Molecular architecture and assembly principles of Vibrio cholerae biofilms

Intestinal biofilms: pathophysiological relevance, host defense, and therapeutic opportunities

SUMMARYThe human intestinal tract harbors a profound variety of microorganisms that live in symbiosis with the host and each other. It is a complex and highly dynamic environment whose homeostasis directly relates to human health. Dysbiosis of the gut microbiota and polymicrobial biofilms have been associated with gastrointestinal diseases, including irritable bowel syndrome, inflammatory bowel diseases, and colorectal cancers. This review covers the molecular composition and organization of intestinal biofilms, mechanistic aspects of biofilm signaling networks for bacterial communication and behavior, and synergistic effects in polymicrobial biofilms. It further describes the clinical relevance and diseases associated with gut biofilms, the role of biofilms in antimicrobial resistance, and the intestinal host defense system and therapeutic strategies counteracting biofilms. Taken together, this review summarizes the latest knowledge and research on intestinal biofilms and their role in gut disorders and provides directions toward the development of biofilm-specific treatments.

Marine bacteria Alteromonas spp. require UDP-glucose-4-epimerase for aggregation and production of sticky exopolymer

The physiology and ecology of particle-associated marine bacteria are of growing interest, but our knowledge of their aggregation behavior and mechanisms controlling their association with particles remains limited. We have found that a particle-associated isolate, Alteromonas sp. ALT199 strain 4B03, and the related type-strain A. macleodii 27126 both form large (>500 μm) aggregates while growing in rich medium. A non-clumping variant (NCV) of 4B03 spontaneously arose in the lab, and whole-genome sequencing revealed a partial deletion in the gene encoding UDP-glucose-4-epimerase (galEΔ308-324). In 27126, a knock-out of galE (ΔgalE::kmr) resulted in a loss of aggregation, mimicking the NCV. Microscopic analysis shows that both 4B03 and 27126 rapidly form large aggregates, whereas their respective galE mutants remain primarily as single planktonic cells or clusters of a few cells. Strains 4B03 and 27126 also form aggregates with chitin particles, but their galE mutants do not. Alcian Blue staining shows that 4B03 and 27126 produce large transparent exopolymer particles (TEP), but their galE mutants are deficient in this regard. This study demonstrates the capabilities of cell-cell aggregation, aggregation of chitin particles, and production of TEP in strains of Alteromonas, a widespread particle-associated genus of heterotrophic marine bacteria. A genetic requirement for galE is evident for each of the above capabilities, expanding the known breadth of requirement for this gene in biofilm-related processes.

IMPORTANCE

Heterotrophic marine bacteria have a central role in the global carbon cycle. Well-known for releasing CO2 by decomposition and respiration, they may also contribute to particulate organic matter (POM) aggregation, which can promote CO2 sequestration via the formation of marine snow. We find that two members of the prevalent particle-associated genus Alteromonas can form aggregates comprising cells alone or cells and chitin particles, indicating their ability to drive POM aggregation. In line with their multivalent aggregation capability, both strains produce TEP, an excreted polysaccharide central to POM aggregation in the ocean. We demonstrate a genetic requirement for galE in aggregation and large TEP formation, building our mechanistic understanding of these aggregative capabilities. These findings point toward a role for heterotrophic bacteria in POM aggregation in the ocean and support broader efforts to understand bacterial controls on the global carbon cycle based on microbial activities, community structure, and meta-omic profiling.

Screening and identification of functional bacterial attachment genes in aerobic granular sludge

The screening and identification of attachment genes is important to exploring the formation mechanism of biofilms at the gene level. It is helpful to the development of key culture technologies for aerobic granular sludge (AGS). In this study, genome-wide sequencing and gene editing were employed for the first time to investigate the effects and functions of attachment genes in AGS. With the help of whole-genome analysis, ten attachment genes were screened from thirteen genes, and the efficiency of gene screening was greatly improved. Then, two attachment genes were selected as examples to further confirm the gene functions by constructing gene-knockout recombinant mutants of Stenotrophomonas maltophilia; when the two attachment genes were knocked out, the attachment potential was reduced by 50.67% and 43.93%, respectively. The results provide a new theoretical principle and efficient method for the development of AGS from the perspective of attachment genes.

Metal-polyphenol coordination nanosheets with synergistic peroxidase-like and photothermal properties for efficient antibacterial treatment

Bacterial infections pose a serious threat to human health and socioeconomics worldwide. In the post-antibiotic era, the development of novel antimicrobial agents remains a challenge. Polyphenols are natural compounds with a variety of biological activities such as intrinsic antimicrobial activity and antioxidant properties. Metal-polyphenol obtained by chelation of polyphenol ligands with metal ions not only possesses efficient antimicrobial activity but also excellent biocompatibility, which has great potential for application in biomedical and food packaging fields. Herein, we developed metal-polyphenol coordination nanosheets named copper oxidized tannic acid quinone (CuTAQ) possessing efficient antibacterial and anti-biofilm effects, which was synthesized by a facile one-pot method. The synthesis was achieved by chelation of partially oxidized tannic acid (TA) with Cu2+ under mild conditions, which supports low-cost and large-scale production. It was demonstrated that CuTAQ exhibited high antibacterial activity via disrupting the integrity of bacterial cell membranes, inducing oxidative stress, and interfering with metabolism. In addition, CuTAQ exhibits excellent peroxidase catalytic activity and photothermal conversion properties, which play a significant role in enhancing its bactericidal and biofilm scavenging abilities. This study provides insights for rational design of innovative metal-polyphenol nanomaterials with efficient antimicrobial properties.

Enhanced Chemoradiotherapy for MRSA-Infected Osteomyelitis Using Immunomodulatory Polymer-Reinforced Nanotherapeutics

The eradication of osteomyelitis caused by methicillin-resistant Staphylococcus aureus (MRSA) poses a significant challenge due to its development of biofilm-induced antibiotic resistance and impaired innate immunity, which often leads to frequent surgical failure. Here, the design, synthesis, and performance of X-ray-activated polymer-reinforced nanotherapeutics that modulate the immunological properties of infectious microenvironments to enhance chemoradiotherapy against multidrug-resistant bacterial deep-tissue infections are reported. Upon X-ray radiation, the proposed polymer-reinforced nanotherapeutic generates reactive oxygen species and reactive nitrogen species. To robustly eradicate MRSA biofilms at deep infection sites, these species can specifically bind to MRSA and penetrate biofilms for enhanced chemoradiotherapy treatment. X-ray-activated nanotherapeutics modulate the innate immunity of macrophages to prevent the recurrence of osteomyelitis. The remarkable anti-infection effects of these nanotherapeutics are validated using a rat osteomyelitis model. This study demonstrates the significant potential of a synergistic chemoradiotherapy and immunotherapy method for treating MRSA biofilm-infected osteomyelitis.

Elevated concentrations of polymyxin B elicit a biofilm-specific resistance mechanism in Vibrio cholerae

Vibrio cholerae can form biofilms in the aquatic environment and in the human intestine, facilitating the release of hyper-infectious aggregates. Due to the increasing antibiotic resistance, alternatives need to be found. One of these alternatives is antimicrobial peptides, including polymyxin B (PmB). In this study, we first investigated the resistance of V. cholerae O1 El Tor strain A1552 to various antimicrobials under aerobic and anaerobic conditions. An increased resistance to PmB is observed in anaerobiosis, with a 3-fold increase in the dose required for 50 % growth inhibition. We then studied the impact of the PmB on the formation and the degradation of V. cholerae biofilms to PmB. Our results show that PmB affects more efficiently biofilm formation under anaerobic conditions. On the other hand, preformed biofilms are susceptible to degradation by PmB at concentrations close to the minimal inhibitory concentration. At higher concentrations, we observe an opacification of the biofilm structures within 20 min post-treatment, suggesting a densification of the structure. This densification does not seem to result from the overexpression of matrix genes but rather from DNA release through massive cell lysis, likely forming a protective shield that limits the penetration of the PmB into the biofilm.

