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

"This book is a valuable source of ideas, facts and references ... I will be recommending that our library buys copies to be accessed by students ranging from enthusiastic first-year undergraduates taking my Genetics course to PhD students researching topics for a dissertation ... the text is clear with good subheadings and is easy to dip into." from Chris Thomas (University of Birmingham, UK) writing in Microbiology Today (2013) read more ...

Horizontal Gene Transfer in Microorganisms Edited by: M. Pilar Francino ISBN: 978-1-908230-10-2 Publisher: Caister Academic Press Publication Date: September 2012 Cover: hardback "a valuable source of ideas, facts and references" (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

"it is very timely that we should have a book dedicated to the subject area ... it provides an in-depth analysis of the state of the union and some vision of where the field is heading ... explore(s) the limits and pitfalls of modern metagenomics ... covers a wide range of areas in which metagenomics has made an impact and provides the reader with sufficient scope to see how this approach can be used. It should show any reader that the method is highly applicable to any complex microbial community for which it is either not possible or practical to access the different organisms and isolate them for further analysis." from Julian R Marchesi (Cardiff University, UK) writing in Future Microbiology (2012) 7(7): 813-814. read more ...

Metagenomics: Current Innovations and Future Trends Edited by: Diana Marco ISBN: 978-1-904455-87-5 Publisher: Caister Academic Press Publication Date: September 2011 Cover: hardback "an in-depth analysis" (Future Micro.)

from M. Pilar Francino writing in Horizontal Gene Transfer in Microorganisms:

As genome sequences have accumulated for closely related bacteria, our view of bacterial genomes has radically changed. Genome comparisons have demonstrated that little 16S sequence divergence can be accompanied by large differences in total gene repertoire, and even populations of a single 16S rRNA species are made up of vast numbers of genomic varieties. Much of the observed variation among closely related genomes is attributable to gains and losses of genes that are acquired horizontally, in addition to genomic rearrangements, including gene duplications. The genomic flexibility that results from these mechanisms certainly contributes to the ability of bacteria to survive and adapt in varying environmental challenges. However, the duplicability and transferability of individual genes imply that natural selection should operate, not only at the organismal level, but also at the level of the gene. Therefore, it can be argued that genes are semiautonomous entities capable of responding to natural selection at different levels: selfishly, because they can "reproduce" by duplication and "migrate" by Horizontal Gene Transfer (HGT), and cooperatively, because their long-term survival depends on their ability to be replicated as parts of integrated, emerging genomes. The extent of gene autonomy, or the tightness of the association between gene and genome, can greatly vary, mostly depending on the relative strengths of the selective processes acting at each of these two different, but directly related, levels of organization.

Further reading: Horizontal Gene Transfer in Microorganisms

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 Florent Lassalle and Vincent Daubin writing in Horizontal Gene Transfer in Microorganisms:

Since the discovery of the two ancient "kingdoms" of Bacteria and Archaea, molecular biologists have been constantly revising their perception of the abundance and variety of microbial life, and the processes driving their evolution. In the last years, genome sequences from closely related species and strains of the same species have revealed a yet unforeseen diversity of gene repertoires, much larger than could have been predicted by their morphologies or biochemical capabilities. The origins and the functional significance of these differences still need to be understood, and the techniques to address these questions have yet by large to be invented. In this review, we will present a review of the current knowledge on the mechanisms responsible for the diversity of gene repertoires in prokaryotes.

Further reading: Horizontal Gene Transfer in Microorganisms

"This book edited by Diana Marco highlights the current state of the art of metagenomics and introduces the reader to recent advances in this field. More than twenty international experts have contributed chapters covering a very broad range of topics. The topics addressed extend from theoretical questions (such as the concepts of metagenomics, its integration with other approaches in life sciences or sequence data management) to metagenomic studies of various habitats (e.g. the human microbiome, plant-microbe interactions) and chapters with a strongly applied focus (e.g. bioremediation, biotechnology) to philosophical questions raised through the results of metagenome research. Generally, the mixture of theory/background and practice/applications is well balanced. Lucid descriptions of methodical approaches and technical details are given. Accounts of specific limitations and problems related to metagenomics in a certain area are simultaneously provided with a wealth of references for further reading ... the book can be highly recommended to advanced students or anyone starting research in this field. " from Kathleen Schleinitz (Helmholtz Centre for Environmental Research, Leipzig, Germany) writing in Biotechnol. J. (2011) 6: 124-125. read more ...

Metagenomics: Theory, Methods and Applications Edited by: Diana Marco ISBN: 978-1-904455-54-7 Publisher: Caister Academic Press Publication Date: January 2010 Cover: hardback "highly recommended" (Biotechnol. J.)

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 Fernando González-Candelas and M. Pilar Francino writing in Horizontal Gene Transfer in Microorganisms:

The existence of numerous types of barriers to Horizontal Gene Transfer (HGT) is well documented. Nevertheless, no barrier is impervious, and all kinds of genes can occasionally find their way into organisms different from the ones in which they evolved. This by no means implies a free flow of genes across taxa, but, rather, the existence of complex networks of loopholes across barriers that could potentially connect all kinds of organisms through gene transfer. Loopholes may be provided by way of a small fraction of the individuals in an otherwise inaccessible population and, if exogenous genes are incorporated into the chromosome, homology-assisted recombination processes may further spread them across wild type individuals. HGT networks should be very fluid, as they depend heavily on fortuitous events and transient circumstances, such as the presence of Mobile Genetic Elements (MGEs) in a potential donor that may extend the transfer network in particular directions. Moreover, HGT networks should be highly evolvable, as a result of 1) the multiplicity of processes with the potential to modulate, modify or alleviate the different barriers to transfer, 2) the constantly changing selective pressures operating on them and 3) the enormous plasticity of MGEs. Finally, HGT networks should be gene-specific, as different genes should have an unequal likelihood of passing through or being incorporated into new genomes.

