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Heather Huot Creasy - One of the best experts on this subject based on the ideXlab platform.
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hmpdacc a Human Microbiome Project multi omic data resource
Nucleic Acids Research, 2021Co-Authors: Heather Huot Creasy, Victor Felix, Jain Aluvathingal, Jonathan Crabtree, Olukemi O Ifeonu, James Matsumura, Carrie Mccracken, Lance Nickel, Joshua Orvis, Mike SchorAbstract:The Human Microbiome Project (HMP) explored microbial communities of the Human body in both healthy and disease states. Two phases of the HMP (HMP and iHMP) together generated >48TB of data (public and controlled access) from multiple, varied omics studies of both the Microbiome and associated hosts. The Human Microbiome Project Data Coordination Center (HMPDACC) was established to provide a portal to access data and resources produced by the HMP. The HMPDACC provides a unified data repository, multi-faceted search functionality, analysis pipelines and standardized protocols to facilitate community use of HMP data. Recent efforts have been put toward making HMP data more findable, accessible, interoperable and reusable. HMPDACC resources are freely available at www.hmpdacc.org.
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The Integrative Human Microbiome Project
Nature, 2019Co-Authors: Lita M. Proctor, Heather Huot Creasy, Jennifer M. Fettweis, Jason Lloyd-price, Gregory A. Buck, Michael Snyder, Jerome F. Strauss, Anup Mahurkar, Wenyu Zhou, George M WeinstockAbstract:The NIH Human Microbiome Project (HMP) has been carried out over ten years and two phases to provide resources, methods, and discoveries that link interactions between Humans and their Microbiomes to health-related outcomes. The recently completed second phase, the Integrative Human Microbiome Project, comprised studies of dynamic changes in the Microbiome and host under three conditions: pregnancy and preterm birth; inflammatory bowel diseases; and stressors that affect individuals with prediabetes. The associated research begins to elucidate mechanisms of host-Microbiome interactions under these conditions, provides unique data resources (at the HMP Data Coordination Center), and represents a paradigm for future multi-omic studies of the Human Microbiome.
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Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project
Nature, 2017Co-Authors: Jason Lloyd-price, Heather Huot Creasy, Anup Mahurkar, Jonathan Crabtree, Carrie Mccracken, Joshua Orvis, Gholamali Rahnavard, Arthur Brady, A. Brantley Hall, Michelle G GiglioAbstract:Nature 550, 61–66 (2017); doi:10.1038/nature23889 This Article should have contained an associated Creative Commons statement in the Author Information section. This has been corrected in the online versions of the Article.
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strains functions and dynamics in the expanded Human Microbiome Project
Nature, 2017Co-Authors: Anup Mahurkar, Jonathan Crabtree, Joshua Orvis, Jason Lloydprice, Gholamali Rahnavard, Brantley A Hall, Arthur Brady, Heather Huot CreasyAbstract:The characterization of baseline microbial and functional diversity in the Human Microbiome has enabled studies of Microbiome-related disease, diversity, biogeography, and molecular function. The National Institutes of Health Human Microbiome Project has provided one of the broadest such characterizations so far. Here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to provide new characterizations of Microbiome personalization. Strain identification revealed subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, Human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline Human microbial diversity and enables an understanding of personalized Microbiome function and dynamics.
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a framework for Human Microbiome research
Nature, 2012Co-Authors: Barbara A Methe, Heather Huot Creasy, Karen E Nelson, Michelle G Giglio, Curtis Huttenhower, Dirk Gevers, Joseph F Petrosino, Sahar Abubucker, Jonathan H BadgerAbstract:The Human Microbiome Project Consortium has established a population-scale framework to study a variety of microbial communities that exist throughout the Human body, enabling the generation of a range of quality-controlled data as well as community resources.
Curtis Huttenhower - One of the best experts on this subject based on the ideXlab platform.
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HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor.