Proteus mirabilis biofilm expansion microscopy yields over 4-fold magnification for super-resolution of biofilm structure and subcellular DNA organization

Bacterial biofilms form when bacteria attach to surfaces and generate an extracellular matrix that embeds and stabilizes a growing community. Detailed visualization and quantitative analysis of biofilm architecture by optical microscopy are limited by the law of diffraction. Expansion Microscopy (ExM) is a novel Super-Resolution technique where specimens are physically enlarged by a factor of ∼4, prior to observation by conventional fluorescence microscopy. ExM requires homogenization of rigid constituents of biological components by enzymatic digestion. We developed an ExM approach capable of expanding 48-h old Proteus mirabilis biofilms 4.3-fold (termed PmbExM), close to the theoretic maximum expansion factor without gross shape distortions. Our protocol, based on lytic and glycoside-hydrolase enzymatic treatments, degrades rigid components in bacteria and extracellular matrix. Our results prove PmbExM to be a versatile and easy-to-use Super-Resolution approach for enabling studies of P. mirabilis biofilm architecture, assembly, and even intracellular features, such as DNA organization.

Substrate geometry affects population dynamics in a bacterial biofilm

Biofilms inhabit a range of environments, such as dental plaques or soil micropores, often characterized by noneven surfaces. However, the impact of surface irregularities on the population dynamics of biofilms remains elusive, as most experiments are conducted on flat surfaces. Here, we show that the shape of the surface on which a biofilm grows influences genetic drift and selection within the biofilm. We culture Escherichia coli biofilms in microwells with a corrugated bottom surface and observe the emergence of clonal sectors whose size corresponds to that of the corrugations, despite no physical barrier separating different areas of the biofilm. The sectors are remarkably stable and do not invade each other; we attribute this stability to the characteristics of the velocity field within the biofilm, which hinders mixing and clonal expansion. A microscopically detailed computer model fully reproduces these findings and highlights the role of mechanical interactions such as adhesion and friction in microbial evolution. The model also predicts clonal expansion to be limited even for clones with a significant growth advantage-a finding which we confirm experimentally using a mixture of antibiotic-sensitive and antibiotic-resistant mutants in the presence of sublethal concentrations of the antibiotic rifampicin. The strong suppression of selection contrasts sharply with the behavior seen in range expansion experiments in bacterial colonies grown on agar. Our results show that biofilm population dynamics can be affected by patterning the surface and demonstrate how a better understanding of the physics of bacterial growth can be used to control microbial evolution.

Vibrio cholerae virulence and its suppression through the quorum-sensing system

Vibrio cholerae is a cholera-causing pathogen known to instigate severe contagious diarrhea that affects millions globally. Survival of vibrios depend on a combination of multicellular responses and adapt to changes that prevail in the environment. This process is achieved through a strong communication at the cellular level, the process has been recognized as quorum sensing (QS). The severity of infection is highly dependent on the QS of vibrios in the gut milieu. The quorum may exist in a low/high cell density (LCD/HCD) state to exert a positive or negative response to control the regulatory pathogenic networks. The impact of this regulation reflects on the transition of pathogenic V. cholerae from the environment to infect humans and cause outbreaks or epidemics of cholera. In this context, the review portrays various regulatory processes and associated virulent pathways, which maneuver and control LCD and HCD states for their survival in the host. Although several treatment options are existing, promotion of therapeutics by exploiting the virulence network may potentiate ineffective antibiotics to manage cholera. In addition, this approach is also useful in resource-limited settings, where the accessibility to antibiotics or conventional therapeutic options is limited.

Biofilms communities in the soil: characteristic and interactions using mathematical model

There are many different kinds of microorganisms in the soil, and many of them are biofilms because they can make supracellular compounds. Surface-associated microorganisms in a biofilm are encased in a hydrated extracellular polymeric substance that aids in adherence and survival. Numerous different kinds of microorganisms call the soil home. Strong interactions with and among species are made possible by biofilms; this, in turn, might increase the effectiveness with which organic compounds and poisons in soil are degraded. This encouraged us to take a close look at soil biofilm ecosystems, which we do in this paper. In this research, we will look at how soil biofilms arise and how that affects the composition of microbial communities and their function in the soil. Recent years have seen an uptick in interest in questions about biofilm structure and the social interactions of various bacteria. Many concepts elucidating the underlying mathematics of biofilm growth are also presented. Since biofilms are so widespread, this breakthrough in soil biofilm inquiry might help scientists understand soil microbiomes better. Mathematical models further extrapolate the relationships between microbial communities and gives a more precise information as to what is happening in a biofilm. Biofilms can help plants cope with a variety of environmental challenges. Soil quality, plant nourishment, plant protection, bioremediation, and climate change are all influenced by the interplay of biofilm communities. Thus, biofilms play an important role in the development of environmentally friendly and sustainable agriculture.

The role of filamentous matrix molecules in shaping the architecture and emergent properties of bacterial biofilms

Numerous bacteria naturally occur within spatially organised, multicellular communities called biofilms. Moreover, most bacterial infections proceed with biofilm formation, posing major challenges to human health. Within biofilms, bacterial cells are embedded in a primarily self-produced extracellular matrix, which is a defining feature of all biofilms. The biofilm matrix is a complex, viscous mixture primarily composed of polymeric substances such as polysaccharides, filamentous protein fibres, and extracellular DNA. The structured arrangement of the matrix bestows bacteria with beneficial emergent properties that are not displayed by planktonic cells, conferring protection against physical and chemical stresses, including antibiotic treatment. However, a lack of multi-scale information at the molecular level has prevented a better understanding of this matrix and its properties. Here, we review recent progress on the molecular characterisation of filamentous biofilm matrix components and their three-dimensional spatial organisation within biofilms.

Outer membrane vesicles and the outer membrane protein OmpU govern Vibrio cholerae biofilm matrix assembly

Biofilms are matrix-encased microbial communities that increase the environmental fitness and infectivity of many human pathogens including Vibrio cholerae. Biofilm matrix assembly is essential for biofilm formation and function. Known components of the V. cholerae biofilm matrix are the polysaccharide Vibrio polysaccharide (VPS), matrix proteins RbmA, RbmC, Bap1, and extracellular DNA, but the majority of the protein composition is uncharacterized. This study comprehensively analyzed the biofilm matrix proteome and revealed the presence of outer membrane proteins (OMPs). Outer membrane vesicles (OMVs) were also present in the V. cholerae biofilm matrix and were associated with OMPs and many biofilm matrix proteins suggesting that they participate in biofilm matrix assembly. Consistent with this, OMVs had the capability to alter biofilm structural properties depending on their composition. OmpU was the most prevalent OMP in the matrix, and its absence altered biofilm architecture by increasing VPS production. Single-cell force spectroscopy revealed that proteins critical for biofilm formation, OmpU, the matrix proteins RbmA, RbmC, Bap1, and VPS contribute to cell-surface adhesion forces at differing efficiency, with VPS showing the highest efficiency whereas Bap1 showing the lowest efficiency. Our findings provide new insights into the molecular mechanisms underlying biofilm matrix assembly in V. cholerae, which may provide new opportunities to develop inhibitors that specifically alter biofilm matrix properties and, thus, affect either the environmental survival or pathogenesis of V. cholerae.IMPORTANCECholera remains a major public health concern. Vibrio cholerae, the causative agent of cholera, forms biofilms, which are critical for its transmission, infectivity, and environmental persistence. While we know that the V. cholerae biofilm matrix contains exopolysaccharide, matrix proteins, and extracellular DNA, we do not have a comprehensive understanding of the majority of biofilm matrix components. Here, we discover outer membrane vesicles (OMVs) within the biofilm matrix of V. cholerae. Proteomic analysis of the matrix and matrix-associated OMVs showed that OMVs carry key matrix proteins and Vibrio polysaccharide (VPS) to help build biofilms. We also characterize the role of the highly abundant outer membrane protein OmpU in biofilm formation and show that it impacts biofilm architecture in a VPS-dependent manner. Understanding V. cholerae biofilm formation is important for developing a better prevention and treatment strategy framework.