Further reading: Horizontal Gene Transfer in Microorganisms

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 Miriam Barlow, Jared Caywood, Serena Lai, Joshua Finley and Chad Swanlund writing in Horizontal Gene Transfer in Microorganisms:

Recombination is a mechanism that leads to variation in antibiotic resistance genes. We review its importance in the recently emerged nosocomial pathogen Acinetobacter baumannii, where Horizontal Gene Transfer (HGT) and recombination are major sources of variation for resistance phenotypes. We also present our results focusing on the plasmid borne genes of bla_CTX-M, ampC and qac. These results show that random point mutations are not the only major source of variants among the plasmid borne genes, but that homologous recombination is a major contributor of gene variants that can likewise add and remove resistance phenotypes from bacterial populations. Further studies of HGT and recombination are therefore important to determine how their effects can be manipulated to control the occurrence of resistance.

Further reading: Horizontal Gene Transfer in Microorganisms

from Eva C. Berglund and A. Carolin Frank writing in Horizontal Gene Transfer in Microorganisms:

Understanding the origin, evolution, maintenance, and breakdown of host-adaptation is central to diverse areas such as human health and agriculture. Horizontal gene transfer (HGT) is a recurrent theme in the evolution of host-adaptability systems. Why are these genes often successfully transferred and what is the consequence for the recipient genome? Drawing examples from the mammal-adapted bacterium Bartonella, and from plant-adapted rhizobia, we discuss the role of horizontal gene transfer in the evolution and ecology of host-adaptation.

Further reading: Horizontal Gene Transfer in Microorganisms

from Peter Mullany and Adam P. Roberts writing in Horizontal Gene Transfer in Microorganisms:

Mobile genetic elements are discrete segments of nucleic acid that can translocate from one part of the genome to another, and in the case of conjugative elements between genomes in different cells. The vast majority of our knowledge of mobile genetic elements is derived from experimentation on cultivable bacteria and is therefore incomplete. In this chapter we will discuss the methods available for identifying and isolating these elements from metagenomic samples.

Further reading: Horizontal Gene Transfer in Microorganisms

from Iñaki Comas and Fernando González-Candelas writing in Horizontal Gene Transfer in Microorganisms:

Horizontal gene transfer is a pervasive evolutionary process which has developed and is still developing an essential role in shaping biodiversity through providing opportunities for innovation, moving determinants of functions among taxa, opening opportunities for colonization of new niches, or acting as a catalyst for adaptation. However, its importance in evolution has only recently begun to be recognized. Reasons for this relatively late recognition of HGT and its relevance stem from two main sources. One is the availability, or rather the lack thereof, of appropriate information to infer the existence of HGT. This shortcoming has now been widely overcome with the large, and still growing at a very fast rate, number of completely sequenced genomes, which allow for precise phylogenetic reconstructions, along with the deployment of theoretical models necessary for inferring evolutionary events in deep-time. The second source is the appreciation that HGT does not leave an indelible stamp on the transferred genes because these continue evolving under a different genomic, and often ecological, environment which usually act synergistically to erase the initially clear marks that go along with those genes. In this chapter we provide an overview of these processes along with a model proposal that will help to better understand the consequences of the continuous evolution of laterally transferred genes at different evolutionary time-scales.

Further reading: Horizontal Gene Transfer in Microorganisms

from Rustam I. Aminov writing in Horizontal Gene Transfer in Microorganisms:

The importance of horizontal gene transfer (HGT) in bacterial evolution is evident from the retrospective analyses of bacterial genomes, which suggest that a substantial part of bacterial genomes is of foreign origin. Another line of evidence that supports the possibility of rapid adaptation of bacteria through lateral gene exchange is the history of antibiotic use by humans. Within a very brief period of the "antibiotic era" many bacterial pathogens were able to acquire the mechanisms allowing them to withstand the selective pressure of antibiotics. And finally, the field and microcosm studies allowed monitoring HGT events in situ. In this chapter, a brief overview of the milestones of mobile genetic elements (MGEs) research is given, followed by discussion of the conceptual framework development. Then the occurrence and diversity of MGEs as well as the frequencies of HGT in terrestrial, aquatic, intestinal and biofilm communities are described. The role of environmental factors that may affect MGE-mediated HGT in these ecosystems is also discussed.

Further reading: Horizontal Gene Transfer in Microorganisms

"the book comprises 11 papers addressing different applications of biofilm research ... each paper provides a useful update/review of a given area - I particularly like the interactions described in the quorum sensing paper." from Joanna Verran, Manchester Metropolitan University, UK writing in Microbiology Today (2012) read more ...

