uid Project__ProjectID__ArchiveID__accession Project__ProjectID__ArchiveID__archive Project__ProjectDescr__Name Number_of_BioSamples Data size (MB) Project__ProjectDescr__Title Shotgun_or_Amplicon Project__ProjectDescr__Description Project__ProjectDescr__Publication__date Project__ProjectDescr__Publication__id Project__ProjectDescr__Publication__Reference Project__ProjectDescr__Publication__StructuredCitation__Title Project__ProjectDescr__Publication__StructuredCitation__Journal__JournalTitle Project__ProjectDescr__Publication__StructuredCitation__Journal__Year Project__ProjectDescr__Publication__StructuredCitation__AuthorSet__Author__Name__First Project__ProjectDescr__Publication__StructuredCitation__AuthorSet__Author__Name__Last Project__ProjectDescr__Publication__StructuredCitation__AuthorSet__Author__Consortium Project__ProjectType__ProjectTypeSubmission__Target__Organism__taxID Project__ProjectType__ProjectTypeSubmission__Target__Organism__OrganismName Project__ProjectType__ProjectTypeSubmission__ProjectDataTypeSet__DataType Submission__last_update Submission__submitted Submission_year Submission__Description__Organization__Name 294873 PRJDB1786 DDBJ human gut metagenome 1 8 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 246805 PRJDB1794 DDBJ human gut metagenome 9 26 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr02) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294874 PRJDB1800 DDBJ human gut metagenome 1 658 Metgenomic analysis of human gut microbiome in patients with multiple sclerosis (MS). Shotgun 13 individual of Japanese patients with multiple sclerosis. Microbial DNA was sequenced using a 454 GS FLX titanium (Roche). 408170 human gut metagenome Other 2015-09-06 2012-09-05 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294875 PRJDB1826 DDBJ human gut metagenome 1 11 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 246834 PRJDB1846 DDBJ human gut metagenome 8 23 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr12) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294876 PRJDB1849 DDBJ human gut metagenome 1 7 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294877 PRJDB1852 DDBJ human gut metagenome 1 9 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294834 PRJDB1861 DDBJ human gut metagenome 1 11 16S amplicon sequence analysis of human gut microbiome in patients with multiple sclerosis (MS) Amplicon 13 individual of Japanese patients with multiple sclerosis.The V1 and V2 region of the 16S ribosomal RNA gene. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-09-18 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294878 PRJDB1870 DDBJ human gut metagenome 1 22 16S amplicon sequence analysis of human gut microbiome in patients with multiple sclerosis (MS) Amplicon 13 individual of Japanese patients with multiple sclerosis.The V1 and V2 region of the 16S ribosomal RNA gene. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-09-19 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294879 PRJDB1876 DDBJ human gut metagenome 1 743 Metgenomic analysis of human gut microbiome in patients with multiple sclerosis (MS). Shotgun 13 individual of Japanese patients with multiple sclerosis. Microbial DNA was sequenced using a 454 GS FLX titanium (Roche). 408170 human gut metagenome Other 2015-09-06 2012-09-18 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294880 PRJDB1882 DDBJ human gut metagenome 1 678 Metgenomic analysis of human gut microbiome in patients with multiple sclerosis (MS). Shotgun 13 individual of Japanese patients with multiple sclerosis. Microbial DNA was sequenced using a 454 GS FLX titanium (Roche). 408170 human gut metagenome Other 2015-09-06 2012-09-18 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 246872 PRJDB1920 DDBJ human gut metagenome 9 26 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr40) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 246879 PRJDB1933 DDBJ human gut metagenome 9 26 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr39) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294881 PRJDB1942 DDBJ human gut metagenome 1 17 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294882 PRJDB1960 DDBJ human gut metagenome 1 10 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 246906 PRJDB1979 DDBJ human gut metagenome 8 23 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr32) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294883 PRJDB2019 DDBJ human gut metagenome 1 8 16S amplicon sequence analysis of human gut microbiome in patients with multiple sclerosis (MS) Amplicon 13 individual of Japanese patients with multiple sclerosis.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-19 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 246927 PRJDB2021 DDBJ human gut metagenome 9 26 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr31) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294884 PRJDB2028 DDBJ human gut metagenome 1 17 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294885 PRJDB2064 DDBJ human gut metagenome 1 16 16S amplicon sequence analysis of human gut microbiome in patients with multiple sclerosis (MS) Amplicon 13 individual of Japanese patients with multiple sclerosis.The V1 and V2 region of the 16S ribosomal RNA gene. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-09-19 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294886 PRJDB2071 DDBJ human gut metagenome 1 844 Metgenomic analysis of human gut microbiome in patients with multiple sclerosis (MS). Shotgun 13 individual of Japanese patients with multiple sclerosis. Microbial DNA was sequenced using a 454 GS FLX titanium (Roche). 408170 human gut metagenome Other 2015-09-06 2012-09-18 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294887 PRJDB2088 DDBJ human gut metagenome 1 796 Metgenomic analysis of human gut microbiome in patients with multiple sclerosis (MS). Shotgun 13 individual of Japanese patients with multiple sclerosis. Microbial DNA was sequenced using a 454 GS FLX titanium (Roche). 408170 human gut metagenome Other 2015-09-06 2012-09-18 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294888 PRJDB2118 DDBJ human gut metagenome 1 10 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294889 PRJDB2119 DDBJ human gut metagenome 1 722 Metgenomic analysis of human gut microbiome in patients with multiple sclerosis (MS). Shotgun 13 individual of Japanese patients with multiple sclerosis. Microbial DNA was sequenced using a 454 GS FLX titanium (Roche). 408170 human gut metagenome Other 2015-09-06 2012-09-18 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294890 PRJDB2162 DDBJ human gut metagenome 1 11 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294891 PRJDB2181 DDBJ human gut metagenome 1 "1,171" Metgenomic analysis of human gut microbiome in patients with multiple sclerosis (MS). Shotgun 13 individual of Japanese patients with multiple sclerosis. Microbial DNA was sequenced using a 454 GS FLX titanium (Roche). 408170 human gut metagenome Other 2015-09-06 2012-09-18 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294892 PRJDB2244 DDBJ human gut metagenome 1 9 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294893 PRJDB2248 DDBJ human gut metagenome 1 9 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294894 PRJDB2269 DDBJ human gut metagenome 1 889 Metgenomic analysis of human gut microbiome in patients with multiple sclerosis (MS). Shotgun 13 individual of Japanese patients with multiple sclerosis. Microbial DNA was sequenced using a 454 GS FLX titanium (Roche). 408170 human gut metagenome Other 2015-09-06 2012-09-06 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 247071 PRJDB2289 DDBJ human oral metagenome 1 55 16S amplicon sequence analysis of human salivary microbiome from UC patients Amplicon V!-V2 region of 16S amplicon sequence analysis of human salivary microbiome from 19 Japanese UC patients. 447426 human oral metagenome Other 2013-05-10 2013 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294895 PRJDB2307 DDBJ human gut metagenome 1 22 16S amplicon sequence analysis of human gut microbiome in patients with multiple sclerosis (MS) Amplicon 13 individual of Japanese patients with multiple sclerosis.The V1 and V2 region of the 16S ribosomal RNA gene. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-09-19 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294896 PRJDB2311 DDBJ human gut metagenome 1 7 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 247081 PRJDB2312 DDBJ human oral metagenome 1 62 16S amplicon sequence analysis of human salivary microbiome from CD patients Amplicon V!-V2 region of 16S amplicon sequence analysis of human salivary microbiome from 21 Japanse CD patients. 447426 human oral metagenome Other 2013-05-10 2013 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 247094 PRJDB2343 DDBJ human gut metagenome 9 25 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr17) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 247097 PRJDB2351 DDBJ human gut metagenome 8 22 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr09) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294897 PRJDB2353 DDBJ human gut metagenome 1 10 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294898 PRJDB2358 DDBJ human gut metagenome 1 14 16S amplicon sequence analysis of human gut microbiome in patients with multiple sclerosis (MS) Amplicon 13 individual of Japanese patients with multiple sclerosis.The V1 and V2 region of the 16S ribosomal RNA gene. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-09-19 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294899 PRJDB2364 DDBJ human gut metagenome 1 931 Metgenomic analysis of human gut microbiome in patients with multiple sclerosis (MS). Shotgun 13 individual of Japanese patients with multiple sclerosis. Microbial DNA was sequenced using a 454 GS FLX titanium (Roche). 408170 human gut metagenome Other 2015-09-06 2012-09-18 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294900 PRJDB2398 DDBJ human gut metagenome 1 28 16S amplicon sequence analysis of human gut microbiome in patients with multiple sclerosis (MS) Amplicon 13 individual of Japanese patients with multiple sclerosis.The V1 and V2 region of the 16S ribosomal RNA gene. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-09-19 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 247121 PRJDB2401 DDBJ human gut metagenome 9 26 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr22) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294901 PRJDB2402 DDBJ human gut metagenome 1 11 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-19 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294902 PRJDB2435 DDBJ human gut metagenome 1 8 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294903 PRJDB2472 DDBJ human gut metagenome 1 608 Metgenomic analysis of human gut microbiome in patients with multiple sclerosis (MS). Shotgun 13 individual of Japanese patients with multiple sclerosis. Microbial DNA was sequenced using a 454 GS FLX titanium (Roche). 408170 human gut metagenome Other 2015-09-06 2012-09-06 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294904 PRJDB2488 DDBJ human gut metagenome 1 16 16S amplicon sequence analysis of human gut microbiome in patients with multiple sclerosis (MS) Amplicon 13 individual of Japanese patients with multiple sclerosis.The V1 and V2 region of the 16S ribosomal RNA gene. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-09-19 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 247172 PRJDB2499 DDBJ human oral metagenome 1 68 16S amplicon sequence analysis of human salivary microbiome from healthy controls Amplicon V!-V2 region of 16S amplicon sequence analysis of human salivary microbiome from 24 healthy Japanse. 447426 human oral metagenome Other 2013-05-09 2013 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 247176 PRJDB2507 DDBJ human gut metagenome 1 26 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr20) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294905 PRJDB2510 DDBJ human gut metagenome 1 900 Metgenomic analysis of human gut microbiome in patients with multiple sclerosis (MS). Shotgun 13 individual of Japanese patients with multiple sclerosis. Microbial DNA was sequenced using a 454 GS FLX titanium (Roche). 408170 human gut metagenome Other 2015-09-06 2012-09-18 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294906 PRJDB2552 DDBJ human gut metagenome 1 900 Metgenomic analysis of human gut microbiome in patients with multiple sclerosis (MS). Shotgun 13 individual of Japanese patients with multiple sclerosis. Microbial DNA was sequenced using a 454 GS FLX titanium (Roche). 408170 human gut metagenome Other 2015-09-06 2012-09-18 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 247207 PRJDB2570 DDBJ human gut metagenome 9 25 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr23) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 247208 PRJDB2572 DDBJ human gut metagenome 9 26 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr16) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294907 PRJDB2580 DDBJ human gut metagenome 1 7 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294908 PRJDB2582 DDBJ human gut metagenome 1 18 16S amplicon sequence analysis of human gut microbiome in patients with multiple sclerosis (MS) Amplicon 13 individual of Japanese patients with multiple sclerosis.The V1 and V2 region of the 16S ribosomal RNA gene. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-09-19 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 270469 PRJDB2587 DDBJ human oral metagenome 44 114 Identification of microbiota in carious dentin lesions by 16S rRNA pyrosequencing Amplicon "Prevotella in dentinal caries lesions, whereas mutans streptococci had long been assumed to be the main pathogens responsible for human dental caries. This seeming contradiction should be explored in different ethnicities and races. In the present study, bacterial communities in carious dentin in Japanese subjects were analyzed comprehensively. Forty-four carious dentin lesion samples were collected from 32 subjects aged 4_76 years, and bacterial DNA was extracted. The V1-V2 regions of 16S rRNA genes, amplified from the extracted DNA with universal primers, were sequenced with a pyrosequencer." 447426 human oral metagenome Other 2014-12-16 2014-03-31 2014 "Section of Preventive and Public Health Dentistry, Kyushu University Faculty of Dental Science" 247234 PRJDB2617 DDBJ human gut metagenome 8 23 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr37) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294909 PRJDB2647 DDBJ human gut metagenome 1 22 16S amplicon sequence analysis of human gut microbiome in patients with multiple sclerosis (MS) Amplicon 13 individual of Japanese patients with multiple sclerosis.The V1 and V2 region of the 16S ribosomal RNA gene. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-09-19 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294910 PRJDB2665 DDBJ human gut metagenome 1 11 16S amplicon sequence analysis of human gut microbiome in patients with multiple sclerosis (MS) Amplicon 13 individual of Japanese patients with multiple sclerosis.The V1 and V2 region of the 16S ribosomal RNA gene. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-09-18 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294911 PRJDB2695 DDBJ human gut metagenome 1 673 Metgenomic analysis of human gut microbiome in patients with multiple sclerosis (MS). Shotgun 13 individual of Japanese patients with multiple sclerosis. Microbial DNA was sequenced using a 454 GS FLX titanium (Roche). 408170 human gut metagenome Other 2015-09-06 2012-09-18 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294912 PRJDB2697 DDBJ human gut metagenome 1 29 16S amplicon sequence analysis of human gut microbiome in patients with multiple sclerosis (MS) Amplicon 13 individual of Japanese patients with multiple sclerosis.The V1 and V2 region of the 16S ribosomal RNA gene. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-09-19 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 247283 PRJDB2710 DDBJ human gut metagenome 9 26 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr03) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 247287 PRJDB2717 DDBJ human gut metagenome 9 26 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr11) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294913 PRJDB2726 DDBJ human gut metagenome 1 20 16S amplicon sequence analysis of human gut microbiome in patients with multiple sclerosis (MS) Amplicon 13 individual of Japanese patients with multiple sclerosis.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-19 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 247298 PRJDB2737 DDBJ human gut metagenome 9 26 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr19) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294914 PRJDB2771 DDBJ human gut metagenome 1 7 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 247325 PRJDB2793 DDBJ human gut metagenome 9 26 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr01) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 294915 PRJDB2817 DDBJ human gut metagenome 1 11 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon 18 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Other 2015-09-06 2012-09-20 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 247344 PRJDB2841 DDBJ human gut metagenome 9 26 Robustness of gut microbiota of healthy adult in response to probiotic intervention revealed by high-throughput pyrosequencing (APr29) Amplicon Analysis of 16S rRNA gene (V1-V2 region) sequence of gut microbiota from healthy Japanese adult. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Other 2012-12-15 2012 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 270470 PRJDB2877 DDBJ human oral metagenome 37 44 "Salivary microbiota of Japanese orally healthy adults, pools 1 and 2" Amplicon V1-V2 region of 16S amplicon sequence of human salivary microbiome from 37 orally-healthy Japanese adults were analyzed using a 454 Genome sequencer FLX. The project goal is to clarify the relationship between oral microbiota and human health. 447426 human oral metagenome Targeted Locus (Loci) 2014-12-16 2014-05-16 2014 Kyushu University 270471 PRJDB2878 DDBJ human oral metagenome 51 68 "Salivary microbiota of Japanese orally healthy adults, pool 3" Amplicon V1-V2 region of 16S amplicon sequence of human salivary microbiome from 51 orally-healthy Japanese adults were analyzed using a 454 Genome sequencer FLX. The project goal is to clarify the relationship between oral microbiota and human health. 447426 human oral metagenome Targeted Locus (Loci) 2014-12-16 2014-05-16 2014 Kyushu University 293610 PRJDB3417 DDBJ human gut metagenome 9 38 16S amplicon sequence analysis of human gut microbiome in patients with multiple sclerosis (MS) Amplicon 9 individual of Japanese patients with multiple sclerosis.The V1 and V2 region of the 16S ribosomal RNA gene. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Targeted Locus (Loci) 2014-12-24 2014 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 293611 PRJDB3418 DDBJ human gut metagenome 32 93 16S amplicon sequence analysis of human gut microbiome from healthy subjects Amplicon Gut microbiome from 32 healthy individual of Japanese.The V1 and V2 region of the 16S ribosomal RNA gene. 26367776 10.1371/journal.pone.013742 "Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters." PLoS One 2015 Sachiko Miyake 408170 human gut metagenome Targeted Locus (Loci) 2014-12-24 2014 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 311307 PRJDB3451 DDBJ human oral metagenome 63 72 "Salivary microbiota of Japanese orally healthy adults, pool 4" Amplicon V1-V2 region of 16S amplicon sequence of human salivary microbiome from 63 orally-healthy Japanese adults were analyzed using a 454 Genome sequencer FLX. The project goal is to clarify the relationship between oral microbiota and human health. 447426 human oral metagenome Targeted Locus (Loci) 2016-02-09 2015-01-20 2015 Kyushu University 311308 PRJDB3452 DDBJ human oral metagenome 66 82 "Salivary microbiota of Japanese orally healthy adults, pool 5" Amplicon V1-V2 region of 16S amplicon sequence of human salivary microbiome from 66 orally-healthy Japanese adults were analyzed using a 454 Genome sequencer FLX. The project goal is to clarify the relationship between oral microbiota and human health. 