Drug resistance and influencing factors of biofilm bacteria in upper urinary calculi patients with double J stent indwelling

OBJECTIVE

To analyze the distribution and drug resistance of biofilm bacteria infected with upper urinary calculi patients with double J stent indwelling, and to explore the influencing factors of Biofilm Bacteria Infections.

METHODS

A total of 400 patients with upper urinary calculi who adopted double J stent inserting in our hospital from January 2019 to January 2022 were included. Urine and double J stent samples were collected, pathogen cultures were performed, and then drug sensitivity test analysis was carried out for isolates. Univariate and multivariate logistic regression analyzes were used to analyze the influencing factors of patients with double J stent associated biofilm bacteria infections.

RESULTS

A total of 13 strains (3.2%) of biofilm bacteria were detected in urine samples and 168 strains (42%) in double J stent samples (P < 0.05), 95 strains (23.7%) of pathogenic bacteria were separated from urine samples and 117 strains (29.2%) from double J-stent samples (P > 0.05). Escherichia coli were the most common bacteria. There was significantly higher drug resistance observed in biofilm bacteria versus urine-cultured pathogens (P < 0.05). Advanced age, long-term catheterization, inadequate water intake, hypoproteinemia, abnormal renal function, and diabetes mellitus were independent risk factors for biofilm bacteria infection associated with double J stent(P < 0.05).

CONCLUSION

Among the upper urinary calculi patients with double J stent indwelling, the positive rate and drug resistance of biofilm bacteria obtained from double J stent were significantly higher than that from urine. More attention should be paid to the factors that influence biofilm bacteria infections.

Pleiotropic hubs drive bacterial surface competition through parallel changes in colony composition and expansion

Bacteria commonly adhere to surfaces where they compete for both space and resources. Despite the importance of surface growth, it remains largely elusive how bacteria evolve on surfaces. We previously performed an evolution experiment where we evolved distinct Bacilli populations under a selective regime that favored colony spreading. In just a few weeks, colonies of Bacillus subtilis showed strongly advanced expansion rates, increasing their radius 2.5-fold relative to that of the ancestor. Here, we investigate what drives their rapid evolution by performing a uniquely detailed analysis of the evolutionary changes in colony development. We find mutations in diverse global regulators, RicT, RNAse Y, and LexA, with strikingly similar pleiotropic effects: They lower the rate of sporulation and simultaneously facilitate colony expansion by either reducing extracellular polysaccharide production or by promoting filamentous growth. Combining both high-throughput flow cytometry and gene expression profiling, we show that regulatory mutations lead to highly reproducible and parallel changes in global gene expression, affecting approximately 45% of all genes. This parallelism results from the coordinated manner by which regulators change activity both during colony development-in the transition from vegetative growth to dormancy-and over evolutionary time. This coordinated activity can however also break down, leading to evolutionary divergence. Altogether, we show how global regulators function as major pleiotropic hubs that drive rapid surface adaptation by mediating parallel changes in both colony composition and expansion, thereby massively reshaping gene expression.

Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea

Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.

Diffusiophoretic Particle Penetration into Bacterial Biofilms

Bacterial biofilms are communities of cells adhered to surfaces. These communities represent a predominant form of bacterial life on Earth. A defining feature of a biofilm is the three-dimensional extracellular polymer matrix that protects resident cells by acting as a mechanical barrier to the penetration of chemicals, such as antimicrobials. Beyond being recalcitrant to antibiotic treatment, biofilms are notoriously difficult to remove from surfaces. A promising, but relatively underexplored, approach to biofilm control is to disrupt the extracellular polymer matrix by enabling penetration of particles to increase the susceptibility of biofilms to antimicrobials. In this work, we investigate externally imposed chemical gradients as a mechanism to transport polystyrene particles into bacterial biofilms. We show that preconditioning the biofilm with a prewash step using deionized (DI) water is essential for altering the biofilm so it takes up the micro- and nanoparticles by the application of a further chemical gradient created by an electrolyte. Using different particles and chemicals, we document the transport behavior that leads to particle motion into the biofilm and its further reversal out of the biofilm. Our results demonstrate the importance of chemical gradients in disrupting the biofilm matrix and regulating particle transport in crowded macromolecular environments, and suggest potential applications of particle transport and delivery in other physiological systems.

Molecular imaging of bacterial biofilms-a systematic review

The formation of bacterial biofilms in the human body and on medical devices is a serious human health concern. Infections related to bacterial biofilms are often chronic and difficult to treat. Detailed information on biofilm formation and composition over time is essential for a fundamental understanding of the underlying mechanisms of biofilm formation and its response to anti-biofilm therapy. However, information on the chemical composition, structural components of biofilms, and molecular interactions regarding metabolism- and communication pathways within the biofilm, such as uptake of administered drugs or inter-bacteria communication, remains elusive. Imaging these molecules and their distribution in the biofilm increases insight into biofilm development, growth, and response to environmental factors or drugs. This systematic review provides an overview of molecular imaging techniques used for bacterial biofilm imaging. The techniques included mass spectrometry-based techniques, fluorescence-labelling techniques, spectroscopic techniques, nuclear magnetic resonance spectroscopy (NMR), micro-computed tomography (µCT), and several multimodal approaches. Many molecules were imaged, such as proteins, lipids, metabolites, and quorum-sensing (QS) molecules, which are crucial in intercellular communication pathways. Advantages and disadvantages of each technique, including multimodal approaches, to study molecular processes in bacterial biofilms are discussed, and recommendations on which technique best suits specific research aims are provided.

Biofilm formation on human immune cells is a multicellular predation strategy of Vibrio cholerae

Biofilm formation is generally recognized as a bacterial defense mechanism against environmental threats, including antibiotics, bacteriophages, and leukocytes of the human immune system. Here, we show that for the human pathogen Vibrio cholerae, biofilm formation is not only a protective trait but also an aggressive trait to collectively predate different immune cells. We find that V. cholerae forms biofilms on the eukaryotic cell surface using an extracellular matrix comprising primarily mannose-sensitive hemagglutinin pili, toxin-coregulated pili, and the secreted colonization factor TcpF, which differs from the matrix composition of biofilms on other surfaces. These biofilms encase immune cells and establish a high local concentration of a secreted hemolysin to kill the immune cells before the biofilms disperse in a c-di-GMP-dependent manner. Together, these results uncover how bacteria employ biofilm formation as a multicellular strategy to invert the typical relationship between human immune cells as the hunters and bacteria as the hunted.

