"Who owns your poop?": insights regarding the intersection of human microbiome research and the ELSI aspects of biobanking and related studies

Harnessing the Microbiome: A Comprehensive Review on Advancing Therapeutic Strategies for Rheumatic Diseases

Rheumatic diseases are a group of disorders that affect the joints, muscles, and bones. These diseases, such as rheumatoid arthritis, lupus, and psoriatic arthritis, can cause pain, stiffness, and swelling, leading to reduced mobility and disability. Recent studies have identified the microbiome, the diverse community of microorganisms that live in and on the human body, as a potential factor in the development and progression of rheumatic diseases. Harnessing the microbiome offers a promising new avenue for developing therapeutic strategies for these debilitating conditions. There is growing interest in the role of oral and gut microbiomes in the management of rheumatoid arthritis and other autoimmune disease. Microbial metabolites have immunomodulatory properties that could be exploited for rheumatic disorders. A wide range of microorganisms are present in the oral cavity and are found to be vulnerable to the effects of the environment. The physiology and ecology of the microbiota become intimately connected with those of the host, and they critically influence the promotion of health or progression toward disease. This article aims to provide a comprehensive overview of the current state of knowledge on oral and gut microbiome and its potential future role in the management of rheumatic diseases. This article will also discuss newer treatment strategies such as bioinformatic analyses and fecal transplantation.

An ethical code for collecting, using and transferring sensitive health data: outcomes of a modified Policy Delphi process in Singapore

One of the core goals of Digital Health Technologies (DHT) is to transform healthcare services and delivery by shifting primary care from hospitals into the community. However, achieving this goal will rely on the collection, use and storage of large datasets. Some of these datasets will be linked to multiple sources, and may include highly sensitive health information that needs to be transferred across institutional and jurisdictional boundaries. The growth of DHT has outpaced the establishment of clear legal pathways to facilitate the collection, use and transfer of potentially sensitive health data. Our study aimed to address this gap with an ethical code to guide researchers developing DHT with international collaborative partners in Singapore. We generated this code using a modified Policy Delphi process designed to engage stakeholders in the deliberation of health data ethics and governance. This paper reports the outcomes of this process along with the key components of the code and identifies areas for future research.

Microbiome ownership for Indigenous peoples

Several studies have reported increased microbial diversity, or distinct microbial community compositions, in the microbiomes of Indigenous peoples around the world. However, there is a widespread failure to include Indigenous cultures and perspectives in microbiome research programmes, and ethical issues pertaining to microbiome research involving Indigenous participants have not received enough attention. We discuss the benefits and risks arising from microbiome research involving Indigenous peoples and analyse microbiome ownership as an ethical concept in this context. We argue that microbiome ownership represents an opportunity for Indigenous peoples to steward and protect their resident microbial communities at every stage of research.

Donors' experiences and attitudes of fecal microbiota transplantation: An empirical bioethics study from China

Donor participation is a critical part of ensuring the development of human microbiome research and the clinical application of fecal microbiota transplantation (FMT). Most FMT donors are still not sufficiently aware of the risks associated with the act of donating gut microbiota, especially the risk of data privacy disclosure. Enhanced awareness of the moral responsibility of the researchers and ethical oversight by ethics committees are needed.

Advances and Trends in Omics Technology Development

The human history has witnessed the rapid development of technologies such as high-throughput sequencing and mass spectrometry that led to the concept of “omics” and methodological advancement in systematically interrogating a cellular system. Yet, the ever-growing types of molecules and regulatory mechanisms being discovered have been persistently transforming our understandings on the cellular machinery. This renders cell omics seemingly, like the universe, expand with no limit and our goal toward the complete harness of the cellular system merely impossible. Therefore, it is imperative to review what has been done and is being done to predict what can be done toward the translation of omics information to disease control with minimal cell perturbation. With a focus on the “four big omics,” i.e., genomics, transcriptomics, proteomics, metabolomics, we delineate hierarchies of these omics together with their epiomics and interactomics, and review technologies developed for interrogation. We predict, among others, redoxomics as an emerging omics layer that views cell decision toward the physiological or pathological state as a fine-tuned redox balance.

