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Multispecies Biofilms and Microbial Interactions

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Biofilm".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 42514

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Special Issue Editors

Prof. Maëlle Molmeret

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Guest Editor

Unviersity of Toulon, Avenue de l'Université, 83130 La Garde, France
Interests: biofilm; multispecies/multiorganism biofilms; bacteria–host cell interactions; quorum sensing

Dr. Laurent Urios

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Co-Guest Editor

Institute of Analytical Sciences and Physico-Chemistry for Environment and Materials (IPREM), UMR CNRS 5254, Université de Pau et des Pays de l'Adour, Avenue de l'Université, 64013 Pau CEDEX, France
Interests: microbial diversity; biofilms; biodegradation/biodeterioration
Special Issues, Collections and Topics in MDPI journals

Dr. Raphaël LAMI

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Co-Guest Editor

Microbial Biodiversity and Biotechnology Lab, Sorbonne University, Observatoire Océanologique, 66650 Banyuls-sur-mer, France
Interests: biofilms; quorum sensing; quorum quenching; microbial biodiversity; molecular tools

Dr. Claudine BARAQUET

E-Mail Website
Co-Guest Editor

Unviersity of Toulon, Avenue de l'Université, 83130 La Garde, France
Interests: biofilm; motility; regulation; c-di-GMP

Special Issue Information

Dear Colleagues,

In most environments, microbial community composition is shaped by interdependent metabolic interactions determining interspecies competition or cooperation relationships between organisms. Natural ecosystems are made of a mosaic of microhabitats. Within these microhabitats, bacterial (sub)populations do not obligatorily interact on an intimate level with each other due to an important biofilm heterogeneity. Other organisms, including protists and fungi can be part of these biofilms, thereby altering their structure and properties.

Today, limited information is available on multispecies/multiorganism biofilms and their microhabitats related to their natural environment. There is a missing bridge between mono- and bi-species in vitro and large scale in situ studies. Biofilm behavior can profoundly differ when in multispecies and multiorganism versus in monospecies conditions. Moreover, understanding competition and cooperation interactions can result in the identification of molecules of interest. Studies on multiorganism biofilms can also lead to the identification of uncommon (or novel) interactions, which may explain how they survive in the environment. Overall, studying multispecies biofilms can give information on microhabitats, spatial organization, and microorganism interactions.

The aim of this Special Issue, dedicated to “Multispecies Biofilms and Microbial Interactions”, is to collect research articles and reviews on the mechanisms underlying the formation of multispecies and multiorganism biofilms, their persistence and resistance under modified environmental conditions, the development of appropriate laboratory methods to study these biofilms, and the identification of molecules of interest in relation to microbial interactions and of innovative antibiofilm strategies.

Prof. Maëlle Molmeret
Dr. Claudine BARAQUET
Dr. Raphaël LAMI
Dr. Laurent URIOS
Guest Editors

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Keywords

multispecies/multiorganism biofilms
microbial interactions
microhabitats
persistence
resistance
antibiofilm strategies

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Published Papers (11 papers)

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Research

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13 pages, 3021 KiB

Open AccessArticle

Root Caries Preventive Effect of Varnishes Containing Fluoride or Fluoride + Chlorhexidine/Cetylpyridinium Chloride In Vitro

by Gerd Göstemeyer, Helen Woike, Sebastian Paris, Falk Schwendicke and Sebastian Schlafer

Microorganisms 2021, 9(4), 737; https://doi.org/10.3390/microorganisms9040737 - 1 Apr 2021