Imaging biofilms using fluorescence in situ hybridization: seeing is believing

Biofilms are complex structures with an intricate relationship between the resident microorganisms, the extracellular matrix, and the surrounding environment. Interest in biofilms is growing exponentially given its ubiquity in so diverse fields such as healthcare, environmental and industry. Molecular techniques (e.g., next-generation sequencing, RNA-seq) have been used to study biofilm properties. However, these techniques disrupt the spatial structure of biofilms; therefore, they do not allow to observe the location/position of biofilm components (e.g., cells, genes, metabolites), which is particularly relevant to explore and study the interactions and functions of microorganisms. Fluorescence in situ hybridization (FISH) has been arguably the most widely used method for an in situ analysis of spatial distribution of biofilms. In this review, an overview on different FISH variants already applied on biofilm studies (e.g., CLASI-FISH, BONCAT-FISH, HiPR-FISH, seq-FISH) will be explored. In combination with confocal laser scanning microscopy, these variants emerged as a powerful approach to visualize, quantify and locate microorganisms, genes, and metabolites inside biofilms. Finally, we discuss new possible research directions for the development of robust and accurate FISH-based approaches that will allow to dig deeper into the biofilm structure and function.

Vibrio cholerae biofilms use modular adhesins with glycan-targeting and nonspecific surface binding domains for colonization

Bacterial biofilms are formed on environmental surfaces and host tissues, and facilitate host colonization and antibiotic resistance by human pathogens. Bacteria often express multiple adhesive proteins (adhesins), but it is often unclear whether adhesins have specialized or redundant roles. Here, we show how the model biofilm-forming organism Vibrio cholerae uses two adhesins with overlapping but distinct functions to achieve robust adhesion to diverse surfaces. Both biofilm-specific adhesins Bap1 and RbmC function as a "double-sided tape": they share a β-propeller domain that binds to the biofilm matrix exopolysaccharide, but have distinct environment-facing domains. Bap1 adheres to lipids and abiotic surfaces, while RbmC mainly mediates binding to host surfaces. Furthermore, both adhesins contribute to adhesion in an enteroid monolayer colonization model. We expect that similar modular domains may be utilized by other pathogens, and this line of research can potentially lead to new biofilm-removal strategies and biofilm-inspired adhesives.

Long-range alteration of the physical environment mediates cooperation between Pseudomonas aeruginosa swarming colonies

Pseudomonas aeruginosa makes and secretes massive amounts of rhamnolipid surfactants that enable swarming motility over biogel surfaces. But how these rhamnolipids interact with biogels to assist swarming remains unclear. Here, I use a combination of optical techniques across scales and genetically engineered strains to demonstrate that rhamnolipids can induce agar gel swelling over distances >10,000× the body size of an individual cell. The swelling front is on the micrometric scale and is easily visible using shadowgraphy. Rhamnolipid transport is not restricted to the surface of the gel but occurs through the whole thickness of the plate and, consequently, the spreading dynamics depend on the local thickness. Surprisingly, rhamnolipids can cross the whole gel and induce swelling on the opposite side of a two-face Petri dish. The swelling front delimits an area where the mechanical properties of the surface properties are modified: water wets the surface more easily, which increases the motility of individual bacteria and enables collective motility. A genetically engineered mutant unable to secrete rhamnolipids (ΔrhlA), and therefore unable to swarm, is rescued from afar with rhamnolipids produced by a remote colony. These results exemplify the remarkable capacity of bacteria to change the physical environment around them and its ecological consequences.

Matrix is everywhere: extracellular DNA is a link between biofilm and mineralization in Bacillus cereus planktonic lifestyle

To date, the mechanisms of biomineralization induced by bacterial cells in the context of biofilm formation remain the subject of intensive studies. In this study, we analyzed the influence of the medium components on the induction of CaCO₃ precipitation by the Bacillus cereus cells and composition of the extracellular matrix (ECM) formed in the submerged culture. While the accumulation of extracellular polysaccharides and amyloids appeared to be independent of the presence of calcium and urea during the growth, the accumulation of extracellular DNA (eDNA), as well as precipitation of calcium carbonate, required the presence of both ingredients in the medium. Removal of eDNA, which was sensitive to treatment by DNase, did not affect other matrix components but resulted in disruption of cell network formation and a sixfold decrease in the precipitate yield. An experiment with a cell-free system confirmed the acceleration of mineral formation after the addition of exogenous salmon sperm DNA. The observed pathway for the formation of CaCO₃ minerals in B. cereus planktonic culture included a production of exopolysaccharides and negatively charged eDNA lattice promoting local Ca²⁺ supersaturation, which, together with an increase in the concentration of carbonate ions due to pH rise, resulted in the formation of an insoluble precipitate of calcium carbonate. Precipitation of amorphous CaCO₃ on eDNA matrix was followed by crystal formation via the ACC-vaterite-calcite/aragonite pathway and further formation of larger mineral aggregates in complex with extracellular polymeric substances. Taken together, our data showed that DNA in extracellular matrix is an essential factor for triggering the biomineralization in B. cereus planktonic culture.

Breakdown of clonal cooperative architecture in multispecies biofilms and the spatial ecology of predation

Biofilm formation, including adherence to surfaces and secretion of extracellular matrix, is common in the microbial world, but we often do not know how interaction at the cellular spatial scale translates to higher-order biofilm community ecology. Here we explore an especially understudied element of biofilm ecology, namely predation by the bacterium Bdellovibrio bacteriovorus. This predator can kill and consume many different Gram-negative bacteria, including Vibrio cholerae and Escherichia coli. V. cholerae can protect itself from predation within densely packed biofilm structures that it creates, whereas E. coli biofilms are highly susceptible to B. bacteriovorus. We explore how predator-prey dynamics change when V. cholerae and E. coli are growing in biofilms together. We find that in dual-species prey biofilms, E. coli survival under B. bacteriovorus predation increases, whereas V. cholerae survival decreases. E. coli benefits from predator protection when it becomes embedded within expanding groups of highly packed V. cholerae. But we also find that the ordered, highly packed, and clonal biofilm structure of V. cholerae can be disrupted if V. cholerae cells are directly adjacent to E. coli cells at the start of biofilm growth. When this occurs, the two species become intermixed, and the resulting disordered cell groups do not block predator entry. Because biofilm cell group structure depends on initial cell distributions at the start of prey biofilm growth, the surface colonization dynamics have a dramatic impact on the eventual multispecies biofilm architecture, which in turn determines to what extent both species survive exposure to B. bacteriovorus.

Architecture and matrix assembly determinants of Bordetella pertussis biofilms on primary human airway epithelium

Traditionally, whooping cough or pertussis caused by the obligate human pathogen Bordetella pertussis (Bp) is described as an acute disease with severe symptoms. However, many individuals who contract pertussis are either asymptomatic or show very mild symptoms and yet can serve as carriers and sources of bacterial transmission. Biofilms are an important survival mechanism for bacteria in human infections and disease. However, bacterial determinants that drive biofilm formation in humans are ill-defined. In the current study, we show that Bp infection of well-differentiated primary human bronchial epithelial cells leads to formation of bacterial aggregates, clusters, and highly structured biofilms which are colocalized with cilia. These findings mimic observations from pathological analyses of tissues from pertussis patients. Distinct arrangements (mono-, bi-, and tri-partite) of the polysaccharide Bps, extracellular DNA, and bacterial cells were visualized, suggesting complex heterogeneity in bacteria-matrix interactions. Analyses of mutant biofilms revealed positive roles in matrix production, cell cluster formation, and biofilm maturity for three critical Bp virulence factors: Bps, filamentous hemagglutinin, and adenylate cyclase toxin. Adherence assays identified Bps as a new Bp adhesin for primary human airway cells. Taken together, our results demonstrate the multi-factorial nature of the biofilm extracellular matrix and biofilm development process under conditions mimicking the human respiratory tract and highlight the importance of model systems resembling the natural host environment to investigate pathogenesis and potential therapeutic strategies.

