from Christof Godts, Gitte Loozen, Marc Quirynen and Wim Teughels writing in Oral Microbial Ecology: Current Research and New Perspectives:

The human oral cavity is colonized by a wide variety of bacteria, which form very complex and dynamic biofilms on hard and soft tissues. Certain members of these microbiological communities are associated with oral infections, such as caries and periodontal diseases. New treatment approaches are emerging that do not rely on conventional antibiotic therapies, since complete eradication of pathogenic bacteria from oral biofilms is impossible and antibiotic resistance is becoming problematic. For example, attempts have been made to reduce the overall pathogenicity of tissue-associated biofilms by introducing live beneficial bacteria. Early successes, primarily in the field of gastro-intestinal microbiology, have paved the way for the introduction of probiotics in oral health care. These new anti-/pro-microbial therapies are considered very promising for prevention and treatment of plaque related oral diseases. In this review, the concept of probiotics for oral healthcare is introduced, followed by an overview of the diverse mechanisms of probiotic action in the oral cavity. Since the benefits of probiotics will ultimately be revealed by clinical studies, the clinical outcomes of probiotic applications for combating dental caries and periodontal diseases are addressed. Finally the interactions of probiotics with the oral microbial ecosystem are discussed and future perspectives regarding the oral probiotic concept are presented.

Further reading: Oral Microbial Ecology: Current Research and New Perspectives

from George Hajishengallis writing in Oral Microbial Ecology: Current Research and New Perspectives:

The polymicrobial community that initiates periodontal disease does not represent a random compilation of bacteria. Rather, these bacteria form organized consortia that have evolved through mutually beneficial relationships. This review focuses on microbial immune subversion as a means by which select pathogens may contribute to the adaptive fitness of the entire periodontal biofilm. For instance, Porphyromonas gingivalis expresses specialized virulence traits that undermine immunity and promote non-resolving inflammation, which, respectively, protect the bacteria and facilitate nutrient acquisition. The virulence factors involved (e.g. cysteine proteases and atypical lipopolysaccharide structures) are released as components of readily diffusible membrane vesicles, which can thus become available for the benefit of other biofilm organisms. The elucidation of immune subversion mechanisms of key periopathogens that promote the collective virulence of their communities may provide new avenues of therapeutic intervention in human periodontitis.

Further reading: Oral Microbial Ecology: Current Research and New Perspectives

from John G. Thomas writing in Oral Microbial Ecology: Current Research and New Perspectives:

The link between oral flora and lung infections in mechanically ventilated (MV) patients (the 'Oral Systemic Link') has always been circumstantial, based on clinical and nursing practices and preventative care. At the turn of the 20th century, that began to change as molecular and imaging methods provided tools to better evaluate microbial exchange, refocusing on the importance of the endotracheal tube (ETT) lumen as a potential conduit, devoid of normal cellular defensive components. We undertook the challenge in two phases, first engineering the Adult -Ventilator Endotracheal Lung (A-VEL) simulator to replicate the closed, bi-directional airway and stress of the intubated patient in the intensive care unit (ICU). Of singular importance, was the incorporation of multiple quantitative imaging techniques to define the 3-D biofilm luminal development in Stages (I-IV) from single to complex microbial communities and the incorporation of dental pathogens (Streptococcus mutans and Porphyromonas gingivalis) as an endogenous event, in the preconditioning of the ETT luminal surface, an abiotic medical device. The second phase shifted to the in vivo environment and in multiple clinical studies, unmasked the bi-phasic nature of ETT luminal colonization, oral-endogenous (Early) to systemic - exogenous (Late) at a 3-5 day 'switch'. Further, the ICU studies dramatized the shift from the infectious process in VAP to Work of Breathing (WOB), where the former occurred in 16%, while biofilm accretion, occlusion of the ETT lumen and increased airway resistance occurred in 100% of intubated patients. Most recently, we have used both 16S (microarray) and 18S rRNA (pyrosequencing) to redefine the proportions of bacteria and fungi from oral reservoirs, and been astonished by the richness and diversity of the oral fungal community in the ETT accretion occlusion, often yielding >15 species . Endotracheal Tube Associated Pneumonia (EAP) management continues to elude optimal strategies, but the use of selected oral probiotics coupled with better oral care in both the ICU and admitting institutions is gaining reinforcement: "Oral Stewardship". Further, the utilization of dental professionals in the ICU has importance, as has the recognition that the next fertile area of airway disease (oral to systemic) study is the neonatal intensive care unit (NICU), where 50% of newborns may be intubated and develop EAP with no teeth. How? Why?

