of Medical, Oral, and Biotechnological Sciences, and Center of Excellence on Aging and Translational Medicine (CeSI-MeT) , "G. d'Annunzio" University of Chieti-Pescara , Chieti , Italy
| | - Michel Hébraud
- e INRA Centre Auvergne-Rhône-Alpes , UR454 Microbiologie , Saint-Genès Champanelle , France
| | - Zoran Jaglic
- g Department of Food and Feed Safety, Laboratory of Food Bacteriology , Veterinary Research Institute , Brno , Czech Republic
| | - Miroslava Kačániová
- h Department of Microbiology, Faculty of Biotechnology and Food Sciences , Slovak University of Agriculture in Nitra , Nitra , Slovakia
| | - Susanne Knøchel
- i Department of Food Science (FOOD) , University of Copenhagen , Frederiksberg C , Denmark
| | - Anália Lourenço
- j Department of Computer Science , University of Vigo , Ourense , Spain
| | - Filipe Mergulhão
- b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Rikke Louise Meyer
- k Aarhus University, Interdisciplinary Nanoscience Center (iNANO) , Aarhus , Denmark
| | - George Nychas
- l Agricultural University of Athens, Lab of Microbiology and Biotechnology of Foods , Athens , Greece
| | - Manuel Simões
- b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Odile Tresse
- m LUNAM Université, Oniris, SECALIM UMR1024 INRA , Université de Nantes , Nantes , France
| | - Claus Sternberg
- n Department of Biotechnology and Biomedicine , Technical University of Denmark , Lyngby, Denmark
| |
Collapse
|
25
|
Bucher T, Kartvelishvily E, Kolodkin-Gal I. Methodologies for Studying B. subtilis Biofilms as a Model for Characterizing Small Molecule Biofilm Inhibitors. J Vis Exp 2016. [PMID: 27768058 DOI: 10.3791/54612] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
This work assesses different methodologies to study the impact of small molecule biofilm inhibitors, such as D-amino acids, on the development and resilience of Bacillus subtilis biofilms. First, methods are presented that select for small molecule inhibitors with biofilm-specific targets in order to separate the effect of the small molecule inhibitors on planktonic growth from their effect on biofilm formation. Next, we focus on how inoculation conditions affect the sensitivity of multicellular, floating B. subtilis cultures to small molecule inhibitors. The results suggest that discrepancies in the reported effects of such inhibitors such as D-amino acids are due to inconsistent pre-culture conditions. Furthermore, a recently developed protocol is described for evaluating the contribution of small molecule treatments towards biofilm resistance to antibacterial substances. Lastly, scanning electron microscopy (SEM) techniques are presented to analyze the three-dimensional spatial arrangement of cells and their surrounding extracellular matrix in a B. subtilis biofilm. SEM facilitates insight into the three-dimensional biofilm architecture and the matrix texture. A combination of the methods described here can greatly assist the study of biofilm development in the presence and absence of biofilm inhibitors, and shed light on the mechanism of action of these inhibitors.
Collapse
Affiliation(s)
- Tabitha Bucher
- Department of Molecular Genetics, Weizmann Institute of Science
| | | | | |
Collapse
|
26
|
Abstract
Candida albicans, the most pervasive fungal pathogen that colonizes humans, forms biofilms that are architecturally complex. They consist of a basal yeast cell polylayer and an upper region of hyphae encapsulated in extracellular matrix. However, biofilms formed in vitro vary as a result of the different conditions employed in models, the methods used to assess biofilm formation, strain differences, and, in a most dramatic fashion, the configuration of the mating type locus (MTL). Therefore, integrating data from different studies can lead to problems of interpretation if such variability is not taken into account. Here we review the conditions and factors that cause biofilm variation, with the goal of engendering awareness that more attention must be paid to the strains employed, the methods used to assess biofilm development, every aspect of the model employed, and the configuration of the MTL locus. We end by posing a set of questions that may be asked in comparing the results of different studies and developing protocols for new ones. This review should engender the notion that not all biofilms are created equal.
