The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome
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{"title"=>"The Human Microbiome Project: A Community Resource for the Healthy Human Microbiome", "type"=>"journal", "authors"=>[{"first_name"=>"Dirk", "last_name"=>"Gevers", "scopus_author_id"=>"6603379365"}, {"first_name"=>"Rob", "last_name"=>"Knight", "scopus_author_id"=>"8622605900"}, {"first_name"=>"Joseph F.", "last_name"=>"Petrosino", "scopus_author_id"=>"6603064501"}, {"first_name"=>"Katherine", "last_name"=>"Huang", "scopus_author_id"=>"8627731500"}, {"first_name"=>"Amy L.", "last_name"=>"McGuire", "scopus_author_id"=>"9336287600"}, {"first_name"=>"Bruce W.", "last_name"=>"Birren", "scopus_author_id"=>"7003582624"}, {"first_name"=>"Karen E.", "last_name"=>"Nelson", "scopus_author_id"=>"7403227781"}, {"first_name"=>"Owen", "last_name"=>"White", "scopus_author_id"=>"7006065802"}, {"first_name"=>"Barbara A.", "last_name"=>"Methé", "scopus_author_id"=>"35401400600"}, {"first_name"=>"Curtis", "last_name"=>"Huttenhower", "scopus_author_id"=>"14521138100"}], "year"=>2012, "source"=>"PLoS Biology", "identifiers"=>{"pmid"=>"22904687", "doi"=>"10.1371/journal.pbio.1001377", "sgr"=>"84865741828", "isbn"=>"1545-7885 (Electronic) 1544-9173 (Linking)", "scopus"=>"2-s2.0-84865741828", "issn"=>"15449173", "pui"=>"365577408"}, "id"=>"fab11f4c-3066-3ab2-9a86-c7739b579847", "abstract"=>"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.", "link"=>"http://www.mendeley.com/research/human-microbiome-project-community-resource-healthy-human-microbiome-4", "reader_count"=>447, "reader_count_by_academic_status"=>{"Unspecified"=>8, "Professor > Associate Professor"=>28, "Librarian"=>2, "Researcher"=>101, "Student > Doctoral Student"=>21, "Student > Ph. D. Student"=>98, "Student > Postgraduate"=>12, "Student > Master"=>60, "Other"=>28, "Student > Bachelor"=>58, "Lecturer"=>5, "Lecturer > Senior Lecturer"=>5, "Professor"=>21}, "reader_count_by_user_role"=>{"Unspecified"=>8, "Professor > Associate Professor"=>28, "Librarian"=>2, "Researcher"=>101, "Student > Doctoral Student"=>21, "Student > Ph. D. Student"=>98, "Student > Postgraduate"=>12, "Student > Master"=>60, "Other"=>28, "Student > Bachelor"=>58, "Lecturer"=>5, "Lecturer > Senior Lecturer"=>5, "Professor"=>21}, "reader_count_by_subject_area"=>{"Unspecified"=>19, "Agricultural and Biological Sciences"=>238, "Arts and Humanities"=>3, "Veterinary Science and Veterinary Medicine"=>4, "Business, Management and Accounting"=>3, "Chemistry"=>5, "Computer Science"=>15, "Earth and Planetary Sciences"=>1, "Economics, Econometrics and Finance"=>2, "Engineering"=>2, "Environmental Science"=>12, "Biochemistry, Genetics and Molecular Biology"=>42, "Nursing and Health Professions"=>1, "Materials Science"=>1, "Medicine and Dentistry"=>65, "Neuroscience"=>3, "Pharmacology, Toxicology and Pharmaceutical Science"=>2, "Physics and Astronomy"=>2, "Psychology"=>2, "Social Sciences"=>5, "Immunology and Microbiology"=>20}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>65}, "Social Sciences"=>{"Social Sciences"=>5}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Psychology"=>{"Psychology"=>2}, "Unspecified"=>{"Unspecified"=>19}, "Environmental Science"=>{"Environmental Science"=>12}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>2}, "Arts and Humanities"=>{"Arts and Humanities"=>3}, "Engineering"=>{"Engineering"=>2}, "Chemistry"=>{"Chemistry"=>5}, "Neuroscience"=>{"Neuroscience"=>3}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>20}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>238}, "Computer Science"=>{"Computer Science"=>15}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>3}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>42}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>4}}, "reader_count_by_country"=>{"United States"=>23, "Malaysia"=>2, "Sweden"=>2, "Netherlands"=>2, "Korea (South)"=>1, "Ireland"=>1, "Brazil"=>2, "France"=>2, "Colombia"=>1, "Argentina"=>1, "Japan"=>1, "Tanzania"=>1, "United Kingdom"=>2, "Spain"=>1, "India"=>1, "New Zealand"=>1, "Canada"=>6, "Turkey"=>1, "Belgium"=>1, "Taiwan"=>1, "Denmark"=>1, "Italy"=>1, "South Africa"=>1, "Mexico"=>1, "Germany"=>4, "Indonesia"=>1}, "group_count"=>29}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/591710"], "description"=>"<p>Each circle represents a high-throughput sequence-based 16S or shotgun metagenomic bioproject in NCBI (May 2012), indicating the amount of sequence data produced for each project (circle area and <i>y</i>-coordinate) at the time of publication/registration (<i>x</i>-coordinate). Projects are grouped by human-associated (red), other animal (black), or environmental (green) communities, and shotgun metagenomic projects are marked with a grey band. Selected representative projects are labeled: open ocean <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001377#pbio.1001377-DeLong2\" target=\"_blank\">[68]</a>, deep sea <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001377#pbio.1001377-Sogin1\" target=\"_blank\">[69]</a>, lean