Microbial Biofilms: Current Research and Applications Edited by: Gavin Lear and Gillian D. Lewis ISBN: 978-1-904455-96-7 Publisher: Caister Academic Press Publication Date: February 2012 Cover: hardback "a useful update" Micro. Today

from Francisco Dionisio, Teresa Nogueira, Luís M. Carvalho, Helena Mendes-Soares, Sílvia C. M. Mendonça, Iolanda Domingues, Bernardino Moreira and Ana M. Reis writing in Horizontal Gene Transfer in Microorganisms:

The ubiquity of plasmids in nature contrasts with our ability to understand their maintenance. Despite the ability of plasmids to transfer across different bacterial taxonomic groups and to carry useful genes to bacterial cells, it is unclear which factors are responsible for plasmid maintenance among bacterial populations. In this review, we present several hypotheses aiming at explaining plasmid existence: efficiency of self-transfer, advantageous genes, transitory derepression of conjugative pili synthesis, compensatory mutations, the existence of amplifier strains, positive epistasis between chromosomal mutations and plasmids, selective sweeps, frequent cross-species transfer, as well as three types of social interactions (exploitation avoidance in the production of public goods, pathogen- or parasite-mediated harmful behavior, biofilm formation). These hypotheses imply that plasmids and their hosts are adaptable to variable conditions and even that plasmids can be irreplaceable under particular circumstances.

Further reading: Horizontal Gene Transfer in Microorganisms

from Liping Zhao and Jian Shen writing in Metagenomics: Current Innovations and Future Trends:

A devastating epidemic of chronic diseases is threatening the public health worldwide. Preventive healthcare systems require novel types of health assessment technologies which focus on the early warning biomarkers before the clinical onset of chronic diseases. In light of the systems theory, emergent functions of the human body should be measured for health evaluation. Humans are superorganisms harbouring two integrated genomes, the human genome and the microbiome which is the collective genomes of all symbiotic microorganisms, particularly those inhabiting the gut. The gut microbiota and the host interact intimately. The structure and functions of the gut microbiota, together with the host metabolism as reflected in urine metabolite profiles, are the emergent functions of the human body. Metagenomics and metabonomics can be used to monitor the dynamics of gut microbiota and host metabolism. Large scale cohort studies in which urine and faecal samples are analyzed by the whole body systems approaches may lead to the discovery of patterns of gut microbiota and host metabotypes which can in turn be used as a biomarker for diagnosis or target for developing new therapeutics for chronic diseases. The application of these systems approaches in traditional Chinese medicine and nutritional studies may lead to a significant paradigm shift in modern medicine and nutritional sciences.

Further reading: Metagenomics: Current Innovations and Future Trends

from Anna M. Romaní, Joan Artigas and Irene Ylla writing in Microbial Biofilms: Current Research and Applications:

Biofilms in aquatic ecosystems colonize various compartments (sand, rocks, leaves) and play a key role in the uptake of inorganic and organic nutrients. Due to their extracellular enzyme capabilities, biofilm microorganisms are able to use organic matter from the surrounding water and increasing activities are related to the availability of biodegradable organic carbon. The most common extracellular enzymes analysed are those involved in the decomposition of polysaccharides, peptides and organic phosphorus compounds, and changes in enzyme expression have been related to the use of different sources of organic matter available in the ecosystem (i.e., during drought-storm and/or pollution episodes). Enzymes important for microbial acquisition of nitrogen and phosphorus also respond to nutrient content and/or imbalances in the flowing water. Additionally, biofilm extracellular enzyme activities are modified by the internal recycling of organic matter and microbial interactions (competition/synergism) within the biofilm, such as algal-bacterial and fungal-bacterial interactions. Although an extensive knowledge of the biofilm structure is required for the interpretation of extracellular enzyme activities in aquatic biofilms, they give a very useful, integrative measure of the biofilm community function in relation to organic matter use and cycling.

Further reading: Microbial Biofilms: Current Research and Applications

"Highly recommended is the chapter on interactions between plants and biofilms" from Hans-Curt Flemming (Duisburg, Germany) writing in Biospektrum (2012) 18: 109. read more ...

Microbial Biofilms: Current Research and Applications Edited by: Gavin Lear and Gillian D. Lewis ISBN: 978-1-904455-96-7 Publisher: Caister Academic Press Publication Date: February 2012 Cover: hardback "Highly recommended" (Biospektrum)

from Koichi Nishio, Atsushi Kouzuma, Souichiro Kato and Kazuya Watanabe writing in Microbial Biofilms: Current Research and Applications:

Microbial fuel cells (MFCs) are devices that exploit microbial catabolic activities to generate electricity from a variety of starting materials, including complex organic waste and renewable biomass. The use of these energy sources provides MFCs with a great advantage over chemical fuel cells that utilize only purified reactive fuels (e.g., hydrogen). In an MFC bioreactor, microbes that respire using an anode with organics as electron donors grow preferentially, resulting in accelerated and increased current generation with time. The placement of an anode in either soil or sediment represents a simplified MFC system, known as a sediment MFC, which generates current as soil microbes utilize the anode as an electron acceptor. In addition, the irradiation of an MFC system results in the proliferation of photosynthetic microbes together with anode-respiring microbes, resulting in the syntrophic conversion of light energy into electricity. These examples demonstrate that the MFC system is based on a variety of fundamental and sustainable bioenergy processes, and we suggest that a deeper understanding of how microbes transfer electrons to anodes is essential for further developments of MFC systems.