Collapse
Affiliation(s)
- David R Soll
- Developmental Studies Hybridoma Bank, Department of Biology, The University of Iowa, Iowa City, Iowa, USA
| | - Karla J Daniels
- Developmental Studies Hybridoma Bank, Department of Biology, The University of Iowa, Iowa City, Iowa, USA
| |
Collapse
|
27
|
Majed R, Faille C, Kallassy M, Gohar M. Bacillus cereus Biofilms-Same, Only Different. Front Microbiol 2016; 7:1054. [PMID: 27458448 PMCID: PMC4935679 DOI: 10.3389/fmicb.2016.01054] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 06/23/2016] [Indexed: 12/24/2022] Open
Abstract
Bacillus cereus displays a high diversity of lifestyles and ecological niches and include beneficial as well as pathogenic strains. These strains are widespread in the environment, are found on inert as well as on living surfaces and contaminate persistently the production lines of the food industry. Biofilms are suspected to play a key role in this ubiquitous distribution and in this persistency. Indeed, B. cereus produces a variety of biofilms which differ in their architecture and mechanism of formation, possibly reflecting an adaptation to various environments. Depending on the strain, B. cereus has the ability to grow as immersed or floating biofilms, and to secrete within the biofilm a vast array of metabolites, surfactants, bacteriocins, enzymes, and toxins, all compounds susceptible to act on the biofilm itself and/or on its environment. Within the biofilm, B. cereus exists in different physiological states and is able to generate highly resistant and adhesive spores, which themselves will increase the resistance of the bacterium to antimicrobials or to cleaning procedures. Current researches show that, despite similarities with the regulation processes and effector molecules involved in the initiation and maturation of the extensively studied Bacillus subtilis biofilm, important differences exists between the two species. The present review summarizes the up to date knowledge on biofilms produced by B. cereus and by two closely related pathogens, Bacillus thuringiensis and Bacillus anthracis. Economic issues caused by B. cereus biofilms and management strategies implemented to control these biofilms are included in this review, which also discuss the ecological and functional roles of biofilms in the lifecycle of these bacterial species and explore future developments in this important research area.
Collapse
Affiliation(s)
- Racha Majed
- Micalis Institute, INRA, AgroParisTech, CNRS, Université Paris-SaclayJouy-en-Josas, France; Unité de Recherche Technologies et Valorisation Alimentaire, Laboratoire de Biotechnologie, Université Saint-JosephBeirut, Lebanon
| | - Christine Faille
- UMR UMET: Unité Matériaux et Transformations, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université de Lille Villeneuve d'Ascq, France
| | - Mireille Kallassy
- Unité de Recherche Technologies et Valorisation Alimentaire, Laboratoire de Biotechnologie, Université Saint-Joseph Beirut, Lebanon
| | - Michel Gohar
- Micalis Institute, INRA, AgroParisTech, CNRS, Université Paris-SaclayJouy-en-Josas, France; Unité de Recherche Technologies et Valorisation Alimentaire, Laboratoire de Biotechnologie, Université Saint-JosephBeirut, Lebanon
| |
Collapse
|
28
|
Drago L, Agrappi S, Bortolin M, Toscano M, Romanò CL, De Vecchi E. How to Study Biofilms after Microbial Colonization of Materials Used in Orthopaedic Implants. Int J Mol Sci 2016; 17:293. [PMID: 26927075 PMCID: PMC4813157 DOI: 10.3390/ijms17030293] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/03/2016] [Accepted: 02/06/2016] [Indexed: 12/30/2022] Open
Abstract
Over the years, various techniques have been proposed for the quantitative evaluation of microbial biofilms. Spectrophotometry after crystal violet staining is a widespread method for biofilm evaluation, but several data indicate that it does not guarantee a good specificity, although it is rather easy to use and cost saving. Confocal laser microscopy is one of the most sensitive and specific tools to study biofilms, and it is largely used for research. However, in some cases, no quantitative measurement of the matrix thickness or of the amount of embedded microorganisms has been performed, due to limitation in availability of dedicated software. For this reason, we have developed a protocol to evaluate the microbial biofilm formed on sandblasted titanium used for orthopaedic implants, that allows measurement of biomass volume and the amount of included cells. Results indicate good reproducibility in terms of measurement of biomass and microbial cells. Moreover, this protocol has proved to be applicable for evaluation of the efficacy of different anti-biofilm treatments used in the orthopaedic setting. Summing up, the protocol here described is a valid and inexpensive method for the study of microbial biofilm on prosthetic implant materials.