Disaster Risk Management, Ventilated Improved Pit Latrines, and Sanitation Challenges in South Africa

The current paper provides a review and meta-analysis of the practical implications of disaster risk management related to the ventilated improved latrines in South Africa. This technology is evaluated through its legacy and novel challenges of disaster risk reduction. In the current article, the methodology adopted was a literature review and meta-analyses. The results indicate that the in-situ treatment and breakdown of faecal sludge in the ventilated improved pit latrines is not always taking place and that anaerobic digestion might not always be feasible. New strategies are proposed to manage the sanitation-related risks in South Africa by specifying more exact dimensions for the newly built ventilated improved pit latrines by suggesting the use of novel sanitation additives such as fly ash to enhance on-site and in situ treatment, as well as ex situ treatment of the pit latrine faecal sludge. Regular maintenance can lead to prevention of the dysfunctional character of the ventilated improved pit latrines as a functional sanitation technology and a user-friendly hygiene barrier to the spread of sanitation/WASH-related epidemics or infectious diseases. The implementation of the novel strategies should be enhanced by the application of the (Environmental) Technology Assessment in sanitation service delivery in South Africa.

A comprehensive approach to stool donor screening for faecal microbiota transplantation in China

Background

Faecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridium difficile infections and chronic gastrointestional infections. However, the risks of FMT and the selection process of suitable donors remain insufficiently characterized. The eligibility rate for screening, underlying microbial basis, and core ethical issues of stool donors for FMT are yet to be elucidated in China.

Results

The potential stool donors were screened from December 2017 to December 2019 with the help of an online survey, clinical assessments, and stool and blood testing. Bioinformatics analyses were performed, and the composition and stability of gut microbiota in stool obtained from eligible donors were dynamically observed using metagenomics. Meanwhile, we build a donor microbial evaluation index (DoMEI) for stool donor screening. In the screening process, we also focused on ethical principles and requirements. Of the 2071 participants, 66 donors were selected via the screening process (3.19% success rate). Although there were significant differences in gut microbiota among donors, we found that the changes in the gut microbiota of the same donor were typically more stable than those between donors over time.

Conclusions

DoMEI provides a potential reference index for regular stool donor re-evaluation. In this retrospective study, we summarised the donor recruitment and screening procedure ensuring the safety and tolerability for FMT in China. Based on the latest advances in this field, we carried out rigorous recommendation and method which can assist stool bank and clinicians to screen eligible stool donor for FMT.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01705-0.

Current Status and Future Challenges of Biobank Research in Malaysia

The establishment of MyCohort in 2005 showed that there is a growing interest on the part of the Malaysian government in the creation of biobanks in the country. This project can be considered as the biggest and most comprehensive cohort study in Malaysia, where hundreds of thousands of human samples are stored for epidemiological and biomedical research. However, little is known about the current issues or the situation related to biobank research in Malaysia. There are pressing issues that need answers such as the governance of the national biobank as well as other privately owned biobanks in the nation, the public perspectives and perceptions regarding biobanks, and other matters such as the ethical, legal, and social issues related to biobank research. This article will highlight the status and issues related to biobank research in Malaysia and provide suggestions on future research practices that we feel need to be seriously considered. These suggestions are designed to advance and enlighten researchers' knowledge, as well as provide the public with information on issues associated to biobanking. Good governance increases public knowledge and trust, and religious acceptance of biobank research and accountability can lead to increased participation in biobank research. The direct implications of the discussion about the ethical, legal, and social issues of biobanks are pertinent for the foundation of knowledge relating to biobanks, as well as the forward gestures for future medicine for mankind.

Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice

Humans are inextricably linked to each other and our natural world, and microorganisms lie at the nexus of those interactions. Microorganisms form genetically flexible, taxonomically diverse, and biochemically rich communities, i.e., microbiomes that are integral to the health and development of macroorganisms, societies, and ecosystems. Yet engagement with beneficial microbiomes is dictated by access to public resources, such as nutritious food, clean water and air, safe shelter, social interactions, and effective medicine. In this way, microbiomes have sociopolitical contexts that must be considered. The Microbes and Social Equity (MSE) Working Group connects microbiology with social equity research, education, policy, and practice to understand the interplay of microorganisms, individuals, societies, and ecosystems. Here, we outline opportunities for integrating microbiology and social equity work through broadening education and training; diversifying research topics, methods, and perspectives; and advocating for evidence-based public policy that supports sustainable, equitable, and microbial wealth for all.