Further reading: Microbial Biofilms: Current Research and Applications

from Roger S. Lasken, Mary-Jane Lombardo, Mark Novotny, Joyclyn Yee-Greenbaum and Rashel V. Grindberg writing in Metagenomics: Current Innovations and Future Trends:

Development of a method to sequence DNA from a single cell has enabled new strategies to investigate the microbial world. Only a few years ago, sequencing from one cell was not feasible. A bacterium only contains a few femtograms of DNA which is insufficient for current sequencing technologies. This limitation was overcome with the development of a method to amplify DNA called multiple displacement amplification (MDA) which can generate micrograms of genomic sequence from one cell. Improvements have also been made in our ability to isolate cells by flow cytometry, micromanipulation and microfluidics and to lyse the cells to release the single genome copy as a template for MDA. Large portions of the genome can be obtained from each cell and this has opened up a new front in the effort to sequence uncultivated species. Cells can be isolated from an environment or clinical specimen and directly sequenced with no need to develop culture methods. This chapter will review the current methodologies, the strengths and limitations of the single cell approach and its application to microbial genomics.

Further reading: Metagenomics: Current Innovations and Future Trends

from Steve Flint and Gideon Wolfaardt writing in Microbial Biofilms: Current Research and Applications:

Biofilms can directly or indirectly be attributed to deterioration of the underlying substratum. Corrosion may result, particularly if the surface comprises metal or metal alloy. This phenomenon, referred to as microbially influenced corrosion (MIC) affects many industries from food manufacture to medicine. The economic impact of corrosion is significant due to the need for replacing corroded equipment, repairs and attempts to prevent corrosion. MIC is believed to be responsible for one third of all metallic corrosion. Although there have been many studies into the mechanisms of MIC, the process is relatively poorly understood. Most information relates to pure cultures, however biofilms are rarely composed of single species thus most models are a simplification of the real process. It is likely the MIC depends on the composition of the biofilm and the environment surrounding the biofilm. Prevention and control methods rely on mechanical cleaning of fouling and chemical removal and killing of biofilms. Future control measures are likely to focus on preventing biofilm formation.

Further reading: Microbial Biofilms: Current Research and Applications

from Rainer Gross, Andreas Schmid and Katja Buehler writing in Microbial Biofilms: Current Research and Applications:

Biofilms are mainly known for causing problems in medical and industrial settings due to their persistence towards treatment with bactericides, including antibiotics. However, in the area of bioremediation they are widely recognized for their ability to degrade hazardous or organic compounds to CO₂ and biomass. Biofilms represent a highly interesting biological concept since they unite important characteristics such as the ability of self-immobilization and increased robustness to various physical, chemical and biological stressors, which make them exceedingly attractive for productive catalysis. The following review provides a detailed survey of biofilm applications for productive biocatalysis on lab-, pilot-, and industrial scales, regarding fermentation as well as biotransformation reactions. It discusses technological as well as biological challenges of biofilm driven catalysis, presenting developments in the field of biofilm reactor technology and the latest findings in understanding biofilm dynamics. Biocatalysis related issues like genetic stability, evolution, uncontrolled growth as well as detachment, contamination risks, monitoring of biomass, EPS, chemical and biological heterogeneity are considered.

Further reading: Microbial Biofilms: Current Research and Applications

from Gabriele Pastorella, Giulio Gazzola, Seratna Guadarrama and Enrico Marsili writing in Microbial Biofilms: Current Research and Applications:

Bioremediation uses microorganisms to remove, detoxify, or immobilize pollutants, and does not require addition of harmful chemicals. Bioremediation is particularly suitable for large areas where contaminant concentrations are relatively low and the hydrology of the soil does not support an aggressive chemical remediation strategy. In the last few years, researchers have described the mechanisms of bioremediation for numerous priority pollutants, including chlorinated hydrocarbons, polyaromatic hydrocarbons, and heavy metals. However, most studies published to date have dealt with planktonic cultures grown under controlled laboratory conditions. Microorganisms in the environment occur mostly as biofilms, whose development is encouraged by the presence of solid surfaces and the limited amounts of organic carbon. Therefore, optimization of bioremediation processes in the field requires a thorough knowledge of biofilm structure, dynamic, and interaction with pollutants and other environmental factors. In this chapter, we describe the recent advances in bioremediation, with particular regard to the role of microbial biofilms. We discuss emerging technologies, such as bioelectroremediation and microbially produced surfactants. We also show how genetic engineering technologies may be employed to improve bioremediation effectiveness, both in laboratory and in field applications.

Further reading: Microbial Biofilms: Current Research and Applications

from G.A. Clark Ehlers and Susan J. Turner writing in Microbial Biofilms: Current Research and Applications:

Biofilms occur frequently inside various engineered systems for wastewater treatment. These include traditional trickling filter systems, modified lagoons, and specialized supplementary systems for nutrient removal or treatment of specialized wastes. The major advantages of biofilm systems over suspension treatment is the high microbial density that can be achieved, leading to smaller treatment system footprints, and the inherent development of aerobic, anoxic and anaerobic zones which enable simultaneous biological nutrient removal. The intrinsic resistance of biofilm communities to changing environmental conditions creates the added advantage that biofilm-based treatment systems are more resilient to influent variation in toxicity and nutrient concentrations. In contrast to biofilms of environmental or biomedical relevance comparatively little is known about development and stability in waste treatment systems. The advent of tools that enable the study of biofilms in reactor systems on a molecular level has enabled greater insight into the physiologically and biochemically relevant pathways that may facilitate optimized processes. In this chapter, the current literature on biofilms in wastewater treatment systems is reviewed and opportunities for further development in this field are identified.

