Signal Processing for Metagenomics: Extracting Information from the Soup

Traditionally, studies in microbial genomics have focused on single-genomes from cultured species, thereby limiting their focus to the small percentage of species that can be cultured outside their natural environment. Fortunately, recent advances in high-throughput sequencing and computational analyses have ushered in the new field of metagenomics, which aims to decode the genomes of microbes from natural communities without the need for cultivation. Although metagenomic studies have shed a great deal of insight into bacterial diversity and coding capacity, several computational challenges remain due to the massive size and complexity of metagenomic sequence data. Current tools and techniques are reviewed in this paper which address challenges in 1) genomic fragment annotation, 2) phylogenetic reconstruction, 3) functional classification of samples, and 4) interpreting complementary metaproteomics and metametabolomics data. Also surveyed are important applications of metagenomic studies, including microbial forensics and the roles of microbial communities in shaping human health and soil ecology.     

Genomics: Applications,Challenges, and Opportunities for the U.S. Environmental Protection Agency

Genomics information has great potential to enhance assessment of risks to human health and the environment. Although understanding genomic responses with respect to adverse ecological and human health outcomes is not, as yet, established, it is important to consider the likely future impacts of genomics technologies on risk assessment and decision-making. Four areas are identified as those likely to be influenced by the generation of genomics information within, and the submission of such information to, the U.S. Environmental Protection Agency (USEPA): risk assessment, prioritization of contaminants and contaminated sites, monitoring, and reporting provisions. For each of these risk assessment and regulatory applications, representative activities are presented to illustrate the application. Three major challenges for the USEPA associated with genomics are also identified in the areas of research, technical development, and capacity. The USEPA's initial activities to address these challenges are discussed. The Agency recognizes it must be prepared to use genomics information, and that many scientific, policy, ethical, and legal concerns will need to be addressed. The USEPA also recognizes it is essential to continue to collaborate with other federal agencies, academia, the regulated community, and other stakeholders in order to benefit from ongoing advances in genomics in the wider scientific and regulatory communities.     

WHO fellowships--what do they achieve?

Training health professionals is one of WHO''s major strategies for improving health care in the developing world. The aim, to strengthen a country''s own capacity rather than injecting expertise from outside, is in the best tradition of sustainable development. But how effective is this so called "capacity building in human resources"? Since it accounted for $43m of WHO''s budget in 1992-3 and is considered by WHO to be a major contribution to health in individual countries, it deserves detailed examination.     

The right to be treated against her will

... My sister's inconsistent and intermittent treatment over the past eight years is largely a result of her own indecision and the inconsistencies of her abnormal mental state. The professionals who might have taken control of the situation as her health and functioning deteriorated have not done so and I must presume that they believe they cannot do so. I do not think her case is unique. There are many more people living in the community who are severely ill and are being deprived of treatment they need.     

Protecting communities in health research from exploitation

Guidelines for health research focus on protecting individual research subjects. Yet several commentators have argued that protecting individual subjects, while undoubtedly important, is not sufficient to ensure ethical research. It is also vital to protect the communities involved in health research. In particular, a number of studies have been criticized on the grounds that they exploited host communities. Although these criticisms have received a good deal of attention, there has been no systematic analysis of what constitutes community exploitation in health research, nor an assessment of what safeguards are needed to protect against it. This is a serious deficiency. The absence of an analysis of community exploitation makes it impossible to ensure that host communities are protected against exploitation. The absence of an analysis also raises the possibility that charges of exploitation may block important research, without any way of assessing whether the charges are warranted. The present paper attempts to address these concerns by providing an analysis of community exploitation and, based on this analysis, determining what safeguards are needed to protect communities in health research against exploitation.     

