Seminar paper - Microbiology.docx

International Burch University
Faculty of Engineering and Information Technologies
Department of Genetics and Bioengineering



Academic year: 2016/2017
Semester: Fall
Course: Microbiology
Seminar topic: Biofilms



Authors: Azra Smailagič & Nermin Đuzić, 2nd year students of GBE Department at IBU
Mentor/Evaluator: Mirsada Hukić, PhD.
Assistant: Samira Smajlović, BSc.





Sarajevo, 2017.
CONTENT

Abstract
Definition of biofilms
Historical background
Properties
Formation and development of biofilms
Biofilms in industry and medicine
References

ABSTRACT

Among many studies related to microbiology nowadays, very popular is the study of microorganisms in pure culture of the aqueous planktonic phase, which is considered as "Gold model" for most microbiological examinations, but, however, it does not reflect the real growth of bacteria in nature and therefore, scientist are also paying attention toward understanding of bacterial growth in natural conditions. Considering these studies, it becomes clear that many bacteria tend to exist in complex associations attached to the surfaces and embedded in their own extracellular matrix. Such associations are known as biofilms. Although being best studied and examined in bacteria, the colonization of surfaces and formation of biofilms on them, which actually occurs in several consecutive steps, is also characteristic for fungi, algae, protozoa and some viruses. These microorganisms can use almost every surface in the environment to form biofilms; it does not matter if the material has natural or synthetic origin. Biofilms are present nowadays in medical and industrial settings, having wide applications and both advantages and disadvantages as well as benefits and harms. Considering the fact they have very high rates of resistance to many antibiotics, which makes difficult to deal with them, biofilms, without any doubt, represent the great challenge for microbiologists and clinicians, which they have to face with.
Keywords: biofilm, bacterial attachment, biofilms and their applications, resistance to antibiotics
DEFINITION OF BIOFILMS
According to the IUPAC (International Union of Pure and Applied Chemistry) and their nomenclature system, a biofilm is any group of microorganisms, whose cells stick to each other and adhere to certain surface, being often embedded in their own extracellular matrix or extracellular polymeric substance (EPS) (Vert et al, 2012). Extracellular polymeric substance, also referred to as slime, is actually a polymeric conglomeration generally composed of extracellular DNA, proteins, and polysaccharides (Hall-Stoodley et al, 2004). However, it is important to mention that not every slime represents a biofilm (Lear & Lewis, 2012). Noncellular materials such as mineral crystals, corrosion particles, clay or silt particles, or blood components can also be found in a biofilm matrix, which actually depends on the environment or place where the biofilm developed (Vert et al, 2012). The microbial cells that grow in a biofilm differ from planktonic cells of the same organism in a physiological manner, since planktonic cells are single cells which may float or swim in a liquid medium. Biofilms can be found on a wide variety of surfaces, including indwelling or rusted medical devices used by patients or doctors, living tissues, industrial, natural aquatic systems or systems of potable water (Figure 1) (Lear & Lewis, 2012).

Figure 1: Staphylococcus aureus biofilm on indwelling catheter
HISTORICAL BACKGROUND