Further reading: Microbial Biofilms: Current Research and Applications

from Gavin Lear, Andrew Dopheide, Pierre-Yves Ancion, Kelly Roberts, Vidya Washington, Jo Smith and Gillian D. Lewis writing in Microbial Biofilms: Current Research and Applications:

This chapter reviews our current understanding of the roles biofilm-associated microbial communities play in both maintaining and improving the ecological health of freshwater rivers and streams. Biofilms are where most of the bacteria present in freshwater systems are found, and have been identified as major sites for primary production, carbon and nutrient cycling. Advances in various scientific methodologies have recently been used to characterise the enormous diversity of biofilms, in terms of their structural, chemical and biological traits. The microbial life present within most natural biofilms, as well as associated exudates and lysates have been identified as a valuable, nutrient rich food source for a variety of benthic consumers. Furthermore, the diverse metabolic potential of these complex communities, in combination with various protective traits offered by the biofilm 'mode-of-life', provide biofilms with an excellent ability to degrade, or otherwise transform a vast array of freshwater pollutants. Despite this apparent resilience, we highlight the sensitivity of these poorly studied freshwater biofilm communities to various human activities, and consider their potential as a reliable and sensitive biological indicator of freshwater ecological health.

Further reading: Microbial Biofilms: Current Research and Applications

from James D. Bryers writing in Microbial Biofilms: Current Research and Applications:

Clinically related research on biofilms has expanded exponentially in the past ten years due to the pandemic of nosocomial (hospital-related) infections. Biofilms are thought to cause a significant amount of all human microbial infections, according to the Centers for Disease Control and Prevention. Nosocomial infections are the fifth leading cause of death in the U.S. with more than two million cases annually (or approximately 10% of American hospital patients). The difficulty of eradicating biofilm bacteria with classic systemic antibiotic treatments is a prime concern of medicine. Biofilm bacteria can be up to a thousand times less susceptible to antimicrobial stress than their freely suspended counterparts. This chapter discusses the pathogenesis of a number of biofilm-mediated infections, including: oral infections, biomedical device based infections, osteomyelitis, otitis media, and others. Emerging research in biofilm control and prevention is also reviewed.

Further reading: Microbial Biofilms: Current Research and Applications

from Mette Burmølle, Annelise Kjøller and Søren J. Sørensen writing in Microbial Biofilms: Current Research and Applications:

Biofilms in soil are composed of multiple species microbial consortia attached to soil particles and biotic surfaces including roots, fungal hyphae and decomposing organic material. The bacteria present in these biofilms gain several advantages including protection from predation, desiccation and exposure to antibacterial substances, and optimized acquisition of nutrients released in the mycosphere. Studies of soil biofilms are complicated by the composite structure of the soil environment; therefore, various simplified model systems have been applied to study succession and bacterial interactions in soil biofilms. Model system observations indicate an increased efficiency to degrade and decompose organic material and xenobiotic compounds by these multispecies bacterial communities. Consequently, soil biofilms may be valuable tools for bioremediation and biocontrol. However, soil biofilms may also provide survival sites for opportunistic pathogenic bacteria, providing enhanced protection and increasing their potential to survive and evolve in the soil environment. In this review, we provide evidence that biofilms are of major importance for the fitness of individual bacteria and the wider soil ecology, due to the accumulated selective advantage provided to bacteria by the biofilm mode-of-life.

Further reading: Microbial Biofilms: Current Research and Applications

from Joy D. Van Nostrand, Zhili He and Jizhong Zhou writing in Metagenomics: Current Innovations and Future Trends:

The use of microarrays has revolutionized the field of microbiology. While many types of microarrays are available, the functional gene arrays (FGAs) afford a way to link environmental processes with microbial communities. FGAs probe for a wide range of genes involved in functional activities of interest to microbial ecology (e.g. carbon degradation, N₂-fixation, metal resistance) from many different microorganisms, cultured and uncultured. The most comprehensive FGA reported to date are the GeoChip arrays. GeoChip 3.0 targets tens of thousands of genes involved in the geochemical cycling of carbon, nitrogen, phosphorus, and sulphur, metal resistance and reduction, energy processing, antibiotic resistance and contaminant degradation as well as phylogenetic information (gyrB). This technology has been used successfully to examine the effects of global climate change on microbial communities. This chapter provides an overview of FGA development with a focus on the GeoChip. Several GeoChip studies, which have established the GeoChip's worth as a rapid, sensitive and specific tool for the examination of microbial communities, will be highlighted.

Further reading: Metagenomics: Current Innovations and Future Trends

from Tracy L. Meiring, Rolene Bauer, Ilana Scheepers, Colin Ohlhoff, Marla I. Tuffin and Donald A. Cowan writing in Metagenomics: Current Innovations and Future Trends:

Metagenomics is the cultivation independent analysis of the collective genomes of microbes within a given environment, using sequence- and function-based approaches. Early metagenomic studies, aimed at cataloguing the phylogenetic diversity of different habitats, revealed the vast size and richness of the microbial and viral realms. Access to previously unexplored volumes of sequence space from uncultured organisms has since opened up many new avenues of research, with the number of projects and potential applications ever expanding. The rapid growth of the research area is furthermore a direct reflection of the advances in the throughput, as well as the reduction in cost, of sequencing and screening technologies. In this chapter we present a comprehensive introduction to the current methodologies, applications and challenges of metagenomics. We review the major improvements in the technologies that form the metagenomic toolkit, as well as the limitations they currently place on research. We assess the achievements made thus far in the exploration of novel sequence space. Finally, we consider future research trends in light of recent novel metagenomic approaches and the incorporation of complementary technologies.

