Bacteria that attach to surfaces aggregate in a hydrated polymeric matrix of their own synthesis to form biofilms. Formation of these sessile communities and their inherent resistance to antimicrobial agents are at the root of many persistent and chronic bacterial infections. Studies of biofilms have revealed differentiated, structured groups of cells with community properties. Recent advances in our understanding of the genetic and molecular basis of bacterial community behavior point to therapeutic targets that may provide a means for the control of biofilm infections.

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Bacterial biofilms : A common cause of persistent infections

The microorganisms in biofilms live in a self-produced matrix of hydrated extracellular polymeric substances (EPS) that form their immediate environment. EPS are mainly polysaccharides, proteins, nucleic acids and lipids; they provide the mechanical stability of biofilms, mediate their adhesion to surfaces and form a cohesive, three-dimensional polymer network that interconnects and transiently immobilizes biofilm cells. In addition, the biofilm matrix acts as an external digestive system by keeping extracellular enzymes close to the cells, enabling them to metabolize dissolved, colloidal and solid biopolymers. Here we describe the functions, properties and constituents of the EPS matrix that make biofilms the most successful forms of life on earth.

The biofilm matrix

Biofilms--matrix-enclosed microbial accretions that adhere to biological or non-biological surfaces--represent a significant and incompletely understood mode of growth for bacteria. Biofilm formation appears early in the fossil record (approximately 3.25 billion years ago) and is common throughout a diverse range of organisms in both the Archaea and Bacteria lineages, including the 'living fossils' in the most deeply dividing branches of the phylogenetic tree. It is evident that biofilm formation is an ancient and integral component of the prokaryotic life cycle, and is a key factor for survival in diverse environments. Recent advances show that biofilms are structurally complex, dynamic systems with attributes of both primordial multicellular organisms and multifaceted ecosystems. Biofilm formation represents a protected mode of growth that allows cells to survive in hostile environments and also disperse to colonize new niches. The implications of these survival and propagative mechanisms in the context of both the natural environment and infectious diseases are discussed in this review.

/pdf/bacterial-biofilms-from-the-natural-environment-to-4pdlw3zbzj.pdf

Bacterial biofilms: from the natural environment to infectious diseases.

Though biofilms were first described by Antonie van Leeuwenhoek, the theory describing the biofilm process was not developed until 1978. We now understand that biofilms are universal, occurring in aquatic and industrial water systems as well as a large number of environments and medical devices relevant for public health. Using tools such as the scanning electron microscope and, more recently, the confocal laser scanning microscope, biofilm researchers now understand that biofilms are not unstructured, homogeneous deposits of cells and accumulated slime, but complex communities of surface-associated cells enclosed in a polymer matrix containing open water channels. Further studies have shown that the biofilm phenotype can be described in terms of the genes expressed by biofilm-associated cells. Microorganisms growing in a biofilm are highly resistant to antimicrobial agents by one or more mechanisms. Biofilm-associated microorganisms have been shown to be associated with several human diseases, such as native valve endocarditis and cystic fibrosis, and to colonize a wide variety of medical devices. Though epidemiologic evidence points to biofilms as a source of several infectious diseases, the exact mechanisms by which biofilm-associated microorganisms elicit disease are poorly understood. Detachment of cells or cell aggregates, production of endotoxin, increased resistance to the host immune system, and provision of a niche for the generation of resistant organisms are all biofilm processes which could initiate the disease process. Effective strategies to prevent or control biofilms on medical devices must take into consideration the unique and tenacious nature of biofilms. Current intervention strategies are designed to prevent initial device colonization, minimize microbial cell attachment to the device, penetrate the biofilm matrix and kill the associated cells, or remove the device from the patient. In the future, treatments may be based on inhibition of genes involved in cell attachment and biofilm formation.

Biofilms: Survival Mechanisms of Clinically Relevant Microorganisms

▪ Abstract Quorum sensing is the regulation of gene expression in response to fluctuations in cell-population density. Quorum sensing bacteria produce and release chemical signal molecules called autoinducers that increase in concentration as a function of cell density. The detection of a minimal threshold stimulatory concentration of an autoinducer leads to an alteration in gene expression. Gram-positive and Gram-negative bacteria use quorum sensing communication circuits to regulate a diverse array of physiological activities. These processes include symbiosis, virulence, competence, conjugation, antibiotic production, motility, sporulation, and biofilm formation. In general, Gram-negative bacteria use acylated homoserine lactones as autoinducers, and Gram-positive bacteria use processed oligo-peptides to communicate. Recent advances in the field indicate that cell-cell communication via autoinducers occurs both within and between bacterial species. Furthermore, there is mounting data suggesting that ba...