If we look back to the history, we can find an important information that microorganisms have primarily been characterized as planktonic and freely suspended cells and described according to their growth characteristics in nutritionally rich culture media. However, a rediscovery of a microbiologic phenomenon by Van Leeuwenhoek, which explained that microorganisms attach to and grow universally on exposed surfaces, resulted in studies that gave a rise to biofilms as surface-associated microorganisms, which exhibited a distinct phenotype with respect to gene transcription and growth rate (Lappin-Scott & Costerton, 2003). Beside Van Leeuwenhoek, they are many other scientists that contributed to the development of the study of biofilms. First of all, Heukelekian and Heller observed a so-called "bottle effect" for marine microorganisms, which is actually the fact that bacterial growth and activity were substantially enhanced by the incorporation of a surface to which these microorganisms could attach. Subsequently, Zobbel revealed that the number of bacteria on surfaces was dramatically higher than in the surrounding medium (in this case, seawater). Next important discovery was obtained by Jones and his colleagues, who examined biofilms on trickling filters in a wastewater treatment plant and, using scanning and transmission electron microscopy, revealed that they were composed of a variety of organisms. Not such long ago from now, namely in 1978, Costerton and colleagues put a theory of biofilms, explaining the mechanisms by which microorganisms adhere to living and nonliving materials and benefits achieved by this ecological niche. From that days toward nowadays, the studies of biofilms have become widely and well developed and thus the application of biofilms today can be noticed and monitored not only in industrial and ecological settings but also in medical settings as well (Lappin-Scott & Costerton, 2003).
PROPERTIES
Just like microorganisms, biofilms are ubiquitous or present everywhere, inhabiting every existing environment. Biofilms will form on almost every non-shedding surface in a humid environment (Donlan, 2002). Usually, biofilms can be found submerged in solid substrates or exposed to an aqueous solution, although they can simply float on liquid surfaces and also can exist on the surface of leaves, particularly in regions with high concentration of humidity. Under optimal conditions, having sufficient resources for growth, a biofilm will quickly grow to be macroscopic (visible to the naked eye). Many different microorganisms can be found in biofilm associations, e.g. bacteria, archaea, protozoa, fungi and algae; each of them performing specialized metabolic functions. Not all bacteria have an ability to be included in such associations and to form biofilms (Donlan, 2002).
Hydrophobicity of surface is one of the several factors that play an important role in determining the ability of bacteria to form biofilms since those with increased hydrophobicity have reduced repulsion between the extracellular matrix and the bacterium (Lear & Lewis, 2012).Some species do not have an ability to attach to a surface on their own but can instead anchor themselves to the matrix or directly to earlier colonists. Such cells are able to communicate via so-called quorum sensing during the process of colonization. using products like N-acyl homoserine lactone. Some bacteria are unable to form biofilms because of their limited motility. Non-motile bacteria cannot recognize the surface or aggregate together as easily as motile bacteria (Lear & Lewis, 2012).


FORMATION AND DEVELOPMENT OF BIOFILMS

Microbes can response to many factors which can serve as initiators for biofilm formation: cellular recognition of specific or non-specific attachment sites on a surface, nutritional cues, or in some cases, exposure of planktonic cells to sub-inhibitory concentrations of antibiotics. When switched to the biofilm mode of growth, the cell undergoes a phenotypic shift in behavior in which huge numbers of genes are regulated in different ways (Karatan & Watnick, 2009).
Actually, the formation and development of biofilms occur in several consecutive phases. At the very beginning, in the first phase an initial transport and reversible attachment of bacteria to the surface, with adsorbed organic and inorganic nutrients, occurs. While still not fully understood, it is believed that the first colonists of a biofilm adhere to the surface initially through weak, reversible adhesion via van der Waals forces and hydrophobic effects. If they are not immediately separated from the surface, colonists can anchor themselves more permanently using pili, cell structures responsible for adhesion (Donlan, 2002). Afterward, extracellular polymeric substance (EPS) gets secreted and it forms bridges between individual cells, which results in the irreversible attachment or cementing" of the cells to the surface. Hence it cannot be removed from the surface by gently rinsing. Finally, the last phase of this process is the colonization of the surface (Donlan, 2002). Attached to the surface, bacteria grow and divide, creating microcolonies, which are considered as the elemental organization units of biofilms. The "primary colonizer" secrets substances which attract other planktonic bacteria that are found in the environment (secondary colonization). The final stage of biofilm formation is known as dispersion and is the stage in which the biofilm is established and may only change in shape and size. A completed biofilm has complex architecture, providing an optimal environment for exchange of genetic material between cells, and is made out of bacteria embedded in EPS coated microcolonies, of which there are less dense parts of the matrix with permeable water channels that aid in the transport of nutrients and waste products (An & Parsek, 2007). In conclusion, there are actually five stages of biofilm development, illustrated in Figure 2 below (Monroe, 2007):
Initial attachment.
Irreversible attachment.
Maturation I.
Maturation II.
Dispersion.