American journal of epidemiology, 2019Co-Authors: Lucas Schiffer, Curtis Huttenhower, Rimsha Azhar, Lori Shepherd, Marcel Ramos, Ludwig Geistlinger, Jennifer B. Dowd, Nicola Segata, Levi WaldronAbstract:Phase 1 of the Human Microbiome Project (HMP) investigated 18 body subsites of 242 healthy American adults to produce the first comprehensive reference for the composition and variation of the "healthy" Human Microbiome. Publicly available data sets from amplicon sequencing of two 16S ribosomal RNA variable regions, with extensive controlled-access participant data, provide a reference for ongoing Microbiome studies. However, utilization of these data sets can be hindered by the complex bioinformatic steps required to access, import, decrypt, and merge the various components in formats suitable for ecological and statistical analysis. The HMP16SData package provides count data for both 16S ribosomal RNA variable regions, integrated with phylogeny, taxonomy, public participant data, and controlled participant data for authorized researchers, using standard integrative Bioconductor data objects. By removing bioinformatic hurdles of data access and management, HMP16SData enables epidemiologists with only basic R skills to quickly analyze HMP data.
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Bioinformatics for the Human Microbiome Project
PLoS computational biology, 2012Co-Authors: Dirk Gevers, Mihai Pop, Patrick D. Schloss, Curtis HuttenhowerAbstract:Microbes inhabit virtually all sites of the Human body, yet we know very little about the role they play in our health. In recent years, there has been increasing interest in studying Human-associated microbial communities, particularly since microbial dysbioses have now been implicated in a number of Human diseases [1]–[3]. Dysbiosis, the disruption of the normal microbial community structure, however, is impossible to define without first establishing what “normal microbial community structure” means within the healthy Human Microbiome. Recent advances in sequencing technologies have made it feasible to perform large-scale studies of microbial communities, providing the tools necessary to begin to address this question [4], [5]. This led to the implementation of the Human Microbiome Project (HMP) in 2007, an initiative funded by the National Institutes of Health Roadmap for Biomedical Research and constructed as a large, genome-scale community research Project [6]. Any such Project must plan for data analysis, computational methods development, and the public availability of tools and data; here, we provide an overview of the corresponding bioinformatics organization, history, and results from the HMP (Figure 1).
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The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome
PLOS Biology, 2012Co-Authors: Dirk Gevers, Rob Knight, Barbara A Methe, Karen E Nelson, Joseph F Petrosino, Katherine H. Huang, Amy L. Mcguire, Bruce W. Birren, Owen White, Curtis HuttenhowerAbstract:This manuscript describes the NIH Human Microbiome Project, including a brief review of Human Microbiome research, a history of the Project, and a comprehensive overview of the consortium's recent collection of publications analyzing the Human Microbiome.
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a framework for Human Microbiome research
Nature, 2012Co-Authors: Barbara A Methe, Heather Huot Creasy, Karen E Nelson, Michelle G Giglio, Curtis Huttenhower, Dirk Gevers, Joseph F Petrosino, Sahar Abubucker, Jonathan H BadgerAbstract:The Human Microbiome Project Consortium has established a population-scale framework to study a variety of microbial communities that exist throughout the Human body, enabling the generation of a range of quality-controlled data as well as community resources.
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structure function and diversity of the healthy Human Microbiome
Nature, 2012Co-Authors: Rob Knight, Heather Huot Creasy, Curtis Huttenhower, Dirk Gevers, Sahar Abubucker, Jonathan H Badger, Asif T Chinwalla, Ashlee M. EarlAbstract:The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a Human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the Human Microbiome.
Gholamali Rahnavard - One of the best experts on this subject based on the ideXlab platform.
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host genetic variation and its Microbiome interactions within the Human Microbiome Project
Genome Medicine, 2018Co-Authors: Raivo Kolde, Gholamali Rahnavard, Eric A Franzosa, Andrew Brantley Hall, Hera Vlamakis, Christine Stevens, Mark J DalyAbstract:Despite the increasing recognition that microbial communities within the Human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the composition of these communities. Although host genetic factors play a role in these interactions, these factors have remained relatively unexplored given the requirement for large population-based cohorts in which both genotyping and Microbiome characterization have been performed. We performed whole-genome sequencing of 298 donors from the Human Microbiome Project (HMP) healthy cohort study to accompany existing deep characterization of their Microbiomes at various body sites. This analysis yielded an average sequencing depth of 32x, with which we identified 27 million (M) single nucleotide variants and 2.3 M insertions-deletions. Taxonomic composition and functional potential of the Microbiome covaried significantly with genetic principal components in the gastrointestinal tract and oral communities, but not in the nares or vaginal microbiota. Example associations included validation of known associations between FUT2 secretor status, as well as a variant conferring hypolactasia near the LCT gene, with Bifidobacterium longum abundance in stool. The associations of microbial features with both high-level genetic attributes and single variants were specific to particular body sites, highlighting the opportunity to find unique genetic mechanisms controlling Microbiome properties in the microbial communities from multiple body sites. This study adds deep sequencing of host genomes to the body-wide Microbiome sequences already extant from the HMP healthy cohort, creating a unique, versatile, and well-controlled reference for future studies seeking to identify host genetic modulators of the Microbiome.