Further reading: Oral Microbial Ecology: Current Research and New Perspectives

from Marieke P.T. Otten, Henk J. Busscher, Chris G. van Hoogmoed, Frank Abbas and Henny C. van der Mei writing in Oral Microbial Ecology: Current Research and New Perspectives:

An overview is presented on oral biofilm formation and recent developments in oral biofilm control using mechanical devices (manual or powered toothbrushes and interdental cleaning devices) and biofilm control based on oral chemotherapeutics (antibacterial toothpastes and mouthrinses). For clinical efficacy of oral chemotherapeutics, it is important that the antibacterial remains active in the oral cavity for periods longer than the actual brushing or rinsing time, a characteristic called 'substantivity'. Substantivity can be achieved by adsorption of antibacterials to oral hard and soft tissues followed by release. Mechanical cleaning never results in complete removal of oral biofilm: most notably in fissures, interproximal spaces, gingival pockets and around orthodontic appliances. Recently, it has been demonstrated that this residual biofilm can act as a reservoir for oral chemotherapeutics that are slowly released over time in bio-active concentrations. This function of oral biofilm was already known for fluoride and has been demonstrated to aid in preventing caries. Results from our laboratory showed that residual biofilm after mechanical cleaning can release absorbed antibacterial agents from toothpastes and mouthrinses in bio-active concentrations.

Further reading: Oral Microbial Ecology: Current Research and New Perspectives

"well-written essays to explore a number of microbial ecological theories from population genetic and evolution theory to microbial biogeography ... The academic content of this volume is robust and the questions posted are thought-provoking ... definitely a useful reference book for scientists" from Diane Purchase (Middlesex University, UK) writing in Microbiology Today (2013) read more ...

Microbial Ecological Theory: Current Perspectives Edited by: Lesley A. Ogilvie and Penny R. Hirsch ISBN: 978-1-908230-09-6 Publisher: Caister Academic Press Publication Date: September 2012 Cover: hardback "thought-provoking ... a useful reference book" (Microbiol. Today)

from Michael F. Cole, Katherine A. Wirth and George H. Bowden writing in Oral Microbial Ecology: Current Research and New Perspectives:

In this review we consider the biology of the viridans streptococci in the human oropharynx with a particular focus on the pioneer bacterium Streptococcus mitis. We show that, although this species is a constant component of the human oral cavity, each person harbors a unique and diverse population of stains that appear not to be shared within a family and, apparently, are rarely transmitted from mother to neonate. The population of stains of S. mitis within the mouth of each individual exhibits turnover perhaps in response to pressure exerted by the mucosal immune system since it has been shown that some secretory immunoglobulin A (SIgA) antibodies are clone-specific. We assert that the strains that are successful in establishing in the mouth are physiologically adapted to occupy their niche within their habitat. While it is clear that in vitro experiments and animal models have provided useful information, they are no substitute for studying commensal oral bacteria in their environment, the human oral cavity.

Further reading: Oral Microbial Ecology: Current Research and New Perspectives

from Saswat Sourav Mohapatra and Indranil Biswas writing in Oral Microbial Ecology: Current Research and New Perspectives:

The human oral cavity is estimated to host more than 700 bacterial species formed into distinct biofilm communities, of which more than 50% are yet to be cultured in the laboratory. Though oral streptococci constitute two thirds of the total commensals, only a fraction known as mutans streptococci are involved in producing dental caries. The oral streptococci are the primary colonizers of the tooth and other mucosal surfaces in the oral cavity and initiate plaque biofilm formation. Mutual interaction in the form of cooperation and competition shapes the constitution of the oral microflora. Colonization by Streptococcus mutans, having significant acidogenicity and aciduricity properties, is primarily responsible for dental caries formation. Recent advances in nucleotide sequencing and other high throughput methods have provided significant clues to the biology and gene regulation of S. mutans in a community structure. Many therapeutic methods are being devised to specifically target the S. mutans in the biofilm, without disturbing other bacterial species. Significant among them are targeting the interbacterial signaling, replacing cariogenic flora with non-cariogenic flora, and specifically targeted antimicrobial peptides (STAMPs). As the research progresses in this field, better therapeutic methods are on the horizon.