447426 human oral metagenome Targeted Locus (Loci) 2016-02-09 2015-01-20 2015 Kyushu University 314752 PRJDB3601 DDBJ human gut metagenome 255 "220,000" Metagenomics of Japanese gut microbiomes Shotgun "The human gut microbiome has profound influences on the hostfs health largely through its inter- ference with various intestinal functions. As recent studies have suggested diversity in the human gut microbiome among human populations, it will be interesting to analyse how gut microbiome is correlated with geographical, cultural, and traditional differences. The Japanese people are known to have several characteristic features such as eating a variety of traditional foods and exhibit- ing a low BMI and long life span. In this study, we analysed gut microbiomes of the Japanese by com- paring the metagenomic data obtained from 106 Japanese individuals with those from 11 other nations. We found that the composition of the Japanese gut microbiome showed more abundant in the phylum Actinobacteria, in particular in the genus Bifidobacterium, than other nations. Regard- ing the microbial functions, those of carbohydrate metabolism were overrepresented with a concur- rent decrease in those for replication and repair, and cell motility. The remarkable low prevalence of genes for methanogenesis with a significant depletion of the archaeon Methanobrevibacter smithii and en- richment of acetogenesis genes in the Japanese gut microbiome compared with others suggested a difference in the hydrogen metabolism pathway in the gut between them. It thus seems that the gut microbiome of the Japanese is considerably different from those of other populations, which cannot be simply explained by diet alone. We postulate possible existence of hitherto unknown factors contributing to the population-level diversity in human gut microbiomes." 26951067 10.1093/dnares/dsw002 The gut microbiome of healthy Japanese and its microbial and functional uniqueness. DNA Res 2016 Suguru Nishijima 408170 human gut metagenome Metagenome 2016-03-09 2015-03-16 2015 The University of Tokyo 327546 PRJDB4064 DDBJ human gut metagenome 56 165 microbiota of the feces obtained from 16 Japanese alcoholic patients and 40 healthy Japanese subjects Amplicon microbiota of the feces obtained from 16 Japanese alcoholic patients and 40 healthy Japanese subjects. The V1 and V2 region of the 16S ribosomal RNA gene. 408170 human gut metagenome Targeted Locus (Loci) 2016-07-01 2015-07-14 2015 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 314211 PRJDB4107 DDBJ human oral metagenome 2344 9684 Population-based study on salivary microbiome of Japanese adults Amplicon "We collected saliva from Japanese adults aged over 40 years inhabiting Hisayama town, Fukuoka, Japan in a health examination performed as a part of the follow-up survey of the Hisayama cohort study on 2007. The V1-V2 region of 16S amplicon sequence of human salivary microbiome were analyzed using Ion PGM. The project goal is to identify core and pan salivary microbiome in Japanese adults and to clarify the relationship with host's health and health-related conditions." 447426 human oral metagenome Targeted Locus (Loci) 2016-03-03 2015-07-30 2015 "Section of Preventive and Public Health Dentistry, Kyushu University Faculty of Dental Science" 520750 PRJDB4176 DDBJ human gut metagenome 645 "2,450,000" metagenomic data from human fecal samples Shotgun "Total microbial community DNA was isolated from the fecal samples of Japanese patients who underwent colonoscopy at National Cancer Research Center. The study population contains health, early and advanced cancer stages." 31171880 10.1038/s41591-019-0458-7 Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer. Nat Med 2019 Shinichi Yachida 408170 human gut metagenome Metagenome 2019-02-02 2015-08-20 2015 Tokyo Institute of Technology 347331 PRJDB4177 DDBJ human oral metagenome 100 "8,137" Comprehensive microbiome analysis of tonsillar crypts in IgA nephropathy Amplicon We investigated the relationship between IgA nephropathy and the bacterial flora in the tonsils by analyzing the composition of the bacterial community in the crypts of the tonsils of IgAN patients and compared it to those of recurrent tonsillitis patients without urine abnormalities and children with tonsillar hyperplasia by using a high-throughput multiplexed 16S ribosomal RNA gene sequencing method. 27683270 10.1093/ndt/gfw343 Comprehensive microbiome analysis of tonsillar crypts in IgA nephropathy. Nephrol Dial Transplant 2017 Hirofumi Watanabe 447426 human oral metagenome Targeted Locus (Loci) 2016-10-07 2015-08-20 2015 Tokyo Institute of Technology 295928 PRJDB4231 DDBJ human gut metagenome 10 285 "Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing" Amplicon comparison of the gut microbiota composition between obese and non-obese individual as analysed by next generation sequence. 26261039 10.1186/s12876-015-0330-2 "Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing." BMC gastroenterology 2015 Chika Kasai "Department of Gastroenterology, Mie Prefectural General Medical Center, 5450-132 Hinaga, Yokkaichi, Mie, 510-8561, Japan. cpkasai@tg7.so-net.ne.jp." 408170 human gut metagenome Other 2015-09-17 2015-09-15 2015 "Department of Gastroenterology, Mie Prefectural General Medical Center" 323835 PRJDB4360 DDBJ human gut metagenome 495 "2,787" Microbiota composition in healthy Japanese Amplicon Fecal samples from 367 healthy Japanese subjects were analyzed by high-throughput sequencing of amplicons derived from the V3-V4 region of the 16S rRNA gene. 27220822 10.1186/s12866-016-0708-5 Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study. BMC microbiology 2016 Toshitaka Odamaki "Next Generation Science Institute, Morinaga Milk Industry Co., Ltd., Zama, Kanagawa, Japan. t-odamak@morinagamilk.co.jp." 408170 human gut metagenome Targeted Locus (Loci) 2016-05-31 2015-11-17 2015 "Morinagamilk Industry CO.,LTD." 768681 PRJDB4525 DDBJ human gut metagenome 36 "260,000" Shotgun metagenomics of fecal bacterial consortium inhabiting healthy Asian children Shotgun "Recent development in intestinal microbiology has revealed crucial functions of gut microbiota as interface between diet and health and the question has arisen how diet modulates gut microbial community. In this context, Asia is an interesting association of cohorts with their own food habit unique to each country or region. To investigate the correlation among diet, health, and gut microbiota, Asian Microbiome Project (AMP) has been established with ten countries and Phase I study was already performed by focusing on children gut microbiota, which were expected to more depend on regional food compared to adult. Their microbiota has been analyzed based on 16S rRNA gene sequencing. As a result, we have found two distinctive enterotypes, Bifidobacterium/Bacteroides (BB) enterotype and Prevotella (P) enterotype in these Asian population, as well as local differences unique to each country or region. BB-enterotype was enriched in temperate countries, such as Japan and China, while P-enterotype was frequent in tropical countries. In conjunction with dietary survey, it is suspected that these difference may be a reflection of their dietary habit. To correlate the function of their gut microbial community with diet input, we performed shotgun metagenomic sequencing of those microbial community and gained overview on consortium of functional genes, e.g., network of anabolic and catabolic pathway enriched in each food-oriented enterotype or biosynthesis of beneficial or non-benefical compounds, such as vitamins or secondary bile acids." 408170 human gut metagenome Metagenome 2021-10-05 2016-01-22 2016 Tokyo Institute of Technology 313370 PRJDB4592 DDBJ human gut metagenome 101 212 Intestinal microbiota associate with menstrual cycle-dependent complaints and plasma female hormones in young Japanese women Amplicon "To evaluate the hypothesis that intestinal microbiota affects menstrual cycle-dependent complaints and plasma levels of female hormones, we conducted an observational pilot study in healthy young females for 12 weeks (2 or 3 menstrual cycles). We recruited 10 subjects (mean age: 20.9 ? 1.3 years, body mass index: 20.67 ? 1.71) from the college student. Fecal samples were collected on a weekly basis. From the samples, we got the DNA extraction by using commercially available kit (QIAamp DNA stool mini kit, Qiagen) and RNase A (Qiagen). Pyrosequencing of 16S rRNA gene was performed with the samples to amplify the V1-V2 region of 16S rRNA gene by using 454 GS JUNIOR sequencing (Roche Applied Science, Penzberg, Germany). Menstrual cycle was classified into 4 phases, an ovulation phase (12 to 16 days before the beginning of menstruation), a luteal phase (1 to 11 days before the beginning of menstruation), a menstruation phase (during menstruation) and a follicular phase (between the menstruation phase and the ovulation phase) based on the Ogino-Knaus theory. Fecal samples also classified the 4 phases." 408170 human gut metagenome Targeted Locus (Loci) 2016-02-28 2016-02-22 2016 "Kagome Co.,LTD" 353991 PRJDB4998 DDBJ human gut metagenome 516 "1,192" Fecal microbiota of Japanese healthy adults Amplicon Fecal microbiota of Japanese healthy adults. 16s rRNA gene library of V1-V2 hyper variable regions derived from the fecal samples of 516 subjects. 27894251 10.1186/s12866-016-0898-x Comprehensive analysis of the fecal microbiota of healthy Japanese adults reveals a new bacterial lineage associated with a phenotype characterized by a high frequency of bowel movements and a lean body type. BMC microbiology 2016 Kaihei Oki "Yakult Central Institute, 5-11 Izumi, Kunitachi, Tokyo, 186-8650, Japan. kaihei.oki@yher.be." 408170 human gut metagenome Targeted Locus (Loci) 2016-07-14 2016 Yakult Central Institute 475901 PRJDB5064 DDBJ human skin metagenome 148 63 16S amplicon sequence analysis of skin microbiomes from Japanese individual Amplicon "The V1 and V2 region sequence data of the 16S ribosomal RNA gene. Skin samples of 37 Japanese individuals sampled from Cheek, Forearm, Forehead and Scalp." 2017-09-05T00:00:00Z 28874721 10.1038/s41598-017-10834-9 Aging-related changes in the diversity of women's skin microbiomes associated with oral bacteria. Scientific reports 2017 Nakako Shibagaki "Nihon L'Oreal Research & Innovation, KSP, Sakado, Takatsu, Kawasaki, Kanagawa, 213-0012, Japan." 539655 human skin metagenome Targeted Locus (Loci) 2018-06-13 2016-07-29 2016 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 506554 PRJDB5310 DDBJ human gut metagenome 104 52 Gut microbiota of 104 Japanese adults Amplicon "Feces samples of 104 healthy Japanese adults were collected (Nishijima et al.). The 16S rRNA gene hypervariable V1-V2 regions were PCR-amplified using universal primers (a barcoded 27Fmod and 338R) and, multiplexed amplicon pyrosequencing was carried out using 454 GS FLX Titanium or 454 GS JUNIOR (Roche Applied Science)." 