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With the advancement ofhumanmicrobiomeresearch, it is inevitable that a growing number of biobanks will include a collection of microbiota specimens to characterize the microbial communities that inhabit thehuman body and explore the relationships between the microbiota and theirhuman hosts. Biobanks ofhuman microbiota and their associated genetic information may become a valuable health resource. But, this area ofresearch also presents ethical and social problems, some of which are (...) distinct from those faced by biobanks that storehuman tissue samples. This paper examines four core issues which are considered highly relevant tomicrobiome biobanking: the nature ofhumanmicrobiome samples and how different understandings have an impact on benefit/risk evaluation, privacy, informed consent, and returning the result to participants. We argue that these issues should be addressed early on inmicrobiomeresearch projects and also call for adjusting or developing new governance mechanism to better accommodate these changes. (shrink)

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BackgroundBiobanks are considered to be key infrastructures forresearch development and have generated a lot of debate about their ethical, legal and social implications. While the focus has been onhuman genomicresearch, rapid advances inhumanmicrobiomeresearch further complicate the debate.DiscussionWe draw on two cystic fibrosis biobanks in Toronto, Canada, to illustrate our points. The biobanks have been established to facilitate sample and data sharing forresearch into the link between disease (...) progression and microbial dynamics in the lungs of pediatric and adult patients. We begin by providing an overview of some of the ELSI associated withhumanmicrobiomeresearch, particularly on the implications for the broader society. We then discuss ethical considerations regarding the identifiability of samples biobanked forhumanmicrobiomeresearch, and examine the issue of return of results and incidental findings. We argue that, for the purposes ofresearch ethics oversight,humanmicrobiomeresearch samples should be treated with the same privacy considerations ashuman tissues samples. We also suggest that returning individualmicrobiome-related findings could provide a powerful clinical tool for care management, but highlight the need for a more grounded understanding of contextual factors that may be unique tohumanmicrobiomeresearch.ConclusionsWe revisit the ELSI of biobanking and consider the impact thathumanmicrobiomeresearch might have. Our discussion focuses on identifiability ofhumanmicrobiomeresearch samples, and return ofresearch results and incidental findings for clinical management. (shrink)

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Humanmicrobiomeresearch has revealed that legions of bacteria, viruses, and fungi live on our skin and within the cavities of our bodies. New knowledge from these recent studies shows that humans are superorganisms and that themicrobiome is indispensible to our lives and our health. This volume explores some of the science on thehumanmicrobiome and considers the ethical, legal, and social concerns that are raised by thisresearch.

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Background Continued advances inhumanmicrobiomeresearch and technologies raise a number of ethical, legal, and social challenges. These challenges are associated not only with the conduct of theresearch, but also with broader implications, such as the production and distribution of commercial products promising maintenance or restoration of good physical health and disease prevention. In this article, we document several ethical, legal, and social challenges associated with the commercialization ofhumanmicrobiomeresearch, (...) focusing particularly on how thisresearch is mobilized within economic markets for new public health uses. Methods We conducted in-depth, semi-structured interviews (2009–2010) with 63 scientists, researchers, and National Institutes of Health project leaders (“investigators”) involved withhumanmicrobiomeresearch. Interviews explored a range of ethical, legal, and social dimensions ofhumanmicrobiomeresearch, including investigators’ perspectives on commercialization. Using thematic content analysis, we identified and analyzed emergent themes and patterns. Results Investigators discussed the commercialization ofhumanmicrobiomeresearch in terms of (1) commercialization, probiotics, and issues of safety, (2) public awareness of the benefits and risks of dietary supplements, and (3) regulation. Conclusion The prevailing theme of ethical, legal, social concern focused on the need to find a balance between the marketplace, scientificresearch, and the public’s health. The themes we identified are intended to serve as points for discussions about the relationship between scientificresearch and the manufacture and distribution of over-the-counter dietary supplements in the United States. (shrink)