The impact of cross-kingdom molecular forensics on genetic privacy

Recent advances in metagenomic technology and computational prediction may inadvertently weaken an individual's reasonable expectation of privacy. Through cross-kingdom genetic and metagenomic forensics, we can already predict at least a dozen human phenotypes with varying degrees of accuracy. There is also growing potential to detect a "molecular echo" of an individual's microbiome from cells deposited on public surfaces. At present, host genetic data from somatic or germ cells provide more reliable information than microbiome samples. However, the emerging ability to infer personal details from different microscopic biological materials left behind on surfaces requires in-depth ethical and legal scrutiny. There is potential to identify and track individuals, along with new, surreptitious means of genetic discrimination. This commentary underscores the need to update legal and policy frameworks for genetic privacy with additional considerations for the information that could be acquired from microbiome-derived data. The article also aims to stimulate ubiquitous discourse to ensure the protection of genetic rights and liberties in the post-genomic era. Video abstract.

Governing Personalized Health: A Scoping Review

Genetic research is advancing rapidly. One important area for the application of the results from this work is personalized health. These are treatments and preventive interventions tailored to the genetic profile of specific groups or individuals. The inclusion of personalized health in existing health systems is a challenge for policymakers. In this article, we present the results of a thematic scoping review of the literature dealing with governance and policy of personalized health. Our analysis points to four governance challenges that decisionmakers face against the background of personalized health. First, researchers have highlighted the need to further extend and harmonize existing research infrastructures in order to combine different types of genetic data. Second, decisionmakers face the challenge to create trust in personalized health applications, such as genetic tests. Third, scholars have pointed to the importance of the regulation of data production and sharing to avoid discrimination of disadvantaged groups and to facilitate collaboration. Fourth, researchers have discussed the challenge to integrate personalized health into regulatory-, financing-, and service provision structures of existing health systems. Our findings summarize existing research and help to guide further policymaking and research in the field of personalized health governance.

Microbiomics: Were we all wrong before?

Periodontal microbiology has historically been based on an "us against them" paradigm, one that focuses mainly on identifying microbes and viruses that cause disease. However, such a bottom-up approach limits our appreciation of the incredible diversity of this ecosystem and the essential ways in which microbial interactions contribute to health and homeostasis of the subgingival niche. Microbiomics-the science of collectively characterizing and quantifying molecules responsible for the structure, function, and dynamics of a microbial community-has enabled us to study these communities in their natural habitat, thereby revolutionizing our knowledge of host-associated microbes and reconceptualizing our definition of "human." When this systems-biology approach is combined with ecologic principles, it explicates the complex relationship that exist between microbiota and between them and us, the human. In this volume of Periodontology 2000, a group of 12 female scientists take the lead in investigating how metagenomics, genomics, metatranscriptomics, proteomics, metaproteomics, and metabolomics have achieved the following: (a) widened our view of the periodontal microbiome; (b) expanded our understanding of the evolution of the human oral microbiome; (c) shone a light on not just bacteria, but also other prokaryotic and eukaryotic members of the community; (d) elucidated the effects of anthropogenic behavior and systemic diseases on shaping these communities; and (e) influenced traditional patterns of periodontal therapeutics.

Public understanding of science and common sense: Social representations of the human microbiome among the expert and non-expert public

The aim of this investigation is to examine the structure and the content of different social groups' representations of the human microbiome. We employed a non-probabilistic sample comprising two groups of participants. The first group (n = 244) included university students. The second group included lay people (n = 355). We chose a mixed-method approach. The data obtained were processed using IRaMuTeQ software. The results allow us to identify the anchoring and objectification processes activated by the two different groups of interviewees. The results could be useful to those in charge of implementing campaigns aimed at promoting health literacy.

Framing the discussion of microorganisms as a facet of social equity in human health

What do “microbes” have to do with social equity? These microorganisms are integral to our health, that of our natural environment, and even the “health” of the environments we build. The loss, gain, and retention of microorganisms—their flow between humans and the environment—can greatly impact our health. It is well-known that inequalities in access to perinatal care, healthy foods, quality housing, and the natural environment can create and arise from social inequality. Here, we focus on the argument that access to beneficial microorganisms is a facet of public health, and health inequality may be compounded by inequitable microbial exposure.

What do microbes have to do with social equity? This Essay explores the argument that access to beneficial microorganisms is a facet of public health, and that health inequality may be compounded by inequitable microbial exposure.