The biofilm matrix: multitasking in a shared space

The biofilm matrix can be considered to be a shared space for the encased microbial cells, comprising a wide variety of extracellular polymeric substances (EPS), such as polysaccharides, proteins, amyloids, lipids and extracellular DNA (eDNA), as well as membrane vesicles and humic-like microbially derived refractory substances. EPS are dynamic in space and time and their components interact in complex ways, fulfilling various functions: to stabilize the matrix, acquire nutrients, retain and protect eDNA or exoenzymes, or offer sorption sites for ions and hydrophobic substances. The retention of exoenzymes effectively renders the biofilm matrix an external digestion system influencing the global turnover of biopolymers, considering the ubiquitous relevance of biofilms. Physico-chemical and biological interactions and environmental conditions enable biofilm systems to morph into films, microcolonies and macrocolonies, films, ridges, ripples, columns, pellicles, bubbles, mushrooms and suspended aggregates - in response to the very diverse conditions confronting a particular biofilm community. Assembly and dynamics of the matrix are mostly coordinated by secondary messengers, signalling molecules or small RNAs, in both medically relevant and environmental biofilms. Fully deciphering how bacteria provide structure to the matrix, and thus facilitate and benefit from extracellular reactions, remains the challenge for future biofilm research.

Instantaneous Clearing of Biofilm (iCBiofilm): an optical approach to revisit bacterial and fungal biofilm imaging

Whole-biofilm imaging at single-cell resolution is necessary for system-level analysis of cellular heterogeneity, identification of key matrix component functions and response to immune cells and antimicrobials. To this end, we developed a whole-biofilm clearing and imaging method, termed instantaneous clearing of biofilm (iCBiofilm). iCBiofilm is a simple, rapid, and efficient method involving the immersion of biofilm samples in a refractive index-matching medium, enabling instant whole-biofilm imaging with confocal laser scanning microscopy. We also developed non-fixing iCBiofilm, enabling live and dynamic imaging of biofilm development and actions of antimicrobials. iCBiofilm is applicable for multicolor imaging of fluorescent proteins, immunostained matrix components, and fluorescence labeled cells in biofilms with a thickness of several hundred micrometers. iCBiofilm is scalable from bacterial to fungal biofilms and can be used to observe biofilm-neutrophil interactions. iCBiofilm therefore represents an important advance for examining the dynamics and functions of biofilms and revisiting bacterial and fungal biofilm formation.

New Insights into Vibrio cholerae Biofilms from Molecular Biophysics to Microbial Ecology

With the discovery that 48% of cholera infections in rural Bangladesh villages could be prevented by simple filtration of unpurified waters and the detection of Vibrio cholerae aggregates in stools from cholera patients it was realized V. cholerae biofilms had a central function in cholera pathogenesis. We are currently in the seventh cholera pandemic, caused by O1 serotypes of the El Tor biotypes strains, which initiated in 1961. It is estimated that V. cholerae annually causes millions of infections and over 100,000 deaths. Given the continued emergence of cholera in areas that lack access to clean water, such as Haiti after the 2010 earthquake or the ongoing Yemen civil war, increasing our understanding of cholera disease remains a worldwide public health priority. The surveillance and treatment of cholera is also affected as the world is impacted by the COVID-19 pandemic, raising significant concerns in Africa. In addition to the importance of biofilm formation in its life cycle, V. cholerae has become a key model system for understanding bacterial signal transduction networks that regulate biofilm formation and discovering fundamental principles about bacterial surface attachment and biofilm maturation. This chapter will highlight recent insights into V. cholerae biofilms including their structure, ecological role in environmental survival and infection, regulatory systems that control them, and biomechanical insights into the nature of V. cholerae biofilms.

Multispecies biofilm architecture determines bacterial exposure to phages

Numerous ecological interactions among microbes-for example, competition for space and resources, or interaction among phages and their bacterial hosts-are likely to occur simultaneously in multispecies biofilm communities. While biofilms formed by just a single species occur, multispecies biofilms are thought to be more typical of microbial communities in the natural environment. Previous work has shown that multispecies biofilms can increase, decrease, or have no measurable impact on phage exposure of a host bacterium living alongside another species that the phages cannot target. The reasons underlying this variability are not well understood, and how phage-host encounters change within multispecies biofilms remains mostly unexplored at the cellular spatial scale. Here, we study how the cellular scale architecture of model 2-species biofilms impacts cell-cell and cell-phage interactions controlling larger scale population and community dynamics. Our system consists of dual culture biofilms of Escherichia coli and Vibrio cholerae under exposure to T7 phages, which we study using microfluidic culture, high-resolution confocal microscopy imaging, and detailed image analysis. As shown previously, sufficiently mature biofilms of E. coli can protect themselves from phage exposure via their curli matrix. Before this stage of biofilm structural maturity, E. coli is highly susceptible to phages; however, we show that these bacteria can gain lasting protection against phage exposure if they have become embedded in the bottom layers of highly packed groups of V. cholerae in co-culture. This protection, in turn, is dependent on the cell packing architecture controlled by V. cholerae biofilm matrix secretion. In this manner, E. coli cells that are otherwise susceptible to phage-mediated killing can survive phage exposure in the absence of de novo resistance evolution. While co-culture biofilm formation with V. cholerae can confer phage protection to E. coli, it comes at the cost of competing with V. cholerae and a disruption of normal curli-mediated protection for E. coli even in dual species biofilms grown over long time scales. This work highlights the critical importance of studying multispecies biofilm architecture and its influence on the community dynamics of bacteria and phages.

Evidence of a possible multicellular life cycle in Escherichia coli

Biofilms are surface-attached multicellular microbial communities. Their genetics have been extensively studied, but the cell-scale morphogenetic events of their formation are largely unknown. Here, we recorded the entirety of morphogenesis in Escherichia coli, and discovered a previously unknown multicellular self-assembly process. Unattached, single-cells formed 4-cell rosettes which grew into constant-width chains. After ∼10 cell generations, these multicellular chains attached to surfaces and stopped growing. Chains remained clonal throughout morphogenesis. We showed that this process generates biofilms, which we found are composed of attached clonal chains, aligned in parallel. We investigated genetics of chain morphogenesis: Ag43 facilitates rosette formation and clonality; type-1 fimbriae and curli promote stability and configuration; and extracellular polysaccharide production facilitates attachment. Our study establishes that E. coli, a unicellular organism, can follow a multistage, clonal, genetically-regulated, rosette-initiated multicellular life cycle. These findings have implications for synthetic biology, multicellular development, and the treatment and prevention of bacterial diseases.

Donor-strand exchange drives assembly of the TasA scaffold in Bacillus subtilis biofilms

Many bacteria in nature exist in multicellular communities termed biofilms, where cells are embedded in an extracellular matrix that provides rigidity to the biofilm and protects cells from chemical and mechanical stresses. In the Gram-positive model bacterium Bacillus subtilis, TasA is the major protein component of the biofilm matrix, where it has been reported to form functional amyloid fibres contributing to biofilm structure and stability. Here, we present electron cryomicroscopy structures of TasA fibres, which show that, rather than forming amyloid fibrils, TasA monomers assemble into fibres through donor-strand exchange, with each subunit donating a β-strand to complete the fold of the next subunit along the fibre. Combining electron cryotomography, atomic force microscopy, and mutational studies, we show how TasA fibres congregate in three dimensions to form abundant fibre bundles that are essential for B. subtilis biofilm formation. Our study explains the previously observed biochemical properties of TasA and shows how a bacterial extracellular globular protein can assemble from monomers into β-sheet-rich fibres, and how such fibres assemble into bundles in biofilms.