Science and policy: valuing framing, language and listening

This paper considers the context for science contributing to policy development and explores some critical issues that should inform science advocacy and influence with policy makers. The paper argues that the key challenges are at least as much in educating conservation scientists and science communicators about society and policy making as they are in educating society and policy makers about science. The importance of developing processes to ensure that scientists and science communicators invest in the development of relationships based on respect and understanding of their audience in both communities and amongst policy makers provides a critical first step. The objectives of the Global Strategy for Plant Conservation acknowledge the importance of developing the capacities and public engagement necessary to implement the Strategy, including knowledge transfer and community capacity building. However, the development of targets to equip institutions and plant conservation professionals to explicitly address the barriers to influencing policy development through knowledge transfer and integration require further consideration.     

Effects of high latitude protected areas on bird communities under rapid climate change

Anthropogenic climate change is rapidly becoming one of the main threats to biodiversity, along with other threats triggered by human‐driven land‐use change. Species are already responding to climate change by shifting their distributions polewards. This shift may create a spatial mismatch between dynamic species distributions and static protected areas (PAs). As protected areas represent one of the main pillars for preserving biodiversity today and in the future, it is important to assess their contribution in sheltering the biodiversity communities, they were designated to protect. A recent development to investigate climate‐driven impacts on biological communities is represented by the community temperature index (CTI). CTI provides a measure of the relative temperature average of a community in a specific assemblage. CTI value will be higher for assemblages dominated by warm species compared with those dominated by cold‐dwelling species. We here model changes in the CTI of Finnish bird assemblages, as well as changes in species densities, within and outside of PAs during the past four decades in a large boreal landscape under rapid change. We show that CTI has markedly increased over time across Finland, with this change being similar within and outside PAs and five to seven times slower than the temperature increase. Moreover, CTI has been constantly lower within than outside of PAs, and PAs still support communities, which show colder thermal index than those outside of PAs in the 1970s and 1980s. This result can be explained by the higher relative density of northern species within PAs than outside. Overall, our results provide some, albeit inconclusive, evidence that PAs may play a role in supporting the community of northern species. Results also suggest that communities are, however, shifting rapidly, both inside and outside of PAs, highlighting the need for adjusting conservation measures before it is too late.     

“One Health” or Three? Publication Silos Among the One Health Disciplines

The One Health initiative is a global effort fostering interdisciplinary collaborations to address challenges in human, animal, and environmental health. While One Health has received considerable press, its benefits remain unclear because its effects have not been quantitatively described. We systematically surveyed the published literature and used social network analysis to measure interdisciplinarity in One Health studies constructing dynamic pathogen transmission models. The number of publications fulfilling our search criteria increased by 14.6% per year, which is faster than growth rates for life sciences as a whole and for most biology subdisciplines. Surveyed publications clustered into three communities: one used by ecologists, one used by veterinarians, and a third diverse-authorship community used by population biologists, mathematicians, epidemiologists, and experts in human health. Overlap between these communities increased through time in terms of author number, diversity of co-author affiliations, and diversity of citations. However, communities continue to differ in the systems studied, questions asked, and methods employed. While the infectious disease research community has made significant progress toward integrating its participating disciplines, some segregation—especially along the veterinary/ecological research interface—remains.     

Traditional medicines as a mechanism for driving research innovation in Africa

The outcomes from recent high profile deliberations concerning African health research and economic development all point towards the need for a mechanism to support health innovation on the continent. The mission of the African Network for Drugs and Diagnostics Innovation (ANDI), is to promote and sustain African-led health product innovation to address African public health needs through the assembly of research networks, and building of capacity to support human and economic development. ANDI is widely viewed as the vehicle to implementing some of these recommendations. There is tremendous opportunity for Africa, to leverage the expertise in natural products and traditional medicines in support of this objective to kick-start innovation. This report highlights key recommendations that have emerged through expert forums convened by ANDI on the challenges, opportunities and prospects for investing in this important area of research.     