Fecal microbiota transplantation: donor relation, fresh or frozen, delivery methods, cost-effectiveness

Fecal microbiota transplantation (FMT) has evolved into a robust and efficient means for treating recurrent Clostridium difficile infection (CDI). Our narrative review looks at the donor selection, preparation, delivery techniques and cost-effectiveness of FMT. We searched electronic databases, including PubMed, MEDLINE, Google Scholar, and Cochrane Databases, for studies that compared the biological effects of donor selection, fresh or frozen fecal preparation, and various delivery techniques. We also evaluated the cost-effectiveness and manually searched references to identify additional relevant studies. Overall, there is a paucity of studies that directly compare outcomes associated with related and non-related stool donors. However, inferences from prior studies indicate that the success of FMT does not depend on the donor-patient relationship. Over time, the use of unrelated donors has increased because of the formation of stool banks and the need to save processing time and capital. However, longitudinal studies are needed to clarify the optimal freezing time before microbial function declines. Several FMT techniques have been developed, such as colonoscopy, enema, nasogastric or nasojejunal tubes, and capsules. The comparable and high efficacy of FMT capsules, combined with their convenience, safety and aesthetically tolerable mode of delivery, makes it an attractive option for many patients. Cost-effective models comparing these various approaches support the use of FMT via colonoscopy as being the best strategy for the treatment of recurrent CDI.

Sustainability in Biobanking

Biobanks are storage places for biospecimens that can be used for current and future scientific research. Biospecimens are exceptional sources of biological data that can be potentially translated from molecular and genetic information to clinically relevant treatment modalities. Examples of such biospecimens include, but are not limited to, blood, skin, hair, saliva, stem cells, DNA, and RNA. The volume of biospecimens worldwide continues to grow at an extraordinary rate posing a challenge for biobanks to manage this growth. Due to the vital role of biobanks in research, an understanding of biobanking sustainability is important. Simply starting to collect biospecimens without strategic planning and cost analysis can lead to failure. Components vital to sustainability include fostering public support, cost-effective banking, funding development, standardized protocols, and interoperability.

Model framework for governance of genomic research and biobanking in Africa - a content description

Genomic research and biobanking are expanding globally, with a promise to fast-track the research needed to improve approaches to disease treatment and prevention through scientific collaborations such as the Human Heredity and Health in Africa (H3Africa) initiative. Integral to this type of research is the availability of samples and data for research. The need for broad access brings along a host of ethical concerns, including those related to privacy and confidentiality, as well as fairness and equity in access and capacity to utilise these samples between scientists from the high income and low income countries. Addressing these concerns while promoting genomic research, especially in Africa, requires the implementation of a sound governance framework. In this paper, we describe the contents of a Framework for Best Practice for Genomics Research and biobanking in Africa that was developed, under the auspices of the H3Africa initiative. This framework is broad enough to be used and adapted by African countries to facilitate the development of country-specific guidelines and to help improve the conduct and governance of genomics research.

Model framework for governance of genomic research and biobanking in Africa - a content description

Genomic research and biobanking are expanding globally, with a promise to fast-track the research needed to improve approaches to disease treatment and prevention through scientific collaborations such as the Human Heredity and Health in Africa (H3Africa) initiative. Integral to this type of research is the availability of samples and data for research. The need for broad access brings along a host of ethical concerns, including those related to privacy and confidentiality, as well as fairness and equity in access and capacity to utilise these samples between scientists from the high income and low income countries. Addressing these concerns while promoting genomic research, especially in Africa, requires the implementation of a sound governance framework. In this paper, we describe the contents of a Framework for Best Practice for Genomics Research and biobanking in Africa that was developed, under the auspices of the H3Africa initiative. This framework is broad enough to be used and adapted by African countries to facilitate the development of country-specific guidelines and to help improve the conduct and governance of genomics research.

The perception of different social agents in Colombia regarding biobanks for research purposes

Introduction: Biobanks for research purposes are public assets that require active participation from all interested parties; therefore, it is important to discern and investigate the perception that the general public in Colombia has with regards to their participation in a biobank. Objective: To question different healthy Colombian social agents about the perception they have on donating human biological material to be stored in a biobank for future research purposes. Materials and methods: We conducted an exploratory quantitative and qualitative research by means of an anonymous survey on healthy members of the Colombian community in order to evaluate their knowledge and stances related to biobanks. Results: Three hundred sixty-eight (368) individuals completed the survey, including health-care researchers, lawyers and members of research ethics committees. Ninety-six percent (96%) of the subjects stated their willingness to donate biological material to biobanks, although 60% expressed distress about their samples being used for certain research activities, mainly human cloning. Even though about half of the participants reported knowing what a biobank is, less than 3% of the individuals had a clear concept of them. Conclusion: Participants showed their willingness to donate and store their biological material for research purposes. Similarly, they expressed their opinion about issues related to the management of biobanks. It is necessary to take into account the opinions of the general public in the development of policies that regulate biobanks for research purposes in Colombia.