Ultrasound-Activatable Phase-Shift Nanoparticle as a Targeting Antibacterial Agent for Efficient Eradication of Pseudomonas aeruginosa Biofilms

Biofilms are physical barriers composed of extracellular polymeric substances (EPS) that enable planktonic bacteria to resist host responses and antibacterial treatments, complicating efforts to clear bacteria such as Pseudomonas aeruginosa (P. aeruginosa) and thereby contributing to persistently chronic infections. As such, it is critical to develop a robust antimicrobial strategy capable of effectively eradicating P. aeruginosa biofilms and to further address aggressive clinical infection. In this study, ultrasound-activatable targeted nanoparticles were designed by using poly(lactic-co-glycolic acid) (PLGA) nanoparticles to encapsulate phase-transformable perfluoropentane (PFP) and the antibiotic meropenem via a double emulsion approach, followed by conjugation with anti-P. aeruginosa antibodies. In this strategy, ultrasound exposure can trigger PFP to produce microbubbles, inducing ultrasonic cavitation effects that can disrupt EPS components and allow nanoparticles to release meropenem to kill P. aeruginosa directly and accelerate the associated wound healing. These nanoparticles eradicated biofilms effectively and cleared bacteria in vitro as well as exhibited potent anti-infective activity in vivo. In summary, this study demonstrates the efficacy of a sonobactericidal strategy as a means of effectively and reliably eliminating biofilms.

Quorum-sensing control of matrix protein production drives fractal wrinkling and interfacial localization of Vibrio cholerae pellicles

Bacterial cells at fluid interfaces can self-assemble into collective communities with stunning macroscopic morphologies. Within these soft, living materials, called pellicles, constituent cells gain group-level survival advantages including increased antibiotic resistance. However, the regulatory and structural components that drive pellicle self-patterning are not well defined. Here, using Vibrio cholerae as our model system, we report that two sets of matrix proteins and a key quorum-sensing regulator jointly orchestrate the sequential mechanical instabilities underlying pellicle morphogenesis, culminating in fractal patterning. A pair of matrix proteins, RbmC and Bap1, maintain pellicle localization at the interface and prevent self-peeling. A single matrix protein, RbmA, drives a morphogenesis program marked by a cascade of ever finer wrinkles with fractal scaling in wavelength. Artificial expression of rbmA restores fractal wrinkling to a ΔrbmA mutant and enables precise tuning of fractal dimensions. The quorum-sensing regulatory small RNAs Qrr1-4 first activate matrix synthesis to launch pellicle primary wrinkling and ridge instabilities. Subsequently, via a distinct mechanism, Qrr1-4 suppress fractal wrinkling to promote fine modulation of pellicle morphology. Our results connect cell-cell signaling and architectural components to morphogenic patterning and suggest that manipulation of quorum-sensing regulators or synthetic control of rbmA expression could underpin strategies to engineer soft biomaterial morphologies on demand.

Calibrating spatiotemporal models of microbial communities to microscopy data: A review

Spatiotemporal models that account for heterogeneity within microbial communities rely on single-cell data for calibration and validation. Such data, commonly collected via microscopy and flow cytometry, have been made more accessible by recent advances in microfluidics platforms and data processing pipelines. However, validating models against such data poses significant challenges. Validation practices vary widely between modelling studies; systematic and rigorous methods have not been widely adopted. Similar challenges are faced by the (macrobial) ecology community, in which systematic calibration approaches are often employed to improve quantitative predictions from computational models. Here, we review single-cell observation techniques that are being applied to study microbial communities and the calibration strategies that are being employed for accompanying spatiotemporal models. To facilitate future calibration efforts, we have compiled a list of summary statistics relevant for quantifying spatiotemporal patterns in microbial communities. Finally, we highlight some recently developed techniques that hold promise for improved model calibration, including algorithmic guidance of summary statistic selection and machine learning approaches for efficient model simulation.

Homogeneously and heterogeneously structured biofilm models for wastewater treatment

Biofilm, a layer comprising extracellular polymeric substances, is the platform where the embedded living cells degrade the substances in the wastewaters. Biofilm models have been developed as part of the comprehensive models for the wastewater treatment process. This review summarizes the biofilm models applied in contemporary literature based on the spatial dimensions adopted for model build-up. The most commonly applied biofilm models are null-dimensional, considering the biofilm active biomass for the substrate sink's biological reaction. The one-dimensional, multi-species models are the second standard models for contemporary studies, providing transport and reaction resistances of substrates in the biofilm matrix and the interactions of competing or collaborating strains in the biofilm. The structural homogeneity of the biofilm challenges the validity of the uniformly structured models, highlighting the need to re-examine the validity of the uniformly structured models. The challenges and prospects of biofilm model developments and applications are outlined.

Biofilm with highly heterogeneous interior structure for pollutant removal: Effects of individual extracellular polymeric substance

For the first time, this study reveals the effects of an individual component of extracellular polymeric substances on the substrate consumption rates by the embedded cells based on the highly heterogeneous interior structures of a working biofilm. The flow-across mode in operation established a boundary-layer flow field with high transport resistance, making the uniformly structured model valid. Conversely, the flow field of the flow-through mode is determined by 46% jointly by proteins and β-d-glucopyranose polysaccharides. The substrate consumption rates hindered by β-d-glucopyranose polysaccharide is up to 60% over the 20%-40% biofilm height from the bottom, much lower than expected by the uniformly structured models. The strategies to maximize the biofilm performance have been suggested.

Functional characterization of Vibrio alginolyticus T3SS regulator ExsA and evaluation of its mutant as a live attenuated vaccine candidate in zebrafish (Danio rerio) model

Vibrio alginolyticus, a Gram-negative bacterium, is an opportunistic pathogen of both marine animals and humans, resulting in significant losses in the aquaculture industry. Type III secretion system (T3SS) is a crucial virulence mechanism of V. alginolyticus. In this study, the T3SS regulatory gene exsA, which was cloned from V. alginolyticus wild-type strain HY9901, is 861 bp encoding a protein of 286 amino acids. The ΔexsA was constructed by homologous recombination and Overlap-PCR. Although there was no difference in growth between HY9901 and ΔexsA, the ΔexsA exhibited significantly decreased extracellular protease activity and biofilm formation. Besides, the ΔexsA showed a weakened swarming phenotype and an ~100-fold decrease in virulence to zebrafish. Antibiotic susceptibility testing showed the HY9901ΔexsA was more sensitive to kanamycin, minocycline, tetracycline, gentamicin, doxycycline and neomycin. Compared to HY9901 there were 541 up-regulated genes and 663 down-regulated genes in ΔexsA, screened by transcriptome sequencing. qRT-PCR and β-galactosidase reporter assays were used to analyze the transcription levels of hop gene revealing that exsA gene could facilitate the expression of hop gene. Finally, Danio rerio, vaccinated with ΔexsA through intramuscular injection, induced a relative percent survival (RPS) value of 66.7% after challenging with HY9901 wild type strain. qRT-PCR assays showed that vaccination with ΔexsA increased the expression of immune-related genes, including GATA-1, IL6, IgM, and TNF-α in zebrafish. In summary, these results demonstrate the importance of exsA in V. alginolyticus and provide a basis for further investigations into the virulence and infection mechanism.

