▪ Abstract Biofilms can be defined as communities of microorganisms attached to a surface. It is clear that microorganisms undergo profound changes during their transition from planktonic (free-swimming) organisms to cells that are part of a complex, surface-attached community. These changes are reflected in the new phenotypic characteristics developed by biofilm bacteria and occur in response to a variety of environmental signals. Recent genetic and molecular approaches used to study bacterial and fungal biofilms have identified genes and regulatory circuits important for initial cell-surface interactions, biofilm maturation, and the return of biofilm microorganisms to a planktonic mode of growth. Studies to date suggest that the planktonic-biofilm transition is a complex and highly regulated process. The results reviewed in this article indicate that the formation of biofilms serves as a new model system for the study of microbial development.

Biofilm Formation as Microbial Development

Biofilms are complex communities of microorganisms attached to surfaces or associated with interfaces. Despite the focus of modern microbiology research on pure culture, planktonic (free-swimming) bacteria, it is now widely recognized that most bacteria found in natural, clinical, and industrial settings persist in association with surfaces. Furthermore, these microbial communities are often composed of multiple species that interact with each other and their environment. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies (clusters of cells) relative to one another, has profound implications for the function of these complex communities. Numerous new experimental approaches and methodologies have been developed in order to explore metabolic interactions, phylogenetic groupings, and competition among members of the biofilm. To complement this broad view of biofilm ecology, individual organisms have been studied using molecular genetics in order to identify the genes required for biofilm development and to dissect the regulatory pathways that control the plankton-to-biofilm transition. These molecular genetic studies have led to the emergence of the concept of biofilm formation as a novel system for the study of bacterial development. The recent explosion in the field of biofilm research has led to exciting progress in the development of new technologies for studying these communities, advanced our understanding of the ecological significance of surface-attached bacteria, and provided new insights into the molecular genetic basis of biofilm development.

Microbial Biofilms: from Ecology to Molecular Genetics

Helicobacter pylori is the first formally recognized bacterial carcinogen and is one of the most successful human pathogens, as over half of the world's population is colonized with this gram-negative bacterium. Unless treated, colonization usually persists lifelong. H. pylori infection represents a key factor in the etiology of various gastrointestinal diseases, ranging from chronic active gastritis without clinical symptoms to peptic ulceration, gastric adenocarcinoma, and gastric mucosa-associated lymphoid tissue lymphoma. Disease outcome is the result of the complex interplay between the host and the bacterium. Host immune gene polymorphisms and gastric acid secretion largely determine the bacterium's ability to colonize a specific gastric niche. Bacterial virulence factors such as the cytotoxin-associated gene pathogenicity island-encoded protein CagA and the vacuolating cytotoxin VacA aid in this colonization of the gastric mucosa and subsequently seem to modulate the host's immune system. This review focuses on the microbiological, clinical, immunological, and biochemical aspects of the pathogenesis of H. pylori.

Pathogenesis of Helicobacter pylori Infection

Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Integrative Genomics Viewer

Biofilms probably comprise the normal environment for most microbial cells in many natural and artificial habitats, and as such are complex associations of cells, extracellular products and detritus either trapped within the biofilm or released from cells which have lysed as the biofilm ages (Christensen, 1989). The main ‘cement ’ for all these cells and products is the mixture of polysaccharides secreted by the cells established within the biofilm. Probably the nearest analogy is processed food, in which a mixture of macromolecules of all types interact in variousways to form a recognizable structure. Within such a structure, cells, water, ions and soluble low-and high-molecular-mass products are trapped. In many biofilms, as in food, the hydrated polysaccharides may be in a semi-solid state. The major component in the biofilm matrix is water – up to 97% (Zhang et al., 1998), and the characteristics of the solvent are determined by the solutes dissolved in it. The exact structure of any biofilm is probably a unique feature of the environment in which it develops. As pointed out by Stoodley et al. (1999a), nutritional and physical conditions greatly affect the nature of laboratory biofilms and this is equally true for other types. Wimpenny & Colasanti (1997) have also suggested that biofilm structure is largely determined by the concentration of substrate. They further postulated that such differences also validate at least three conceptual models of biofilms – heterogeneous mosaics, structures penetrated by water channels, and dense confluent biofilms.