Further reading: Metagenomics: Current Innovations and Future Trends

from Varun Shah, Kunal Jain, Chirayu Desai and Datta Madamwar writing in Metagenomics: Current Innovations and Future Trends:

Implementation of efficacious bioremediation strategies relies heavily on intrinsic microbial community dynamics, structure and function. Any one particular microorganism is incapable of processing all the metabolic reactions to degrade environmental pollutants, however a group of diverse organisms form a community and collectively process all the metabolic reactions for bioremediation. Therefore, metagenomics based analyses of entire microbial community genomes becomes imperative to delineate the metabolic pathways responsible for biodegradation. The essential genes for bioremediation may be present, however to ascertain how many of them are involved in bioremediation we need high throughput metatranscriptomics and metaproteomics, transcriptome and proteome analyses of entire community respectively. Metametabolomics, analyses of the entire repertoire of microbial community metabolites and fluxomics, real time flux analysis of molecules/metabolites over a time period provide the missing links about regulation of metabolism of anthropogenic/xenobiotic compounds. Interactive studies between metagenomics, metatranscriptomics, metaproteomics and metametabolomics have become a trend in microbial bioremediation. In this chapter, we discuss the potential of recent innovative breakthroughs in molecular and '-omics' technologies such as molecular profiling, ultrafast pyro-sequencing, microarrays, mass spectrometry and other novel techniques and applications along with bioinformatics tools to gain insights of indigenous microbial communities and their mechanism in bioremediation of environmental pollutants.

Further reading: Metagenomics: Current Innovations and Future Trends

from Valeria Bianciotto, Erica Lumini, Alberto Orgiazzi, Roberto Borriello and Paola Bonfante writing in Metagenomics: Current Innovations and Future Trends:

Metagenomics studies have recently offered new approaches that shed light on microbial communities in a variety of environments. In this context, DNA pyrosequencing is being used more and more to investigate prokaryotic assemblages in soil environment. Fungi, which are crucial components of soil microbial communities, functioning as decomposers, pathogens and mycorrhizal symbionts, have instead been largely neglected. However, the last year has been characterized by an explosion of metagenomic studies applied to fungal communities, based on the pyrosequencing technology. The aim of this chapter is to focus on Arbuscular Mycorrhizal Fungi (AMF), the most widespread symbionts in many ecosystems, and to demonstrate how metagenomics may help us to understand the composition and dynamics of AMF communities. At the moment, only two studies have investigated AMF biodiversity using the pyrosequencing approach and SSU rDNA as the target gene. Although both studies targeted the same group of fungi, they focused on different habitats. Compared to similar studies, carried out using a cloning-sequencing approach or DNA barcoding, the main outcome that emerged from pyrosequencing analyses applied to AMF and to other fungal communities is the unexpected fungal biodiversity observed in the analyzed environments. Interestingly, the pyrosequencing approach applied to isolated spores of AMF has demonstrated that they are a niche for highly polymorphic endobacterial communities. The data confirm the powerfulness of the pyrosequencing approach, which represents a promising new tool to better understand the natural distribution of an essential group of soil microorganisms, such as fungi. The large number of reads that have been obtained increases the likelihood of capturing sequences from rare organisms, which would instead remain undetected with the cloning- sequencing approach.

Further reading: Metagenomics: Current Innovations and Future Trends

from Vincent Montoya, Eunice C. Chen, Charles Y. Chiu and Patrick Tang writing in Metagenomics: Current Innovations and Future Trends:

Viruses are the most abundant and genetically diverse biological entities on Earth and the vast majority is yet to be discovered. Therefore, systematic surveillance for viruses requires techniques that have both broad specificity and high sensitivity. Conventional laboratory techniques in virology often fail to detect a specific etiology in many syndromes that are thought be caused by viruses. Metagenomics-based tools such as pan-viral microarrays and ultra-high-throughput sequencing have significantly improved our ability to detect and characterize divergent as well as novel viruses. Some of these methods rely on the fact that any one virus will possess some degree of conservation within its genomic sequence with other members of the same family. Thus, nucleic acid amplification tests targeting conserved regions in the viral families associated with a particular disease can often lead to a successful diagnosis. However, metagenomics-based techniques such as pan-viral microarrays are able to transcend our predetermined lists of viruses associated with each syndrome and allow for the simultaneous interrogation of thousands of conserved and specific genetic regions within all taxa of known virus families. Second generation high-throughput sequencing offers the unique opportunity to discover novel pathogens with no a priori sequence information with sensitivities comparable to that of PCR. As the costs for these techniques continue to decrease and the technology becomes more widely available, they will have the potential to revolutionize our approach to detecting viruses and diagnosing viral diseases.