VxrB Influences Antagonism within Biofilms by Controlling Competition through Extracellular Matrix Production and Type 6 Secretion

The human pathogen Vibrio cholerae grows as biofilms, communities of cells encased in an extracellular matrix. When growing in biofilms, cells compete for resources and space. One common competitive mechanism among Gram-negative bacteria is the type six secretion system (T6SS), which can deliver toxic effector proteins into a diverse group of target cells, including other bacteria, phagocytic amoebas, and human macrophages. The response regulator VxrB positively regulates both biofilm matrix and T6SS gene expression. Here, we directly observe T6SS activity within biofilms, which results in improved competition with strains lacking the T6SS. VxrB significantly contributes to both attack and defense via T6SS, while also influencing competition via regulation of biofilm matrix production. We further determined that both Vibrio polysaccharide (VPS) and the biofilm matrix protein RbmA can protect cells from T6SS attack within mature biofilms. By varying the spatial mixing of predator and prey cells in biofilms, we show that a high degree of mixing favors T6SS predator strains and that the presence of extracellular DNA in V. cholerae biofilms is a signature of T6SS killing. VxrB therefore regulates both T6SS attack and matrix-based T6SS defense, to control antagonistic interactions and competition outcomes during mixed-strain biofilm formation.

RapD Is a Multimeric Calcium-Binding Protein That Interacts With the Rhizobium leguminosarum Biofilm Exopolysaccharide, Influencing the Polymer Lengths

Rhizobium leguminosarum synthesizes an acidic polysaccharide mostly secreted to the extracellular medium, known as exopolysaccharide (EPS) and partially retained on the bacterial surface as a capsular polysaccharide (CPS). Rap proteins, extracellular protein substrates of the PrsDE type I secretion system (TISS), share at least one Ra/CHDL (cadherin-like) domain and are involved in biofilm matrix development either through cleaving the polysaccharide by Ply glycanases or by altering the bacterial adhesive properties. It was shown that the absence or excess of extracellular RapA2 (a monomeric CPS calcium-binding lectin) alters the biofilm matrix’s properties. Here, we show evidence of the role of a new Rap protein, RapD, which comprises an N-terminal Ra/CHDL domain and a C-terminal region of unknown function. RapD was completely released to the extracellular medium and co-secreted with the other Rap proteins in a PrsDE-dependent manner. Furthermore, high levels of RapD secretion were found in biofilms under conditions that favor EPS production. Interestingly, size exclusion chromatography of the EPS produced by the ΔrapA2ΔrapD double mutant showed a profile of EPS molecules of smaller sizes than those of the single mutants and the wild type strain, suggesting that both RapA2 and RapD proteins influence EPS processing on the cell surface. Biophysical studies showed that calcium triggers proper folding and multimerization of recombinant RapD. Besides, further conformational changes were observed in the presence of EPS. Enzyme-Linked ImmunoSorbent Assay (ELISA) and Binding Inhibition Assays (BIA) indicated that RapD specifically binds the EPS and that galactose residues would be involved in this interaction. Taken together, these observations indicate that RapD is a biofilm matrix-associated multimeric protein that influences the properties of the EPS, the main structural component of the rhizobial biofilm.

Social evolution of shared biofilm matrix components

Biofilm formation is an important and ubiquitous mode of growth among bacteria. Central to the evolutionary advantage of biofilm formation is cell-cell and cell-surface adhesion achieved by a variety of factors, some of which are diffusible compounds that may operate as classical public goods-factors that are costly to produce but may benefit other cells. An outstanding question is how diffusible matrix production, in general, can be stable over evolutionary timescales. In this work, using Vibrio cholerae as a model, we show that shared diffusible biofilm matrix proteins are indeed susceptible to cheater exploitation and that the evolutionary stability of producing these matrix components fundamentally depends on biofilm spatial structure, intrinsic sharing mechanisms of these components, and flow conditions in the environment. We further show that exploitation of diffusible adhesion proteins is localized within a well-defined spatial range around cell clusters that produce them. Based on this exploitation range and the spatial distribution of cell clusters, we constructed a model of costly diffusible matrix production and related these length scales to the relatedness coefficient in social evolution theory. Our results show that production of diffusible biofilm matrix components is evolutionarily stable under conditions consistent with natural biofilm habitats and host environments. We expect the mechanisms revealed in this study to be relevant to other secreted factors that operate as cooperative public goods in bacterial communities and the concept of exploitation range and the associated analysis tools to be generally applicable.

Targeting the Holy Triangle of Quorum Sensing, Biofilm Formation, and Antibiotic Resistance in Pathogenic Bacteria

Chronic and recurrent bacterial infections are frequently associated with the formation of biofilms on biotic or abiotic materials that are composed of mono- or multi-species cultures of bacteria/fungi embedded in an extracellular matrix produced by the microorganisms. Biofilm formation is, among others, regulated by quorum sensing (QS) which is an interbacterial communication system usually composed of two-component systems (TCSs) of secreted autoinducer compounds that activate signal transduction pathways through interaction with their respective receptors. Embedded in the biofilms, the bacteria are protected from environmental stress stimuli, and they often show reduced responses to antibiotics, making it difficult to eradicate the bacterial infection. Besides reduced penetration of antibiotics through the intricate structure of the biofilms, the sessile biofilm-embedded bacteria show reduced metabolic activity making them intrinsically less sensitive to antibiotics. Moreover, they frequently express elevated levels of efflux pumps that extrude antibiotics, thereby reducing their intracellular levels. Some efflux pumps are involved in the secretion of QS compounds and biofilm-related materials, besides being important for removing toxic substances from the bacteria. Some efflux pump inhibitors (EPIs) have been shown to both prevent biofilm formation and sensitize the bacteria to antibiotics, suggesting a relationship between these processes. Additionally, QS inhibitors or quenchers may affect antibiotic susceptibility. Thus, targeting elements that regulate QS and biofilm formation might be a promising approach to combat antibiotic-resistant biofilm-related bacterial infections.

Mechanisms Underlying Vibrio cholerae Biofilm Formation and Dispersion

Biofilms are a widely observed growth mode in which microbial communities are spatially structured and embedded in a polymeric extracellular matrix. Here, we focus on the model bacterium Vibrio cholerae and summarize the current understanding of biofilm formation, including initial attachment, matrix components, community dynamics, social interactions, molecular regulation, and dispersal. The regulatory network that orchestrates the decision to form and disperse from biofilms coordinates various environmental inputs. These cues are integrated by several transcription factors, regulatory RNAs, and second-messenger molecules, including bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP). Through complex mechanisms, V. cholerae weighs the energetic cost of forming biofilms against the benefits of protection and social interaction that biofilms provide. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Impact of Gene Repression on Biofilm Formation of Vibrio cholerae

Vibrio cholerae, the etiological agent of cholera, is a facultative intestinal pathogen which can also survive in aquatic ecosystems in the form of biofilms, surface-associated microbial aggregates embedded in an extracellular matrix, which protects them from predators and hostile environmental factors. Biofilm-derived bacteria and biofilm aggregates are considered a likely source for cholera infections, underscoring the importance of V. cholerae biofilm research not just to better understand bacterial ecology, but also cholera pathogenesis in the human host. While several studies focused on factors induced during biofilm formation, genes repressed during this persistence stage have been fairly neglected. In order to complement these previous studies, we used a single cell-based transcriptional reporter system named TetR-controlled recombination-based in-biofilm expression technology (TRIBET) and identified 192 genes to be specifically repressed by V. cholerae during biofilm formation. Predicted functions of in-biofilm repressed (ibr) genes range from metabolism, regulation, surface association, transmembrane transport as well as motility and chemotaxis. Constitutive (over)-expression of these genes affected static and dynamic biofilm formation of V. cholerae at different stages. Notably, timed expression of one candidate in mature biofilms induced their rapid dispersal. Thus, genes repressed during biofilm formation are not only dispensable for this persistence stage, but their presence can interfere with ordered biofilm development. This work thus contributes new insights into gene silencing during biofilm formation of V. cholerae.