408170 human gut metagenome Targeted Locus (Loci) 2018-11-22 2016-11-18 2016 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 450760 PRJDB5316 DDBJ human gut metagenome 312 "6,311" Infants stool microbiome Amplicon "Bacterial colonization in infancy is critical window for ordinary development of immune system and its disturbance may cause allergy development in late life. In the present study, we surveyed signatures in the developmental gut microbiota associated with childhood allergy. We conducted a prospective study on the relationship between developmental food allergy in 2 years of age and gut microbiota in infancy. fecal samples were collected at 1, 2, 6 months and 1 year of life form infants who were born in St. Mary's hospital in Kurume city, Japan, and 16S rRNA V1-V2 region was sequenced by MiSeq. We show that gut microbiota in food allergy infants had a significantly difference at lactation and weaning." 408170 human gut metagenome Other 2018-04-18 2016-11-11 2016 "Lab. of Microbial Technology, Faculty of Agriculture, Kyushu University" 506918 PRJDB5338 DDBJ human oral metagenome 50 29 Salivary microbiota of jet-lagged 2 adults Amplicon "Salivary samples of 2 healthy Japanese adults were collected (1 female and 1 male) immediately after returning Japan from New York whose time-zone is 13 hours behind Japan time. The 16S rRNA gene hypervariable V1-V2 regions were PCR-amplified using universal primers (a barcoded 27Fmod and 338R) and, multiplexed amplicon pyrosequencing was carried out using 454 GS FLX Titanium or 454 GS JUNIOR (Roche Applied Science)." 447426 human oral metagenome Targeted Locus (Loci) 2018-11-26 2016-11-25 2016 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 489620 PRJDB5459 DDBJ human skin metagenome 73 930 Skin microbiome by different collection methods Amplicon "We have developed a novel collection method for skin microbiota. To validate the efficacy of the developed method, we planned to compare the novel method with traditional swabbing by 16S amplicon sequencing. The back skin of healthy volunteers was swabbed, and the novel method was applied to the area adjacent to the swabbed region. The collected samples were processed and sent to the outsourcing research center for 16S amplicon analysis." 539655 human skin metagenome Targeted Locus (Loci) 2018-09-06 2017-01-12 2017 "SAKIGAKE Project, Wellness Promotion Science Center, Kanazawa University" 592914 PRJDB5697 DDBJ human gut metagenome 29 624 Generic sample from human gut 16s amplicon-sequencing(sequence by miseq) Amplicon Total microbial community DNA was isolated from the fecal samples of Japanese healthy person. We use *miseq* in this project. 408170 human gut metagenome Targeted Locus (Loci) 2019-12-02 2017-04-17 2017 Metagen Inc. 592915 PRJDB5698 DDBJ human gut metagenome 29 55 Generic sample from human gut 16s amplicon-sequencing(sequence by miniseq) Amplicon Total microbial community DNA was isolated from the fecal samples of Japanese healthy person. We use *miniseq* in this project. 408170 human gut metagenome Targeted Locus (Loci) 2019-12-02 2017-04-17 2017 Metagen Inc. 540782 PRJDB5741 DDBJ human gut metagenome 104 42 Gut microbiota of 104 Japanese adults Amplicon "Feces samples of 104 healthy Japanese adults were collected (Nishijima et al.). The 16S rRNA gene hypervariable V1-V2 regions were PCR-amplified using universal primers (a barcoded 27Fmod and 338R) and, multiplexed amplicon pyrosequencing was carried out using MiSeq (illumina)." 408170 human gut metagenome Targeted Locus (Loci) 2019-05-02 2017-05-01 2017 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 478864 PRJDB5860 DDBJ human gut metagenome 292 "2,548" Asian Microbiome Project Amplicon "Asia differs substantially among and within its regions populated by diverse ethnic groups, which maintain their own respective cultures and dietary habits. On the other hand, Oriental and Western cultures are now merging at many sites in Asia and affecting our life style, especially daily diets. To inquire into diversity in gut microbiota of Asian people, which must respond to daily diets and link to host health, Asian Microbiome Project (AMP) was established in 2009. AMP aims to build a basal microbiome database of Asians covering entire region and age group and gain an insight into the link between life style and gut microbiota. By sharing information and gained knowledge obtained in this project, we hope to promote health of Asian people." 408170 human gut metagenome Targeted Locus (Loci) 2018-07-02 2017-06-12 2017 "Lab. of Microbial Technology, Faculty of Agriculture, Kyushu University" 555513 PRJDB5944 DDBJ human oral metagenome 75 226 Subgingival microbiota of 30 Japanese healthy or periodontitis adults Amplicon "Gingival crevicular fluid samples of 30 Japanese adults were collected (Ikeda et al.). The 16S rRNA gene hypervariable V1-V2 regions were PCR-amplified using universal primers (a barcoded 27Fmod and 338R) and, multiplexed amplicon pyrosequencing was carried out using 454 GS FLX Titanium or 454 GS JUNIOR (Roche Applied Science)." 447426 human oral metagenome Targeted Locus (Loci) 2019-07-19 2017-07-18 2017 "Hattori Laboratory, Department of Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo" 560354 PRJDB6133 DDBJ human gut metagenome 78 "3,115" 16S amplicon sequence analysis of human gut microbiome in patients with Inflammatory bowel disease (IBD) Amplicon "Abnormal composition of gut microbiota, termed dysbiosis, has been implicated in pathogenesis of inflammatory bowel diseases (IBD). In order to investigate associations between dysbiosis and fecal metabolites, we performed 16S ribosomal RNA (rRNA) amplicon sequence analysis of fecal samples from 23 Japanese healthy subjects, 30 ulcerative colitis patients and 25 Crohn's disease patients. The V3 and V4 regions of the 16S rRNA gene were sequenced with a MiSeq 600 cycle v3 kit (Illumina)." 408170 human gut metagenome Targeted Locus (Loci) 2019-08-15 2017-08-02 2017 "Hase Labratory, Division of Biochemistry, Faculty of Pharmacy, Keio University" 483574 PRJDB6472 DDBJ human gut metagenome 96 "3,044" Bacteroides vulgatus and Bacteroides dorei reduce gut microbial lipopolysaccharide production and inhibit atherosclerosis Amplicon "Increasing evidence suggests gut microbiota play a pivotal role in development of atherosclerotic cardiovascular disease. However, it still remains unclear how the specific gut bacteria contributes to the atherosclerosis progression. Here, we compared the gut microbiome in patients with or without coronary artery disease (CAD), and studied the underlying mechanisms using mice model. Fecal 16S rRNA gene sequencing revealed lower abundance of Bacteroides vulgatus and Bacteroides dorei in patients with CAD. Gavage with live-B. vulgatus and B. dorei ameliorated the atherosclerotic lesion formation in atherosclerosis-prone mice. Markedly decreasing gut microbial lipopolysaccharide production and intestinal permeability attributed to the attenuation of endotoxemia and suppression of the proinflammatory immune response. Furthermore, significant increasing gut microbial lipopolysaccharide production in CAD patients was observed. Our findings identify causal link between specific gut bacteria and atherosclerosis, and provide a novel intervention in CAD by targeting the gut microbiota." 2018-11-27T00:00:00Z 30571343 Bacteroides vulgatus and Bacteroides dorei Reduce Gut Microbial Lipopolysaccharide Production and Inhibit Atherosclerosis. Circulation 2018 Naofumi Yoshida "Division of Cardiovascular Medicine (N.Y., T.E., T.Y., T.H., T.T., N.S., T.M., H.Z.A., K.H.), Kobe University Graduate School of Medicine, Japan." 408170 human gut metagenome Targeted Locus (Loci) 2017-10-27 2017 "Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan" 474293 PRJDB6814 DDBJ human gut metagenome 22 "1,003" Conventional culture methods with commercially available media unveil the presence of novel culturable bacteria; 16S metagenomics of healthy Japanese individual derived-gut microbiome Amplicon "Recent metagenomic analysis has revealed that our gut microbiota plays an important role in not only the maintenance of our health but also various diseases. However, most intestinal bacteria are considered unculturable bacteria, and their functions remain unknown. To date, various culturing methods have been attempted to obtain these unculturable bacteria, but most such methods require advanced techniques. Here, we have tried to isolate possible unculturable bacteria from a healthy Japanese individual by using commercially available media. A 16S metagenomic analysis revealed that each culture medium showed bacterial growth depending on its selective features and a possibility of the presence of novel bacterial species. Whole genome sequencing of these candidate strains suggested the isolation of 8 novel bacterial species classified in the Actinobacteria and Firmicutes phyla. As a result, we have obtained novel gut bacteria from a healthy Japanese individual using a combination of comprehensive genomics and conventional culturing methods. Our approach indicates that a number of intestinal bacteria hitherto considered unculturable are potentially culturable and can be cultured on commercially available media." 408170 human gut metagenome Targeted Locus (Loci) 2018-06-02 2018-03-05 2018 "Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases" 485284 PRJDB7021 DDBJ human oral metagenome 100 561 Characterization of salivary microbiota of healthy adults Amplicon We collected saliva samples from 100 healthy men in Japan. The project goal is to characterize the salivary microbiota profiles of healthy adults and to reveal the association between the bacterial composition of the microbiota and health outcomes. 447426 human oral metagenome Targeted Locus (Loci) 2018-08-09 2018-05-12 2018 "Section of Preventive and Public Health Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University" 635039 PRJDB7053 DDBJ human gut metagenome 120 "2,559" Generic sample from human gut 16s amplicon-sequencing Amplicon Total microbial community DNA was isolated from the fecal samples of Japanese healthy person. We use MiSeq for the same sample. 