Cited by 9 | Viewed by 2781

Abstract

Caries preventive varnishes containing only fluoride might differ from those containing a combination of fluoride and antimicrobial components in terms of mineralization properties and their impact on the cariogenic biofilm. We compared a fluoride and a fluoride + chlorhexidine (CHX)/cetylpyridinium chloride (CPC) varnish on root caries formation in vitro. One hundred bovine root dentin samples were allocated to five groups (n = 20/group): (1) 7700 ppm fluoride varnish (Fluorprotector S (F)), (2) experimental placebo varnish for F (F-P), (3) 1400 ppm fluoride + 0.3% CHX/0.5% CPC varnish (Cervitec F (CF)), (4) experimental placebo varnish for CF (CF-P), (5) untreated control. Cariogenic challenge was provided using a multi-station, continuous-culture 3-species (Streptococcus mutans (SM), Lactobacillus rhamnosus (LR), Actinomyces naeslundii (AN)) biofilm model for 10 days. Mineral loss (ΔZ) was evaluated using transversal microradiography and bacterial counts in the biofilm assessed as colony-forming units. Fluorescence in situ hybridization (FISH) and confocal microscopy were performed to assess the three-dimensional biofilm architecture. Mean ± SD (vol% × μm) ΔZ was significantly lower for F (9133 ± 758) and CF (9835 ± 1677) compared to control (11362 ± 919) (p < 0.05), without significant differences between F and CF. SM counts were significantly lower and LR counts significantly higher in F- and CF-biofilms compared to control. AN counts were significantly higher in the F-biofilms than in all other groups. According to FISH, SM and LR invaded dentinal tubules only in the control-group. In the CF-group, the basal biofilm layer did not contain SM and AN. Both F and CF varnishes had similar caries-preventive effects and a considerable impact on biofilm structure and composition. Full article

(This article belongs to the Special Issue Multispecies Biofilms and Microbial Interactions)

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16 pages, 1719 KiB

Open AccessArticle

Probiotic Lactobacillus sp. Strains Inhibit Growth, Adhesion, Biofilm Formation, and Gene Expression of Bacterial Vaginosis-Inducing Gardnerella vaginalis

by Zhixiang Qian, Hui Zhu, Dan Zhao, Ping Yang, Fei Gao, Chunyi Lu, Yu Yin, Shidong Kan and Daijie Chen

Microorganisms 2021, 9(4), 728; https://doi.org/10.3390/microorganisms9040728 - 31 Mar 2021

Cited by 22 | Viewed by 5701

Abstract

Gardnerella vaginalis contributes significantly to bacterial vaginosis, which causes an ecological imbalance in vaginal microbiota and presents with the depletion of Lactobacillus sp. Lactobacillus supplementation was reported to be an approach to treat bacterial vaginosis. We investigated the applicability of three Lactobacillus sp. strains (Lactobacillus delbrueckii DM8909, Lactiplantibacillus plantarum ATCC14917, and Lactiplantibacillus plantarum ZX27) based on their probiotic abilities in vitro. The three candidate Lactobacillus sp. strains for bacterial vaginosis therapy showed distinct properties in auto-aggregation ability, hydrophobicity, adhesion to cervical epithelial cells, and survivability in 0.01% hydrogen peroxide. Lpb. plantarum ZX27 showed a higher yield in producing short-chain fatty acids and lactic acid among the three candidate strains, and all three Lactobacillus sp. strains inhibited the growth and adhesion of G. vaginalis. Furthermore, we discovered that the culture supernatant of Lactobacillus sp. exhibited anti-biofilm activity against G. vaginalis. In particular, the Lpb. plantarum ZX27 supernatant treatment decreased the expression of genes related to virulence factors, adhesion, biofilm formation, metabolism, and antimicrobial resistance in biofilm-forming cells and suspended cells. Moreover, Lactobacillus sp. decreased the upregulated expression of interleukin−8 in HeLa cells induced by G. vaginalis or hydrogen peroxide. These results demonstrate the efficacy of Lactobacillus sp. application for treating bacterial vaginosis by limiting the growth, adhesion, biofilm formation, and virulence properties of G. vaginalis. Full article

(This article belongs to the Special Issue Multispecies Biofilms and Microbial Interactions)

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16 pages, 4393 KiB

Open AccessArticle

In Vitro Anti-Biofilm and Antibacterial Properties of Streptococcus downii sp. nov.

by Maigualida Cuenca, María Carmen Sánchez, Pedro Diz, Lucía Martínez-Lamas, Maximiliano Álvarez, Jacobo Limeres, Mariano Sanz and David Herrera

Microorganisms 2021, 9(2), 450; https://doi.org/10.3390/microorganisms9020450 - 22 Feb 2021

