An open-source computational tool for measuring bacterial biofilm morphology and growth kinetics upon one-sided exposure to an antimicrobial source.

Bacillus subtilis biofilms are well known for their complex and highly adaptive morphology. Indeed, their phenotypical diversity and intra-biofilm heterogeneity make this gram-positive bacterium the subject of many scientific papers on the structure of biofilms. The "robustness" of biofilms is a term often used to describe their level of susceptibility to antimicrobial agents and various mechanical and molecular inhibition/eradication methods. In this paper, we use computational analytics to quantify Bacillus subtilis morphological response to proximity to an antimicrobial source, in the form of the antiseptic chlorhexidine. Chlorhexidine droplets, placed in proximity to Bacillus subtilis macrocolonies at different distances result in morphological changes, quantified using Python-based code, which we have made publicly available. Our results quantify peripheral and inner core deformation as well as differences in cellular viability of the two regions. The results reveal that the inner core, which is often characterized by the presence of wrinkled formations in the macrocolony, is more preserved than the periphery. Furthermore, the paper describes a crescent-shaped colony morphology which occurs when the distance from the chlorhexidine source is 0.5 cm, as well as changes observed in the growth substrate of macrocolonies exposed to chlorhexidine.

Cannabigerol Effect on Streptococcus mutans Biofilms-A Computational Approach to Confocal Image Analysis.

Biofilms are complex bacterial structures in which bacterial cells thrive as a community. Many bacterial species, including pathogens, form biofilms of high complexity and adaptability to a wide range of environmental conditions. One example of these is Streptococcus mutans, a gram-positive bacterium that has been associated with caries. Cannabigerol, a non-psychoactive cannabinoid, has been shown to affect S. mutans biofilms. In order to better characterize the effect of cannabigerol on biofilms of S. mutans, this paper provides a series of computational assays for biofilm analysis, applied on confocal images of S. mutans biofilms treated with cannabigerol. Confocal images are ubiquitous in biofilm analysis-they are often used to visualize the complex structure and molecular composition of biofilm macrocolonies. In this article, we demonstrate how confocal imaging data can be used to reveal more comprehensive insights into biofilm structure and measure specific anti-biofilm effects. This is accomplished by a series of computational assays, each focusing on a different aspect of biofilm structure.

Topography and Expansion Patterns at the Biofilm-Agar Interface in Bacillus subtilis Biofilms.

Bacterial biofilms are complex microbial communities that are formed on various natural and synthetic surfaces. In contrast to bacteria in their planktonic form, biofilms are characterized by their relatively low susceptibility to anti-microbial treatments, in part due to limited diffusion throughout the biofilm and the complex distribution of bacterial cells within. The virulence of biofilms is therefore a combination of the structural properties and patterns of adhesion that anchor them to their host surface. In this paper, we analyze the topographical properties of Bacillus subtilis' biofilm-agar interface across different growth conditions. B. subtilis colonies were grown to maturity on biofilm-promoting agar-based media (LBGM), under standard and stress-inducing growth conditions. The biofilm-agar interface of the colony-type biofilms was modeled using confocal microscopy and computational analysis. Profilometry data were obtained from the macrocolonies and used for the analysis of the surface topography as it relates to the adhesion modes present at the biofilm-agar interface. Fluorescent microspheres were utilized to monitor the expansion patterns present at the interface between the macrocolonies and the solid growth medium. Contact surface analysis revealed topographical changes that could have a direct effect on the adhesion strength of the biofilm to its host surface, thus affecting its potential susceptibility to anti-microbial agents. The topographical characteristics of the biofilm-agar interface partially define the macrocolony structure and may have significant effects on bacterial survival and virulence.

The Adaptive Morphology of Bacillus subtilis Biofilms: A Defense Mechanism against Bacterial Starvation.

Biofilms are commonly defined as accumulations of microbes, embedded in a self-secreted, polysaccharide-rich extra-cellular matrix. This study aimed to characterize specific morphological changes that occur in Bacillus subtilis biofilms under nutrient-limiting growth conditions. Under varying levels of nutrient depletion, colony-type biofilms were found to exhibit different rates of spatial expansion and green fluorescent protein production. Specifically, colony-type biofilms grown on media with decreased lysogeny broth content exhibited increased spatial expansion and more stable GFP production over the entire growth period. By modeling the surface morphology of colony-type biofilms using confocal and multiphoton microscopy, we analyzed the appearance of distinctive folds or "wrinkles" that form as a result of lysogeny broth content reduction in the solid agar growth media. When subjected to varying nutritional conditions, the channel-like folds were shown to alter their morphology; growth on nutrient-depleted media was found to trigger the formation of large and straight wrinkles connecting the colony core to its periphery. To test a possible functional role of the formed channels, a fluorescent analogue of glucose was used to demonstrate preferential native uptake of the molecules into the channels' interiors which supports their possible role in the transport of molecules throughout biofilm structures.

Bacillus subtilis Biofilm Development - A Computerized Study of Morphology and Kinetics.

Biofilm is commonly defined as accumulation of microbes, embedded in a self-secreted extra-cellular matrix, on solid surfaces or liquid interfaces. In this study, we analyze several aspects of Bacillus subtilis biofilm formation using tools from the field of image processing. Specifically, we characterize the growth kinetics and morphological features of B. subtilis colony type biofilm formation and compare these in colonies grown on two different types of solid media. Additionally, we propose a model for assessing B. subtilis biofilm complexity across different growth conditions. GFP-labeled B. subtilis cells were cultured on agar surfaces over a 4-day period during which microscopic images of developing colonies were taken at equal time intervals. The images were used to perform a computerized analysis of few aspects of biofilm development, based on features that characterize the different phenotypes of B. subtilis colonies. Specifically, the analysis focused on the segmented structure of the colonies, consisting of two different regions of sub-populations that comprise the biofilm - a central "core" region and an "expanding" region surrounding it. Our results demonstrate that complex biofilm of B. subtillis grown on biofilm-promoting medium [standard lysogeny broth (LB) supplemented with manganese and glycerol] is characterized by rapidly developing three-dimensional complex structure observed at its core compared to biofilm grown on standard LB. As the biofilm develops, the core size remains largely unchanged during development and colony expansion is mostly attributed to the expansion in area of outer cell sub-populations. Moreover, when comparing the bacterial growth on biofilm-promoting agar to that of colonies grown on LB, we found a significant decrease in the GFP production of colonies that formed a more complex biofilm. This suggests that complex biofilm formation has a diminishing effect on cell populations at the biofilm core, likely due to a combination of reduced metabolic rate and increased levels of cell death within this region.