408170 human gut metagenome Targeted Locus (Loci) 2020-05-26 2018-05-23 2018 Metabologenomics Inc. 637838 PRJDB7111 DDBJ human blood metagenome 27 "1,263" Diagnosis of infectious diseases by sequencing Amplicon "Prompt identification of causative pathogenic bacteria is imperative for the treatment of patients suffering from infectious diseases including sepsis and pneumonia. However, current culture-based methodologies have several drawbacks including the limitation to culturable bacterial species. To circumvent these problems, we aimed to detect bacterial DNA in the blood using next-generation DNA sequencing (NGS) technology." 1504969 human blood metagenome Targeted Locus (Loci) 2020-06-07 2018-06-08 2018 "Biomedical Informatics Laboratory, Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine" 483575 PRJDB7124 DDBJ human oral metagenome 506 "2,591" Population-based study on tongue microbiota composition of Japanese elderly adults Amplicon Tongue coating samples were collected from Japanese community-dwelling elderly adults aged 70-80 years in a health examination performed as a part of the follow-up survey of the Hisayama cohort study on 2016. The V1-V2 regions of 16S rRNA gene amplicons were analyzed using Ion PGM. The project goal is to understand the variation among normal tongue microbiota observed the community-dwelling elderly adults. 447426 human oral metagenome Targeted Locus (Loci) 2018-07-31 2018-06-12 2018 "Section of Preventive and Public Health Dentistry, Kyushu University Faculty of Dental Science" 593437 PRJDB7378 DDBJ human gut metagenome 50 "180,000" Generic sample from human gut metagenome Shotgun "Total microbial community DNA was isolated from the fecal samples of Japanese patients who underwent colonoscopy at National Cancer Research Center. The study population contains health, gastrectomy." 31171880 10.1038/s41591-019-0458-7 Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer. Nat Med 2019 Shinichi Yachida 408170 human gut metagenome Metagenome 2019-12-04 2018-08-29 2018 Tokyo Institute of Technology 729666 PRJDB7462 DDBJ human lung metagenome 1 247 The genomic analysis of an unclutured bacterium IOLA detected from a patient with chronic respiratory disease Shotgun "The unclassified microorganisms temporarily named "IOLA" were discovered from the bronchoalveolar lavage fluid (BALF) specimens from patients with respiratory tract infection. Here we show the IOLA genomic sequence determined without isolating of IOLA with culture methods. The genome of IOLA is the smallest (303,838 bp) in bacteria obtained from human clinical specimens, and there are only 310 CDSs. Each protein shows low similarity with known sequences, and a half over of them (167 CDSs) is still "function unknown"." 2014-07-31T00:00:00Z 10.1371/journal.pone.0103646 10.1371/journal.pone.0103646 An Unclassified Microorganism: Novel Pathogen Candidate Lurking in Human Airways PLoS ONE 2014 Kazumasa Fukuda 646099 human metagenome Other 2021-05-13 2018-09-04 2018 "Microbiology, Graduate School of Medical Sciences, Kyushu University" 675216 PRJDB7616 DDBJ human gut metagenome 194 "2,599" Comparison of gut microbiota from healthy adult populations living in India and Japan Amplicon We analyzed gut bacterial and fungal compostion of healthy adult populations living in India and Japan by next generation sequencer. 31885873 10.1038/s41522-019-0110-9 Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi. NPJ Biofilms Microbiomes 2019 Siddhika Pareek 408170 human gut metagenome Targeted Locus (Loci) 2020-11-07 2018-11-01 2018 Osaka University 676047 PRJDB7649 DDBJ human oral metagenome 12 "1,471" Genomic and metagenomic sequencing of tonsillar crypts microbiome Amplicon We investigated the relationship between IgA nephropathy and the bacterial flora in the tonsils by comparing the bacterial community in the crypts of the tonsils of IgAN patients and those of recurrent tonsillitis patients using metagenomic sequencing and genomic sequencing of isolated bacterial strains. 33099625 10.1093/ndt/gfaa223 Aberrant mucosal immunoreaction to tonsillar microbiota in immunoglobulin A nephropathy. Nephrol Dial Transplant 2021 Hiroki Yamaguchi 447426 human oral metagenome Metagenome 2020-11-11 2018-11-09 2018 "Genome Evolution Laboratory, Center for Information Biology, National Institute of Genetics" 609424 PRJDB7687 DDBJ human skin metagenome 229 "3,924" Skin microbiome of Japanese elderly in relation to the onset of pressure ulcers Amplicon "It is widely known that Japan is in a "super-aging" society; one in four is older than 65 years old. One of the most prevalence and challenging problems for elderly in Japan is the onset of pressure ulcers (PU) during being cared in hospitals and/or their home. Infections after PU development is also the problem. Our team has been devoted to clarify the nature of PU onset and deterioration, focusing on the dysbiosis of skin. This study is aiming to discover how differently elderly people in Japan harbor skin microbiome in comparison with young and healthy elderly people." 539655 human skin metagenome Targeted Locus (Loci) 2020-02-29 2018-11-22 2018 "Wellness Promotion Science Center, Kanazawa University" 804729 PRJDB8001 DDBJ human gut metagenome 161 "4,000" Oral immunotherapy for cow's milk allergy Amplicon "Feces samples of 35 Japanese children who had cow's milk allergy and received oral immunotherapy were collected (Ohno et al.). The 16S rRNA gene hypervariable V1-V2 regions were PCR-amplified using universal primers (a barcoded 27Fmod and 338R) and, multiplexed amplicon pyrosequencing was carried out using MiSeq (illumina)." 408170 human gut metagenome Targeted Locus (Loci) 2022 "Laboratory for Microbiome Sciences, Center for Integrative Medical Sciences, RIKEN" 701808 PRJDB8027 DDBJ human gut metagenome 73 "1,117" PBC microbiome Amplicon "Although the relationship between chronic liver disease and gut microbiome should be attractive enough for paying some definite attention, the analysis of gut microbiome in patients with primary biliary cholangitis (PBC) has been insufficient so far. Then, the reactivity to ursodeoxycholic acid (UDCA) could predict the long-term prognosis of patients with PBC, whereas little is known about the significance of gut microbiome in patients with PBC. The aim of this comparative study is to demonstrate the relations between biochemical reactivity to UDCA and the composition of gut microbiota in Japanese patients with PBC." 408170 human gut metagenome Genome sequencing 2021-02-14 2019-02-12 2019 "Third department of internal medicine, Nara Medical University" 527441 PRJDB8081 DDBJ human gut metagenome 47 605 analysis of duodenal microbiome Amplicon We analyzed duodenal microbiome of patients with Helicobacter pylori infection and healthy participants using NGS 408170 human gut metagenome Targeted Locus (Loci) 2019-03-16 2019-03-13 2019 "general medicine, microbiology, omori hospital, toho university" 553436 PRJDB8270 DDBJ human lung metagenome 37 747 Comparison of lung microbiota between antineutrophil cytoplasmic antibody-associated vasculitis and sarcoidosis Amplicon "Bacterial involvements for the pathogenesis have been suggested in both antineutrophil cytoplasmic antibody-associated vasculitis (AAV) and sarcoidosis, which have lung involvements. However, exhaustive researches to assess the bacteria in the lung in AAV and in sarcoidosis have not been performed to elucidate the differences in bacterial characteristics. We sought to elucidate the distinct lung microbiota suggesting contributions of dysbiosis in the lung to the pathogenesis of AAV and sarcoidosis." 433733 human lung metagenome Targeted Locus (Loci) 2019-05-06 2019 "Immunology and Rheumatology, Nagasaki University" 726650 PRJDB8511 DDBJ human gut metagenome 114 "1,199" Metabologenomic approach reveals the feature of intestinal environment associated with barley-induced blood parameter improvements in Japanese cohort: a randomised controlled trial Amplicon "Consumption of barley has been known to have beneficial effects on metabolic disorders; however, the inter-individual difference in the response has also been reported. Recent evidences have suggested that such individually different effects are mediated by the intestinal environment. Therefore, to understand its mechanisms, evaluating both intestinal environment and metabolic disorders marker is crucial. Here we report a randomised controlled trial in Japanese subjects with 4-week consumption of barley or control-food. In this study, we analysed intestinal environment, which include both microbiota and their metabolites by metabologenomic approach, and blood parameter were integratedly assessed. We found that groups of subjects who exhibited the improvement in glucose tolerance and reduction of total cholesterol by barley consumption were predictable by machine learning from their intestinal metabologenomic data. Also, rate of increase in abundance of cholesterol-degrading bacteria ([Eubacterium] coprostanoligenes group) by barley consumption in subjects who showed decrease in total cholesterol was significantly higher than the other subjects, which may contribute to the reduction of blood total cholesterol. Our findings indicate the effects of barley consumption are partly defined by the intestinal environment of consumers, which shed light on quantitative measurement of dietary effect from intestinal environment." 408170 human gut metagenome Targeted Locus (Loci) 2021-05-01 2019-07-04 2019 "Metabologenomics, Inc." 560192 PRJDB8669 DDBJ human oral metagenome 60 "2,521" Interdental plaque microbiota treated with NO Amplicon "The deterioration of human oral microbiota is known not only to cause oral diseases but also to affect systemic health. Various environmental factors are thought to influence the disruption and restoration of oral ecosystem. In this study, we focused on the effect of nitric oxide (NO) produced by denitrification and immune cells on plaque flora. Interdental plaques collected from 10 subjects were exposed with NO donor sodium nitroprusside (SNP), and cultured in SHI medium. This study has provided an overview of how oral plaque microbiota shifts with exposure to NO and may contribute to the development of a method for adjusting the balance of the oral microbiome." 447426 human oral metagenome Targeted Locus (Loci) 2019-08-14 2019-08-09 2019 Osaka Dental University 561727 PRJDB8690 DDBJ human lung metagenome 25 993 16S rRNA gene amplicon sequencing of lower respiratory sample in Japanese patients Amplicon "During a multicenter, open-label Phase 3 clinical trial of lascufloxacin intravenously administered to patients with respiratory tract infections, 17 of aspiration pneumonia and 11 of lung abscess patients were enrolled in this study." 