Cited by 6 | Viewed by 3119

Abstract

The aim of this study was to evaluate the potential anti-biofilm and antibacterial activities of Streptococcus downii sp. nov. To test anti-biofilm properties, Streptococcus mutans, Actinomyces naeslundii, Veillonella parvula, Fusobacterium nucleatum, Porphyromonas gingivalis, and Aggregatibacter actinomycetemcomitans were grown in a biofilm model in the presence or not of S. downii sp. nov. for up to 120 h. For the potential antibacterial activity, 24 h-biofilms were exposed to S. downii sp. nov for 24 and 48 h. Biofilms structures and bacterial viability were studied by microscopy, and the effect in bacterial load by quantitative polymerase chain reaction. A generalized linear model was constructed, and results were considered as statistically significant at p < 0.05. The presence of S. downii sp. nov. during biofilm development did not affect the structure of the community, but an anti-biofilm effect against S. mutans was observed (p < 0.001, after 96 and 120 h). For antibacterial activity, after 24 h of exposure to S. downii sp. nov., counts of S. mutans (p = 0.019) and A. actinomycetemcomitans (p = 0.020) were significantly reduced in well-structured biofilms. Although moderate, anti-biofilm and antibacterial activities of S. downii sp. nov. against oral bacteria, including some periodontal pathogens, were demonstrated in an in vitro biofilm model. Full article

(This article belongs to the Special Issue Multispecies Biofilms and Microbial Interactions)

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12 pages, 3155 KiB

Open AccessArticle

Methyl Potassium Siliconate and Siloxane Inhibit the Formation of Multispecies Biofilms on Ceramic Roof Tiles: Efficiency and Comparison of Two Common Water Repellents

by Mattea Romani, Claire Carrion, Frédéric Fernandez, Philippe Lebaron and Raphaël Lami

Microorganisms 2021, 9(2), 394; https://doi.org/10.3390/microorganisms9020394 - 15 Feb 2021

Cited by 5 | Viewed by 2555

Abstract

Ceramic roof tiles are widespread marketed building materials, rapidly colonized by microorganisms that form multispecies biofilms on their surface and play crucial roles in biodeterioration processes. Coating tiles with water repellents is a pervasive industrial strategy employed to prevent liquid water penetration and slow biodeterioration. Very few studies have examined the links between the characteristics of water-repellent coatings and biofilm colonization patterns. Our work aims to compare the effects of coating tiles with two common water repellents (siliconate and siloxane) on the growth of colonizing microbes. We combined in situ exposure of tiles for over six years and macroscopic and microscopic observations with in vitro biotests, relying on the use of algal and fungal models. Our data showed that (1) tiles coated with water repellents were macroscopically less colonized by lichens (2) a significant fungal biofilm development at the microscopic scale (3) water repellents had very contrasting effects on our model strains. These data reinforce the great interest for industry to conduct more studies linking the nature of the water repellents with the composition of colonizing multispecies biofilms. The long-term objective is to improve the available water repellents and better adapt their selection to the nature of microbial colonization. Full article

(This article belongs to the Special Issue Multispecies Biofilms and Microbial Interactions)

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14 pages, 12442 KiB

Open AccessArticle

Antimicrobial Photoinactivation of In Situ Oral Biofilms by Visible Light Plus Water-Filtered Infrared A and Tetrahydroporphyrin-tetratosylate (THPTS)

by Lamprini Karygianni, Sandra Ruf, Elmar Hellwig, Marie Follo, Kirstin Vach and Ali Al-Ahmad

Microorganisms 2021, 9(1), 145; https://doi.org/10.3390/microorganisms9010145 - 11 Jan 2021

Cited by 8 | Viewed by 2853

Abstract

The aim of this study was to examine the effect of aPDT with visual light (VIS) + water-filtered infrared A (wIRA) as a light source, and tetrahydroporphyrin-tetratosylate (THPTS) as a photosensitizer on in situ initial and mature oral biofilms. The samples were incubated, ex situ, with THPTS for two minutes, followed by irradiation with 200 mW cm − 2 VIS + wIRA for five minutes at 37 °C. The adherent microorganisms were quantified, and the biofilm samples were visualized using live/dead staining and confocal laser scanning microscopy (CLSM). The THPTS-mediated aPDT resulted in significant decreases in both the initially adherent microorganisms and the microorganisms in the mature oral biofilms, in comparison to the untreated control samples (>99.99% each; p = 0.018 and p = 0.0066, respectively). The remaining vital bacteria significantly decreased in the aPDT-treated biofilms during initial adhesion (vitality rate 9.4% vs. 71.2% untreated control, 17.28% CHX). Of the mature biofilms, 25.67% remained vital after aPDT treatment (81.97% untreated control, 16.44% CHX). High permeability of THPTS into deep layers could be shown. The present results indicate that the microbial reduction in oral initial and mature oral biofilms resulting from aPDT with VIS + wIRA in combination with THPTS has significant potential for the treatment of oral biofilm-associated diseases. Full article