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Thehumanmicrobiome is the bacteria, viruses, and fungi that cover our skin, line our intestines, and flourish in our body cavities. Work on thehumanmicrobiome is new, but it is quickly becoming a leading area of biomedicalresearch. What scientists are learning about humans and our microbiomes could change medical practice by introducing new treatment modalities. This new knowledge redefines us as superorganisms comprised of thehuman body and the collection of microbes (...) that inhabit it and reveals how much we are a part of our environment. The understanding that microbes are not only beneficial but sometimes necessary for survival recasts our interaction with microbes from adversarial to neighborly. This volume explores some of the science that makeshumanmicrobiomeresearch possible. It then considers ethical, legal, and social concerns raised bymicrobiomeresearch. Chapters explore issues related to personal identity, property rights, and privacy. The authors reflect on howhumanmicrobiomeresearch challenges reigning views on public health andresearch ethics. They also address the need for thoughtful policies and procedures to guide the use of the biobankedhuman samples required for advancing this new domain ofresearch. In the course of these explorations, they introduce examples from the history of biomedical science and recent legal cases that shed light on the issues and inform the policy recommendations they offer at the end of each topic's discussion.This volume is the product of an NIHHumanMicrobiome Project grant. It represents three years of conversations focused on consensus formation by the twenty-seven members of the interdisciplinaryMicrobiome Working Group. (shrink)

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Microbiomeresearch shows thathuman health is foundationally intertwined with the ecology of microbial communities living on and in our bodies. This challenges the categorical separation of organisms from environments that has been central to biomedicine, and questions the boundaries between them. Biomedicine is left with an empirical problem: how to understand causal pathways between host health, microbiota and environment? We propose a conceptual tool – environmentality – to think through this problem. Environmentality is the state or (...) quality of being an environment for something else in a particular context: a fully perspectival proposition. Its power lies partly in what Isabelle Stengers has called the efficacy of the word itself, contrasting the dominant sense of the word environment as something both external and fixed. Through three case studies, we argue that environmentality can help think about the causality of microbiota vis-a-vis host health in a processual, relational and situated manner, across scales and temporalities. We situate this intervention within historical trajectories of thought in biomedicine, focusing on the challengemicrobiomeresearch poses to an aperspectival body. We argue that addressing entanglements between microbial andhuman lives requires that the environment is brought into the clinic, thus shortening the conceptual gap between medicine and public health. (shrink)

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This essay, written by a biologist, a microbial ecologist, a biological anthropologist, and an anthropologist‐historian, examines tensions and translations inmicrobiomeresearch on animals in the laboratory and field. The authors trace howresearch questions and findings in the laboratory are extrapolated into the field and vice versa, and the shifting evidentiary standards that theseresearch settings require. Showing how complexities of microbiomes challenge traditional standards of causation, the authors contend that these challenges require new approaches (...) to inferences used in ecology, anthropology, and history. As social scientists incorporate investigations of microbial life into theirhuman studies,microbiome researchers venture into field settings to develop mechanistic understandings about the functions of complex microbial communities. These efforts generate new possibilities for cross‐fertilizations and inference frameworks to interpretmicrobiome findings.Microbiomeresearch should integrate multiple scales, levels of variability, and other disciplinary approaches to tackle questions spanning conditions from the laboratory to the field. (shrink)

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Research on thehumanmicrobiome has gen- erated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units—the metagenome, coremicrobiome, and entero- type—have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statisti- cal methods, coupled with a translational imperative, are the primary drivers of this new (...) ontology. By reducing the dimensionality of variation in thehumanmicrobiome, these new units render it more tractable and easier to interpret, and hence serve an important heuristic role. Nonetheless, there are several reasons to be cautious about these new categories prematurely ‘‘hardening’’ into natural units: a lack of constraints on what can be sequenced metagenomically, freedom of choice in taxonomic level in defining a ‘‘coremicrobiome,’’ typological framing of some of the concepts, and possible reification of statistical constructs. Finally, lessons from theHuman Genome Project have led to a translational imperative: a drive to derive results from the exploration ofmicrobiome variation that can help to articulate the emerging paradigm of per- sonalized genomic medicine (PGM). There is a tension between the typologizing inherent in much of thisresearch and the personal in PGM. (shrink)

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Starting in June 2012, a series of articles in the journal Nature and in the online journals of the Public Library of Science made public the first results of a massive, international collaborative scientific endeavor known as the “HumanMicrobiome Project” . This project, which is attempting to categorize the vast number of microbiological species and organisms that live in and on the “healthy”human body, raises important questions about what it means to be a whole individual (...) organism, especially if that individual involves a community of some hundreds of trillions of others. In this article, we will explore a handful of political, ethical, and philosophical issues that this newresearch raises .. (shrink)

