"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