Further reading: Metagenomics: Current Innovations and Future Trends

from John Walshaw, Graham J. Etherington and Dan MacLean writing in Metagenomics: Current Innovations and Future Trends:

Next-generation sequencing approaches enable us to gather many more times sequence data than was possible a few years ago. Next-generation sequencers from the main vendors, Illumina, 454 and ABI SOLiD are distinct and varied technologies with unique approaches to sequencing that produce sequence reads with different strengths and weaknesses. We describe these technologies in detail and also discuss the applicability of the co-evolving new approaches for manipulation of reads and assembly and alignment of the high volume of reads that have also been developed to tackle the particular challenges of the shorter read format. By using next-generation sequence data in metagenomics experiments a wide range of new analyses are possible and we discuss the scope, goals, utility and practicality of these in modern laboratories including analysing environmental communities with partial assembly, clustering of taxonomically related reads to identify community structure, phylogenetic classification of unclustered reads and functional analyses that rely on identification of specific pathways or gene family members in samples. Metagenomic study has an increasingly powerful partner in the next-generation sequence technology and this partnership is likely to get more productive as software and hardware mature.

Further reading: Metagenomics: Current Innovations and Future Trends

from Robert J. Goldstone, Roman Popat, Matthew P. Fletcher, Shanika A. Crusz and Stephen P. Diggle writing in Microbial Biofilms: Current Research and Applications:

It is now well recognised that populations of bacteria from many Gram-positive and Gram-negative species cooperate and communicate to perform diverse social behaviours including swarming, toxin production and biofilm formation. Communication between bacterial cells involves the production and detection of diffusible signal molecules and has become commonly known as quorum sensing (QS). In addition, an evolutionary perspective on QS illuminates important phenomena which help in understanding the prevalence and diversity of QS phenotypes and strategies under various conditions. The research fields of QS and biofilm formation often overlap with a number of studies demonstrating that QS is an important regulatory mechanism of biofilm formation in a variety of bacterial species. However in contrast, there are conflicting reports, demonstrating that QS appears to play a minimal role in the development of biofilms. Our aim in this review is to highlight the key findings with respect to QS and the subsequent impact on biofilm formation. We also discuss QS and cooperation in the context of social evolution and how this may impact on the development and maintenance of microbial biofilms.

Further reading: Microbial Biofilms: Current Research and Applications

from Venkatachalam Lakshmanan, Amutha Sampath Kumar and Harsh P. Bais writing in Microbial Biofilms: Current Research and Applications:

Microorganisms have historically been studied as planktonic or free-swimming cells, but most exist as sessile communities attached to surfaces, in multicellular assemblies known as biofilms. In the process of coping with both the pathogenic and beneficial interactions, the rhizosphere of plant roots encourages formation of sessile communities that begins with the attachment of free-floating microorganisms to a surface. Certain bacteria such as plant growth promoting rhizobacteria not only induce plant growth but also protect plants from soil-borne pathogens in a process known as biocontrol. Contrastingly, other rhizobacteria in a biofilm matrix may cause pathogenesis in plants. Although research suggests that biofilm formation on plants is associated with biological control and pathogenic response, little is known about how plants regulate this association. The scope of this chapter is restricted to biofilm-forming bacteria and their interactions with terrestrial plants, specifically emphasizing recent work. After an overview of documented interactions between bacteria and plant tissues, we examine some of the more prominent mechanisms of biofilm formation on and around plant surfaces.

Further reading: Microbial Biofilms: Current Research and Applications

from Robert L. Dorit and Margaret A. Riley writing in Metagenomics: Current Innovations and Future Trends:

The importance of horizontal gene transfer (HGT) in bacterial evolution has led many bacteriologists to question the very existence of bacterial species. If gene transfer is as rampant as comparative genomic and metagenomic studies suggest, how could bacterial species survive such genomic fluidity? Indeed, some go so far as to propose the metagenome as the appropriate unit of evolutionary distinction. The coherence and continuity of the metagenome remains, for us, an open question. Whatever the ultimate fate of metagenome-based phylogenetic reconstructions, we contend that genetic information in the bacterial world still comes in discrete, discernible and discontinuous packages that retain their integrity over evolutionary time. Despite the many fascinating instances of horizontal gene transfer that have been documented, the genetic coherence of bacterial species has not devolved into a continuous smear of promiscuously shared genetic information. The distinctions that we see and name in the microbial world are not arbitrary slicings of a continuous distribution, but natural breakpoints and boundaries that reflect the operation of time, history and selection on bacterial populations.

Further reading: Metagenomics: Current Innovations and Future Trends

from Jing Chen, Shulei Sun, Weizhong Li and John C. Wooley writing in Metagenomics: Current Innovations and Future Trends:

The sustained deluge of complex experimental data in metagenomics opens extraordinary opportunities for this new science, but also requires an advanced, cyberinfrastructure-based knowledge resource that provides a platform for rigorous analysis of the data sets and in turn, of the microbial communities. In response, we established the Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis or CAMERA and recently released a very major extension to this resource, termed CAMERA 2.0. In this chapter, we describe the essential attributes of CAMERA 2.0 and their relationship to expectations of the experimental and computational researchers in metagenomics. An analysis portal provides access to a semantically aware database along with computational infrastructure. Meticulous attention is paid to annotating the sequence data with metadata, the associated contextual information (environmental parameters). Using the standards established by the Genomics Standard Consortium, CAMERA 2.0 enables ready depositing, locating, analyzing, visualizing and sharing data and the use of a range of actual analytical processes or workflows. These workflows, most notably, are user-selected, allowing a flexible approach in which an investigator can set their own requirements for a given sequential analysis. The analytical and computational history is archived, allowing accurate reproducibility, detailed further analysis, and validation.