(This article belongs to the Special Issue Multispecies Biofilms and Microbial Interactions)

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25 pages, 10837 KiB

Open AccessArticle

Marine Bacteria Display Different Escape Mechanisms When Facing Their Protozoan Predators

by Richard Guillonneau, Claudine Baraquet and Maëlle Molmeret

Microorganisms 2020, 8(12), 1982; https://doi.org/10.3390/microorganisms8121982 - 12 Dec 2020

Cited by 4 | Viewed by 3565

Abstract

Free-living amoeba are members of microbial communities such as biofilms in terrestrial, fresh, and marine habitats. Although they are known to live in close association with bacteria in many ecosystems such as biofilms, they are considered to be major bacterial predators in many ecosystems. Little is known on the relationship between protozoa and marine bacteria in microbial communities, more precisely on how bacteria are able survive in environmental niches where these bacterial grazers also live. The objective of this work is to study the interaction between the axenized ubiquitous amoeba Acanthamoeba castellanii and four marine bacteria isolated from immersed biofilm, in order to evaluate if they would be all grazed upon by amoeba or if they would be able to survive in the presence of their predator. At a low bacteria-to-amoeba ratio, we show that each bacterium is phagocytized and follows a singular intracellular path within this host cell, which appears to delay or to prevent bacterial digestion. In particular, one of the bacteria was found in the amoeba nucleolar compartment whereas another strain was expelled from the amoeba in vesicles. We then looked at the fate of the bacteria grown in a higher bacteria-to-amoeba ratio, as a preformed mono- or multi-species biofilm in the presence of A. castellanii. We show that all biofilms were subjected to detachment from the surface in the presence of the amoeba or its supernatant. Overall, these results show that bacteria, when facing the same predator, exhibit a variety of escape mechanisms at the cellular and population level, when we could have expected a simple bacterial grazing. Therefore, this study unravels new insights into the survival of environmental bacteria when facing predators that they could encounter in the same microbial communities. Full article

(This article belongs to the Special Issue Multispecies Biofilms and Microbial Interactions)

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19 pages, 9460 KiB

Open AccessArticle

Disinfectant, Soap or Probiotic Cleaning? Surface Microbiome Diversity and Biofilm Competitive Exclusion

by Wendy Stone, Janke Tolmay, Keira Tucker and Gideon M. Wolfaardt

Microorganisms 2020, 8(11), 1726; https://doi.org/10.3390/microorganisms8111726 - 4 Nov 2020

Cited by 19 | Viewed by 6055

Abstract

This study extends probiotic cleaning research to a built environment. Through an eight-month cleaning trial, we compared the effect of three cleaning products (disinfectant, plain soap, and a probiotic cleaner containing a patented Bacillus spore consortium), and tap water as the control, on the resident microbiome of three common hospital surfaces (linoleum, ceramic, and stainless steel). Pathogens, Escherichia coli and Staphylococcus aureus, were deposited and desiccated, and competitive exclusion was assessed for each microbiome. Cell survival was shown to be an incomplete tool for measuring microbial competitive exclusion. Biofilm competition offered a fuller understanding of competitive dynamics. A test for culturable cell survival showed that both plain soap and probiotic cleaner regimes established a surface microbiome that outcompeted the two pathogens. A different picture emerged when observing biofilms with a deposited and desiccated GFP-labeled pathogen, Pseudomonas aeruginosa. Competitive exclusion was again demonstrated. On surfaces cleaned with disinfectant the pathogen outcompeted the microbiomes. On surfaces cleaned with plain soap, the microbiomes outcompeted the pathogen. However, on surfaces cleaned with probiotic cleaner, despite the exponentially higher surface microbial loads, the microbiome did not completely outcompete the pathogen. Thus, the standard culturable cell test for survival on a surface confirmed the competitive advantage that is typically reported for probiotic cleaners. However, observation of competition in biofilms showed that the more diverse microbiome (according to alpha and beta indices) established on a surface cleaned with plain soap had a better competitive advantage than the monoculture established by the probiotic cleaner. Therefore, microbial diversity appears to be as critical to the competitive exclusion principle as cell numbers. The study showed that both plain soap and probiotic cleaner fostered competitive exclusion far more effectively than disinfectant. Probiotic cleaners with microbial diversity could be worth considering for hospital cleaning. Full article

