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

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

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

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

Further reading: Microbial Ecological Theory: Current Perspectives

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

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

Further reading: Microbial Ecological Theory: Current Perspectives

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

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

Further reading: Microbial Ecological Theory: Current Perspectives

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

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

Further reading: Microbial Ecological Theory: Current Perspectives

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

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

Further reading: Microbial Ecological Theory: Current Perspectives

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

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

Further reading: Microbial Ecological Theory: Current Perspectives

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 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 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 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