Promises and Prospects of Microbiome Studies

Since Anthony van Leeuwenhoek, first microscopic observations of the unseen microbiota and the more recent realization that little of the microbes in the biosphere are known, humans have developed a deep curiosity to fully understand the inner workings of the microbial realm. Our ability to characterize the complexity of microbial communities in their natural habitats has dramatically improved over the past decade thanks to advances in high-throughput methodologies. By eliminating the need to isolate and culture individual species, metagenomics approaches have removed many of the obstacles that hindered research in the ecology of mixed microbial consortia, providing valuable information about the diversity, composition, function, and metabolic capability of the community. Microbes are the unseen majority with the capability to colonize every environment, including our bodies. The establishment and composition of a stable human microbiome is determined by the host genetics, immunocompetence, and life-style choices. Our life-style choices determine our exposure to many external and internal environmental factors that permanently or temporarily can influence our microbiome composition. Figure 1 illustrates some of the life-style-related factors that might influence the microbiota of the skin, mouth, and gut. It is not limited to what we carry, touch, breath, and eat. Other dispersal vectors include secretion, excretions, aerosols, air flow, animals, moving surfaces, water, beverages, food, contact, wind, tools, toiletry, and others. These influence the microbiome membership, who are present, and they have the ability to participate in the microbiome dynamic within an environment. The establishment of a microbial community is dependent on many environmental factors, including pH, temperature, altitude, weather, soil type, nutrient availability, relative humidity, air quality, pollutants, microbial competitors, and others. In other words, we are superorganisms interconnected with other living forms on this Earth

\u3ci\u3eMetagenomics for Microbiology:\u3c/i\u3e Preface

It is well known that only a small fraction of extant microbial life has been identified. Metagenomics, the direct sequencing and characterization of genes and genomes present in complex microbial ecosystems (e.g., metagenomes), has revolutionized the practice of microbiology by bypassing the hurdle of pure culture isolation. Metagenomics shows promise of advancing our understanding of the diversity, function, and evolution of the uncultivated majority. Metagenomics as a field arose in the 1990s after the application of molecular biology techniques to genomic material directly extracted from microbial assemblages present in diverse habitats, including the human body. The application of metagenomic approaches allows for the acquisition of genetic/genomic information from the viruses, bacteria, archaea, fungi, and protists forming complex assemblages. The field of metagenomics addresses the fundamental questions of which microbes are present and what their genes are potentially doing. In the mid-2000s, the availability of high-throughput or next-generation sequencing technologies propelled the field by lowering the monetary and time constraints imposed by traditional DNA sequencing technologies. These advances have allowed the scientific community to examine the microbiome of diverse environments/habitats, follow spatial and temporal changes in community structure, and study the response of the communities to treatment or environmental modifications. In 2012, the publication of the large-scale characterization of the microbiome of healthy adults created high expectations about the influence of the microbiota in human health and disease. With the publication of the results of the Human Microbiome Project, metagenomics has emerged as a major research area in microbiology, particularly, when it comes to the characterization of the role of microbiota in complex disorders, such as obesity. With contributions by leading researchers in the field, we provide a series of chapters describing best practices for the collection and analysis of metagenomic data, as well as the promises and challenges of the field. The chapters have been dedicated to different aspects of metagenomics

Treponema denticola in Disseminating Endodontic Infections

Treponema denticola is a consensus periodontal pathogen that has recently been associated with endodontic pathology. In this study, the effect of mono-infection of the dental pulp with T. denticola and with polymicrobial “red-complex” organisms (RC) (Porphyromonas gingivalis, Tannerella forsythia, and T. denticola) in inducing disseminating infections in wild-type (WT) and severe-combined-immunodeficiency (SCID) mice was analyzed. After 21 days, a high incidence (5/10) of orofacial abscesses was observed in SCID mice mono-infected with T. denticola, whereas abscesses were rare in SCID mice infected with the red-complex organisms or in wildtype mice. Splenomegaly was present in all groups, but only mono-infected SCID mice had weight loss. T. denticola DNA was detected in the spleen, heart, and brain of mono-infected SCID mice and in the spleen from mono-infected wild-type mice, which also had more periapical bone resorption. The results indicate that T. denticola has high pathogenicity, including dissemination to distant organs, further substantiating its potential importance in oral and linked systemic conditions