Using successional theory to measure marine ecosystem health

Marine ecosystems are diverse and complex, providing significant challenges to the development of generalizable metrics of ecosystem health. Of particular concern is the varied form of change caused by multiple human activities, which limits the capacity to generate a single measure to encapsulate the overall condition of the ecosystem. Here we consider how successional theory can help to simplify our understanding of marine community structure, especially when viewed in context of human disturbance. During succession, the emergent properties of communities change in predictable ways. As communities mature, there is an increase in total production and biomass, the mean size of organisms, the level of internal recycling of food and nutrients, and the mean trophic level. Using a set of multi-species trophic models, we explore the changes in community structure that are likely to occur during succession. These changes include increases in biomass within trophic levels due to decreased rates of energy and food loss through trophic and production inefficiencies, and potential shifts from top-down control early in succession to bottom-up later. Because human activities disproportionately favor early-successional species, we can gain insights by considering community degradation in the context of succession being played in reverse. Indicators of health based on ecological succession thus provide a mechanistic view to measure the impact of human activities (both positive and negative) on marine ecosystems.     

Microbiota of the chicken gastrointestinal tract: influence on health,productivity and disease

Recent advances in the technology available for culture-independent methods for identification and enumeration of environmental bacteria have invigorated interest in the study of the role of chicken intestinal microbiota in health and productivity. Chickens harbour unique and diverse bacterial communities that include human and animal pathogens. Increasing public concern about the use of antibiotics in the poultry industry has influenced the ways in which poultry producers are working towards improving birds’ intestinal health. Effective means of antibiotic-independent pathogen control through competitive exclusion and promotion of good protective microbiota are being actively investigated. With the realisation that just about any change in environment influences the highly responsive microbial communities and with the abandonment of the notion that we can isolate and investigate a single species of interest outside of the community, came a flood of studies that have attempted to profile the intestinal microbiota of chickens under numerous conditions. This review aims to address the main issues in investigating chicken microbiota and to summarise the data acquired to date.     

Plants Replacing Plants: The Future of Community Modeling and Research

Over the past few decades, several conceptual and mathematical models of plant community organization and dynamics have been put forward. While each of these models has attempted to explain important plant community patterns by attributing them to some aspect of plant niches, or to a higher-level process, their predictive success has been very limited. Here I explore why this has happened by reviewing and summarizing each model individually by highlighting the plant community pattern each is trying to explain and predict, by identifying the mechanisms, tolerances, and/or processes authors propose are producing those patterns and describing how they work within the model, and by examining the assumptions of each model. I then discuss common misconceptions and shortcomings among the models, and finally propose a unifying synthesis and comprehensive framework that can serve as a basis for future plant community modeling and research. This synthesis is composed of three key ideas (1) that plant-plant replacements are the “fundamental process” of plant communities which produce every community-level terrestrial plant pattern, (2) that plants respond to mechanisms and tolerances which work both in spaces inside plants and in those spaces outside plants that influence them and/or they may be able to influence, and (3) that those responses make up plant niches which may be able to predict how plants replace themselves over time and space. Consequently I suggest to future field researchers that the best way to understand plant community patterns is to study plant-plant replacements, first by sampling long-term vegetation plots in order to map them, and then by manipulating mechanisms and tolerances in field experiments in order to understand what causes them.     

人体鼻咽部微生物群落多样性研究进展

定殖于鼻咽部的微生物与人体始终处于动态生态平衡,对于维持人体健康发挥着重要作用,也与多种上呼吸道疾病的发生发展有密切关系。鼻咽部微生物之间及其与宿主之间的相互作用是引发人体上呼吸道疾病的重要因素。微生物的培养方法与分子生物学技术的结合使人们越来越深入地了解人体鼻咽部微生物群落的组成和结构。定殖于人体鼻咽部的微生物以肺炎链球菌(Streptococcus pneumoniae)和流感嗜血杆菌(Haemophilus influenzae)等潜在致病菌为主。本文将分别从鼻咽部微生物与机体的平衡关系、鼻咽部微生物群落的研究方法以及鼻咽部微生物群落的组成及其相互关系三个方面,综述近年来鼻咽部微生物群落结构的相关研究进展,从而为指导实践提供可靠的理论依据。     

