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

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          Abstract

          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.

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          Most cited references15

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          Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency.

          Nonalcoholic fatty liver disease affects up to 30% of the US population, but the mechanisms underlying this condition are incompletely understood. We investigated how diet standardization and choline deficiency influence the composition of the microbial community in the human gastrointestinal tract and the development of fatty liver under conditions of choline deficiency. We performed a 2-month inpatient study of 15 female subjects who were placed on well-controlled diets in which choline levels were manipulated. We used 454-FLX pyrosequencing of 16S ribosomal RNA bacterial genes to characterize microbiota in stool samples collected over the course of the study. The compositions of the gastrointestinal microbial communities changed with choline levels of diets; each individual's microbiome remained distinct for the duration of the experiment, even though all subjects were fed identical diets. Variations between subjects in levels of Gammaproteobacteria and Erysipelotrichi were directly associated with changes in liver fat in each subject during choline depletion. Levels of these bacteria, change in amount of liver fat, and a single nucleotide polymorphism that affects choline were combined into a model that accurately predicted the degree to which subjects developed fatty liver on a choline-deficient diet. Host factors and gastrointestinal bacteria each respond to dietary choline deficiency, although the gut microbiota remains distinct in each individual. We identified bacterial biomarkers of fatty liver that result from choline deficiency, adding to the accumulating evidence that gastrointestinal microbes have a role in metabolic disorders. Copyright © 2011 AGA Institute. Published by Elsevier Inc. All rights reserved.
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            The Human Microbiome Project in 2011 and beyond.

            The human microbiome comprises the genes and genomes of the microbiota that inhabit the body. We highlight Human Microbiome Project (HMP) resources, including 600 microbial reference genomes, 70 million 16S sequences, 700 metagenomes, and 60 million predicted genes from healthy adult microbiomes. Microbiome studies of specific diseases and future research directions are also discussed. Copyright © 2011 Elsevier Inc. All rights reserved.
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              A novel abundance-based algorithm for binning metagenomic sequences using l-tuples.

              Metagenomics is the study of microbial communities sampled directly from their natural environment, without prior culturing. Among the computational tools recently developed for metagenomic sequence analysis, binning tools attempt to classify the sequences in a metagenomic dataset into different bins (i.e., species), based on various DNA composition patterns (e.g., the tetramer frequencies) of various genomes. Composition-based binning methods, however, cannot be used to classify very short fragments, because of the substantial variation of DNA composition patterns within a single genome. We developed a novel approach (AbundanceBin) for metagenomics binning by utilizing the different abundances of species living in the same environment. AbundanceBin is an application of the Lander-Waterman model to metagenomics, which is based on the l-tuple content of the reads. AbundanceBin achieved accurate, unsupervised, clustering of metagenomic sequences into different bins, such that the reads classified in a bin belong to species of identical or very similar abundances in the sample. In addition, AbundanceBin gave accurate estimations of species abundances, as well as their genome sizes-two important parameters for characterizing a microbial community. We also show that AbundanceBin performed well when the sequence lengths are very short (e.g., 75 bp) or have sequencing errors. By combining AbundanceBin and a composition-based method (MetaCluster), we can achieve even higher binning accuracy. Supplementary Material is available at www.liebertonline.com/cmb .
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                Author and article information

                Journal
                BMC Med Ethics
                BMC Med Ethics
                BMC Medical Ethics
                BioMed Central
                1472-6939
                2012
                30 October 2012
                : 13
                : 28
                Affiliations
                [1 ]Center for Medical Ethics and Health Policy, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
                [2 ]University of Texas School of Public Health, Center for Health Promotion and Prevention Research, 7000 Fannin Street, Houston, TX, 77030, USA
                [3 ]Department of Family and Community Medicine, Baylor College of Medicine, 3701 Kirby Drive, Suite 600, Houston, TX, 77098, USA
                Article
                1472-6939-13-28
                10.1186/1472-6939-13-28
                3512494
                23110633
                331b0092-1d5a-41aa-99d7-e74798cc95f7
                Copyright ©2012 Slashinski et al.; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 2 May 2012
                : 15 October 2012
                Categories
                Research Article

                Medicine
                commercialization,dietary supplements,human microbiome,qualitative research,ethical legal and social implications (elsi)

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