Biofilms are widespread in nature and constitute an important strategy implemented by microorganisms to survive in sometimes harsh environmental conditions. They can be beneficial or have a negative impact particularly when formed in industrial settings or on medical devices. As such, research into the formation and elimination of biofilms is important for many disciplines. Several new methodologies have been recently developed for, or adapted to, biofilm studies that have contributed to deeper knowledge on biofilm physiology, structure and composition. In this review, traditional and cutting-edge methods to study biofilm biomass, viability, structure, composition and physiology are addressed. Moreover, as there is a lack of consensus among the diversity of techniques used to grow and study biofilms. This review intends to remedy this, by giving a critical perspective, highlighting the advantages and limitations of several methods. Accordingly, this review aims at helping scientists in finding the most appropriate and up-to-date methods to study their biofilms. ARTICLE HISTORY

Phages are recognized as the most abundant and diverse entities on the planet. Their diversity is determined predominantly by their dynamic adaptation capacities when confronted with different selective pressures in an endless cycle of coevolution with a widespread group of bacterial hosts. At the end of the infection cycle, progeny virions are confronted with a rigid cell wall that hinders their release into the environment and the opportunity to start a new infection cycle. Consequently, phages encode hydrolytic enzymes, called endolysins, to digest the peptidoglycan. In this work, we bring to light all phage endolysins found in completely sequenced double-stranded nucleic acid phage genomes and uncover clues that explain the phage-endolysin-host ecology that led phages to recruit unique and specialized endolysins.

Staphylococcus epidermidis is now well established as a major nosocomial pathogen associated with infections of indwelling medical devices. The major virulence factor of these organisms is their ability to adhere to devices and form biofilms. However, it has not been established that adherence and biofilm formation are closely linked phenotypes for clinical isolates. In this study, the initial adhesion to different materials (acrylic and glass) of 9 clinical isolates of S. epidermidis, along with biofilmpositive and biofilm-negative control strains, was assayed using physico-chemical interactions to analyze the basis for bacterial adherence to the substratum. X-ray photo electron spectroscopy (XPS) analysis of the cell surface elemental composition was also performed in an attempt to find a relationship between chemical composition and adhesion capabilities. Biofilm formation on the two surfaces was evaluated by dry weight measurements. Human erythrocytes were used to evaluate the ability of S. epidermidis strains to cause hemagglutination, an indicator of the production of a poly-N -acetyl glucosamine cell surface polysaccharide also involved in biofilm formation. The clinical isolates exhibited different cell wall physico-chemical properties, resulting in differing abilities to adhere to surfaces. Adhesion to hydrophobic substrata for all strains occurred to a greater extent than that to hydrophilic surfaces. Bacterial cell hydrophobicity seemed to have little or no influence on adhesion. X-ray photoelectron spectroscopy analysis showed a high ratio of oxygen/carbon for all strains, which is a common characteristic of S. epidermidis species. No relevant relationship was found between XPS data and adhesion values. All strains forming biofilms were able to agglutinate erythrocytes. However, no direct relationship was found between the amount of biofilm formed and the initial adhesion extent. These results indicate that high levels of initial adherence do not necessarily lead to thick biofilm formation. These two aspects of the pathogenesis of medical device related-infection may need to be evaluated independently to ascertain the contribution of each to the virulence of S. epidermidis causing device-related infections.

Bacterial vaginosis (BV) is the most common cause of vaginal discharge. It is associated with an increased risk of preterm delivery, pelvic inflammatory disease, and an increased risk of acquisition of sexually transmitted infections including human immunodeficiency virus (HIV). The epidemiology of BV supports sexual transmission. However, its etiology remains unknown. At the center of the debate is whether BV is caused by a primary pathogen or a polymicrobial consortium of microorganisms that are sexually transmitted. We previously published a conceptual model hypothesizing that BV is initiated by sexual transmission of Gardnerella vaginalis. Critics of this model have iterated that G. vaginalis is found in virginal women and in sexually active women with a normal vaginal microbiota. In addition, colonization does not always lead to BV. However, recent advances in BV pathogenesis research have determined the existence of 13 different species within the genus Gardnerella. It may be that healthy women are colonized by nonpathogenic Gardnerella species, whereas virulent strains are involved in BV development. Based on our results from a recent prospective study, in addition to an extensive literature review, we present an updated conceptual model for the pathogenesis of BV that centers on the roles of virulent strains of G. vaginalis, as well as Prevotella bivia and Atopobium vaginae.