Impact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancement

Recent studies indicate that the human intestinal microbiota could impact the outcome of infection by Vibrio cholerae, the etiological agent of the diarrheal disease cholera. A commensal bacterium, Paracoccus aminovorans, was previously identified in high abundance in stool collected from individuals infected with V. cholerae when compared to stool from uninfected persons. However, if and how P. aminovorans interacts with V. cholerae has not been experimentally determined; moreover, whether any association between this bacterium alters the behaviors of V. cholerae to affect the disease outcome is unclear. Here, we show that P. aminovorans and V. cholerae together form dual-species biofilm structure at the air–liquid interface, with previously uncharacterized novel features. Importantly, the presence of P. aminovorans within the murine small intestine enhances V. cholerae colonization in the same niche that is dependent on the Vibrio exopolysaccharide and other major components of mature V. cholerae biofilm. These studies illustrate that multispecies biofilm formation is a plausible mechanism used by a gut microbe to increase the virulence of the pathogen, and this interaction may alter outcomes in enteric infections.

Biofilm with highly heterogeneous interior structure for pollutant removal: Cell distribution and manipulated mass transport

Biofilm wastewater treatment had been applied in practice. Conventionally the biofilm was modeled as a uniform structure to simplify the analysis. This study for the first time established a three-dimensional biofilm model with distributions separating living cells, Extracellular polymeric substances (EPS) and pores, based on which the local fluid flow velocity and pollutant diffusion and reaction fluxes inside the biofilm were numerically evaluated. Both the uniform structured and previously proposed heterogeneous models had been confirmed to overestimate the performances of a biofilm for wastewater treatment. The survival strategies of living cells in biofilm were discussed. Besides exposing to fresh pollutants for maximizing pollutant uptake, the tendency to form small aggregates of cells for shortening diffusion length so furnishing the pollutant with reduced diffusional resistance to living cells was also for the first time noted. This communication advanced the knowledge to comprehend the detailed processes in biofilm.

Genome-wide mapping of Vibrio cholerae VpsT binding identifies a mechanism for c-di-GMP homeostasis

Many bacteria use cyclic dimeric guanosine monophosphate (c-di-GMP) to control changes in lifestyle. The molecule, synthesized by proteins having diguanylate cyclase activity, is often a signal to transition from motile to sedentary behaviour. In Vibrio cholerae, c-di-GMP can exert its effects via the transcription factors VpsT and VpsR. Together, these proteins activate genes needed for V. cholerae to form biofilms. In this work, we have mapped the genome-wide distribution of VpsT in a search for further regulatory roles. We show that VpsT binds 23 loci and recognises a degenerate DNA palindrome having the consensus 5'-W-5R-4[CG]-3Y-2W-1W+1R+2[GC]+3Y+4W+5-3'. Most genes targeted by VpsT encode functions related to motility, biofilm formation, or c-di-GMP metabolism. Most notably, VpsT activates expression of the vpvABC operon that encodes a diguanylate cyclase. This creates a positive feedback loop needed to maintain intracellular levels of c-di-GMP. Mutation of the key VpsT binding site, upstream of vpvABC, severs the loop and c-di-GMP levels fall accordingly. Hence, as well as relaying the c-di-GMP signal, VpsT impacts c-di-GMP homeostasis.

Mechanical forces drive a reorientation cascade leading to biofilm self-patterning

In growing active matter systems, a large collection of engineered or living autonomous units metabolize free energy and create order at different length scales as they proliferate and migrate collectively. One such example is bacterial biofilms, surface-attached aggregates of bacterial cells embedded in an extracellular matrix that can exhibit community-scale orientational order. However, how bacterial growth coordinates with cell-surface interactions to create distinctive, long-range order during biofilm development remains elusive. Here we report a collective cell reorientation cascade in growing Vibrio cholerae biofilms that leads to a differentially ordered, spatiotemporally coupled core-rim structure reminiscent of a blooming aster. Cell verticalization in the core leads to a pattern of differential growth that drives radial alignment of the cells in the rim, while the growing rim generates compressive stresses that expand the verticalized core. Such self-patterning disappears in nonadherent mutants but can be restored through opto-manipulation of growth. Agent-based simulations and two-phase active nematic modeling jointly reveal the strong interdependence of the driving forces underlying the differential ordering. Our findings offer insight into the developmental processes that shape bacterial communities and provide ways to engineer phenotypes and functions in living active matter.

Joint protection strategies for Saccharomyces boulardii: exogenous encapsulation and endogenous biofilm structure

Biofilms are heterogeneous structures composed of microorganisms and the surrounding extracellular polymeric substances (EPS) that protect the microbial cells from harsh environments. Saccharomyces boulardii is the first yeast classified as a probiotic strain with unique properties. However, tolerance of S. boulardii biofilms to harsh environments especially during production and in the gastrointestine remains unknown. In this study, S. boulardii cells were encapsulated in alginate microcapsules and subsequently cultured to form biofilms, and their survival and tolerance were evaluated. Microencapsulation provided S. boulardii a confined space that enhanced biofilm formation. The thick alginate shell and the mature biofilm improved the ability of S. boulardii to survive under harsh conditions. The exogenous encapsulation and the endogenous biofilm structure together enhanced the gastrointestinal tolerance and thermotolerance of S. boulardii. Besides, as the alginate shell became thinner with an increase in the subsequent culture duration, the EPS of S. boulardii biofilms exerted an important protective effect in resisting high temperatures. The encapsulated biofilm of S. boulardii after 24-h culture exhibited 60 × higher thermotolerance at 60 °C (10 min), while those after 6-h and 24-h culture showed 1000 × to 550,000 × higher thermotolerance at 120 °C (1 min) compared with the planktonic cells without encapsulation. The present study's findings suggest that a combination of encapsulation and biofilm mode efficiently enhanced gastrointestinal tolerance and thermotolerance of S. boulardii. KEY POINTS: • Encapsulated S. boulardii in biofilm mode showed enhanced tolerance. • Exogenous shell and endogenous biofilm provided dual protection to S. boulardii.

Computerized fluorescence microscopy of microbial cells

The upgrading of fluorescence microscopy by the introduction of computer technologies has led to the creation of a new methodology, computerized fluorescence microscopy (CFM). CFM improves subjective visualization and combines it with objective quantitative analysis of the microscopic data. CFM has opened up two fundamentally new opportunities for studying microorganisms. The first is the quantitative measurement of the fluorescence parameters of the targeted fluorophores in association with certain structures of individual cells. The second is the expansion of the boundaries of visualization/resolution of intracellular components beyond the "diffraction limit" of light microscopy into the nanometer range. This enables to obtain unique information about the localization and dynamics of intracellular processes at the molecular level. The purpose of this review is to demonstrate the potential of CFM in the study of fundamental aspects of the structural and functional organization of microbial cells. The basics of computer processing and analysis of digital images are briefly described. The fluorescent molecules used in CFM with an emphasis on fluorescent proteins are characterized. The main methods of super-resolution microscopy (nanoscopy) are presented. The capabilities of various CFM methods for exploring microbial cells at the subcellular level are illustrated by the examples of various studies on yeast and bacteria.