Figure 2: 5 stages of biofilm development
BIOFILMS IN FOOD INDUSTRY AND MEDICINE
Because of their ability to form on different plants and during industrial processes, biofilms have become an important problem in several food industries. The fact is that many bacteria is capable of surviving long periods of time in various, even harsh, conditions like in animal manure, in water, soil, under high temperatures and therefore causing biofilm formation on plants, animals or processing equipment (Srey et al, 2013). It further increases a health risk to consumers due to its ability to make food less susceptible and more resistant to disinfectants. Also, during the washing process, biofilms are able to resist sanitization and disinfection processes and allow bacteria to spread across the produce (Tarvel, 2009). According to some statistical data, biofilms are tightly connected with more than 80% of bacterial infection in the USA. Nowadays, new forms of cleaning procedures are being tested in order to reduce biofilm formation in these processes which will lead to safer and more productive food processing industries (Srey et al).
In another hand, being considered from the medical aspect, biofilms are thought to be involved in a wide variety of microbial infections affecting the human body and health. These infections include urinary tract infections, catheter infections, middle-ear infections, formation of dental plaque, gingivitis, coating contact lenses, and less common but also there are more lethal processes like bacterial endocarditis, infections which can result in cystic fibrosis or, finally, infections such as those of permanent indwelling devices like heart valves and joint prostheses (Parsek et al, 2003). Perhaps the most common infection is a dental plaque, which is considered as an oral biofilm that adheres to the teeth and consists of many species of both bacteria and fungi (such as Streptococcus mutants and Candida albicans), embedded in salivary polymers and microbial extracellular products (Rogers, 2008). The accumulation of microorganisms affects the teeth and surrounding tissues, which results in dental disease. We can conclude that, if an infection develops a biofilm, it becomes even harder to treat it. As the bacteria change, they become more resistant to antibiotics and the body's own host defenses and immunity. Future studies are thus directed toward needs to find ways of identifying and monitoring biofilm colonization at the bedside in order to permit timely initiation of treatment (Roger, 2008). However, not everything is as bad as it seems to be. Namely, sometimes biofilms can have a protective role, especially in humans. For example, the gut commensal flora forms biofilms, that attach to epithelial cells, making a barrier which prevents the penetration of pathogens. In other words, considering another example, dental plaque is made out of different bacterial biofilms, but the decline of teeth is a consequence of the proliferation of pathogenic strains in the same (Hukić & Ibrišimović, 2016).
REFERENCES
An, D., & Parsek, M. R. (2007). The promise and peril of transcriptional profiling in biofilm communities. Current opinion in microbiology, 10(3), 292-296.

Donlan, R. M. (2002). Biofilms: microbial life on surfaces. Emerg Infect Dis, 8(9).

Hall-Stoodley, L., Costerton, J. W., & Stoodley, P. (2004). Bacterial biofilms: from the natural environment to infectious diseases. Nature reviews microbiology, 2(2), 95-108.

Hukić, M. & Ibrišimović-Avdić M. (2016); Biofilms. BurchGene magazine, 2(1), 8-9.

Karatan, E., & Watnick, P. (2009). Signals, regulatory networks, and materials that build and break bacterial biofilms. Microbiology and Molecular Biology Reviews, 73(2), 310-347.

Lappin-Scott, H. M., & Costerton, J. W. (2003). Microbial biofilms (Vol. 5). Cambridge University Press.

Lear, G., & Lewis, G. D. (Eds.). (2012). Microbial biofilms: current research and applications. Horizon Scientific Press.

Monroe, D. (2007). Looking for chinks in the armor of bacterial biofilms. PLoS Biol, 5(11), e307.

Parsek, M. R., & Singh, P. K. (2003). Bacterial biofilms: an emerging link to disease pathogenesis. Annual Reviews in Microbiology, 57(1), 677-701.

Rogers, A. H. (2008). Molecular oral microbiology. Horizon Scientific Press.

Srey, S., Jahid, I. K., & Ha, S. D. (2013). Biofilm formation in food industries: a food safety concern. Food Control, 31(2), 572-585.

Vert, M., Hellwich, K. H., Hess, M., Hodge, P., Kubisa, P., Rinaudo, M., & Schué, F. (2012).
Terminology for biorelated polymers and applications (IUPAC Recommendations 2012). Pure and Applied Chemistry, 84(2), 377-410.

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