Collapse
Affiliation(s)
- Lorenzo Drago
- Laboratory of Clinical Chemistry and Microbiology, IRCCS Galeazzi Orthopaedic Institute, via R. Galeazzi 4, 20161 Milan, Italy.
- Laboratory of Clinical Microbiology, Department of Biomedical Sciences for Health, University of Milan, via L. Mangiagalli 31, 20133 Milan, Italy.
| | - Serse Agrappi
- Laboratory of Clinical Chemistry and Microbiology, IRCCS Galeazzi Orthopaedic Institute, via R. Galeazzi 4, 20161 Milan, Italy.
| | - Monica Bortolin
- Laboratory of Clinical Chemistry and Microbiology, IRCCS Galeazzi Orthopaedic Institute, via R. Galeazzi 4, 20161 Milan, Italy.
| | - Marco Toscano
- Laboratory of Clinical Microbiology, Department of Biomedical Sciences for Health, University of Milan, via L. Mangiagalli 31, 20133 Milan, Italy.
| | - Carlo Luca Romanò
- Department of Bone and Joint Infections and Reconstructive Surgery, IRCCS Galeazzi Orthopaedic Institute, via R. Galeazzi 4, 20161 Milan, Italy.
| | - Elena De Vecchi
- Laboratory of Clinical Chemistry and Microbiology, IRCCS Galeazzi Orthopaedic Institute, via R. Galeazzi 4, 20161 Milan, Italy.
| |
Collapse
|
29
|
Pérez-Zárate P, Aragón-Piña A, Soria-Guerra RE, González-Amaro AM, Pérez-Urizar J, Pérez-González LF, Martinez-Gutierrez F. Risk factors and biofilm detection on central venous catheters of patients attended at tertiary hospital. Micron 2015. [PMID: 26218801 DOI: 10.1016/j.micron.2015.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AIM To determinate the significance of risk factors with the presence of biofilm on catheters of patients attended at tertiary hospital cares. MATERIAL AND METHODS A total of 126 patients were included, data collection by observing the handling of the CVC, clinical history and microbiological isolation methods of CVCs tips (Roll-plate, sonication and scanning electron microscopy) were evaluated. RESULTS Certain factors, such as the lack of proper hand washing, the use of primary barriers and preparing medications in the same hospital service, showed an important relationship between biofilm formation in CVCs. The sonication method presented that most of the samples had isolation of multispecies 29 samples (64%); in contrast with the roll-plate method, just one sample (3%) was isolated. CONCLUSIONS The importance of the strict aseptic techniques of insertion and of the handlings of CVC was highlighted, the failure of both techniques was related to the biofilm formation and was evidenced using the scanning electron microscopy. Since this tool is not available in most hospitals, we present the correlation of those evidences with other standard microbiological methods and risk factors, which are necessary for the sensible detection of the different steps of the biofilm formation on CVC and their correct interpretation with clinical evidences.