646099 human metagenome Targeted Locus (Loci) 2019-08-23 2019-08-16 2019 Toho University 596690 PRJDB8768 DDBJ human oral metagenome 9 12 "Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan" Amplicon "DNA metabarcoding analysis of dental calculus from Edo people, Japan. We used trnL P6 primer set for plant and ITS primer set for fungi" 2018-03-13T00:00:00Z 10.1371/journal.pone.0226654 10.1371/journal.pone.0226654 "Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan" PLoS One 2020 Rikai Sawafuji 447426 human oral metagenome Targeted Locus (Loci) 2019-12-19 2019-09-09 2019 University of the Ryukyus 612449 PRJDB8820 DDBJ human gut metagenome 255 "3,751" Comparison study of gut microbiome and health status Amplicon "We performed medical examination including oral condition, nutrients intake, and the structure of human gut microbiota in Noto district, Ishikawa Prefecture, Japan, and determined relationship between them." 408170 human gut metagenome Targeted Locus (Loci) 2020-03-13 2019-09-25 2019 Kanazawa University 768691 PRJDB8956 DDBJ human gut metagenome 20 "73,000" An efficient and accurate reconstruction of the full-length phage genomes by chimera-free long-read metagenomics of the human gut virome Shotgun Fecal samples of five healthy Japanese adults were collected (Kiguchi et al.). The DNA of viral-like particles (VLPs) were extracted and subjected to the multiple displacement amplification (MDA). The whole metagenomic sequencing of MDA-treated VLPs DNA was performed by MiSeq (Illumina) and Sequel (PacBio). 10.1093/dnares/dsab019 10.1093/dnares/dsab019 Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads DNA Res 2021 Yuya Kiguchi 408170 human gut metagenome Other 2021 "Laboratory for Microbiome Sciences, Center for Integrative Medical Sciences, RIKEN" 788396 PRJDB9093 DDBJ human metagenome 130 "45,371" Fecal and salivary microbiomes in Japanese HIV-1-infected patients Amplicon We sought to identify characters of fecal and salivary microbiomes in Japanese HIV-1-infected patients. 646099 human metagenome Targeted Locus (Loci) 2021-12-13 2019-12-11 2019 "Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center" 692121 PRJDB9239 DDBJ human gut metagenome 120 882 Stratification of population who improve the blood parameters by Chlorella consumption Amplicon Total microbial community DNA that was isolated from the fecal samples of Japanese healthy person before and after ingestion. We use Miseq for sequence. 408170 human gut metagenome Targeted Locus (Loci) 2021-01-14 2020-01-15 2020 "Metabologenomics, Inc." 691773 PRJDB9256 DDBJ human skin metagenome 25 "1,765" Amplicon sequencing of CRISPRs in human skin Amplicon Amplicon sequencing of CRISPRs in human skin. Spacers of the three CRISPRs were amplified by the primer pairs targeting DRs and then sequenced by Miseq. 539655 human skin metagenome Targeted Locus (Loci) 2020-01-23 2020 National Research Institute of Police Science 734802 PRJDB9274 DDBJ human oral metagenome 52 "2,144" Evaluating the transition of bacterial composition around dental implants over time Amplicon To evaluate the transition of bacterial composition around dental implants which are placed into patients by submerged insertion and to clarify the factors contributing to such changes. 447426 human oral metagenome Targeted Locus (Loci) 2021-06-03 2020-01-29 2020 "Oral Implantology and Regenerative Dental Medicine, Tokyo Medical and Dental University" 675336 PRJDB9334 DDBJ human gut metagenome 14 777 Study on the gut microbiota associated with long-term withdrawal of Adalimumab in ulcerative colitis paitients. Amplicon "Adalimumab is an anti-tumor necrosis factor alpha (anti-TNF-alpha) agent used to suppress intestinal inflammation in ulcerative colitis (UC) patients. However, it is known that suppression of TNF-alpha by Adalimumab cause side effects related to lowered immune system function. Therefore, it is of importance to be able to identify UC patients who can discontinue Adalimumab treatment without relapse for a longer period of time. For this purpose, through sequencing bacterial 16S rRNA amplicons, we examined gut microbiota of two groups of UC patients who relapsed within 12 months after the withdrawal of Adalimumab and those who relapsed after 12 months after the withdrawal of Adalimumab, at two time points: pre and post treatment." 408170 human gut metagenome Targeted Locus (Loci) 2020-11-08 2020-02-12 2020 "Kindai University, Department of Gastroenterology and Hepatology" 798278 PRJDB9512 DDBJ human skin metagenome 171 "2,292" A comparative study of skin microbiome in Japanese and Cameroonian healthy people Amplicon "Skin is the largest organ of our body, serving a physical barrier which protects our body from external insults. Skin microbiota, or skin bacteria and fungi, is also reported to participate in the skin barrier function, in terms of maturation of skin immunity, producing bactericidal materials to prevent pathogenic bacteria to flourish, and keeping the skin physiological function healthy (e.g., sebum decomposition to fatty acids to keep skin pH mildly acidic). In this study, we are interested in the difference in skin microbiome between Japanese and other countries' people, especially in Africa, which is yet to be clarified. As we could successfully make a collaborative research team between Japan and Cameroon, here we show the skin microbiome of Japanese and Cameroonian healthy people." 31956235 "Feasibility of microbial sample collection on the skin from people in Yaound_, Cameroon." Drug discoveries & therapeutics 2019 Nana C Benderli "The Biotechnology Center, University of Yaound_ I, Yaound_, Cameroon." 539655 human skin metagenome Targeted Locus (Loci) 2022-01-18 2020-03-17 2020 "Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University" 700382 PRJDB9705 DDBJ human gut metagenome 58 446 Resistant maltodextrin intake reduces virulent metabolites in the gut environment: randomised control study Amplicon "Objective: In recent years, there have been many reports on the effects of prebiotics on the intestinal health. In particular, consuming indigestible dextrin has been reported to be beneficial. However, there is no reported that the comprehensive quantification of the effect of gut metabolites. Therefore, this study aimed to quantify the effects of indigestible dextrin on the intestine, especially intestinal metabolites. Design: A randomised, double-blind controlled trial was conducted in 29 Japanese subjects. Subjects consumed indigestible dextrin or placebo twice per day for half a year. Blood and faecal samples were collected before and after the intake. The intestinal environment was assessed by sequencing the microbiome and mass spectrometry-based metabologenomics analyses. Results: The intake of indigestible dextrin increased the levels of Bifidobacterium and Fusicatenibacter, and decreased deoxycholate. In addition, intake of the indigestible dextrin lowered the levels of some virulent metabolites, such as imidazole propionate and trimethylamine, in subjects with an initially high amount of those metabolites. Conclusion: Indigestible dextrin might have beneficial effects for gut environments such as increasing of commensal microbiota and decreasing of virulence metabolites reported as a causation factor of several disease, but its effect partially depends on their baseline gut environments." 408170 human gut metagenome Targeted Locus (Loci) 2021-02-07 2020-04-11 2020 "Metabologenomics, Inc." 742248 PRJDB9921 DDBJ human skin metagenome 0 0 Human and murine skin microbiota of atopic dermatitis Amplicon "Human skin swab samples were collected from Japanese healthy volunteers and patients with atopic dermatitis (AD). Swab samples were also collected from neck skin of SPF Tmem79-/- AD model mice and Tmem79-/- mice colonized with complex AD microbiota. The 16S rRNA gene hypervariable V1-V2 regions were PCR-amplified using universal primers (a barcoded 27F and 354R) and, multiplexed amplicon pyrosequencing was carried out using MiSeq (illumina)." 1338477 skin metagenome Targeted Locus (Loci) 2021-06-29 2020-05-18 2020 "Laboratory for Microbiome Sciences, Center for Integrative Medical Sciences, RIKEN" 718780 PRJDB9936 DDBJ human gut metagenome 366 "4,499" 16S rRNA gene V1-V2 amplicon sequencing of healthy Japanese adults Amplicon "To clarify the features of gut microbiota in Japanese, fecal samples of 366 healthy Japanese adults were sampled and analyzed by 16S rRNA gene amplicon sequencing." 10.1016/j.funeco.2020.101036 10.1016/j.funeco.2020.101036 Saprotrophic and ectomycorrhizal fungi exhibit contrasting richness patterns along elevational gradients in cool-temperate montane forests Fungal Ecology 2021 Nobuhiko Shigyo 408170 human gut metagenome Targeted Locus (Loci) 2021-03-31 2020-05-21 2020 "Analytical Science Laboratory IV, Analytical Science Department, Yakult Central Institute" 679204 PRJDB9975 DDBJ human gut metagenome 97 "3,382" Cultural isolation of spore-forming bacteria in human feces using bile acids Amplicon "Structurally-diversified bile acids (BAs) are involved in shaping of intestinal microbiota as well as absorption of dietary lipids. Taurocholic acid, a conjugated form of BA, has been reported to be a factor triggering germination of a wide range of spore-forming bacteria in intestine. To test a hypothesis that other BAs also promote germination of intestinal bacteria, we attempted culture of bacteria from ethanol-treated feces by using a series of BAs. Among tested BAs, two glycine-conjugated BAs, namely glycodeoxycholic acid and glycochenodeoxycholic acid, most dramatically increased the number of colonies formed on the agar plate. These colonized bacteria mostly belonged to class Clostridia, mainly consisting of families Lachnospiraceae, Clostridiaceae, and Oscillospiraceae. There were several types of bacteria associated with different sensitivity to each BA. Eventually, we isolated 72 bacterial species of which 61 are known and 11 novel. These results demonstrate that the culturable range of bacteria in intestine can be widened using the germination-inducing activity of BAs. This approach would advance the research on spore-forming Clostridia that contains important but difficult-to-cultured bacteria associate with host health and diseases." 