Further reading: Oral Microbial Ecology: Current Research and New Perspectives

from Paul Wilmes writing in Microbial Ecological Theory: Current Perspectives:

The recent application of high-throughput molecular biology methods to natural microbial communities is profoundly changing our view on the microbial world. In particular, our understanding of microbial population-level differentiation involved in ecological adaptation that leads to microbial divergence and speciation has been profoundly altered. Numerous processes that underlie microbial differentiation have been identified but determining the relative significance of these processes remains challenging. For example, a major unresolved question is how much of observed genetic heterogeneity is due to neutral versus adaptive processes. Sequence-based and modelling analyses suggest that much of the observed variation is neutral but recent functional "meta-OMIC" data suggest that at least some of this fine-scale variation is functionally relevant and, thus, involved in adaption and divergence. From the limited amount of largely disjointed metagenomic and functional data obtained to date, extensive intra- and inter-system as well as extensive intra- and inter-population differences are apparent. Consequently, it is difficult to ascertain specific molecular patterns that define specific microbial groups that would be congruent with the definition of a microbial species. Future concomitant analysis of community genomic complements, transcriptomes, proteomes and metabolomes over relevant spatial and temporal scales will result in detailed molecular descriptions of distinct taxonomic entities. Such a system-level molecular organismal classification system will need to be solidly grounded in ecological theory, population genetic theory and evolutionary theory, and may be universally applicable to the three domains of life.

Further reading: Microbial Ecological Theory: Current Perspectives

from Nicholas S. Jakubovics writing in Oral Microbial Ecology: Current Research and New Perspectives:

A core component of microbial biofilms is the extracellular matrix, which binds together the assembled micro-organisms and regulates the passage of small molecules to and from cells. The scaffolding of the matrix is composed of biological macromolecules including carbohydrates, nucleic acids and proteins. The production and function of extracellular polysaccharides in oral biofilms has been the subject of a great deal of research over many decades, and is considered in a separate review. More recently, it has become clear that proteins and extracellular DNA (eDNA) play key roles in maintaining the structure of many different biofilms, including oral biofilms. This paper reviews the recent research on proteins and eDNA in the biofilm matrix, and discusses the evidence that oral micro-organisms utilise these macromolecules for specific functions within mixed-species biofilms.

Further reading: Oral Microbial Ecology: Current Research and New Perspectives

from Justin Merritt and Jens Kreth writing in Oral Microbial Ecology: Current Research and New Perspectives:

Oral streptococci encounter an exceptionally wide range of environmental stresses and population densities. These stimuli are sensed by efficient detection systems that also coordinate the appropriate adaptive genetic responses. The majority of these detection systems utilize membrane bound sensory proteins that are directly or indirectly regulated by their sensed stimuli. Such systems play an intimate role in mitigating the potential damage caused by changes in redox potential, fluctuations in local pH, and toxicity from antimicrobial agents. In addition, the typical life cycle of oral streptococci includes a transition from growth in a relatively low cell density planktonic state to an extremely high cell density biofilm environment. Consequently, various sensory systems are dedicated to detecting this increase in population density and regulating the genetic pathways that are essential for persistence in a highly competitive multispecies biofilm environment. Recent studies have identified many of the targets of these sensory systems and have provided unprecedented insight into the intimate connection between the constantly changing oral environment and the genetic machinery of oral bacteria.

Further reading: Oral Microbial Ecology: Current Research and New Perspectives

from William Wade writing in Oral Microbial Ecology: Current Research and New Perspectives:

The oral microbiota is highly diverse and includes fungi, protozoa, viruses and bacteria. Both domains of prokaryotes, Archaea and Bacteria are present. Representatives of the Archaea are restricted to a few taxa in the genus Methanobrevibacter, while there are over 600 species of Bacteria, from at least 12 phyla. The full diversity of bacterial populations in the mouth has been recognised following the application of culture-independent methods of analysis, based on 16S rRNA gene sequence comparisons. Because oral bacteria are typically slow-growing and fastidious, and around half cannot be grown in the laboratory at all, the taxonomic process of classifying and naming bacterial species is ongoing and over 100 cultivable taxa have still to be named. In recent years, attempts have been made to culture the not-yet-cultured portion of the microbiota. There are a number of reasons why certain taxa are uncultivable and these include a need for a specific nutrient, extreme oxygen sensitivity and dependence on other organisms. The inter-dependence among members of the oral microbial community may relate to cooperative degradation of natural substrates for growth or the need to participate in signalling networks that control growth rate and resuscitation from dormancy. Novel culture media and methods are being developed that reproduce the in vivo environment and thus encourage previously uncultured organisms to grow in the laboratory.