Collapse
Affiliation(s)
- Pamela Pérez-Zárate
- Laboratorio de Microbiología, Facultad de Ciencias Químicas, UASLP, San Luis Potosí, SLP, Mexico
| | | | - Ruth Elena Soria-Guerra
- Laboratorio de Microbiología, Facultad de Ciencias Químicas, UASLP, San Luis Potosí, SLP, Mexico
| | - Ana María González-Amaro
- Laboratorio Multidisciplinario de la Maestría en Endodoncia, Facultad de Estomatología, UASLP, San Luis Potosí, SLP, Mexico
| | - José Pérez-Urizar
- Laboratorio de Farmacología, Facultad de Ciencias Químicas, UASLP, San Luis Potosí, SLP, Mexico
| | | | - Fidel Martinez-Gutierrez
- Laboratorio de Microbiología, Facultad de Ciencias Químicas, UASLP, San Luis Potosí, SLP, Mexico.
| |
Collapse
|
30
|
Biofilm formation and extracellular polymeric substances (EPS) production by Bacillus subtilis depending on nutritional conditions in the presence of polyester film. Folia Microbiol (Praha) 2015; 61:91-100. [PMID: 26139336 DOI: 10.1007/s12223-015-0406-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 06/08/2015] [Indexed: 10/23/2022]
Abstract
The influence of biofilm formation as the mode of microorganism growth on degradation of synthetic polymers represents an important research topic. This study focuses on the effect of biofilm developed by Bacillus subtilis (BS) cultivated submerged under various nutrition conditions on biodeterioration of poly(ε-caprolactone) film. Polymer in the film form (thickness 0.7 mm) was incubated for 21 days either continuously or by regularly renewed system. The scission of polyester chain bonds took place in all biotic media and was enhanced by biofilm formation in nutrient-rich media.
Collapse
|
31
|
Randrianjatovo I, Girbal-Neuhauser E, Marcato-Romain CE. Epicocconone, a sensitive and specific fluorescent dye for in situ quantification of extracellular proteins within bacterial biofilms. Appl Microbiol Biotechnol 2015; 99:4835-44. [PMID: 25913004 DOI: 10.1007/s00253-015-6570-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 03/17/2015] [Accepted: 03/24/2015] [Indexed: 12/15/2022]
Abstract
Biofilms are ecosystems of closely associated bacteria encapsulated in an extracellular matrix mainly composed of polysaccharides and proteins. A novel approach was developed for in situ quantification of extracellular proteins (ePNs) in various bacterial biofilms using epicocconone, a natural, fluorescent compound that binds amine residues of proteins. Six commercial proteins were tested for their reaction with epicocconone, and bovine serum albumin (BSA) was selected for assay optimization. The optimized protocol, performed as a microassay, allowed protein amounts as low as 0.7 μg to as high as 50 μg per well to be detected. Addition of monosaccharides or polysaccharides (glucose, dextran or alginate) to the standard BSA solutions (0 to 250 μg ml(-1)) showed little or no sugar interference up to 2000 μg ml(-1), thus providing an assessment of the specificity of epicocconone for proteins. The optimized protocol was then applied to three different biofilms, and in situ quantification of ePN showed contrasted protein amounts of 22.1 ± 3.1, 38.3 ± 7.1 and 0.3 ± 0.1 μg equivalent BSA of proteins for 48-h biofilms of Pseudomonas aeruginosa, Bacillus licheniformis and Weissella confusa, respectively. Possible interference due to global matrix compounds on the in situ quantification of proteins was also investigated by applying the standard addition method (SAM). Low error percentages were obtained, indicating a correct quantification of both the ePN and the added proteins. For the first time, a specific and sensitive assay has been developed for in situ determination of ePN produced by bacterial cells. This advance should lead to an accurate, rapid tool for further protein labelling and microscopic observation of the extracellular matrix of biofilms.