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This article reformulates Stephan Helmreich´s the ¨microbiomisation of race¨ as the historiality of otherness in the foundations ofhumanmicrobiome science. Through the lens of my ethnographic fieldwork of a transnational community ofmicrobiome scientists that conducted a landmarkhumanmicrobiomeresearch on indigenous microbes and its affiliated and first personalisedmicrobiome initiative, the American Gut Project, I follow and trace the key actors, experimental systems and onto-epistemic claims in the emergence of (...) class='Hi'>humanmicrobiome science a decade ago. In doing so, I show the links between the reinscription of race, comparativeresearch on the microbial genetic variation ofhuman populations and the remining of bioprospected data for personalised medicine. In these unpredictableresearch movements, themicrobiome of non-Western peoples and territories is much more than a side project or a specific approach within the field: it constitutes the nucleus of its experimental system, opening towards subsequent and cumulativeresearch processes and knowledge production inhumanmicrobiome science. The article demonstrates that whilehumanmicrobiome science is articulated upon the microbial ‘makeup’ of non-wester(nised) communities, societies, and locales, its results and therapeutics are only applicable to medical conditions affecting rich nations (i.e., inflammatory, autoimmune, and metabolic diseases). My reformulation of ¨microbiomisation of race¨ as the condition of possibility ofhumanmicrobiome science reveals that its individual dimension is sustained by microbial DNA data fromhuman populations through bioprospecting practices and gains meaning through personalised medicine initiatives, informal online networks of pseudoscientific and commodified microbial-related evidence. (shrink)

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Microbiomeresearch is changing how ecosystems, including animal bodies, are understood. In the case of humans,microbiome knowledge is transforming medical approaches and applications. However, the field is still young, and many conceptual and explanatory issues need resolving. These include howmicrobiome causality is understood, and how to conceptualize the role microbiomes have in the health status of their hosts and other ecosystems. A key concept that crops up in the medicalmicrobiome literature is “balance.” (...) A balancedmicrobiome is thought to produce health and an imbalanced one disease. Based on a quantitative and qualitative analysis of how balance is used in themicrobiome literature, this “think again” essay critically analyses each of the several subconceptions of balance. As well as identifying problems with these uses, the essay suggests some starting points for filling this conceptual gap inmicrobiomeresearch. (shrink)

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The target article suggests inter-individual variability is a weakness of microbiota-gut-brainresearch, but we discuss why it is actually a strength. We comment on how accounting for individual differences can help researchers systematically understand the observed variance in microbiota composition, interpret null findings, and potentially improve the efficacy of therapeutic treatments in future clinicalmicrobiomeresearch.

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Human evolution has been punctuated by climate anomalies, structuring environments, deadly infections, and altering landscapes. How well humans adapted to these new circumstances had direct effects on fitness and survival. Here, how the gutmicrobiome could have contributed tohuman evolutionary success through contributions to host nutritional buffering and infectious disease resistance is reviewed. How changes inhuman genetics, diet, disease exposure, and social environments almost certainly altered microbial community composition is also explored. Emergingresearch (...) points to themicrobiome as a key player in host responses to environmental change. Therefore, the reciprocal interactions between humans and their microbes are likely to have shapedhuman patterns of local adaptation throughout our shared evolutionary history. Recent alterations inhuman lifestyle, however, are alteringhuman microbiomes in unprecedented ways. The consequences of interrupted host–microbe relationships forhuman adaptive potential in the future are unknown. (shrink)

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The complexity of thehuman mind and its interaction with the environment is one of the main epistemological debates throughout history. Recent ideas, framed as the 4E perspective to cognition, highlight thathuman experience depends causally on both cerebral and extracranial processes, but also is embedded in a particular sociomaterial context and is a product of historical accumulation of trajectory changes throughout life. Accordingly, thehumanmicrobiome is one of the most intriguing actors modulating brain function (...) and physiology. Here, we present the 4E approach to theHumanMicrobiome for understanding mental processes from a broader perspective, encompassing one's body physiology and environment throughout their lifespan, interconnected bymicrobiome community structure and dynamics. We review evidence supporting the approach theoretically and motivates the study of the global set of microbial ecosystem networks encountered by a person across their lifetime (from skin to gut to natural and built environments). We furthermore trace future empirical implementation of the approach. We finally discuss novelresearch opportunities and clinical interventions aimed toward developing low‐cost/high‐benefit integrative and personalized bio‐psycho‐socio‐environmental treatments for mental health and including the brain‐gut‐microbiome axis. (shrink)

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Humanmicrobiomeresearch makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. (...) When Koch’s postulates are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas ofmicrobiomeresearch, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated bymicrobiomeresearch are weak or misleading. We focus on the stability, specificity and proportionality of proposedmicrobiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues ofresearch. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (shrink)