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host genetic variation and its Microbiome interactions within the Human Microbiome Project
Genome Medicine, 2018Co-Authors: Raivo Kolde, Gholamali Rahnavard, Eric A Franzosa, Andrew Brantley Hall, Hera Vlamakis, Christine Stevens, Mark J DalyAbstract:Despite the increasing recognition that microbial communities within the Human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the composition of these communities. Although host genetic factors play a role in these interactions, these factors have remained relatively unexplored given the requirement for large population-based cohorts in which both genotyping and Microbiome characterization have been performed. We performed whole-genome sequencing of 298 donors from the Human Microbiome Project (HMP) healthy cohort study to accompany existing deep characterization of their Microbiomes at various body sites. This analysis yielded an average sequencing depth of 32x, with which we identified 27 million (M) single nucleotide variants and 2.3 M insertions-deletions. Taxonomic composition and functional potential of the Microbiome covaried significantly with genetic principal components in the gastrointestinal tract and oral communities, but not in the nares or vaginal microbiota. Example associations included validation of known associations between FUT2 secretor status, as well as a variant conferring hypolactasia near the LCT gene, with Bifidobacterium longum abundance in stool. The associations of microbial features with both high-level genetic attributes and single variants were specific to particular body sites, highlighting the opportunity to find unique genetic mechanisms controlling Microbiome properties in the microbial communities from multiple body sites. This study adds deep sequencing of host genomes to the body-wide Microbiome sequences already extant from the HMP healthy cohort, creating a unique, versatile, and well-controlled reference for future studies seeking to identify host genetic modulators of the Microbiome.
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Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project
Nature, 2017Co-Authors: Jason Lloyd-price, Heather Huot Creasy, Anup Mahurkar, Jonathan Crabtree, Carrie Mccracken, Joshua Orvis, Gholamali Rahnavard, Arthur Brady, A. Brantley Hall, Michelle G GiglioAbstract:Nature 550, 61–66 (2017); doi:10.1038/nature23889 This Article should have contained an associated Creative Commons statement in the Author Information section. This has been corrected in the online versions of the Article.
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strains functions and dynamics in the expanded Human Microbiome Project
Nature, 2017Co-Authors: Anup Mahurkar, Jonathan Crabtree, Joshua Orvis, Jason Lloydprice, Gholamali Rahnavard, Brantley A Hall, Arthur Brady, Heather Huot CreasyAbstract:The characterization of baseline microbial and functional diversity in the Human Microbiome has enabled studies of Microbiome-related disease, diversity, biogeography, and molecular function. The National Institutes of Health Human Microbiome Project has provided one of the broadest such characterizations so far. Here we introduce a second wave of data from the study, comprising 1,631 new metagenomes (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to provide new characterizations of Microbiome personalization. Strain identification revealed subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, Human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline Human microbial diversity and enables an understanding of personalized Microbiome function and dynamics.
Richard A. Gibbs - One of the best experts on this subject based on the ideXlab platform.