Collapse
Affiliation(s)
- I Randrianjatovo
- Université de Toulouse, Laboratoire de Biotechnologies Alimentaire et Environnementale, EA 4565 (LBAE), Institut Universitaire de Technologie, Université Paul Sabatier, 24 rue d'Embaquès, F-32000, Auch, France
| | | | | |
Collapse
|
32
|
Peterson BW, He Y, Ren Y, Zerdoum A, Libera MR, Sharma PK, van Winkelhoff AJ, Neut D, Stoodley P, van der Mei HC, Busscher HJ. Viscoelasticity of biofilms and their recalcitrance to mechanical and chemical challenges. FEMS Microbiol Rev 2015; 39:234-45. [PMID: 25725015 PMCID: PMC4398279 DOI: 10.1093/femsre/fuu008] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
We summarize different studies describing mechanisms through which bacteria in a biofilm mode of growth resist mechanical and chemical challenges. Acknowledging previous microscopic work describing voids and channels in biofilms that govern a biofilms response to such challenges, we advocate a more quantitative approach that builds on the relation between structure and composition of materials with their viscoelastic properties. Biofilms possess features of both viscoelastic solids and liquids, like skin or blood, and stress relaxation of biofilms has been found to be a corollary of their structure and composition, including the EPS matrix and bacterial interactions. Review of the literature on viscoelastic properties of biofilms in ancient and modern environments as well as of infectious biofilms reveals that the viscoelastic properties of a biofilm relate with antimicrobial penetration in a biofilm. In addition, also the removal of biofilm from surfaces appears governed by the viscoelasticity of a biofilm. Herewith, it is established that the viscoelasticity of biofilms, as a corollary of structure and composition, performs a role in their protection against mechanical and chemical challenges. Pathways are discussed to make biofilms more susceptible to antimicrobials by intervening with their viscoelasticity, as a quantifiable expression of their structure and composition. Recalcitrance of biofilms against mechanical and chemical challenges has been looked at for ages from a microbiological perspective, but an approach based on viscoelastic properties of biofilms yields new insights in this recalcitrance.
Collapse
Affiliation(s)
- Brandon W Peterson
- University of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Yan He
- University of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands University of Groningen and University Medical Center Groningen, Department of Orthodontics, Hanzeplein 1, 9700 RB Groningen, The Netherlands
| | - Yijin Ren
- University of Groningen and University Medical Center Groningen, Department of Orthodontics, Hanzeplein 1, 9700 RB Groningen, The Netherlands
| | - Aidan Zerdoum
- Department of Chemical Engineering and Materials Science, Stevens Institute of Technology, Hoboken, NJ 07030, Hoboken, New Jersey, USA
| | - Matthew R Libera
- Department of Chemical Engineering and Materials Science, Stevens Institute of Technology, Hoboken, NJ 07030, Hoboken, New Jersey, USA
| | - Prashant K Sharma
- University of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Arie-Jan van Winkelhoff
- University of Groningen and University Medical Center Groningen, Center for Dentistry and Oral Hygiene, Anatonius Deusinglaan 1, 9713 AV Groningen, The Netherlands University of Groningen and University Medical Center Groningen, Department of Medical Microbiology, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
| | - Danielle Neut
- University of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Paul Stoodley
- Departments of Microbial Infection and Immunity and Orthopedics, Center for Microbial Interface Biology, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA National Centre for Advanced Tribology at Southampton (nCATS), Engineering Sciences, University of Southampton, SO17 1BJ, UK
| | - Henny C van der Mei
- University of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Henk J Busscher
- University of Groningen and University Medical Center Groningen, Department of Biomedical Engineering, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| |
Collapse
|
33
|
Peters LB, Peterson B, Jaramillo DE, van der Sluis L. The Use of Scanning Electron Microscopy (SEM) in Visualizing the Root Canal Biofilm. SPRINGER SERIES ON BIOFILMS 2015. [DOI: 10.1007/978-3-662-47415-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
34
|
Simões LC, Simões M, Lima N. Kinetics of biofilm formation by drinking water isolated Penicillium expansum. BIOFOULING 2015; 31:349-362. [PMID: 26010032 DOI: 10.1080/08927014.2015.1042873] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/16/2015] [Indexed: 06/04/2023]
Abstract