mouse <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001377#pbio.1001377-Turnbaugh3\" target=\"_blank\">[70]</a>, diarrheal illness <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001377#pbio.1001377-Nakamura1\" target=\"_blank\">[71]</a>, costal ocean <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001377#pbio.1001377-Gilbert1\" target=\"_blank\">[72]</a>, lean/obese gut <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001377#pbio.1001377-Turnbaugh2\" target=\"_blank\">[53]</a>, human microbiome <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001377#pbio.1001377-Costello1\" target=\"_blank\">[56]</a>, MetaHIT (gut) <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001377#pbio.1001377-Qin1\" target=\"_blank\">[58]</a>, cow rumen <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001377#pbio.1001377-Hess1\" target=\"_blank\">[73]</a>, soil (NCBI BioProject PRJNA50473), and human gut <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001377#pbio.1001377-Yilmaz1\" target=\"_blank\">[74]</a>. Note that HMP has deposited a total of 7.44 terabases of shotgun data in SRA, of which 49% is host DNA derived data that was filtered and only available through protected access in dbGaP project phs000228.</p>", "links"=>[], "tags"=>["microbial", "studies", "high-throughput"], "article_id"=>262193, "categories"=>["Genetics"], "users"=>["Dirk Gevers", "Rob Knight", "Joseph F. Petrosino", "Katherine Huang", "Amy L. McGuire", "Bruce W. Birren", "Karen E. Nelson", "Owen White", "Barbara A. Methé", "Curtis Huttenhower"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1001377.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Timeline_of_microbial_community_studies_using_high_throughput_sequencing_/262193", "title"=>"Timeline of microbial community studies using high-throughput sequencing.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 00:50:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/591785"], "description"=>"<p>(A) Initiatives within the HMP coordinated to isolate samples, generate data, perform analysis, and publish results. <i>Technology development</i> was employed to develop novel bacterial culture and DNA isolation techniques. <i>Ethical Legal and Social Implications (ELSI)</i> work anticipated societal implications and guided policies associated with human subject microbiomes. <i>Clinical sites</i> were collected samples from large cohorts of healthy individuals, with nucleotide sequence information derived at four <i>sequencing centers</i> at the Baylor College of Medicine (BCM), the Broad Institute, the J. Craig Venter Institute (JCVI), and the Washington University Genome Institute (WUGI). Additional <i>demonstration projects</i> assessed primarily microbiome alterations related to disease. In addition to analysis throughout the HMP consortium, <i>computational tools</i> were funded to address, for example, genome assembly, microbial ecology, and statistical modeling. A <i>data analysis and coordination center</i> provided a portal to all data generated. (B) Overview of the analysis approaches that were the ultimate product of the HMP consortium, corresponding to data products and protocols available at <a href=\"http://hmpdacc.org\" target=\"_blank\">http://hmpdacc.org</a>.</p>", "links"=>[], "tags"=>["consortium", "activities", "microbiome"], "article_id"=>262275, "categories"=>["Genetics"], "users"=>["Dirk Gevers", "Rob Knight", "Joseph F. Petrosino", "Katherine Huang", "Amy L. McGuire", "Bruce W. Birren", "Karen E. Nelson", "Owen White", "Barbara A. Methé", "Curtis Huttenhower"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1001377.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_HMP_consortium_activities_as_a_model_for_microbiome_data_generation_and_analyses_/262275", "title"=>"HMP consortium activities as a model for microbiome data generation and analyses.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 00:50:39"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[322, 550, 671, 773, 864, 955, 1048, 1135, 1223, 1308, 1387, 1465, 1534, 1602, 1673, 1744, 1813, 1885, 1955, 2026, 2093, 2160, 2228, 2290, 2349]}, {"subject_area"=>"/Biology and life sciences/Ecology", "average_usage"=>[350, 552, 657, 754, 839, 932, 1023, 1103, 1197, 1274, 1359, 1436, 1499, 1564, 1640, 1726, 1794, 1865, 1933, 2021, 2101, 2181, 2239, 2324, 2376]}, {"subject_area"=>"/Biology and life sciences/Mycology", "average_usage"=>[375, 602, 746, 847, 942, 1060, 1162, 1258, 1358, 1453, 1528, 1646, 1768, 1830, 1928, 1980, 2060, 2153, 2240, 2316, 2380, 2453, 2540, 2617, 2695]}, {"subject_area"=>"/Ecology and environmental sciences/Ecology", "average_usage"=>[347, 547, 641, 742, 836, 927, 1016, 1099, 1184, 1267, 1348, 1418, 1484, 1555, 1631, 1705, 1788, 1843, 1917, 1985, 2052, 2115, 2190, 2258, 2333]}, {"subject_area"=>"/Social sciences", "average_usage"=>[354, 585, 710, 810, 904, 998, 1090, 1181, 1268, 1361, 1435, 1525, 1594, 1657, 1731, 1813, 1878, 1948, 2016, 2094, 2158, 2219, 2294, 2347, 2410]}]}
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