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The gut mycobiome of the Human Microbiome Project healthy cohort
Microbiome, 2017Co-Authors: Andrea K. Nash, Thomas A. Auchtung, Jonathan R. Gesell, Matthew C. Ross, Daniel P. Smith, Christopher J. Stewart, Matthew C Wong, Ginger A Metcalf, Donna M Muzny, Richard A. GibbsAbstract:BackgroundMost studies describing the Human gut Microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal Microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our Microbiome. To date, Human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the Human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene.ResultsThree hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia, and Candida, with S. cerevisiae, M. restricta, and C. albicans operational taxonomic units (OTUs) present in 96.8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta, and C. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents.ConclusionsCompared to bacterial communities, the Human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia, and Candida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual’s mycobiome is no more similar to itself over time than to another person’s. Nonetheless, several fungal species persisted across a majority of samples, evidence that a core gut mycobiome may exist. ITS2 sequencing data provided greater resolution of the mycobiome membership compared to metagenomic and 18S rRNA gene sequencing data, suggesting that it is a more sensitive method for studying the mycobiome of stool samples.
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The gut mycobiome of the Human Microbiome Project healthy cohort.
Microbiome, 2017Co-Authors: Andrea K. Nash, Thomas A. Auchtung, Jonathan R. Gesell, Matthew C. Ross, Daniel P. Smith, Christopher J. Stewart, Matthew C Wong, Ginger A Metcalf, Donna M Muzny, Richard A. GibbsAbstract:Most studies describing the Human gut Microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal Microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our Microbiome. To date, Human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the Human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene. Three hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia, and Candida, with S. cerevisiae, M. restricta, and C. albicans operational taxonomic units (OTUs) present in 96.8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta, and C. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents. Compared to bacterial communities, the Human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia, and Candida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual’s mycobiome is no more similar to itself over time than to another person’s. Nonetheless, several fungal species persisted across a majority of samples, evidence that a core gut mycobiome may exist. ITS2 sequencing data provided greater resolution of the mycobiome membership compared to metagenomic and 18S rRNA gene sequencing data, suggesting that it is a more sensitive method for studying the mycobiome of stool samples.
Dirk Gevers - One of the best experts on this subject based on the ideXlab platform.
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Bioinformatics for the Human Microbiome Project
PLoS computational biology, 2012Co-Authors: Dirk Gevers, Mihai Pop, Patrick D. Schloss, Curtis HuttenhowerAbstract:Microbes inhabit virtually all sites of the Human body, yet we know very little about the role they play in our health. In recent years, there has been increasing interest in studying Human-associated microbial communities, particularly since microbial dysbioses have now been implicated in a number of Human diseases [1]–[3]. Dysbiosis, the disruption of the normal microbial community structure, however, is impossible to define without first establishing what “normal microbial community structure” means within the healthy Human Microbiome. Recent advances in sequencing technologies have made it feasible to perform large-scale studies of microbial communities, providing the tools necessary to begin to address this question [4], [5]. This led to the implementation of the Human Microbiome Project (HMP) in 2007, an initiative funded by the National Institutes of Health Roadmap for Biomedical Research and constructed as a large, genome-scale community research Project [6]. Any such Project must plan for data analysis, computational methods development, and the public availability of tools and data; here, we provide an overview of the corresponding bioinformatics organization, history, and results from the HMP (Figure 1).
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The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome
PLOS Biology, 2012Co-Authors: Dirk Gevers, Rob Knight, Barbara A Methe, Karen E Nelson, Joseph F Petrosino, Katherine H. Huang, Amy L. Mcguire, Bruce W. Birren, Owen White, Curtis HuttenhowerAbstract:This manuscript describes the NIH Human Microbiome Project, including a brief review of Human Microbiome research, a history of the Project, and a comprehensive overview of the consortium's recent collection of publications analyzing the Human Microbiome.