Quorum Sensing in Bacteria

For several years, Science policy has required that published X-ray crystallographic coordinates be deposited with a publically accessible database (e.g., Brookhaven Protein Data Bank). That policy recognized the high costs and risks of solving important structures to accord those who have made such investments successfully the time to reap their intellectual benefits. Wlodawer et al. (below) assert that recent technical enhancements have reduced “the time needed to solve a structure (to less than) than the allowed hold period” and have called for immediate release of the data. In cooperative discussions with our colleagues at Nature and other journals, Science wishes to evaluate how best to fulfill our responsibilities to the community. We urge readers to respond to a survey now underway (see ) and to us, so that future policy may be modified on the basis of scientific judgement.

# Immediate Release of Crystallographic Data: A Proposal {#article-title-2}

There has been an incredibly rapid increase in the rate of determination of three-dimensional (3D) structures of biomacromolecules, as reflected by the deposition of a new structure in the Protein Data Bank (PDB) at the Brookhaven National Laboratory ([1][1]), on average, every 5 hours. Unfortunately, in parallel, an increasing proportion of depositors take advantage of the PDB's policy of allowing structures to be kept “on hold” for up to a year after coordinate deposition. Despite a recent drop in the number of structures put “on hold,” nearly half the entries deposited are not released immediately. The policy of the PDB is based on rules drawn up by the International Union of Crystallography (IUCr) in the late 1980s for papers published in IUCr journals. These rules ([2][2]) also provide the basis for the policies of most other scientific journals and of a number of government funding agencies, such as the National Institutes of Health, for work undertaken with grant support.

It is time to consider whether this policy is still appropriate. When it was debated and accepted by the community 10 years ago, the time needed to solve a macromolecular structure was often measured in years and was rarely less than 1 year. The time needed for detailed analysis of such structures was also fairly long. The 1-year hold on coordinates was therefore instituted to allow the authors to reap the fruit of their tremendous investment of time and effort. Because of recent advances in protein expression and purification, crystallization procedures, x-ray instrumentation, and computer software, the time needed to solve a structure is often shorter than the allowed hold period. In light of such developments, it is difficult to justify withholding coordinates for any period once the paper has been published.

Biomolecular structure analysis has succeeded in bringing 3D structures to the forefront of molecular biological research. This success has expanded both the interest in and utility of the information being deposited in the PDB. The molecular modeling community has grown and evolved considerably, due to the expansion of this source of experimental data. The value of the data rests in their availability to the broader community. Methods are continuously being developed to analyze new structures and their relationships to the collection of existing structures. New uses for these data, such as statistical potentials for folding and threading calculations, and interface recognition tools, are evolving rapidly. No single research group can fully exhaust this wealth of information. The value of the resource grows proportionally to the timeliness of the data and to the number of scientists who have access to them. Three-dimensional structural information is also a crucial link elucidating the role of a translated region of a DNA sequence of unknown function.

The time has come to change the rules of deposition so as to ensure that the coordinates are released concomitantly with publication of the paper (or papers) describing the structure. We are convinced that without access to the coordinates, the structures cannot be used for comparison with other proteins, for theoretical analysis or, more and more important, for drug design.

We propose that coordinates deposited at the PDB should be marked as either “for immediate release” or “to be released upon publication.” We also recommend that the maximum hold for primary data (that is, x-ray structure factors, and nuclear magnetic resonance proton-proton distance and dihedral angle restraints) be reduced from 4 years to 1 year. The PDB is already working on a “layered approach” to deposition so that it will be possible to release entries as submitted, after the authors have checked for outliers and errors through the PDB's WEB-based AutoDep procedure, on the same day that they are deposited (with the permission of authors), or when the article related to the structure is published, if the authors request “release on publication date” rather than “hold for a year.” It is clear that such a change in policy will require cooperation of both the granting agencies and the scientific journals, as well as the overwhelming support of the scientists doing the research. It should be stressed that even the current policy is not uniformly enforced. These changes would bring macromolecular crystallography into line with the requirements of other fields, such as gene sequencing, which have never allowed extended hold periods. We hope that this proposed change in the deposition policy will be publicly debated and ultimately accepted.

1. [↵][3] .
 

2. [↵][4]International Union of Crystallography, Acta Crystallogr. A45, 658 (1989).
 [OpenUrl][5]

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Immediate release of crystallographic data: a proposal.

The use of signal molecules to manipulate the behavior of biofilm bacteria

The goal of this study is to explore a new self-healing concept in which
fungi are used as a self-healing agent to promote calcium mineral precipitation
to fill the cracks in concrete. Although many species of fungi have been
reported to be able to promote calcium mineralization, they have not yet been
investigated in the application of self-healing concrete, thus an initial
screening of different species of fungi has been conducted. The experimental
results showed that, due to the leaching of Ca(OH)2 from concrete, the pH of
the growth medium increased from its original value of 6.5 to 13.0. Despite the
drastic pH increase, Trichoderma reesei (ATCC13631) spores germinated into
hyphal mycelium and grew equally well with or without concrete. We employed
material characterization techniques including X-ray diffraction (XRD) and
scanning electron microscope (SEM), both of which confirmed that the crystals
precipitated on the fungal hyphae were composed of calcite.