景感生态学视角下的健康社区构建

景感生态学是基于中国传统人居环境营造理论与实践结合现代生态学基本原理形成的新兴学科,注重探讨生态系统服务与可持续发展的关系。可持续发展目标中健康与福祉是其重要内容,因此健康人居环境的营造也是景感生态学的重要应用领域之一。在健康人居环境的营造过程中,健康社区构建具有作为"细胞工程"的基础性作用。因此,从景感生态学的视角探讨健康社区的构建,有助于景感生态学进一步应用于可持续发展与人居环境营造的实践,为健康与福祉的顺利实现提供支撑。从健康社区的定义和主要理念出发,基于健康社区构建的需求本体和供给客体及其相互作用关系,结合生态环境科学的"时-空-量-序"的视角,探讨了生态环境研究应用于健康社区构建的作用及面临的系统性不足、人文性不足和耦合性不足等挑战;进而以景感生态学作为连接生态环境学科与建筑规划学科的纽带,探讨了景感生态学在应对上述挑战中的作用。从景感生态学视角来看,健康社区构建就是将人类健康这一愿景融入到社区健康需求本体与健康供给客体及其相互关系的调控与营造,从而实现社区及人群的健康和可持续发展。健康社区的构建强调社区人群主观健康需求与客观健康供给之间的互动与耦合,与景感生态学强调"景"与...     

Community Members' Engagement with and Involvement in Genomic Research: Lessons to Learn from the Field

In this paper, we describe the potential role laypersons on ethics committees can play in ensuring community concerns are addressed in the design and implementation of genomic research. We draw inferences from the outcome of an empirical study of the impact of training of laypersons to address community engagement issues in ethics review of research protocol. While this paper does not advocate a particular solution, it describes the importance of community engagement in genomic research, the current limitations there are in engaging communities in the design of these research projects and how communities can be indirectly engaged in the design and implementation of genomic research through the engagement of laypersons on ethics committees. However, to ensure that these laypersons can play this role, their capacity needs to be built to play this role appropriately. There is evidence to show that where resources are invested in building the capacity of laypersons to play their role as community ‘watchdogs’ in research, they play this role aptly. Community engagement is important in genomic research as genomic researchers will increasingly require community perspectives in critical ethics decision making.     

In vitro anaerobic biofilms of human colonic microbiota

The human gastrointestinal tract hosts a complex community of microorganisms that grow as biofilms on the intestinal mucosa. These bacterial communities are not well characterized, although they are known to play an important role in human health. This study aimed to develop a model for culturing biofilms (surface-adherent communities) of intestinal microbiota. The model utilizes adherent mucosal bacteria recovered from colonic biopsies to create multi-species biofilms. Culture on selective media and confocal microscopy indicated the biofilms were composed of a diverse community of bacteria. Molecular analyses confirmed that several phyla were represented in the model, and demonstrated stability of the community over 96 h when cultured in the device. This model is novel in its use of a multi-species community of mucosal bacteria grown in a biofilm mode of growth.     