Current knowledge on drinking water (DW) biofilms has been obtained mainly from studies on bacterial biofilms. Very few reports on filamentous fungi (ff) biofilms are available, although they can contribute to the reduction in DW quality. This study aimed to assess the dynamics of biofilm formation by Penicillium expansum using microtiter plates under static conditions, mimicking water flow behaviour in stagnant regions of drinking water distribution systems. Biofilms were analysed in terms of biomass (crystal violet staining), metabolic activity (resazurin, fluorescein diacetate and 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide [MTT]) and morphology (epifluorescence [calcofluor white M2R, FUN-1, FDA and acridine orange] and bright-field microscopies). Biofilm development over time showed the typical sigmoidal curve with noticeable different phases in biofilm formation (induction, exponential, stationary, and sloughing off). The methods used to assess metabolic activity provided similar results. The microscope analysis allowed identification of the involvement of conidia in initial adhesion (4 h), germlings (8 h), initial monolayers (12 h), a monolayer of intertwined hyphae (24 h), mycelial development, hyphal layering and bundling, and development of the mature biofilms (≥48 h). P. expansum grows as a complex, multicellular biofilm in 48 h. The metabolic activity and biomass of the fungal biofilms were shown to increase over time and a correlation between metabolism, biofilm mass and hyphal development was found.
Collapse
Affiliation(s)
- Lúcia Chaves Simões
- a CEB, Centre of Biological Engineering , University of Minho , Braga , Portugal
| | | | | |
Collapse
|
35
|
Gomes IB, Simões M, Simões LC. An overview on the reactors to study drinking water biofilms. WATER RESEARCH 2014; 62:63-87. [PMID: 24937357 DOI: 10.1016/j.watres.2014.05.039] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 05/21/2014] [Accepted: 05/22/2014] [Indexed: 06/03/2023]
Abstract
The development of biofilms in drinking water distribution systems (DWDS) can cause pipe degradation, changes in the water organoleptic properties but the main problem is related to the public health. Biofilms are the main responsible for the microbial presence in drinking water (DW) and can be reservoirs for pathogens. Therefore, the understanding of the mechanisms underlying biofilm formation and behavior is of utmost importance in order to create effective control strategies. As the study of biofilms in real DWDS is difficult, several devices have been developed. These devices allow biofilm formation under controlled conditions of physical (flow velocity, shear stress, temperature, type of pipe material, etc), chemical (type and amount of nutrients, type of disinfectant and residuals, organic and inorganic particles, ions, etc) and biological (composition of microbial community - type of microorganism and characteristics) parameters, ensuring that the operational conditions are similar as possible to the DWDS conditions in order to achieve results that can be applied to the real scenarios. The devices used in DW biofilm studies can be divided essentially in two groups, those usually applied in situ and the bench top laboratorial reactors. The selection of a device should be obviously in accordance with the aim of the study and its advantages and limitations should be evaluated to obtain reproducible results that can be transposed into the reality of the DWDS. The aim of this review is to provide an overview on the main reactors used in DW biofilm studies, describing their characteristics and applications, taking into account their main advantages and limitations.
Collapse
Affiliation(s)
- I B Gomes
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal
| | - M Simões
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal
| | - L C Simões
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal; CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| |
Collapse
|
36
|
Gomes LC, Moreira JMR, Simões M, Melo LF, Mergulhão FJ. Biofilm localization in the vertical wall of shaking 96-well plates. SCIENTIFICA 2014; 2014:231083. [PMID: 24834360 PMCID: PMC4009116 DOI: 10.1155/2014/231083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 12/19/2013] [Indexed: 06/03/2023]
Abstract
Microtiter plates with 96 wells are being increasingly used for biofilm studies due to their high throughput, low cost, easy handling, and easy application of several analytical methods to evaluate different biofilm parameters. These methods provide bulk information about the biofilm formed in each well but lack in detail, namely, regarding the spatial location of the biofilms. This location can be obtained by microscopy observation using optical and electron microscopes, but these techniques have lower throughput and higher cost and are subjected to equipment availability. This work describes a differential crystal violet (CV) staining method that enabled the determination of the spatial location of Escherichia coli biofilms formed in the vertical wall of shaking 96-well plates. It was shown that the biofilms were unevenly distributed on the wall with denser cell accumulation near the air-liquid interface. The results were corroborated by scanning electron microscopy and a correlation was found between biofilm accumulation and the wall shear strain rates determined by computational fluid dynamics. The developed method is quicker and less expensive and has a higher throughput than the existing methods available for spatial location of biofilms in microtiter plates.