Further reading: Oral Microbial Ecology: Current Research and New Perspectives

from Purnima S Kumar, Matthew R Mason and Janel Yu writing in Oral Microbial Ecology: Current Research and New Perspectives:

Dental plaque biofilm is composed of a diverse microbial community. Several decades of research have been focused on the role played by the subgingival biofilm in the etiology of periodontal diseases. However, recent evidence from other ecosystems within the human body indicates that these biofilms also play an important role in maintaining health. The purpose of this review is to explore the health benefits of subgingival plaque, and to outline the development of the biofilm as well as to characterize the bacteria present in the plaque biofilm in health and disease. Additionally, the virulence mechanisms of health and disease-associated biofilms will be outlined.

Further reading: Oral Microbial Ecology: Current Research and New Perspectives

from David Beighton, Sadaf Rasheed Mughal and Thuy Do writing in Oral Microbial Ecology: Current Research and New Perspectives:

The oral biofilm proliferates in the mouth by primarily utilizing components of saliva as dietary foods are rapidly cleared. The complex microbial community functions in a concerted manner to obtain nutrients, sugars and amino acids, from salivary components including mucins, by the production of a range of glycosidic enzymes including sialidase, β-galactosidase, N-acetylglucosaminidases, α-fucosidase and mannosidases and exo- and endo-proteolytic activities. Degradation of glycans occurs sequentially and in vitro studies indicate that liberated sugars are rapidly transported though evidence of cross-feeding between species, utilizing liberated sugars, is evident. Streptococcus oralis is a species with the greatest ability to deglycosylate both N- and O-linked glycans and has been used extensively in model systems. New research should take advantage of modern high throughput sequencing techniques to determine the biofilm transcriptome of humans receiving defined diet, including fasting, to ascertain the response of the biofilm to in vivo conditions.

Further reading: Oral Microbial Ecology: Current Research and New Perspectives

from Alexander H. Rickard, Adam J. Underwood and William Nance writing in Oral Microbial Ecology: Current Research and New Perspectives:

Mature dental-plaque biofilm communities contain hundreds of bacterial species. The potential for these communities to cause caries or periodontal disease relates to bacterial spatiotemporal biofilm development and species composition. At least three forms of inter-species interactions can conceivably mediate altered biofilm development and species composition. These are coaggregation, metabolic interactions, and cell-cell signaling. Coaggregation is the specific recognition and adhesion of different species of bacteria and likely contributes toward the ordered (sequential) integration of species into biofilms as well as improving species retention in a flowing environment. 'Metabolic interactions' is an umbrella term that describes the exchange of metabolites or environmental protection afforded between adjacent species within dental plaque. Cell-cell signaling is a phenomenon that has gained increasing research interest over the past decade. One broad inter-species signaling molecule system consists of a collection of inter-convertible cell-cell signal molecules that are collectively called autoinducer-2 (AI-2). Evidence indicates that AI-2 can alter bacterial phenotypes, when present in saliva at concentrations as low as the nanomolar range. It is the aim of this review to describe each of these inter-species phenomena, with case-examples, and extrapolate singular and combined roles in the spatio-temporal development of dental plaque. The potential for these phenomena to create shifts in community species composition have implications for the development of polymicrobial diseases.

Further reading: Oral Microbial Ecology: Current Research and New Perspectives

from Zhanshan (Sam) Ma, Jiawei Geng, Zaid Abdo and Larry J. Forney writing in Microbial Ecological Theory: Current Perspectives:

Microbial community dynamics is one of the most important central themes of microbial community ecology, which seems to be experiencing its first golden era thanks to the rapidly expanding datasets derived using metagenomic and other "omics" methods in microbial biology. For example, much of the ongoing NIH-HMP (Human Microbiome Project) focus has been centered on the dynamics of human microbiome communities. Microbial ecologists are beginning to actively draw upon ecological theories from macro ecology to study microbial communities. In this article, we present a brief review on several selected topics of ecological theories that are most relevant to community dynamics, including the diversity-stability paradigm, intermediate disturbance hypothesis (IDH), species area/time curves (SAT), species abundance distribution (SAD), and neutral community theory. In perspective, we suggest that the study of microbial community dynamics can not only benefit from applying ecological theories originally developed in macro ecology, but also contribute to the development and testing of new ecological theories. These bidirectional interactions are of critical importance to the flourishing of theoretical microbial ecology, and studies of microbial community dynamics offers tremendous opportunities for these intellectual exchanges to occur.