\u3ci\u3eMetagenomics for Microbiology:\u3c/i\u3e Preface

It is well known that only a small fraction of extant microbial life has been identified. Metagenomics, the direct sequencing and characterization of genes and genomes present in complex microbial ecosystems (e.g., metagenomes), has revolutionized the practice of microbiology by bypassing the hurdle of pure culture isolation. Metagenomics shows promise of advancing our understanding of the diversity, function, and evolution of the uncultivated majority. Metagenomics as a field arose in the 1990s after the application of molecular biology techniques to genomic material directly extracted from microbial assemblages present in diverse habitats, including the human body. The application of metagenomic approaches allows for the acquisition of genetic/genomic information from the viruses, bacteria, archaea, fungi, and protists forming complex assemblages. The field of metagenomics addresses the fundamental questions of which microbes are present and what their genes are potentially doing. In the mid-2000s, the availability of high-throughput or next-generation sequencing technologies propelled the field by lowering the monetary and time constraints imposed by traditional DNA sequencing technologies. These advances have allowed the scientific community to examine the microbiome of diverse environments/habitats, follow spatial and temporal changes in community structure, and study the response of the communities to treatment or environmental modifications. In 2012, the publication of the large-scale characterization of the microbiome of healthy adults created high expectations about the influence of the microbiota in human health and disease. With the publication of the results of the Human Microbiome Project, metagenomics has emerged as a major research area in microbiology, particularly, when it comes to the characterization of the role of microbiota in complex disorders, such as obesity. With contributions by leading researchers in the field, we provide a series of chapters describing best practices for the collection and analysis of metagenomic data, as well as the promises and challenges of the field. The chapters have been dedicated to different aspects of metagenomics

Combination of carbon nanotubes and two-photon absorbers for broadband optical limiting

New systems are required for optical limiting against broadband laser pulses. We demonstrate that the association of non-linear scattering from single-wall carbon nanotubes (SWNT) and multiphoton absorption (MPA) from organic chromophores is a promising approach to extend performances of optical limiters over broad spectral and temporal ranges. Such composites display high linear transmission and good neutral colorimetry and are particularly efficient in the nanosecond regime due to cumulative effects.Comment: 5 avril 200

Periplasm Organization in \u3ci\u3eTreponema denticola\u3c/i\u3e as Studied by Cryo-electron Tomography

As a spirochete, the genus Treponema is one of the few major bacterial groups whose natural phylogenic relationships are evident at the level of gross phenotypic characteristics such as their morphology. Treponema spp. are highly invasive due to their unique motility in dense media, and their ability to penetrate cell layers [1]. This feature is associated with the helical cell body and the presence of flagellar filaments in the periplasm [2]. Treponema denticola is an oral pathogen involved in endodontic infections and periodontal diseases. The presence and quantity of T. denticola in the subgingival biofilm is correlated with the severity of periodontal disease and tissue destruction [3,4]. The organism has also been detected in 75% of severe endodontic abscesses [5]. A better understanding of Treponema ultrastructure and motility will aid development of new strategies to control infection. Because of the similarity in ultrastructural organization among spirochetes, knowledge gained from T. denticola can be applied to other spirochetes causing diseases in human and animals (syphilis, digital dermatitis, Lyme disease, relapsing fever, leptospirosis, etc.)

The Unseen World: Environmental Microbial Sequencing and Identification Methods for Ecologists

Microorganisms inhabit almost every environment, comprise the majority of diversity on Earth, are important in biogeochemical cycling, and may be vital to ecosystem responses to large-scale climatic change. In recent years, ecologists have begun to use rapidly advancing molecular techniques to address questions about microbial diversity, biogeography, and responses to environmental change. Studies of microbes in the environment generally focus on three broad objectives: determining which organisms are present, what their functional capabilities are, and which are active at any given time. However, comprehending the range of methodologies currently in use can be daunting. To provide an overview of environmental microbial sequence data collection and analysis approaches, we include case studies of microbiomes ranging from the human mouth to geothermal springs. We also suggest contexts in which each technique can be applied and highlight insights that result from their use

The effect of induced sadness and moderate depression on attention networks

This study investigates how sadness and minor/moderate depression influences the three functions of attention: alerting, orienting, and executive control using the attention network test. The aim of the study is to investigate whether minor to moderate depression is more similar to sadness or clinical depression with regards to attentional processing. It was predicted that both induced sadness and minor to moderate depression will influence executive control by narrowing spatial attention and in turn this will lead to less interference from the flanker items (i.e., less effects of congruency) due to a focused attentional state. No differences were predicted for alerting or orienting functions. The results from the two experiments, the first inducing sadness (Experiment 1) and the second measuring subclinical depression (Experiment 2), show that, as expected, participants who are sad or minor to moderately depressed showed less flanker interference compared to participants who were neither sad nor depressed. This study provides strong evidence, that irrespective of its aetiology, sadness and minor/moderate depression have similar effects on spatial attention