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There has been a spurt in both fundamental and translationalresearch that examines the underlying mechanisms of thehumanmicrobiome in psychiatric disorders. The personalized and dynamic features of thehumanmicrobiome suggest the potential of its manipulation for precision psychiatry in ways to improve mental health and avoid disease. However, findings in the field ofmicrobiome also raise philosophical and ethical questions. From a philosophical point of view, they may yet be another attempt (...) at providing a biological cause for phenomena that ultimately cannot be so easily localized. From an ethical point of view, it is relevant that thehuman gutmicrobiome comprises data on the individual’s lifestyle, disease history, previous medications, and mental health. Massive datasets ofmicrobiome sequences are collected to facilitate comparative studies to identify specific links between themicrobiome and mental health. Although this emergingresearch domain may show promise for psychiatric patients, it is surrounded by ethical challenges regarding patient privacy, health risks, effects on personal identity, and concerns about responsibility. This narrative overview displays the roles and advances ofmicrobiomeresearch in psychiatry and discusses the philosophical and ethical implications ofmicrobiome big data andmicrobiome-based interventions for psychiatric patients. We also investigate whether these issues are really “new,” or “old wine in new bottles.”. (shrink)

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Microbiome science asserts humans are made up of more microbial cells and genes thanhuman ones, and that each person harbors their own unique microbial population.Humanmicrobiome studies gesture toward the post-racial aspirations of personalized medicine—characterizing states ofhuman health and illness microbially. By viewing humans as “supraorganisms” made up of millions of microbial partners, somemicrobiome science seems to disrupt binding historical categories often grounded in racist biology, allowing interspeciality to supersede race. (...) But inevitably, unexamined categories of race and ethnicity surface in a myriad of studies on microbiota. This paper approaches race as a ghost variable acrossmicrobiomeresearch and asks, what is race doing in studies of themicrobiome? Why is it there, and how is it functioning? I examine thisresearch to argue that social scientists must work with biological scientists to help put microbial differences into perspective—to investigate how microbiomes and race are entangled embodiments of the social, environmental, and biological. Ultimately, transdisciplinary collaboration is required to address racial health disparities inmicrobiomeresearch without reifying race as a straightforward biological or social designation. (shrink)

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The use of thehumanmicrobiome as a subject of study for forensic purposes raises a number of issues, ranging from a challenge to our traditional concept of identity to respect for privacy and the type of consent to be obtained when amicrobiome sample is taken. The particular nature of this study requires the joint work of a multidisciplinary team made up of specialists in ethics, forensic science, law, microbiology, philosophy and political science.

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Recentresearch about themicrobiome points to a picture in which we, humans, are ‘living through’ nature, and nature itself is living in us. Our bodies are hosting—and depend on—the multiple species that constitutehuman microbiota. This article will discuss currentresearch on themicrobiome through the ideas of Japanese ecologist Imanishi Kinji (1902–1992). First, some of Imanishi’s key ideas regarding the world of living beings and multispecies societies are presented. Second, seven types of relationships (...) concerning thehumanmicrobiome,human beings, and the environment are explored. Third, inspired by Imanishi’s work, this paper develops the idea of dynamic, porous, and complex multispecies societies in which different living beings or species are codependent on others, including microbiota andhuman beings. (shrink)

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Now characterised by high-throughput sequencing methods that enable the study of microbes without lab culture, thehuman “microbiome” (the microbial flora of the body) is said to have revolutionary implications for biology and medicine. According to many experts, we must now understand ourselves as “holobionts” like lichen or coral, multispecies superorganisms that consist of animal and symbiotic microbes in combination, because normal physiological function depends on them. Here I explore the 1960sresearch of biologist René Dubos, a (...) forerunner figure mentioned in some historical accounts of themicrobiome, and argue that he arrived at the superorganism concept 40 years before theHumanMicrobiome Project. This raises the question of why his contribution was not hailed as revolutionary at the time and why Dubos is not remembered for it. (shrink)