Further reading: Microbial Ecological Theory: Current Perspectives

from Diego Fontaneto and Joaquín Hortal writing in Microbial Ecological Theory: Current Perspectives:

The distribution of microscopic organisms (that is, those smaller than 2 mm) has been historically considered non relevant for biogeography, because of the idea that due to their small size, dispersal abilities, resting stages and quick reproductive rates, the presence of microscopic organisms in any place was not limited by geographical barriers and distances. Recent studies challenge this idea, and provide theoretical and empirical evidence in support of the existence of spatial patterns at different scales, and of biogeographical processes affecting many groups of microscopic organisms. Here we review the current state of the art for microbial biogeography, summarising sources of problems and misconceptions, but also their solutions advancing the general understanding of biogeography, and conclude suggesting new avenues for future research.

Further reading: Microbial Ecological Theory: Current Perspectives

from Penny R Hirsch and Tim H. Mauchline writing in Microbial Ecological Theory: Current Perspectives:

Mutualism is responsible for the genesis of green plants and is implicated in their colonisation of land. Current knowledge of plant-microorganism symbioses includes a range of associations with different degrees of intimacy and mutual dependence but the mutual benefits are not always clear. Complex signalling is involved when the plant immune system recognises beneficial endosymbionts although many have also evolved mechanisms to evade or moderate plant defence pathways. A wide range of bacteria inhabit intercellular spaces but only a few are true endosymbionts able to penetrate living cells whilst remaining membrane-bound, accessing plant carbon compounds in a manner analogous to biotrophic pathogens. Unlike pathogens, they provide nutrients to the plant in exchange. The best-known examples are rhizobia, bacteria that induce root nodules on leguminous plants and fix atmospheric nitrogen; and arbuscular mycorrhizal fungi that sequester phosphate and organic N from soil and provide it to their plant hosts. Both secrete factors prior to contacting plant cells which appear to prepare the hosts for mutual rather than pathogenic interactions and suppress the defence mechanisms. The processes involved in these symbioses are compared to less intimate interactions and the nature of mutualism is discussed.

Further reading: Microbial Ecological Theory: Current Perspectives

from Anna Oliver, Andrew K. Lilley and Christopher J. van der Gast writing in Microbial Ecological Theory: Current Perspectives:

The identification of spatial patterns and their relationships to ecological events is an important specialization within ecology which is now branching into the microbial world. In spatial ecology, the detection of patterns at a given spatial scale can be used to explain ecological mechanisms and processes. Furthermore, through the application of spatial statistical analyses, factors leading to ecological events can be determined and verified. One of the most commonly studied aspects of spatial ecology, recently applied in microbial ecology, is the species‰ÛÒarea relationship (SAR). The temporal analogue of the SAR, the species‰ÛÒtime relationship (STR), on the other hand has received far less attention, even in the science of general ecology. Like SARs, the STRs are influenced by a variety of factors including dispersal, abiotic and biotic interactions, and species-species interactions. The application of these ecological conceptual tools to microbial ecology is a rapidly developing field. This chapter proposes that the STRs are a powerful and appropriate tool for studies of microbial diversity and that they make a contribution to understanding ecological communities. From a fundamental perspective, we focus on how microbial STRs compare with those for animals and plant communities, and how they are improving our understanding of community assembly and dynamics. As we believe a key future importance of studying STRs will be for applied benefit, we also discuss how microbial STRs have been used to distinguish between anthropogenic perturbations and underlying natural dynamics and have provided ecological insights for clinical benefit in bacterial infections.

Further reading: Microbial Ecological Theory: Current Perspectives

from Lesley A. Ogilvie, Andrew D.J. Overall and Brian V. Jones writing in Microbial Ecological Theory: Current Perspectives:

Humans enter into a range of symbioses with resident and transiently colonising microbes, which span a dynamic continuum from antagonistic to mutualistic. These interactions are shaped by a complex set of selective forces, which include both host and microbially-derived selective pressures. Given the significant impact that both resident and pathogenic microbes can have on our health, there is now a move to develop a theoretical framework that may guide studies of human-microbe interactions. This should enable the deeper level of understanding required to model, predict and ultimately control human diseases related to antagonistic or aberrant host-microbe interactions. Here we explore the human‰ÛÒmicrobe coevolutionary continuum in the context of current and emerging theory, and with a focus on the opposite ends of the spectrum: mutualism and antagonism. In doing so we highlight areas in which theory is helping to enhance the understanding of this dynamic continuum and where current theory fails as well as suggesting future avenues of research.

Further reading: Microbial Ecological Theory: Current Perspectives