2020-12-01T00:00:00Z 10.1038/s41598-020-71883-1 10.1038/s41598-020-71883-1 Cultural isolation of spore-forming bacteria in human feces using bile acids Scientific Reports 2020 Masaru Tanaka 408170 human gut metagenome Targeted Locus (Loci) 2020-05-25 2020 "Lab. of Microbial Technology, Faculty of Agriculture, Kyushu University" 725688 PRJDB10526 DDBJ human gut metagenome 297 "17,842" Gut microbiota of healthy Japanese adult Amplicon "16S rDNA amplicon sequence of gut microbiota of healthy Japanese adult living in Shinjuku, Tokyo, Japan." 2021-05-20T00:00:00Z 34016052 Comprehensive analysis of gut microbiota of a healthy population and covariates affecting microbial variation in two large Japanese cohorts. BMC microbiology 2021 Jonguk Park "Laboratory of Bioinformatics, Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan." 408170 human gut metagenome Targeted Locus (Loci) 2020-09-07 2020 "Laboratory of Bioinformatics Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition" 725689 PRJDB10527 DDBJ human gut metagenome 91 "7,123" Gut microbiota of healthy Japanese adult Amplicon "16S rDNA amplicon sequence of gut microbiota of healthy Japanese adult living in Shinjuku, Tokyo, Japan." 2021-05-20T00:00:00Z 34016052 Comprehensive analysis of gut microbiota of a healthy population and covariates affecting microbial variation in two large Japanese cohorts. BMC microbiology 2021 Jonguk Park "Laboratory of Bioinformatics, Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan." 408170 human gut metagenome Targeted Locus (Loci) 2020-09-08 2020 "Laboratory of Bioinformatics, Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition" 725690 PRJDB10528 DDBJ human gut metagenome 387 "22,518" Gut microbiota of healthy Japanese adult Amplicon "16S rDNA amplicon sequence of gut microbiota of healthy Japanese adult living in Minamiuonuma, Niigata, Japan." 2021-05-20T00:00:00Z 34016052 Comprehensive analysis of gut microbiota of a healthy population and covariates affecting microbial variation in two large Japanese cohorts. BMC microbiology 2021 Jonguk Park "Laboratory of Bioinformatics, Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan." 408170 human gut metagenome Targeted Locus (Loci) 2020-09-08 2020 "Laboratory of Bioinformatics, Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition" 725691 PRJDB10529 DDBJ human gut metagenome 87 "8,198" Gut microbiota of healthy Japanese adult Amplicon "16S rDNA amplicon sequence of gut microbiota of healthy Japanese adult living in Osaka, Osaka, Japan." 2021-05-20T00:00:00Z 34016052 Comprehensive analysis of gut microbiota of a healthy population and covariates affecting microbial variation in two large Japanese cohorts. BMC microbiology 2021 Jonguk Park "Laboratory of Bioinformatics, Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan." 408170 human gut metagenome Targeted Locus (Loci) 2020-09-08 2020 "Laboratory of Bioinformatics, Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition" 725692 PRJDB10530 DDBJ human gut metagenome 92 "7,263" Gut microbiota of healthy Japanese adult Amplicon "16S rDNA amplicon sequence of gut microbiota of healthy Japanese adult living in Shunan, Yamaguchi, Japan." 2021-05-20T00:00:00Z 34016052 Comprehensive analysis of gut microbiota of a healthy population and covariates affecting microbial variation in two large Japanese cohorts. BMC microbiology 2021 Jonguk Park "Laboratory of Bioinformatics, Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, 567-0085, Japan." 408170 human gut metagenome Targeted Locus (Loci) 2020-09-08 2020 "Laboratory of Bioinformatics, Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition" 740186 PRJDB10651 DDBJ human oral metagenome 94 187 "16S amplicon sequence analysis of saliva from patients with IgA Nephropathy, chronic tonsillitis and healthy control" Amplicon "Japan has the second highest incidence of immunoglobulin A nephropathy (IgAN) or Berger's Disease in the world ( 39-45 million cases per million population per year), and 20 to 50 percent of Japanese with IgAN develop fatal end stage kidney disease. The pathogenesis of IgAN is poorly understood and development of diagnostic methods that do not rely on renal biopsy has been slow. Therefore the objective of this study is to compare the salivary microbiome of IgAN patients with healthy controls (HCs) and related mucosal diseases. Saliva was collected pre-operatively from 43 IgAN patients, 20 Chronic tonsillitis patients and 50 HCs. Total microbial DNA extracted from these samples was then analysed by amplicon sequencing of V1-V2 region16S rRNA using 454 pyrosequencing technology." 34078780 Dysbiosis in the Salivary Microbiome Associated with IgA Nephropathy-?A? ?Japanese Cohort Study. Microbes and environments 2021 Anushka Khasnobish "Laboratory of Animal Applied Microbiology, Graduate School of Environmental and Life Science, Okayama University." 1679718 human saliva metagenome Targeted Locus (Loci) 2020-10-06 2020 "Animal Applied Microbiology Laboratory, Department of Animal Science, Graduate School of Environment and Life Sciences" 786494 PRJDB10718 DDBJ human gut metagenome 152 "3,605" gut microbiota of men with prostate cancer Amplicon "This project was conducted to investigate the association between prostate cancer and gut flora in Japanese men. Rectal swabs of 152 Japanese men with suspected prostate cancer were sampled. The samples were suspended in phosphate buffered saline and the bacterial DNA was extracted from the suspension using DNeasy Power Soil Kit (Qiagen). Amplicons targeting the V1-V2 variable regions of 16S rRNA gene were generated,and a 251-bp paired-end sequencing of the amplicons was performed, using a MiSeq (Illumina)." 408170 human gut metagenome Targeted Locus (Loci) 2021-12-06 2020-10-23 2020 "Urology, Graduate School of Medicine, OSAKA UNIVERSITY" 809214 PRJDB10829 DDBJ human gut metagenome 112 "683,000" Generic sample from human gut metagenome Shotgun Total microbial community DNA was isolated from the fecal samples of Japanese patients who underwent colonoscopy at National Cancer Research Center. The study population contains CRC and postoperative patients. 408170 human gut metagenome Random survey 2022 Tokyo Institute of Technology 792347 PRJDB11094 DDBJ human oral metagenome 46 518 Analysis of bacterial community in denture plaque. Amplicon "This study was performed to clarify the difference in the bacterial composition between denture and dental plaques. Denture plaque is a multispecies biofilm that grows on the resin surface of removable prosthodontic devices (dentures), and is closely associated with denture-related stomatitis. Methods: Thirty denture plaque and 16 dental plaque samples were collected from 18 denture wearers (mean age, 80.3 years) with normal systemic conditions. After DNA extraction, a meta 16S rDNA amplicon library was constructed using universal PCR primers 341F and 805R, targeting the V3-V4 hypervariable region of bacteria. The 460-bp amplicon was evaluated by high-throughput sequencing using Illumina MiSeq, followed by bacterial population analysis using QIIME 2." 447426 human oral metagenome Targeted Locus (Loci) 2021-12-26 2021-01-17 2021 "Department of Microbiology, Aichi Gakuin University" 799489 PRJDB11117 DDBJ human lung metagenome 80 "1,906" microbiota analysis of specimens with respiratory infections Amplicon Methods: This study targeted 35 patients with lung abscess and 45 patients with pneumonia with aspiration risks. Objectives: This study was conducted to investigate the optimal clustering threshold of 16S ribosomal RNA gene sequences into operational taxonomic units. 433733 human lung metagenome Targeted Locus (Loci) 2022-01-22 2021-01-20 2021 "University of Occupational and Environmental Health, Japan" 721039 PRJDB11461 DDBJ human lung metagenome 25 429 Lower airway microbiota in patients with clinically suspected Mycobacterium avium complex lung disease Amplicon "We tried to put some light on the relationship between Non-tuberculous mycobacterial lung disease and lower airway microbiota, based on clinical characterization of the patients and 16s rRNA sequencing. The results reported Other than the genus Pseudomonas, there was no clear difference in the composition of and no significant difference in the diversity of the bacterial flora between the Mycobacterium Avium Complex-Lung Disease (MAC-LD) and non-MAC-LD groups. We found that the genus Pseudomonas and Mycobacterium Avium Complex tended to exist exclusively." 1712573 human tracheal metagenome Targeted Locus (Loci) 2021-04-10 2021-04-01 2021 "Internal medicine, Toho University Sakura Medical Center" 743446 PRJDB11894 DDBJ human gut metagenome 336 "3,738" Gut microbiota of Japanese centenarians Amplicon "We performed 16S rRNA gene amplicon sequencing on gut microbiota from centenarians (100-115 yo; average 107 yo; n=162), elderly (85-89 yo; average 86.4 yo; n=112), young (21-55 yo; average 31 yo; n=40) individuals and lineal relatives of centenarians (48-95 yo; average 74.7 yo; n=22). The 16S rRNA gene hypervariable V1-V2 regions were PCR-amplified using universal primers (a barcoded 27Fmod and 338R) and, multiplexed amplicon pyrosequencing was carried out using Illumina MiSeq. We have identified that microbiota composition of centenarians was significant different from those of control groups." 408170 human gut metagenome Targeted Locus (Loci) 2021-07-03 2021-06-23 2021 "Laboratory for Microbiome Sciences, Center for Integrative Medical Sciences, RIKEN" 747645 PRJDB11918 DDBJ human gut metagenome 41 "1,476" 16S rRNA amplicon sequencing of colon mucosal tissue and feces obtained from patients with gastrointestinal immune-related adverse events Amplicon 16S rRNA amplicon was sequenced to investigate microbial diversity on patients with gastrointestinal immune-related adverse events. 2021-07-16T00:00:00Z 34270845 Integrative analysis of gut microbiome and host transcriptomes reveals associations between treatment outcomes and immunotherapy-induced colitis. Molecular oncology 2021 Toshiharu Sakurai "Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osaka, Japan." 646099 human metagenome Targeted Locus (Loci) 2021-06-28 2021 Kindai University Faculty of Medicine 751782 PRJDB11949 DDBJ human gut metagenome 169 "7,846" microbiome analysis for patietns with HIV Amplicon "A project to clarify the intestinal microbiota of Japanese HIV carriers. The purpose of this project is to compare and analyze the intestinal microflora of Japanese healthy individuals and patients with HIV, and to clarify the alterations in the intestinal microflora associated with pathological conditions." 