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the Human Microbiome Project a community resource for the healthy Human Microbiome
PLOS Biology, 2012Co-Authors: Dirk Gevers, Rob Knight, Karen E Nelson, Joseph F Petrosino, Katherine H. Huang, Amy L. Mcguire, Bruce W. Birren, Owen White, Barbara A MetheAbstract:The Human Microbiome Project (HMP) [1],[2] is a concept that was long in the making. After the Human Genome Project, interest grew in sequencing the “other genome" of microbes carried in and on the Human body [3],[4]. Microbial ecologists, realizing that >99% of environmental microbes could not be easily cultured, developed approaches to study microorganisms in situ [5], primarily by sequencing the 16S ribosomal RNA gene (16S) as a phylogenetic and taxonomic marker to identify members of microbial communities [6]. The need to develop corresponding new methods for culture-independent studies [7],[8] in turn precipitated a sea change in the study of microbes and Human health, inspiring the new term “metagenomics" [9] both to describe a technological approach—sequencing and analysis of the genes from whole communities rather than from individual genomes—and to emphasize that microbes function within communities rather than as individual species. This shift from a focus on individual organisms to microbial interactions [10] culminated in a National Academy of Science report [11], which outlined challenges and promises for metagenomics as a way of understanding the foundational role of microbial communities both in the environment and in Human health. Pioneering medical microbiologists applied these approaches, finding far more microbial diversity than expected even in well-studied body site habitats [12]. Technological advances further enabled sequencing of communities across the Human body, and immunologists began exploring the fundamental role of microorganisms in the maturation of the innate and adaptive immune systems. Initial metagenomic studies of Human-associated microbial communities were performed using the traditional Sanger platform [13],[14]. Upon introduction of pyrosequencing [15], the number of 16S-based data sets increased dramatically [16],[17]. The time was right to invest in a concerted study of the microbial communities associated with the Human body and the metabolic capabilities they provide—the Human Microbiome (Figure 1) [18]. Figure 1 Timeline of microbial community studies using high-throughput sequencing. To coordinate these efforts relating the Microbiome to Human health, the NIH Common Fund launched the HMP as a community resource program (http://commonfund.nih.gov/hmp/) [19]. One of its main goals was to create a baseline view of the healthy Human Microbiome in five major areas (airways, skin, oral cavity, gastrointestinal tract, and vagina) and to make this resource available to the broad scientific community. Characterizing the baseline state of the microbiota is a critical first step in determining how altered microbial states contribute to disease (e.g., [13],[20]–[23]). Previous work showed wide inter- and intra-personal diversity of Human-associated microbes [24], necessitating analysis of a large number of subjects and characterization of many reference bacterial genomes [25] to assist in interpretation of metagenomic data. The scope of the HMP thus required a particularly diverse consortium (Figure 2A), and collaboration among these teams ultimately stimulated research growth throughout the field and produced a study including the first consistent sampling of many clinically relevant body habitats, within a large population, with paired 16S profiling and deep metagenomic sequencing coverage for hundreds of microbial communities. Figure 2 HMP consortium activities as a model for Microbiome data generation and analyses. The HMP required careful consideration of ethical, legal, and social implications (ELSI) unique to the study of the Microbiome [26]. Such research raises questions regarding traditional distinctions between self and non-self, Human and non-Human, genetics and environment, and health and disease. The prospect of manipulating the microbiota in ways that could permanently alter an individual's biological identity requires the development of new ethical paradigms analogous to, but not identical to, those already considered for gene therapy. Likewise, just as gene patents have proven controversial, defining who “owns" a Microbiome raises difficult questions of intellectual property. The ELSI team helped to develop an appropriate sample collection protocol, to draft a template for informed consent, and consulted on ethical issues arising during the study, such as the possibility that unique Human Microbiome “signatures" [27] might compromise participant privacy. A portion of the HMP's dedicated research budget continues to be committed to integrating multidisciplinary approaches (including philosophical, social science, and legal methods) to study these issues and involve stakeholders including study participants, scientists, policy makers, patients, and indigenous populations.
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a framework for Human Microbiome research
Nature, 2012Co-Authors: Barbara A Methe, Heather Huot Creasy, Karen E Nelson, Michelle G Giglio, Curtis Huttenhower, Dirk Gevers, Joseph F Petrosino, Sahar Abubucker, Jonathan H BadgerAbstract:The Human Microbiome Project Consortium has established a population-scale framework to study a variety of microbial communities that exist throughout the Human body, enabling the generation of a range of quality-controlled data as well as community resources.
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structure function and diversity of the healthy Human Microbiome
Nature, 2012Co-Authors: Rob Knight, Heather Huot Creasy, Curtis Huttenhower, Dirk Gevers, Sahar Abubucker, Jonathan H Badger, Asif T Chinwalla, Ashlee M. EarlAbstract:The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a Human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the Human Microbiome.