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The US National Institute of Health’sHumanMicrobiome Project aims to use genomic techniques to understand the microbial communities that live on thehuman body. The emergent field ofmicrobiome science brought together diverse disciplinary perspectives and technologies, thus facilitating the negotiation of differing values. Here, we describe how values are conceptualized and negotiated withinmicrobiomeresearch. Analyzing discussions from a series of interdisciplinary workshops conducted withmicrobiome researchers, we argue that negotiations of (...) epistemic, social, and institutional values were inextricable from the reflective and strategic category work that defined and organized themicrobiome as an object of study and a potential future site of biomedical intervention. Negotiating the divergence or tension between emerging scientific and regulatory classifications also activated “values levers” and opened up reflective discussions of how classifications embody values and how these values might differ across domains. These data suggest that scholars at the intersections of science and technology studies, ethics, and policy could leverage such openings to identify and intervene in the ways that ethical/regulatory and scientific/technical practices are coproduced within unfoldingresearch. (shrink)

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As the international genomicresearch community moves from the tool-making efforts of theHuman Genome Project into biomedical applications of those tools, new metaphors are being suggested as useful to understanding how our genes work - and for understanding who we are as biological organisms. In this essay we focus on theHumanMicrobiome Project as one such translational initiative. The HMP is a new 'metagenomic'research effort to sequence the genomes ofhuman microbiological (...) flora, in order to pursue the interesting hypothesis that our 'microbiome' plays a vital and interactive role with ourhuman genome in normalhuman physiology. Rather than describing thehuman genome as the 'blueprint' forhuman nature, the promoters of the HMP stress the ways in which our primate lineage DNA is interdependent with the genomes of our microbiological flora. They argue that thehuman body should be understood as an ecosystem with multiple ecological niches and habitats in which a variety of cellular species collaborate and compete, and thathuman beings should be understood as 'superorganisms' that incorporate multiple symbiotic cell species into a single individual with very blurry boundaries. These metaphors carry interesting philosophical messages, but their inspiration is not entirely ideological. Instead, part of their cachet within genome science stems from the ways in which they are rooted in genomicresearch techniques, in what philosophers of science have called a 'tools-to-theory' heuristic. Their emergence within genome science illustrates the complexity of conceptual change in translationalresearch, by showing how it reflects both aspirational and methodological influences. (shrink)

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Thehuman intestinal ecosystem, previously called the gut microflora is now known as theHuman Gut Microbiota.Microbiomeresearch has emphasized the potential role of this ecosystem inhuman homeostasis, offering unexpected opportunities in therapeutics, far beyond digestive diseases. It has also highlighted ethical, social and commercial concerns related to the gut microbiota. As diet factors are accepted to be the major regulator of the gut microbiota, the modulation of its composition, either by antibiotics or (...) by food intake, should be regarded as a fascinating tool for improving thehuman health. Scientists, the food industry, consumers and policymakers alike are involved in this new field of nutrition. Defining how knowledge about the HGM is being translated into public perception has never been addressed before. This raises the question of metaphors associated with the HGM, and how they could be used to improve public understanding, and to influence individual decision-making on healthcare policy. This article suggests that a meeting of stakeholders from the social sciences, basicresearch and the food industry, taking an epistemological approach to the HGM, is needed to foster close, innovative partnerships that will help shape public perception and enable novel behavioural interventions that would benefit public health. (shrink)

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We argue for the importance of looking at the microbiota-gut-brain axis from ahuman developmental perspective. For this purpose, we first briefly highlight emergingresearch with infants attesting that themicrobiome plays a role in early brain and cognitive development. We then discuss the use of developmentally informed humanized mouse models and implications ofmicrobiomeresearch that go beyond probiotic administration.

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Emphatic claims of a “microbiome revolution” aside, the study of the gut microbiota and its role in organismal development and evolution is a central feature of so-called postgenomics; namely, a conceptual and/or practical turn in contemporary life sciences, which departs from genetic determinism and reductionism to explore holism, emergentism and complexity in biological knowledge-production. This paper analyses the making of postgenomic knowledge about developmental symbiosis in Drosophila melanogaster by a specific group ofmicrobiome scientists. Drawing from both practical (...) philosophy of science and Science and Technology Studies, the paper documents epistemological questions of artefactuality and representativeness of model organisms as they emerge in the day-to-day labour producing and being produced by the “microbiome revolution." Specifically, the paper builds on all the written and editorial exchanges involved in the troubled publication of aresearch paper studying the symbiotic role of the microbiota in the flies’ development. These written materials permit us to delimit the network of justifications, evidence, standards of knowledge-production, trust in the tools andresearch designs that make up the conditions of possibility of a postgenomic fact. More than reframing the organism as a radically novel multiplicity of reactive genomes, we conclude, doing postgenomicresearch on the microbiota and symbiosis means producing a story that deviates from the scripts embedded into the sociotechnical experimental systems of post-Human Genome Project life sciences. (shrink)