Microbial forensics: new breakthroughs and future prospects

Recent advances in genetic data generation, through massive parallel sequencing (MPS), storage and analysis have fostered significant progresses in microbial forensics (or forensic microbiology). Initial applications in circumstances of biocrime, bioterrorism and epidemiology are now accompanied by the prospect of using microorganisms (i) as ancillary evidence in criminal cases; (ii) to clarify causes of death (e.g., drownings, toxicology, hospital-acquired infections, sudden infant death and shaken baby syndromes); (iii) to assist human identification (skin, hair and body fluid microbiomes); (iv) for geolocation (soil microbiome); and (v) to estimate postmortem interval (thanatomicrobiome and epinecrotic microbial community). When compared with classical microbiological methods, MPS offers a diverse range of advantages and alternative possibilities. However, prior to its implementation in the forensic context, critical efforts concerning the elaboration of standards and guidelines consolidated by the creation of robust and comprehensive reference databases must be undertaken.

How Chinese clinicians face ethical and social challenges in fecal microbiota transplantation: a questionnaire study

BACKGROUND

Fecal microbiota transplantation (FMT) is reportedly the most effective therapy for relapsing Clostridium Difficile infection (CDI) and a potential therapeutic option for many diseases. It also poses important ethical concerns. This study is an attempt to assess clinicians' perception and attitudes towards ethical and social challenges raised by fecal microbiota transplantation.

METHODS

A questionnaire was developed which consisted of 20 items: four items covered general aspects, nine were about ethical aspects such as informed consent and privacy issues, four concerned social and regulatory issues, and three were about an FMT bank. This was distributed to participants at the Second China gastroenterology and FMT conference in May 2015. Basic descriptive statistical analyses and simple comparative statistical tests were performed.

RESULTS

Nearly three quarters of the 100 respondents were gastro-enterologist physicians. 89% of all respondents believed FMT is a promising treatment modality for some diseases and 88% of whom chose clinical efficacy as the primary reason for recommending FMT. High expectation from patients and pressure on clinicians (33%) was reported as the most frequent reasons for not recommending FMT. The clinicians who had less familiarity with FMT reported significantly more worry related to the dignity and psychological impact of FMT compared to those who have high familiarity with FMT (51.6% vs 27.8%, p = 0.021).More than half of the respondents (56.1%) were concerned about the commercialization of FMT, although almost one in five respondents did not see this as a problem.

CONCLUSIONS

We found most respondents have positive attitudes towards FMT but low awareness of published evidence. Informed consent for vulnerable patients, privacy and protection of donors were perceived as the most challenging ethical aspects of FMT. This study identified areas of limited knowledge and ways of addressing ethical issues and indicates the need to devise the education and training for clinicians on FMT.

Ethical Issues in Fecal Microbiota Transplantation in Practice

Fecal microbiota transplantation (FMT) has demonstrated efficacy and is increasingly being used in the treatment of patients with recurrent Clostridium difficile infection. Despite a lack of high-quality trials to provide more information on the long-term effects of FMT, there has been great enthusiasm about the potential for expanding its applications. However, FMT presents many serious ethical and social challenges that must be addressed as part of a successful regulatory policy response. In this article, we draw on a sample of the scientific and bioethics literatures to examine clusters of ethical and social issues arising in five main areas: (1) informed consent and the vulnerability of patients; (2) determining what a "suitable healthy donor" is; (3) safety and risk; (4) commercialization and potential exploitation of vulnerable patients; and (5) public health implications. We find that these issues are complex and worthy of careful consideration by health care professionals. Desperation of a patient should not be the basis for selecting treatment with FMT, and the patient's interests should always be of paramount concern. Authorities must prioritize development of appropriate and effective regulation of FMT to safeguard patients and donors, promote further research into safety and efficacy, and avoid abuse of the treatment.

Human Microbiome and Learning Healthcare Systems: Integrating Research and Precision Medicine for Inflammatory Bowel Disease