(This article belongs to the Special Issue Multispecies Biofilms and Microbial Interactions)

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16 pages, 3475 KiB

Open AccessArticle

Regulating Oral Biofilm from Cariogenic State to Non-Cariogenic State via Novel Combination of Bioactive Therapeutic Composite and Gene-Knockout

by Hong Chen, Yingming Yang, Michael D. Weir, Quan Dai, Lei Lei, Negar Homayounfar, Thomas W. Oates, Kai Yang, Ke Zhang, Tao Hu and Hockin H. K. Xu

Microorganisms 2020, 8(9), 1410; https://doi.org/10.3390/microorganisms8091410 - 13 Sep 2020

Cited by 6 | Viewed by 2472

Abstract

The objectives were to investigate a novel combination of gene-knockout with antimicrobial dimethylaminohexadecyl methacrylate (DMAHDM) composite in regulating oral biofilm from a cariogenic state toward a non-cariogenic state. A tri-species biofilm model included cariogenic Streptococcus mutans (S. mutans), and non-cariogenic Streptococcus sanguinis (S. sanguinis) and Streptococcus gordonii (S. gordonii). Biofilm colony-forming-units (CFUs), lactic acid and polysaccharide production were measured. TaqMan real-time-polymerase-chain reaction was used to determine the percentage of each species in biofilm. The rnc gene-knockout for S. mutans with DMAHDM composite reduced biofilm CFU by five logs, compared to control (p < 0.05). Using parent S. mutans, an overwhelming S. mutans percentage of 68.99% and 69.00% existed in biofilms on commercial composite and 0% DMAHDM composite, respectively. In sharp contrast, with a combination of S. mutans rnc knockout and DMAHDM composite, the cariogenic S. mutans percentage in biofilm was reduced to only 6.33%. Meanwhile, the non-cariogenic S. sanguinis + S. gordonii percentage was increased to 93.67%. Therefore, combining rnc-knockout with bioactive and therapeutic dental composite achieved the greatest reduction in S. mutans, and the greatest increase in non-cariogenic species, thereby yielding the least lactic acid-production. This novel method is promising to obtain wide applications to regulate biofilms and inhibit dental caries. Full article

(This article belongs to the Special Issue Multispecies Biofilms and Microbial Interactions)

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20 pages, 2723 KiB

Open AccessArticle

Anti-Biofilm Activity of a Low Weight Proteinaceous Molecule from the Marine Bacterium Pseudoalteromonas sp. IIIA004 against Marine Bacteria and Human Pathogen Biofilms

by Ibtissem Doghri, Emilie Portier, Florie Desriac, Jean Michel Zhao, Alexis Bazire, Alain Dufour, Vincent Rochette, Sophie Sablé and Isabelle Lanneluc

Microorganisms 2020, 8(9), 1295; https://doi.org/10.3390/microorganisms8091295 - 25 Aug 2020

Cited by 8 | Viewed by 3016

Abstract

Pseudoalteromonas bacteria are known as potential bioactive metabolite producers. Because of the need to obtain natural molecules inhibiting the bacterial biofilms, we investigated the biofilm inhibitory activity of the marine bacterium Pseudoalteromonas sp. IIIA004 against the pioneer surface colonizer Roseovarius sp. VA014. The anti-biofilm activity from the culture supernatant of Pseudoalteromonas sp. IIIA004 (SN_IIIA004) was characterized in microtiter plates (static conditions/polystyrene surface) and in flow cell chambers (dynamic conditions/glass surface). The Pseudoalteromonas exoproducts exhibited an inhibition of Roseovarius sp. VA014 biofilm formation as well as a strong biofilm dispersion, without affecting the bacterial growth. Microbial adhesion to solvent assays showed that SN_IIIA004 did not change the broad hydrophilic and acid character of the Roseovarius strain surface. Bioassay-guided purification using solid-phase extraction and C₁₈ reverse-phase-high-performance liquid chromatography (RP-HPLC) was performed from SN_IIIA004 to isolate the proteinaceous active compound against the biofilm formation. This new anti-biofilm low weight molecule (< 3kDa), named P₀₀₄, presented a wide spectrum of action on various bacterial biofilms, with 71% of sensitive strains including marine bacteria and human pathogens. Pseudoalteromonas sp. IIIA004 is a promising source of natural anti-biofilm compounds that combine several activities. Full article