Collapse
Affiliation(s)
- Luciana C. Gomes
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Joana M. R. Moreira
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Manuel Simões
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Luís F. Melo
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Filipe J. Mergulhão
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| |
Collapse
|
37
|
Vuotto C, Donelli G. Field emission scanning electron microscopy of biofilm-growing bacteria involved in nosocomial infections. Methods Mol Biol 2014; 1147:73-84. [PMID: 24664827 DOI: 10.1007/978-1-4939-0467-9_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Scanning electron microscopy (SEM) provides useful information on the shape, size, and localization within the biofilm of single bacteria as well as on the steps of biofilm formation process, on bacterial interactions, and on production of extracellular polymeric substances.When biofilms are constituted by microbial species involved in health care-associated infections, information provided by SEM can be fruitfully used not only for basic researches but also for diagnostic purposes.The protocols currently used in our laboratory for biofilm investigation by SEM are reported here. Particularly, the procedures to fix, dehydrate, and metalize in vitro-developed biofilms or ex vivo clinical specimens colonized by biofilm-growing microorganisms are described as well as the advantages of the observation of these samples by field emission scanning electron microscopy.
Collapse
Affiliation(s)
- Claudia Vuotto
- Microbial Biofilm Laboratory, Fondazione Santa Lucia IRCCS, Via Ardeatina 306, 00179, Rome, Italy
| | | |
Collapse
|
38
|
Gomes LC, Moreira JMR, Miranda JM, Simões M, Melo LF, Mergulhão FJ. Macroscale versus microscale methods for physiological analysis of biofilms formed in 96-well microtiter plates. J Microbiol Methods 2013; 95:342-9. [PMID: 24140575 DOI: 10.1016/j.mimet.2013.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 10/01/2013] [Accepted: 10/08/2013] [Indexed: 12/24/2022]
Abstract
Microtiter plates with 96 wells have become one of the preferred platforms for biofilm studies mainly because they enable high-throughput assays. In this work, macroscale and microscale methods were used to study the impact of hydrodynamic conditions on the physiology and location of Escherichia coli JM109(DE3) biofilms formed in microtiter plates. Biofilms were formed in shaking and static conditions, and two macroscale parameters were assayed: the total amount of biofilm was measured by the crystal violet assay and the metabolic activity was determined by the resazurin assay. From the macroscale point of view, there were no statistically significant differences between the biofilms formed in static and shaking conditions. However, at a microscale level, the differences between both conditions were revealed using scanning electron microscopy (SEM). It was observed that biofilm morphology and spatial distribution along the wall were different in these conditions. Simulation of the hydrodynamic conditions inside the wells at a microscale was performed by computational fluid dynamics (CFD). These simulations showed that the shear strain rate was unevenly distributed on the walls during shaking conditions and that regions of higher shear strain rate were obtained closer to the air/liquid interface. Additionally, it was shown that wall regions subjected to higher shear strain rates were associated with the formation of biofilms containing cells of smaller size. Conversely, regions with lower shear strain rate were prone to have a more uniform spatial distribution of adhered cells of larger size. The results presented on this work highlight the wealth of information that may be gathered by complementing macroscale approaches with a microscale analysis of the experiments.
Collapse
Affiliation(s)
- L C Gomes
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, Porto, Portugal
| | | | | | | | | | | |
Collapse
|