Healthcare institutions face widespread challenges of delivering high-quality and cost-effective care, while keeping up with rapid advances in biomedical knowledge and technologies. Moreover, there is increased emphasis on developing personalized or precision medicine targeted to individuals or groups of patients who share a certain biomarker signature. Learning healthcare systems (LHS) have been proposed for integration of research and clinical practice to fill major knowledge gaps, improve care, reduce healthcare costs, and provide precision care. To date, much discussion in this context has focused on the potential of human genomic data, and not yet on human microbiome data. Rapid advances in human microbiome research suggest that profiling of, and interventions on, the human microbiome can provide substantial opportunity for improved diagnosis, therapeutics, risk management, and risk stratification. In this study, we discuss a potential role for microbiome science in LHSs. We first review the key elements of LHSs, and discuss possibilities of Big Data and patient engagement. We then consider potentials and challenges of integrating human microbiome research into clinical practice as part of an LHS. With rapid growth in human microbiome research, patient-specific microbial data will begin to contribute in important ways to precision medicine. Hence, we discuss how patient-specific microbial data can help guide therapeutic decisions and identify novel effective approaches for precision care of inflammatory bowel disease. To the best of our knowledge, this expert analysis makes an original contribution with new insights poised at the emerging intersection of LHSs, microbiome science, and postgenomics medicine.

Using typing techniques in a specific outbreak: the ethical reflection of public health professionals

Typing techniques are laboratory methods used in outbreak management to investigate the degree to which microbes found within an outbreak are related. Knowledge about relational patterns between microbes benefits outbreak management, but inevitably also tells us something about the relational patterns of the people hosting them. Since the technique is often used without explicit consent of all individuals involved, this may raise ethical questions. The aim of this study was to unravel the complex ethical deliberation of professionals over the use of such techniques. We organised group discussions (n = 3) with Dutch outbreak managers (n = 23). The topic list was based on previously identified ethical issues and discussions were analysed for recurrent themes. We found that outbreak managers first and foremost reflect on the balance of individual harm with public health benefit. This key question was approached by way of discussing four more specific ethical themes: (1) justification of governmental intervention, (2) responsibility to prevent infections, (3) scientific uncertainty and (4) legal consequences. The themes found in this study, rephrased into accessible questions, represent the shared ethical understanding of professionals and can help to articulate the ethical dimensions of using molecular science in response to infectious disease outbreaks.

Navigating social and ethical challenges of biobanking for human microbiome research

BACKGROUND

Biobanks are considered to be key infrastructures for research development and have generated a lot of debate about their ethical, legal and social implications (ELSI). While the focus has been on human genomic research, rapid advances in human microbiome research further complicate the debate.

DISCUSSION

We draw on two cystic fibrosis biobanks in Toronto, Canada, to illustrate our points. The biobanks have been established to facilitate sample and data sharing for research 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 with human microbiome research, particularly on the implications for the broader society. We then discuss ethical considerations regarding the identifiability of samples biobanked for human microbiome research, and examine the issue of return of results and incidental findings. We argue that, for the purposes of research ethics oversight, human microbiome research samples should be treated with the same privacy considerations as human tissues samples. We also suggest that returning individual microbiome-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 to human microbiome research.

CONCLUSIONS

We revisit the ELSI of biobanking and consider the impact that human microbiome research might have. Our discussion focuses on identifiability of human microbiome research samples, and return of research results and incidental findings for clinical management.

Treating Obesity and Metabolic Syndrome with Fecal Microbiota Transplantation

The worldwide prevalence of metabolic syndrome, which includes obesity and its associated diseases, is rising rapidly. The human gut microbiome is recognized as an independent environmental modulator of host metabolic health and disease. Research in animal models has demonstrated that the gut microbiome has the functional capacity to induce or relieve metabolic syndrome. One way to modify the human gut microbiome is by transplanting fecal matter, which contains an abundance of live microorganisms, from a healthy individual to a diseased one in the hopes of alleviating illness. Here we review recent evidence suggesting efficacy of fecal microbiota transplant (FMT) in animal models and humans for the treatment of obesity and its associated metabolic disorders.

Engineering Human Microbiota: Influencing Cellular and Community Dynamics for Therapeutic Applications

The complex relationship between microbiota, human physiology, and environmental perturbations has become a major research focus, particularly with the arrival of culture-free and high-throughput approaches for studying the microbiome. Early enthusiasm has come from results that are largely correlative, but the correlative phase of microbiome research has assisted in defining the key questions of how these microbiota interact with their host. An emerging repertoire for engineering the microbiome places current research on a more experimentally grounded footing. We present a detailed look at the interplay between microbiota and host and how these interactions can be exploited. A particular emphasis is placed on unstable microbial communities, or dysbiosis, and strategies to reestablish stability in these microbial ecosystems. These include manipulation of intermicrobial communication, development of designer probiotics, fecal microbiota transplantation, and synthetic biology.