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Debates about obesity in bioethics tend to unfold in predictable epicycles between individual choices and behaviours and the oppressive socio-economic structures constraining them. Here, we argue that recent work from two cutting-edgeresearch programmes in microbiology and social psychology can advance this conceptual stalemate in the literature. We begin in section 1 by discussing two promising lines of obesityresearch involving thehumanmicrobiome and relationship partners. Then, in section 2, we show how thisresearch (...) has made viable novel strategies for fighting obesity, including microbial therapies and dyad-level interventions. Finally, in section 3, we consider objections to our account and conclude by arguing that attention to the most immediate features of our biological and social environment offers a middle ground solution, while also raising important new issues for bioethicists. (shrink)

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As understanding of thehumanmicrobiome improves, novel therapeutic targets to improvehuman health with microbial therapeutics will continue to expand. We outline key considerations of balancing risks and benefits, optimising access, returning key results toresearch participants, and potential conflicts of interest.

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. Earlymicrobiomeresearch found numerous associations between microbial community patterns and host physiological states. These findings hinted at community-level explanations. “Top-down” experiments, working with whole communities, strengthened these explanatory expectations. Now, “bottom-up” mechanism-seeking approaches are dissecting communities to focus on specific microbes carrying out particular biochemical activities. To understand the interplay between methodological and explanatory scales, we examine claims of “dysbiosis,” when host illness is proposed as the consequence of a community state. Our analysis concludes with general (...) observations about how methodologies relate to explanations, and the implications formicrobiomeresearch. (shrink)

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The public health issue of bacterial multi‐resistance to antibiotics has gained awareness among the public, researchers, and the pharmaceutical sector. Nevertheless, the spread of antimicrobial resistance has been considerably aggravated byhuman activities, climate change, and the subsequent increased release of antibiotics, drug‐resistant bacteria, and antibiotic resistance genes in the environment. The extensive use of antibiotics for medical and veterinary purposes has not only induced increasing resistance but also other health problems, including negative effects on the patient'smicrobiome. (...) Preventive strategies, new treatment modalities, and increased surveillance are progressively set up. A comprehensive approach is, however, lacking for urgently tackling this adverse situation. To address this challenge, we discussed here the main causes driving antimicrobial resistance and pollution of the environment by factors favorable to the emergence of drug resistance. We next propose some key priorities forresearch, prevention, surveillance, and education to supervise an effective clinical and sustainable response. (shrink)

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It has become increasingly clear that there is a vast array of microorganisms on and in thehuman body, known collectively as thehumanmicrobiome. Our microbiomes are extraordinarily complex, and this complexity has been linked tohuman health and well-being. Given the complexity and importance of our microbiomes, we struggle with how to think about them. There is a long list of competing metaphors that we use to refer to our microbiomes, including as an “organ” (...) containing our “second genome,” as a “symbiont” in thehuman “holobiont,” and as an ecological “community” in thehuman “ecosystem,” among others. Each of these makes different assumptions about the fundamental biology of thehuman-microbe system, with important implications for how we choose to study microbiomes, and the therapies we envision for correctingmicrobiome-linked disorders. We believe that it is time to move beyond metaphors, and we propose a scientifically pluralist approach that focuses on characterizing fundamental biological properties of microbiomes such as heritability, transmission mode, rates of dispersal rates, and strength of local selection. Such an approach will allow us to break out of the confines of narrow conceptual frameworks, and to guide the exploration of our complexity as chimeric beings. (shrink)

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We argue thatmicrobiomeresearch should be more reflective on the methods that it relies on to build its datasets due to the danger of facing a methodological problem which we call “epistemic misalignment.” An epistemic misalignment occurs when the method used to answer specific scientific questions does not track justified answers, due to the material constraints imposed by the very method. For example, relying on 16S rRNA to answer questions about the function of themicrobiome generates (...) epistemic misalignments, due to the different temporal scales that 16S rRNA provides information about and the temporal scales that are required to know about the functionality of some microorganisms. We show how some of these exist in contemporarymicrobiome science and urgemicrobiome scientists to take some measures to avoid them, as they may question the credibility of the field as a whole. (shrink)