Screening of Fungi for Self-Healing of Concrete Cracks

Atherosclerosis, or hardening of the arteries, is a leading cause of congestive heart failure, heart attack, and stroke in humans. Mounting evidence, in the literature and from our lab, points to the regular involvement of bacteria within arterial plaque deposits in patients with advanced atherosclerosis. ABSTRACT The association of bacteria with arterial plaque lesions in patients with atherosclerosis has been widely reported. However, the role these bacteria play in the progression of atherosclerosis is still unclear. Previous work in our lab has demonstrated that bacteria exist in carotid artery plaques as biofilm deposits. Biofilms are communities of microorganisms enmeshed within a protective, self-produced extracellular matrix and have been shown to contribute to chronic infections in humans. Biofilm communities have the potential to impact surrounding tissues in an infection if they undergo a dispersion response, releasing bacteria into the surrounding environment by enzymatic degradation of the extracellular matrix. One concern relating to these enzymes is that they could cause collateral damage to host tissues. In this study, we present an in vitro multispecies biofilm culturing model used to investigate the potential role of bacterial biofilm dispersion in the progression of atherosclerosis. This work has demonstrated an increase in cell release from mixed-species biofilms formed by bacteria associated with human carotid arterial plaque deposits following treatment with iron or a combination of norepinephrine and transferrin. Greater extracellular lipase, protease, and collagenase/gelatinase activity was also associated with iron-treated biofilms. The results of this work suggest that bacteria in this model undergo iron-induced biofilm dispersion, as evidenced by the increased cell release and higher enzyme activity following treatment. This work demonstrates the potential for multispecies biofilm dispersion to contribute to arterial tissue degradation by bacteria and suggests that in atherosclerotic infections, biofilm dispersion may contribute to thrombogenesis, which can lead to heart attack or stroke. IMPORTANCE Atherosclerosis, or hardening of the arteries, is a leading cause of congestive heart failure, heart attack, and stroke in humans. Mounting evidence, in the literature and from our lab, points to the regular involvement of bacteria within arterial plaque deposits in patients with advanced atherosclerosis. Very little is known about the behavior of these bacteria and whether they may contribute to tissue damage in infected arteries. Tissue damage within the arterial plaque lesion can lead to rupture of the plaque contents into the bloodstream, where a clot may form, resulting in a potential heart attack or stroke. This study shows that plaque-associated bacteria, when cultured as mixed-species biofilms in the laboratory, can release degradative enzymes into their environment as the result of a dispersion response triggered by iron. These degradative enzymes can digest proteins and lipids which are associated with the tissues that separate the plaque lesion from the arterial lumen. Thus, this study demonstrates that if mixed species biofilms are induced to undergo dispersion in an infected atherosclerotic lesion when exposed to an elevated concentration of free iron, they have the potential to contribute to the weakening of arterial tissues, which may contribute to atherosclerotic plaque destabilization.

Laboratory Grown Biofilms of Bacteria Associated with Human Atherosclerotic Carotid Arteries Release Collagenases and Gelatinases during Iron-Induced Dispersion

Eine Zusammenfassung umfassend: einen oder mehrere Dispersions-Ausloser, umfassend: wobei eine Einfach- oder Doppel-Kohlenstoff-Kohlenstoff-Bindung ist, m 1 oder 2 ist, n gleich 2 bis 15 ist und R eine Carbonsaure, ein Salz, ein Ester oder ein Amid ist, wobei der Ester oder das Amid isoster oder bioster zu der Carbonsaure sind und ein oder mehrere additive Komponenten, gewahlt aus der Gruppe bestehend aus Bioziden, Tensiden, Antibiotika, Antiseptika, Detergenzien, Chelatbildner, Viruleszenzfaktor-Inhibitoren, Gelen, Polymeren, Pasten, essbaren Produkten und kaubaren Produkten, wobei besagte Zusammensetzung so formuliert ist, dass bei Kontakt mit einem Biofilm, erzeugt durch einen Mikroorganismus, wobei der Biofilm eine Matrix umfasst, und der Mikroorganismus auf einer Oberflache, der Dispersions-Ausloser selektiv auf den Mikroorganismus wirkt und eine geeignete biologische Antwort ausubt, ohne einen notwendigen direkten Effekt auf die Matrix, um den Biofilm zu zerstoren.

David G. Davies

Papers

Immediate release of crystallographic data: a proposal.

The use of signal molecules to manipulate the behavior of biofilm bacteria

Screening of Fungi for Self-Healing of Concrete Cracks

Laboratory Grown Biofilms of Bacteria Associated with Human Atherosclerotic Carotid Arteries Release Collagenases and Gelatinases during Iron-Induced Dispersion

Induktion einer physiologischen Dispersions-Antwort in Bakterien-Zellen in einem Biofilm