Biobanks in the era of personalized medicine: objectives, challenges, and innovation: Overview

Biobanks are an important compound of personalized medicine and strongly support the scientific progress in stratification of population and biomarker discovery and validation due to progress in personalized medicine. Biobanks are an essential tool for new drug discoveries and drug development. Biobanks play an important role in the whole process of patient prevention and prediction, follow-up, and therapy monitoring and optimalization. Biobanks have the specificity in that they cover multidisciplinary approach to the human health combining biological and medical approaches, as well as informative bioinformatics technologies, computationing, and modeling. The importance of biobanks has during the last decade increased in variety and capacity from small collections of samples to large-scale national or international repositories. Collected samples are population-based, disease-specific or rare diseases originating from a diverse profile of individuals. There are various purposes of biobanks, such as diagnostics, pharmacology, or research. Biobanks involve, store, and operate with specific personal information, and as a consequence, such a diversity of biobanking is associated with a broad spectrum of ethical and legal issues. Biobanks are an international phenomenon because any single country, state, or society at the moment is not able to cover all issues involving the whole biobank problematic. Biobanks have an enormous innovative potential in the whole process of biomedical research in the twenty-first century.

Self-tracking the microbiome: where do we go from here?

The quantified self community brings together enthusiasts who are using technological devices to monitor their health and social media to share their personal data with others online. In light of the growing popularity of this movement, self-trackers are challenging the health-care system by raising important questions about data ownership and risk-taking. As we enter a new era of consumer genomics, a significant number of quantified self (QS) individuals are now interested in the monitoring of their microbiome and performing personal interventions. In this paper, we discuss the scientific validity of experiments involving serial observations of a single individual as opposed to randomized clinical trials. We look at self-tracking from an ethical standpoint by questioning the risks and assessing the potential benefits for personalized medicine in general and for microbiome research in particular.

Media Discourse on the Social Acceptability of Fecal Transplants

Advances in human microbiome research have generated considerable interest in elucidating the role of bacteria in health and the application of microbial ecosystem therapies and probiotics. Fecal transplants involve the introduction of gut microbes from a healthy donor's stool to the patient and have been documented as effective for treating Clostridium difficile infections (CDIs) and some other gastrointestinal disorders. However, the treatment has encountered regulatory hurdles preventing widespread uptake. We examined dominant representations of fecal transplants in Canadian media and found that fecal transplants are often represented as being inherently disgusting or distasteful (the "ick factor"). This "ick factor" is used to construct different messages about the treatment's social acceptability and legitimacy. We conclude that an over-emphasis on the "ick factor" constrains public discourse from a more nuanced discussion of the social challenges, scientific concerns, and regulatory issues surrounding the treatment.

Gut Health in the era of the human gut microbiota: from metaphor to biovalue

The human intestinal ecosystem, previously called the gut microflora is now known as the Human Gut Microbiota (HGM). Microbiome research has emphasized the potential role of this ecosystem in human 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 the human 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, basic research 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.

Shrinkage of the human core microbiome and a proposal for launching microbiome biobanks

ABSTRACT: 

The Human Microbiome Project (HMP) revealed the significance of the gut microbiome in promoting health. Disruptions in microbiome composition are associated with the pathogenesis of numerous diseases. The indigenous microflora has co-evolved with humans for millions of years and humans have preserved the inherited microbiomes through consumption of fermented foods and interactions with environmental microbes. Through modernization, traditional foods were abandoned, native food starters were substituted with industrial products, vaccines and antibiotics were used, extreme hygiene measures were taken, the rate of cesarean section increased, and breast feeding changed into formula. These factors have reduced human exposure to microbial symbionts and led to shrinkage of the core microbiome. Reduction in microbiome biodiversity can compromise the human immune system and predispose individuals to several modern diseases. This article suggests launching microbiome biobanks for archiving native microbiomes, supervising antibiotic use, probiotic design and native starter production, as well as advertising a revisit to native lifestyles.

Engaging the next generation of healthcare professionals in genomics: planning for the future

There is broad agreement that healthcare professionals require fundamental training in genomics to keep pace with scientific advancement. Strong models that promote effective genomic education, however, are lacking. Furthermore, curricula at many institutions are now straining to adapt to the integration of additional material on next-generation sequencing and the bioethical and legal issues that will accompany clinical genomic testing. This article advocates for core competencies focused on job function, which will best prepare providers to be end-users of healthcare information. In addition, it argues in favor of online and blended learning models that incorporate student genotyping and specific training in the ethical, legal and social issues raised by genomic testing.