Further reading: Metagenomics: Current Innovations and Future Trends

from Reia Hosokawa-Okamoto and Kentaro Miyazaki writing in Metagenomics: Current Innovations and Future Trends:

Enzymes are environmentally friendly biocatalysts that are widely used in modern life, e.g., in food processing, laundry detergent, and production of medicinal compounds. An increasing demand to shift focus from petrochemicals to biotechnology-based industries has expanded the use of enzymes. To date, most industrially relevant enzymes are of microbial origin. Therefore, mining for microbial enzymes is key to the development of the biotechnology industry; however, less than 1% of environmental bacteria can be cultured in the laboratory at present. To accelerate the discovery of industrially relevant enzymes, it would therefore be advantageous to employ a metagenomic approach to extend the available microbial sources to presently 'unculturable' taxa. However, such an approach also risks a low hit rate; typically, only a few positives are obtained from the hundreds of thousands of library clones screened. This is largely because of the discrepancy between the host's transcriptional/translational machineries and the genetic signals present in the metagenomes. Escherichia coli has long been used as a generic host for cloning and production purposes and is, in most instances, suitable for this purpose. However, several modifications are necessary to overcome the problems of heterologous gene expression. In this chapter, we discuss several approaches that may be useful for developing the utility of E. coli as a host for efficient functional screening of metagenomic libraries.

Further reading: Metagenomics: Current Innovations and Future Trends

from Denis Faure, Mélanie Tannières, Samuel Mondy and Yves Dessaux writing in Metagenomics: Current Innovations and Future Trends:

Though metagenomics is a novel tool in the field of plant-microbe interaction, the technique has already led to remarkable advances. Among these, the identification of yet-uncultivable phytopathogens or the description of the plant and rhizosphere microflora, are two features that may lead to a better description of the quality of agricultural lands, for instance in the case of disease suppressive soils. At a more molecular level, the identification of novel density-dependent regulatory functions (quorum sensing) and antagonizing elements (quorum quenching) that may be used to develop sustainable, biological control strategies directed at plant pathogen, are examples of valuable outcomes of metagenomics in the plant-microbe interaction field.

Further reading: Metagenomics: Current Innovations and Future Trends

from Ondrej Uhlik, Lucie Musilova, Katerina Demnerova, Tomas Macek and Martina Mackova writing in Metagenomics: Current Innovations and Future Trends:

Until recently, investigating functions of microbial populations was restricted to thorough studying of pure cultures. Molecular biology tools enabled scientists to take a much deeper insight into the phylogenetic as well as metabolic diversity but hardly allowed for linking the phylogenetic identity with the metabolic activity which the microbes disposed of. Stable isotope probing (SIP) was one of the first microbial ecology tools to enable such a linkage. SIP consists of providing the community with a stable isotope labelled substrate and subsequent extraction and analysis of the labelled biomarkers. This text summarizes why SIP is a technique of an outstanding importance for microbial ecology and related fields and further focuses on SIP using DNA as a biomarker since DNA is one of the few molecules that bears both phylogenetic and functional information. Much deeper insight into stable isotope labelled DNA has been allowed especially due to current advances in high-throughput sequencing technologies. Metagenomic analyses, however, profit from stable isotope probing as well by reduced complexity of studied DNA (only populations actively performing a particular process). Therefore, when DNA-SIP is used in metagenomics, it is much easier to reconstruct individual genomes of key uncultured microbes as well as detect genes of interest.

Further reading: Metagenomics: Current Innovations and Future Trends

from Corinne F. Maurice and Peter J. Turnbaugh writing in Metagenomics: Current Innovations and Future Trends:

The human body is home to roughly ten times more microbial cells than human cells, containing a vast array of genes and metabolic activities referred to in aggregate as the human microbiome. Metagenomics has recently enabled an initial map of the microbial diversity found in different body habitats, individuals, and populations. These developments include an extensive catalog of genes and genomes, characterization of the human gut viriome, a description of the patterns of succession of the gut microbiota during development, and links between obesity and the gut microbiome. The application of principles from macro-ecology, in addition to studies of defined communities in model organisms, have begun to reveal the basic operating principles that govern community assembly, stability, and function. These studies are beginning to move beyond simple characterizations of the organisms and genes found in a given habitat at a single timepoint, to a systems biology approach that allows the characterization of this complex microbial community at a variety of spatial and temporal scales. In the foreseeable future, studies of the human microbiome promise to reveal new biomarkers for disease, novel strategies for manipulation, and a more comprehensive view of human physiology.

Further reading: Metagenomics: Current Innovations and Future Trends

from Fernando Santos and Josefa Antón writing in Metagenomics: Current Innovations and Future Trends:

Since the publication of the first genomic analysis of a marine uncultured viral community in 2002, the analysis of the viral metagenomes from a wide variety of natural environments has provided a wealth of information on the diversity, abundance and metabolic capabilities of viruses. Here, we summarize how such studies have shed light into the control than viruses exert on prokaryotic communities. We have focused on three main aspects of this control: (i) what metagenomes tell about the dynamics of virus-host interaction and how the well established 'kill-the-winner' theory fits into new metagenomic data; (ii) which picture the analysis of viral metagenomes provides on the extend of lysogeny in the microbial communities; and (iii) which are the new findings on the role of viruses as gene transfer agents. Finally, we give some hints on the analysis of expression of virome genes ("metavirotranscriptomes") and which are, in our opinion, the likely future trends in the "omics" analysis of viruses in nature.

Further reading: Metagenomics: Current Innovations and Future Trends