408170 human gut metagenome Targeted Locus (Loci) 2021-08-03 2021-07-05 2021 "Divisin of Infectious Diseases, Institute of Medical Science, The University of Tokyo" 783555 PRJDB12256 DDBJ human gut metagenome 45 "120,000" Monitoring circulating tumor DNA by using panel-specific sequencing to predict recurrence in colorectal cancer after surgical resection Shotgun "BACKGROUND AND AIMS: Irritable bowel syndrome (IBS) is a disorder of gut-brain interaction, including dysregulation of the hypothalamic-pituitary-adrenal axis with salivary cortisol changes. However, the role of gastrointestinal microbiota during IBS symptom exacerbation remains unclear. We tested the hypothesis that the microbial species, gene transcripts, and chemical composition of fecal and oral samples are altered during the exacerbation of IBS symptoms. METHODS: Fecal, salivary, and dental plaque samples were collected at baseline from 43 men with IBS with diarrhea (IBS-D) and 40 healthy control (HC) men. Samples in the IBS-D patients were also collected during symptom exacerbation. The composition of the fecal microbiota was determined by analyzing the 16S rDNA, RNA-based metatranscriptome, and metabolites in samples from HC and IBS patients with and without symptom exacerbation. Oral samples were also analyzed using omics approaches. RESULTS: The fecal microbiota during IBS symptom exacerbation exhibited significant differences in the phylogenic pattern and short-chain fatty acid metabolites compared with fecal samples during defecation when symptoms were not exacerbated. Although there were no significant differences in the phylogenic pattern of fecal microbiota abundance between HCs and IBS-D patients, significant differences were detected in the expression patterns of bacterial transcriptomes related to butyrate production and neuroendocrine hormones, including tryptophan-serotonin-melatonin synthesis and glutamine/GABA. The composition of plaque microbiota was different between HC and IBS-D patients during normal defecation but there was no overlap with the fecal microbiome. CONCLUSION: Our findings suggest that colonic host-microbial interactions are altered in IBS-D patients during exacerbation of symptoms. There were no overlaps between feces and oral microbiomes." 2705415 human feces metagenome Random survey 2021-11-25 2021-09-03 2021 "Translational Informatics, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center" 792350 PRJDB12349 DDBJ human metagenome 45 "1,906" microbiome analysis for patietns with COVID-19 Shotgun To conduct research that contributes to the control of COVID-19 infections and to contribute to society. 646099 human metagenome Genome sequencing 2021-12-26 2021-09-29 2021 "Division of Infectious Diseases, Advanced Clinical Research Center, Institute of medical science, The University of Tokyo" 771956 PRJDB12388 DDBJ human gut metagenome 16 706 16S rRNA amplicon sequencing of colon mucosal tissue obtained from patients with ulcerative colitis Amplicon 16S rRNA amplicon was sequenced to investigate microbial diversity on patients with ulcerative colitis. 408170 human gut metagenome Targeted Locus (Loci) 2021-10-17 2021-10-04 2021 Kindai University Faculty of Medicine 770551 PRJDB12430 DDBJ human gut metagenome 400 "7,702" Changes in gut microbiome by intake of poly-gamma-glutamic acid and galactooligosaccharide Amplicon Total microbial DNA was isolated from the fecal samples of Japanese healthy people who took test food before and after intervention. We used Miseq for sequence analysis. 408170 human gut metagenome Other 2021-10-12 2021-10-11 2021 "Ajinomoto Co., Inc., Ajinomoto Co., Inc." 771820 PRJDB12444 DDBJ human oral metagenome 60 "3,598" Interdental plaque microbial community changes under in vitro violet Amplicon "Oral microbiome dysbiosis has important links to human health and disease. Although photodynamic therapy influences microbiome diversity, the specific effect of violet light irradiation remains largely unknown. In this study, we analysed the effect of violet light-emitting diode (LED) irradiation on interdental plaque microbiota. Interdental plaque was collected from 12 human subjects, exposed to violet LED irradiation, and cultured in a specialized growth medium. Next-generation sequencing of the 16S ribosomal RNA genes revealed that a-diversity decreased, whereas b-diversity exhibited a continuous change with violet LED irradiation doses. In addition, we identified several operational taxonomic units that exhibited significant shifts during violet LED irradiation." 447426 human oral metagenome Targeted Locus (Loci) 2021-10-16 2021-10-12 2021 Osaka Dental University 798913 PRJDB12514 DDBJ human gut metagenome 1223 "12,851" Development and evaluation of a colorectal cancer screening method using machine learning-based gut microbiota analysis Amplicon The purpose of this study was to develop a non-invasive screening test for colorectal cancer based on gut microbiota analysis. A large number of Japanese feces were used for validation data. 2705415 human feces metagenome eRawSequenceReads 2022-01-20 2021-10-22 2021 "Department of Molecular Microbiology, Research Institute for Microbial Diseases, Osaka University" 782120 PRJDB12569 DDBJ human skin metagenome 58 "4,045" Skin microbiome of Japanese elderly in relation to the onset of pressure ulcers (Staphylococcus species-targeted sequencing) Amplicon "One of the most prevalence and challenging problems for elderly in Japan is the onset of pressure ulcers (PU) during being cared in hospitals and/or their home. We collected bacteria from skins healed from pressure injury (BioProject PRJDB7687). Previously we analyzed 16S rRNA V3-V4 sequences on the healed skins which were suffered from recurrent pressure injury within six weeks and those not suffered within the duration. Additionally, we analyzed abundance of Staphylococcus species in the samples." 539655 human skin metagenome Targeted Locus (Loci) 2021-11-20 2021-11-04 2021 "Institute for Frontier Science Initiative, Kanazawa university" 814097 PRJDB13187 DDBJ human gut metagenome N.D. N.D. Comparison study of gut microbiome and hypertension using shotgun metagenomic sequence Shotgun "We performed shotgun metagenomic analysis of human gut microbiota in Shika Town, Ishikawa Prefecture, Japan, and analyze association between gut microbiota and hypertension." 408170 human gut metagenome Random survey "Shigefumi Okamoto Laboratory, Department of Laboratory Sciences, Faculty of Health Sciences, Kanazawa University" 496632 PRJEB26092 EBI human gut metagenome 0 0 EMG produced TPA metagenomics assembly of the Metagenomics of Japanese gut microbiomes (human gut metagenome) data set. Shotgun "The human gut metagenome Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set: PRJDB3601. This project includes samples from the following biomes: Host-associated, Human, Digestive system, Large intestine." 29069476 "EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies." Nucleic acids research 2018 Alex L Mitchell "EMBL-EBI European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK." Genome sequencing 2018-10-16 2018-10-16 2018 EMG 28117 PRJNA28117 NCBI human gut metagenome 13 0 Gut metagenomes collected from 13 healthy individuals Shotgun "Numerous microbes inhabit the human intestine, many of which are uncharacterized or uncultivable. They form a complex microbial community that deeply affects human physiology. To identify the genomic features common to all human gut microbiomes as well as those variable among them, we performed a large-scale comparative metagenomic analysis of fecal samples from 13 healthy individuals of various ages, including unweaned infants. All the subjects were healthy Japanese individuals. All subjects or their parents were informed of the purpose and protocol of this study. None of the subjects were given dietary restrictions except for antibiotics, probiotics, fermented foods (fermented beans, yogurt, etc.), and well-known functional foods for at least 4 weeks prior to sampling. None had a history of gastrointestinal disorder at the time of sampling, and none had unusual eating behaviors." 17916580 Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA research 2007 Ken Kurokawa "Laboratory of Comparative Genomics, Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan." 408170 human gut metagenome 2007 33495 PRJNA33495 NCBI human gut metagenome 0 0 Metagenomic diagnosis of viral infections - RAPID project Shotgun "454 sequencing was used for viral detection in nasopharyngeal and fecal samples collected during seasonal influenza virus infections and norovirus outbreaks from 2005 to 2007 in Osaka, Japan. Influenza virus and norovirus were directly detected by this approach. <p> The SRA submission can be found using the Project Data link." 408170 human gut metagenome Metagenome 2009-01-05 2009 575808 PRJNA575808 NCBI human reproductive system metagenome 62 "1,068" human reproductive system metagenome Metagenome Amplicon A case-control study of the association between human uterocervical microbiota composition and ovarian cancer status 34856363 10.1016/j.gene.2021.146083 Altered cervicovaginal microbiota in premenopausal ovarian cancer patients. Gene 2022 Asuka Morikawa 1842734 human reproductive system metagenome Other 2019-10-04 2019-10-04 2019 The University of Tokyo 686801 PRJNA686801 NCBI human gut metagenome 571 "1,684" "Yearly change in intestinal microbiota of older people, and the effect on it of Lactobacillus intake Metagenome" Amplicon "Intestinal microbiota of older Japanese, aged 65 or older. V1-V2 region of 16S rRNA gene. Two or three samples per individual" 10.1038/s41598-021-91917-6 10.1038/s41598-021-91917-6 "Yearly changes in the composition of gut microbiota in the elderly, and the effect of lactobacilli intake on these changes" Scientific Reports 2021 Ryuta Amamoto 408170 human gut metagenome metagenome 2020-12-20 2020-12-20 2020 Yakult Central Institute 730993 PRJNA730993 NCBI human gut metagenome 491 0 Metagenome-assembled genomes for new prokaryotic species from Indian and Japanese gut metagenomes. Shotgun Assembled genomes from whole-metagenomic shotgun sequencing data on human feces. 10.1101/2020.11.09.375873 10.1101/2020.11.09.375873 "Human reference gut microbiome comprising 5,414 prokaryotic species, including newly assembled genomes from under-represented Asian metagenomes" 2020 Chan Yeong Kim 408170 human gut metagenome Genome sequencing and assembly 2021-05-19 2021-05-19 2021 Yonsei University