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Biofilm exopolysaccharides: a strong and sticky framework.

Oral Biofilms: Pathogens, Matrix, and Polymicrobial Interactions in Microenvironments.

The role of each of the Streptococcus mutans gtf genes coding for glucan synthesis in cariogenesis was evaluated by using strain UA130 in the specific-pathogen-free (SPF) rat model system. Mutants defective in either or both of the genes required for insoluble glucan synthesis, the gtfB and gtfC genes, exhibited markedly reduced levels of smooth-surface carious lesions relative to that of the parental organism. Likewise, the mutant defective in the gtfD gene coding for the glucosyltransferase-S enzyme synthesizing water-soluble glucans also produced significantly fewer smooth-surface lesions than strain UA130. None of these mutations markedly altered the rate of sulcal caries induction relative to that of the parental organism. In addition, a mutant of strain UA130 defective in the gtfA gene was reexamined in the SPF rat model. In contrast to previous results from a gnotobiotic rat system, these mutants also induced significantly fewer smooth-surface carious lesions compared with that by strain UA130. These results suggest that all four genes are important for smooth-surface caries formation. Furthermore, these results are discussed relative to the differences in the diets utilized in the SPF and gnotobiotic rat model systems for assessing the virulence factors of S. mutans.

Role of the Streptococcus mutans gtf genes in caries induction in the specific-pathogen-free rat model.

The surface of an indwelling medical device can be colonized by human pathogens that can form biofilms and cause infections. In most cases, these biofilms are resistant to antimicrobial therapy and eventually necessitate removal or replacement of the device. An engineered surface microtopography based on the skin of sharks, Sharklet AFTM, has been designed on a poly(dimethyl siloxane) elastomer (PDMSe) to disrupt the formation of bacterial biofilms without the use of bactericidal agents. The Sharklet AFTM PDMSe was tested against smooth PDMSe for biofilm formation of Staphylococcus aureus over the course of 21 days. The smooth surface exhibited early-stage biofilm colonies at 7 days and mature biofilms at 14 days, while the topographical surface did not show evidence of early biofilm colonization until day 21. At 14 days, the mean value of percent area coverage of S. aureus on the smooth surface was 54% compared to 7% for the Sharklet AFTM surface (p<0.01). These results suggest that surface modification of indwelling medical devices and exposed sterile surfaces with the Sharklet AFTM engineered topography may be an effective solution in disrupting biofilm formation of S. aureus.

https://link.springer.com/content/pdf/10.1116%2F1.2751405.pdf

Impact of engineered surface microtopography on biofilm formation of Staphylococcus aureus

pH is a key environmental factor affecting the physiology, ecology and pathogenicity of the oral biofilms colonizing the hard tissues of the human mouth. Much attention has been focused on the production of organic acids through the metabolism of carbohydrates by pathogenic oral bacteria. Now, evidence is emerging that alkali generation, particularly through ammonia production from arginine and urea, plays major roles in pH homeostasis in oral biofilms and may moderate initiation and progression of dental caries. This short review highlights recent progress on understanding molecular genetic and physiologic aspects of ammonia generation by prominent oral bacteria.

Robert A. Burne

Papers

Oral Biofilms: Pathogens, Matrix, and Polymicrobial Interactions in Microenvironments.

Role of the Streptococcus mutans gtf genes in caries induction in the specific-pathogen-free rat model.

Impact of engineered surface microtopography on biofilm formation of Staphylococcus aureus

Alkali production by oral bacteria and protection against dental caries.

Bacterial ureases in infectious diseases