(This article belongs to the Special Issue Multispecies Biofilms and Microbial Interactions)

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Review

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20 pages, 5953 KiB

Open AccessReview

Friends with Benefits: An Inside Look of Periodontal Microbes’ Interactions Using Fluorescence In Situ Hybridization—Scoping Review

by Guilherme Melo Esteves, José António Pereira, Nuno Filipe Azevedo, Andreia Sofia Azevedo and Luzia Mendes

Microorganisms 2021, 9(7), 1504; https://doi.org/10.3390/microorganisms9071504 - 14 Jul 2021

Cited by 6 | Viewed by 3918

Abstract

Fluorescence in situ hybridization (FISH) has proven to be particularly useful to describe the microbial composition and spatial organization of mixed microbial infections, as it happens in periodontitis. This scoping review aims to identify and map all the documented interactions between microbes in periodontal pockets by the FISH technique. Three electronic sources of evidence were consulted in search of suitable articles up to 7 November 2020: MEDLINE (via PubMed), Scopus (Elsevier: Amsterdam, The Netherlands), and Web of Science (Clarivate Analytics: Philadelphia, PA, USA) online databases. Studies that showed ex vivo and in situ interactions between, at least, two microorganisms were found eligible. Ten papers were included. Layered or radially ordered multiple-taxon structures are the most common form of consortium. Strict or facultative anaerobic microorganisms are mostly found in the interior and the deepest portions of the structures, while aerobic microorganisms are mostly found on the periphery. We present a model of the microbial spatial organization in sub- and supragingival biofilms, as well as how the documented interactions can shape the biofilm formation. Despite the already acquired knowledge, available evidence regarding the structural composition and interactions of microorganisms within dental biofilms is incomplete and large-scale studies are needed. Full article

(This article belongs to the Special Issue Multispecies Biofilms and Microbial Interactions)

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19 pages, 5825 KiB

Open AccessReview

Relevance of Biofilm Models in Periodontal Research: From Static to Dynamic Systems

by María Carmen Sánchez, Andrea Alonso-Español, Honorato Ribeiro-Vidal, Bettina Alonso, David Herrera and Mariano Sanz

Microorganisms 2021, 9(2), 428; https://doi.org/10.3390/microorganisms9020428 - 19 Feb 2021

Cited by 25 | Viewed by 5130

Abstract

Microbial biofilm modeling has improved in sophistication and scope, although only a limited number of standardized protocols are available. This review presents an example of a biofilm model, along with its evolution and application in studying periodontal and peri-implant diseases. In 2011, the ETEP (Etiology and Therapy of Periodontal and Peri-Implant Diseases) research group at the University Complutense of Madrid developed an in vitro biofilm static model using representative bacteria from the subgingival microbiota, demonstrating a pattern of bacterial colonization and maturation similar to in vivo subgingival biofilms. When the model and its methodology were standardized, the ETEP research group employed the validated in vitro biofilm model for testing in different applications. The evolution of this model is described in this manuscript, from the mere observation of biofilm growth and maturation on static models on hydroxyapatite or titanium discs, to the evaluation of the impact of dental implant surface composition and micro-structure using the dynamic biofilm model. This evolution was based on reproducing the ideal microenvironmental conditions for bacterial growth within a bioreactor and reaching the target surfaces using the fluid dynamics mimicking the salivary flow. The development of this relevant biofilm model has become a powerful tool to study the essential processes that regulate the formation and maturation of these important microbial communities, as well as their behavior when exposed to different antimicrobial compounds. Full article

(This article belongs to the Special Issue Multispecies Biofilms and Microbial Interactions)

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