Physiological anthropology: past and future

Environmental studies in adaptive human biology by North American anthropologists have a history of strong investigative research. From both laboratory and field work, we have gained major insights into human response to physical and social challenges. While these results were considered by most professionals to belong within evolutionary biology, in fact the intellectual structure sprang almost entirely from physiological equilibrium models. Consequently, physiological process itself was the focus. Further, most of the physiological patterns were not linked directly to important outcomes such as work output, reproductive success or survival.About 1975, American physiological anthropologists, led by Paul Baker, turned to studies of health, change and stress response. These studies were strong, but were still neither genetic nor evolutionary in intellectual structure. Evolutionary human biology was taken over by a new body of theory now called "behavior ecology", positing that selfish genes control human behavior to promote their own reproduction. This was paralleled by strong use of evolutionary theory in some areas of molecular biology. However, although physiological anthropologists have not focused on evolution, we have been developing powerful causal models that incorporate elements of physiology, morphology, physical environment and cultural behavior. In these "proximate" biocultural models, it is of little importance whether outcomes such as work or energy management are genetically based.Our future offers two major challenges. First, we must confirm causal links between specific physiological patterns and outcomes of practical importance to individuals and societies. Second, if we are to take our place in evolutionary biology, the one overarching theory of life on earth, we must understand the heritability of physiological traits, and determine whether they play a role in survival and reproduction.     

Applications of functional gene microarrays for profiling microbial communities

Functional gene arrays (FGAs) have been considered as a specific, sensitive, quantitative, and high throughput metagenomic tool to detect, monitor and characterize microbial communities. Especially GeoChips, the most comprehensive FGAs have been applied to analyze the functional diversity, composition, structure, and metabolic potential or activity of a variety of microbial communities from different habitats, such as aquatic ecosystems, soils, contaminated sites, extreme environments, and bioreactors. FGAs are able to address fundamental questions related to global change, bioremediation, land use, human health, and ecological theories, and link the microbial community structure to environmental properties and ecosystem functioning. This review focuses on applications of FGA technology for profiling microbial communities, including target preparation, hybridization and data processing, and data analysis. We also discuss challenges and future directions of FGA applications.     

“Community Work” in a Climate of Adaptation: Responding to Change in Rural Alaska

We draw on our research experiences with municipal workers in Alaska, where the impacts of climate change are already extensive, to examine adaptation and related concepts, such as resilience and vulnerability, which have become widely used in science and policy formulation for addressing climate change despite also being subject to multiple critiques. We use local people’s experiences with environmental challenges to illustrate limitations of the climate change adaptation paradigm, and offer the additional concept of “community work” — analogous to niche construction — as a counterpart to the adaptive process at the community level. Whereas climate change adaptation insinuates active and purposive change, the reality we have repeatedly encountered is that people in these communities focus not on changing but on building and maintaining capacity and achieving stability: keeping aging and overtaxed infrastructure running while also working toward improving quality of life and services in their communities. We discuss how these findings are congruent with recent calls to better situate climate change adaptation policy in the context of community development, and argue that scientists and policymakers need to understand this context of community work to avoid the pitfalls that potentially accompany the adaptation paradigm.     

The role of competition versus cooperation in microbial community coalescence

New microbial communities often arise through the mixing of two or more separately assembled parent communities, a phenomenon that has been termed “community coalescence”. Understanding how the interaction structures of complex parent communities determine the outcomes of coalescence events is an important challenge. While recent work has begun to elucidate the role of competition in coalescence, that of cooperation, a key interaction type commonly seen in microbial communities, is still largely unknown. Here, using a general consumer-resource model, we study the combined effects of competitive and cooperative interactions on the outcomes of coalescence events. To do so, we simulate coalescence events between pairs of communities with different degrees of competition for shared carbon resources and cooperation through cross-feeding on leaked metabolic by-products (facilitation). We also study how structural and functional properties of post-coalescence communities evolve when they are subjected to repeated coalescence events. We find that in coalescence events, the less competitive and more cooperative parent communities contribute a higher proportion of species to the new community because of their superior ability to deplete resources and resist invasions. Consequently, when a community is subjected to repeated coalescence events, it gradually evolves towards being less competitive and more cooperative, as well as more speciose, robust and efficient in resource use. Encounters between microbial communities are becoming increasingly frequent as a result of anthropogenic environmental change, and there is great interest in how the coalescence of microbial communities affects environmental and human health. Our study provides new insights into the mechanisms behind microbial community coalescence, and a framework to predict outcomes based on the interaction structures of parent communities.