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

\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

Use of remote digital surveys to generate exposure models of residential structures in Chile

This article describes a methodology used to build detailed exposure models of residential structures in three cities of Chile using remote digital surveys. The models provide the location of the structures classified into 18 different structural typologies. Two tools were used simultaneously to build the models: Google StreetView, and GEM’s Inventory Data Capture Tool. The method is described, a summary of the results of the exposure models is presented, and the detailed results of the local models are compared with a previously developed national exposure model for the whole country. The proposed methodology to develop exposure models proved to be useful, simple, and low cost, and can be replicated elsewhere with proper StreetView coverage. The methodology is accurate to count structures, despite presenting certain difficulties to classify the surveyed buildings into different structural typologies. The developed exposure models represent an important input for risk calculations, thus improving technical capabilities for seismic risk management of the country

Immunogenicity and tolerability of an MF59-adjuvanted, egg-derived, A/H1N1 pandemic influenza vaccine in children 6-35 months of age

Background: Vaccines against pandemic A/H1N1 influenza should provide protective immunity in children, because they are at greater risk of disease than adults. This study was conducted to identify the optimal dose of an MF59 (R)-adjuvanted, egg-derived, A/H1N1 influenza vaccine for young children. Methods: Children 6-11 months (N = 144) and 12-35 months (N = 186) of age received vaccine formulations containing either 3.75 mu g antigen with half the standard dose of MF59 or 7.5 mu g antigen with a standard dose of MF59, or a nonadjuvanted formulation containing 15 mu g antigen (children 12-35 months only). Participants were given 2 primary vaccine doses 3 weeks apart, followed by 1 booster dose of MF59-adjuvanted seasonal influenza vaccine 1 year later. Immunogenicity was assessed by hemagglutination inhibition and microneutralization assays. Results: All vaccine formulations were highly immunogenic and met all 3 European licensure criteria after 2 doses. MF59-adjuvanted vaccines met all licensure criteria after 1 dose in both age cohorts, while nonadjuvanted vaccine did not meet all criteria after 1 dose in children 12-35 months. A single booster dose was highly immunogenic, and stable antibody persistence was observed in response to all vaccines. All vaccines were well tolerated. Conclusions: In this study, a single dose of 3.75 mu g antigen with half the standard dose of MF59 was shown to be optimal, providing adequate levels of immediate and long-term antibodies in pediatric subjects 6-35 months of age. These data demonstrated that MF59 adjuvant allowed for reduced antigen content and promoted significant long-term antibody persistence in children, with a satisfactory safety profile

Modeling of the residue transport of lambda cyhalothrin, cypermethrin, malathion and endosulfan in three different environmental compartments in the Philippines

AbstractThis study aims to determine the environmental transport and fate of the residue of four Philippines priority chemicals; i.e., lambda cyhalothrin (L-cyhalothrin), cypermethrin, endosulfan and malathion, in three different environmental compartments (air, water and soil). In the Philippines, pesticide application is the most common method of controlling pests and weeds in rice and vegetable farming. This practice aided the agricultural industry to minimize losses and increase yield. However, indiscriminate use of pesticides resulted to adverse effects to public health and environment. Studies showed that 95% of the applied pesticides went to non-target species. Data from previous studies in Pagsanjan Laguna, Philippines were used as input data. Dispersion, Gaussian plume, and regression equations were employed to simulate the behavior of L-cyhalothrin, cypermethrin, endosulfan and malathion in air, water and soil. Substance decay was calculated using first order reaction. This study showed how L-cyhalothrin, cypermethrin, endosulfan, and malathion behaved in the environment after release from nozzle spray, and its possible duration of stay in the environment. It will also show a tool in determining the percolation depth through soil by endosulfan. This tool can be utilized in determining the depth of contaminated soil during remediation strategic planning and project implementation of similar environmental condition

Distribution and role of benthic diatoms as acid mine drainage indicators in affected water dams

Publicado em "Proceedings of the Energy and Environment Knowledge Week 2014(E2KW2014)". ISBN 978-84-697-1162-

Why long term trawled red algae beds off Balearic Islands (western Mediterranean) still persist?

The bottom morphology, the surface sediments and the epibenthic community of two adjacent areas within the fishing ground traditionally known as Pesquera Rica (Balearic Islands) were characterized using multibeam echosounder, van Veen dredge and beam trawl. Red algae beds predominate in both areas, but one has been exploited by trawling since at least 90 years ago, whereas the presence of natural barriers prevents this fishing activity in the other one. Comparisons between the two areas showed a biomass reduction of 46.8 and 39.3% of dominant red algae taxonomic groups Peyssonneliaceae and Corallinophycidae, respectively, in the trawled area (TA). Similarly, both mean abundance and biomass of most groups of fauna were higher in the not trawled area (NTA). N90 biodiversity index showed higher mean values of algae species in NTA than in TA (7.0 and 4.9, respectively), whereas no differences were detected neither for sessile nor for mobile fauna. SIMPER analysis showed that large species of both sessile and mobile epibenthic fauna (e.g. the ascidia Polycarpa mamillaris and the echinoderm Spatangus purpureus, respectively) presented higher abundance and contribution to within area similarity in NTA than in TA. In coincidence, these are the most abundant epibenthic species in the commercial hauls from the Pesquera Rica. The relatively low fishing effort and the gears used, addressed to avoid large catches of algae allowing longer hauls, may explain the subsistence of red algae beds in the Balearic Islands trawl fishing grounds. However, the detrimental effects shown here claim for urgent management measures aiming to preserve these bedsVersión del edito