Development of a privacy and security policy framework for a multistate comparative effectiveness research network

Comparative effectiveness research (CER) conducted in distributed research networks (DRNs) is subject to different state laws and regulations as well as institution-specific policies intended to protect privacy and security of health information. The goal of the Scalable National Network for Effectiveness Research (SCANNER) project is to develop and demonstrate a scalable, flexible technical infrastructure for DRNs that enables near real-time CER consistent with privacy and security laws and best practices. This investigation began with an analysis of privacy and security laws and state health information exchange (HIE) guidelines applicable to SCANNER participants from California, Illinois, Massachusetts, and the Federal Veteran's Administration. A 7-member expert panel of policy and technical experts reviewed the analysis and gave input into the framework during 5 meetings held in 2011-2012. The state/federal guidelines were applied to 3 CER use cases: safety of new oral hematologic medications; medication therapy management for patients with diabetes and hypertension; and informational interventions for providers in the treatment of acute respiratory infections. The policy framework provides flexibility, beginning with a use-case approach rather than a one-size-fits-all approach. The policies may vary depending on the type of patient data shared (aggregate counts, deidentified, limited, and fully identified datasets) and the flow of data. The types of agreements necessary for a DRN may include a network-level and data use agreements. The need for flexibility in the development and implementation of policies must be balanced with responsibilities of data stewardship.

If microbial ecosystem therapy can change your life, what's the problem?

The increased incidence of morbidity and mortality due to Clostridium difficile infection, had led to the emergence of fecal microbial transplantation (FMT) as a highly successful treatment. From this, a 32 strain stool substitute has been derived, and successfully tested in a pilot human study. These approaches could revolutionize not only medical care of infectious diseases, but potentially many other conditions linked to the human microbiome. But a second revolution may be needed in order for regulatory agencies, society and medical practitioners to accept and utilize these interventions, monitor their long term effects, have a degree of control over their use, or at a minimum provide guidelines for donors and recipients.

Are changes to the common rule necessary to address evolving areas of research? A case study focusing on the human microbiome project

This article examines ways in which research conducted under the Human Microbiome Project, an effort to establish a "reference catalogue" of the micro-organisms present in the human body and determine how changes in those micro-organisms affect health and disease, raise challenging issues for regulation of human subject research. The article focuses on issues related to subject selection and recruitment, group stigma, and informational risks, and explores whether: (1) the Common Rule or proposed changes to the Rule adequately address these issues and (2) the Common Rule is the most appropriate vehicle to provide regulatory oversight and guidance on these topics.

Perspectives on human microbiome research ethics

Study of ethical, legal, and social implications (ELSI) of human microbiome research has been integral to the Human Microbiome Project (HMP). This study explores core ELSI issues that arose during the first phase of the HMP from the perspective of individuals involved in the research. We conducted semi-structured in-depth interviews with investigators and NIH employees ("investigators") involved in the HMP, and with individuals recruited to participate in the HMP Healthy Cohort Study at Baylor College of Medicine ("recruits"). We report findings related to three major ELSI issues: informed consent, data sharing, and return of results. Our findings demonstrate that investigators and recruits were similarly sensitive to these issues yet generally comfortable with study design in light of current knowledge about the microbiome.

"Snake-oil," "quack medicine," and "industrially cultured organisms:" biovalue and the commercialization of human microbiome research

Background

Continued advances in human microbiome research and technologies raise a number of ethical, legal, and social challenges. These challenges are associated not only with the conduct of the research, 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 of human microbiome research, focusing particularly on how this research 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 with human microbiome research. Interviews explored a range of ethical, legal, and social dimensions of human microbiome research, including investigators’ perspectives on commercialization. Using thematic content analysis, we identified and analyzed emergent themes and patterns.

Results

Investigators discussed the commercialization of human microbiome research 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, scientific research, and the public’s health. The themes we identified are intended to serve as points for discussions about the relationship between scientific research and the manufacture and distribution of over-the-counter dietary supplements in the United States.

A Canadian Working Group report on fecal microbial therapy: microbial ecosystems therapeutics

A working group from across Canada comprised of clinician and basic scientists, epidemiologists, ethicists, Health Canada regulatory authorities and representatives of major funding agencies (Canadian Institutes of Health Research and the Crohn's and Colitis Foundation of Canada) met to review the current experience with fecal microbial therapy and to identify the key areas of study required to move this field forward. The report highlights the promise of fecal microbial therapy and related synthetic stool therapy (together called 'microbial ecosystems therapeutics') for the treatment of Clostridium difficile colitis and, possibly, other disorders. It identifies pressing clinical issues that need to be addressed as well as social, ethical and regulatory barriers to the use of these important therapies.