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Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recentresearch is concerned with community functions and their dynamics over time. Models and (...) concepts from traditional ecology have been used to generate new insight into microbial communities, and novel system-level models developed to explain and predict microbial interactions. The process of moving from molecular inventories to functional understanding is complex and challenging, and never more so than when many thousands of dynamic interactions are the phenomena of interest. We outline the process of how epistemic transitions are made from producing catalogues of molecules to achieving functional and predictive insight, and show how those insights not only revolutionize what is known about biological systems but also about how to do biology itself. Examples will be drawn primarily from analyses of differenthuman microbiota, which are the microbial consortia found in and on areas of thehuman body, and their associated microbiomes (the genes of those communities). Molecular knowledge of these microbiomes is transforming microbiological knowledge, as well as broader aspects ofhuman biology, health and disease. (shrink)

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Researchers and others involved in theresearch enterprise from 12 African countries met with those working in ethics and oversight in the United States as part of an effort to developresearch ethics capacity. Drawing on a wealth of experience among participants, discussions at the meeting revealed five categories of issues that warrant careful attention by those engaged in similar efforts as well as international policymakers and those charged with oversight ofresearch. (1) Principal investigators should build (...) ‘trueresearch teams’ where members of the team are meaningfully involved in decisions regarding the protocol and its implementation. (2)There should be explicit discussion about the ‘standard of care’ at the outset of project planning that includes clarification of the terminology that is being used. (3) While internationally collaborativeresearch may involve populations that have inherent vulnerabilities, it is important to recognize the limitations of host country solutions (such as elaborated consent processes) and look for means to negotiate appropriate protections for those willing to participate. (4) In conductingresearch involving biological materials it would be prudent to develop material transfer agreements at the outset of the study to clarify expectations and to minimize the likelihood of harm. (5) Those engaged in internationally collaborativeresearch need to be alert to the potential conflicts of interests of host country ethics committees during the approval process and to take measures to manage them if they indeed exist. (shrink)

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Lynch et al., in an article in this issue, argue that an entiremicrobiome is rarely, if ever, the right target of analysis for causal explanations inmicrobiomeresearch. They argue, using interventionist criteria of proportionality, specificity and stability, for restricting causal claims to the smallest subset of microbes—a causal core—that generate the effect of interest. A further question remains: what kind of interactions generate a consortium of microbes that can operate as causal agents in this manner? (...) Here I introduce two possible kinds of such consortia: ‘trojan horses’ and ‘syntrophic’ individuals. (shrink)

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Geneticresearch has moved from Mendelian genetics to sequence maps to the study of naturalhuman genetic variation at the level of the genome. This past decade of discovery has been accompanied by a shift in emphasis towards the ethical principles of reciprocity, mutuality, solidarity, citizenry and universality.

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Different researchers from psychology and neuroscience state that navigation involves the manipulation of cognitive maps and graphs. In this paper, I will argue that navigating – specifically, journey planning – can be conceived as a process of practical reasoning. First, I will argue that journey planning constitutes a case of means-end reasoning involving inferences with cartographic representations. Then, I will argue that the output of journey planning functions as an instrumental belief in means-end reasoning. More specifically, journey planning can deliver (...) an instrumental rule that plays a normative role in spatial cognition. This approach motivates a pluralist conception of practical reasoning, stating that inferences might run through different representational formats and processes. (shrink)

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Experts from different disciplines offer novel ideas for improvingresearch oversight and protection ofhuman subjects.

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The concepts currently operating in much medicalmicrobiomeresearch bear a curious resemblance to an ancient tradition of Western medicine. This tradition, humoral medicine, is concerned with the four humors: yellow and black bile, phlegm, blood. Both humoral medicine and medicalmicrobiomeresearch use notions of imbalance and balance for broad explanations of disease and health. Both traditions also hold that the composition of humors or microbiomes determines bodily as well as mental states. Causality in each (...) system is often conceived teleologically, meaning that humors or microbiomes "function for" the maintenance of the whole. And ultimately, each framework situates the humors or microbiomes in a multilevel interactionist theory that conceptualizes individual health within a broader environmental context. As well as critically assessing the parallels between these systems, this article sketches some explanations of how they may have arisen. The authors also evaluate the implications of these similarities for the future of medicalmicrobiomeresearch and suggest ways in which the field might move forward. (shrink)

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Thehumanmicrobiome has become one of the dominant biomedical frameworks of the contemporary moment that may be understood to be post-Pasteurian. The recognitions thehumanmicrobiome opens up for thinking about the biological self and the individual have ontological and epistemological ramifications for considering what and who thehuman being is. As this article illustrates, the microbiopolitics of thehumanmicrobiome challenges the immunitarian Pasteurian model in which the organismic self shores itself (...) up and defends itself against a microbial non-self or other. Instead, this theory presents thehuman organism as comprised of multiple ecosystems and as a multitude, suggesting that the thanatopolitical attempts to wipe out microbial others (evident in the overuse and misuse of antibiotics, for example) are giving way to an affirmative microbiopolitics grounded in generative multispecies relationality. This article sets out to make the case for this affirmative microbiopolitics. (shrink)

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In lieu of an abstract, here is a brief excerpt of the content:Kennedy Institute of Ethics Journal 14.1 (2004) 47-54 [Access article in PDF] Ethical Guidelines forHuman Embryonic Stem CellResearch*(A Recommended Manuscript) Adopted on 16 October 2001Revised on 20 August 2002 Ethics Committee of the Chinese NationalHuman Genome Center at Shanghai, Shanghai 201203Human embryonic stem cell (ES)research is a great project in the frontier of biomedical science for the twenty-first century. (...) Be- cause theresearch involves the use ofhuman embryos, it triggers serious debate on ethical issues. Opponents consider the embryo to be an early form ofhuman life that should be respected and not destroyed. However, the majority of scientists support embryonic stem cellresearch, believing that it offers good prospects for the treatment of diseases that have remained incurable until now and so will benefit humankind. The Ethics Committee of the Department of Ethical, Legal, and Social Implications of the Chinese NationalHuman Genome Center at Shanghai seriously discussed the ethical debate initiated by embryonic stem cellresearch. We concluded that we should support the scientists of our country in actively carrying outhuman embryonic stem cellresearch for the noble cause of "medicine being a beneficent art." For the healthy and orderly development ofhuman embryonic stem cellresearch in our country, we put forward the following recommended Ethical Guidelines forHuman Embryonic Stem CellResearch as a reference for leaders, administrative departments, and related scientists. Preface Article 1.Human embryonic stem cells are the primitive cells that play the main role in the growth and development of ahuman body. These [End Page 47] primitive cells have the potential for infinite proliferation, self-renewal, and multi-directional differentiation. If scientists can discover the mechanism of differentiation ofhuman embryonic stem cells, it will be possible to induce differentiation ofhuman embryonic stem cells to form various types ofhuman cells for clinical cell therapy. Ifhuman embryonic stem cellresearch can be integrated with modern biomedical engineering techniques, it also will be possible to make repair and replacement ofhuman tissues and organs a reality. Article 2. There are two ways to classifyhuman embryonic stem cells. One way is to classify them according to their potential for differentiation. There could be three kinds of stem cells: totipotent stem cells, pluripotent stem cells, and unipotent stem cells.A totipotent stem cell has the potential to develop into a whole individual. It can differentiate into the more than 200 cell types in the whole body, construct any tissue or organ of the body, and finally develop into a whole individual. The fertilized egg and the cleavage cells at the very early stage of embryonic development are totipotent stem cells.A pluripotent stem cell has the potential to differentiate into many cell types derived from the three embryonic layers. However, it has lost the capacity to develop into a complete organism.A unipotent stem cell is derived from the further differentiation of the pluripotent stem cell. It can differentiate only into one cell type such as a hematopoietic stem cell, neural stem cell, and others.The other way is to classifyhuman stem cells according to their source. There could be two kinds ofhuman stem cells: embryonic stem cells and tissue stem cells (also called adult stem cells). The former involves experimentation with embryos, which has serious ethical implications. Ethical issues associated with the latter are mainly expressed in the various opinions regarding the allocation of health resources. Article 3.Human embryonic stem cells are the group of cells called the blastocyst inner cell mass during the early stage of embryonic development. They are the main source of totipotent stem cells, and hence the focal and hot point in stem cellresearch. Studies on the clinical application of embryonic stem cells probably will involve use of the somatic cell nucleus transfer (SCNT) technique, which destroys the earlyhuman embryo. At present, the ethical and moral debate is very serious inhuman embryonic stem cellresearch regarding whether theresearch will develop... (shrink)

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A challenge inhuman genomeresearch is how to describe the populations being studied. The use of improper and/or imprecise terms has the potential to both generate and reinforce prejudices and to diminish the clinical value of theresearch. The issue of population descriptors has not attracted enough academic attention outside North America and Europe. In January 2012, we held a two-day workshop, the first of its kind in Japan, to engage in interdisciplinary dialogue between scholars in (...) the humanities, social sciences, medical sciences, and genetics to begin an ongoing discussion of the social and ethical issues associated with population descriptors. (shrink)

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