Table of Contents
メタゲノム解析
ヒト腸内細菌叢解析
健康な日本人の大人と乳幼児計１３人の腸内細菌叢のメタゲノム解析
| サンプル | 年齢 | 性別 | 総解析塩基長(Mb) | 共同研究先 | |||
|---|---|---|---|---|---|---|---|
| 1 | 個人1 | In-A | 45 | 男性 | 52.5 | HMGJ | |
| 2 | 個人2 | In-B | 6ヶ月 | 男性 | 62.8 | HMGJ | |
| 3 | 個人3 | In-D | 35 | 男性 | 55.1 | HMGJ | |
| 4 | 個人4 | In-E | 3ヶ月 | 男性 | 56.8 | HMGJ | |
| 5 | 個人5 | In-M | 4ヶ月 | 女性 | 57.8 | HMGJ | |
| 6 | 個人6 | In-R | 24 | 男性 | 55.4 | HMGJ | |
| 7 | 家族1 | F1-S | 30 | 男性 | 53.6 | HMGJ | |
| 8 | F1-T | 28 | 女性 | 55.4 | HMGJ | ||
| 9 | F1-U | 7ヶ月 | 女性 | 53.9 | HMGJ | ||
| 10 | 家族2 | F2-V | 37 | 男性 | 55.9 | HMGJ | |
| 11 | F2-W | 36 | 女性 | 54,9 | HMGJ | ||
| 12 | F2-X | 3 | 男性 | 56.6 | HMGJ | ||
| 13 | F2-Y | 1.5 | 女性 | 56.3 | HMGJ | ||
| 合計 | 727 |
*HMGJ - Human MetaGenome consortium, Japan
論文
Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, Taylor TD, Noguchi H, Mori H, Ogura Y, Ehrlich DS, Itoh K, Takagi T, Sakaki Y, Hayashi T, Hattori M.
Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes.
DNA Res. (2007) 14:169-81.
TRACE DATAのダウンロード
以下のFTPサイトからダウンロード可能です。
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dta/UTCOB
微生物ゲノム配列解析
| Organism | Status | Size | Publication | Co-Lab. | ||
|---|---|---|---|---|---|---|
| 1 | Adlercreutzia equolifaciens DSM 19450T | Complete | 2,862,633 nt | probiotics | in preparation | 麻布大 |
| 2 | Aeromonas hydrophila | Complete | 4,682,614 nt | pathogen | in preparation | 東京海洋大 |
| 3 | Agromonas oligotrophica S58 | Complete | 8,264,165 nt | soil | in preparation | 東北大 |
| 4 | Arcobacter butzleri ED-1 | Complete | 2,256,675 nt | industrial use | J Bacteriol (2011) | 理研/Univ. Edinburgh |
| 5 | Arcobacter sp. L | Complete | 2,945,673 nt | industrial use | J Bacteriol (2011) | 理研/Univ. Edinburgh |
| 6 | Aspergillus sojae NBRC 4239 | Draft | 39.5 M | industrial use | DNA res (2011) | キッコーマン/東工大 |
| 7 | Azoarcus sp. KH32C | Complete | 5,081,166 nt | soil | in preparation | 東京大 |
| 8 | Bacillus cereus NC7401 | Complete | 5,221,581 nt | pathogen | in preparation | 名古屋大 |
| 9 | Bacillus subtilis ATCC 6051 | Draft | 3.9 M | pathogen | in preparation | NAIST |
| 10 | Bacteroides fragilis YCH46 | Complete | 5,277,274 nt | pathogen | PNAS (2004) | 徳島大 |
| 11 | Bacteroides massiliensis A_03 | Complete | 4,794,082 nt | commensal | in preparation | 徳島大/理研 |
| 12 | Bacteroides sp. A_01 | Incomplete | 5.0 M | commensal | 徳島大/理研 | |
| 13 | Bifidobacterium angulatum JCM 7096 | Complete | 2,021,974 nt | commensal | in preparation | 麻布大 |
| 14 | Bifidobacterium bifidum JCM 1255 | Complete | 2,211,039 nt | commensal | in preparation | 麻布大 |
| 15 | Bifidobacterium breve JCM 1192 | Complete | 2,269,455 nt | commensal | in preparation | 麻布大 |
| 16 | Bifidobacterium catenulatum JCM 1194 | Complete | 2,079,525 nt | commensal | in preparation | 麻布大 |
| 17 | Bifidobacterium dentium JCM 1195 | Complete | 2,385,164 nt | commensal | in preparation | 麻布大 |
| 18 | Bifidobacterium longum subsp. longum ATCC 15707T | Complete | 3,158,347 nt | commensal | Nature (2011) | 麻布大/理研 |
| 19 | Bifidobacterium longum subsp. infantis 157F | Complete | 2,400,312 nt | commensal | Nature (2011) | 麻布大/理研 |
| 20 | Bifidobacterium longum subsp. infantis ATCC 15697 | Complete | 2,828,958 nt | commensal | Nature (2011) | 麻布大/理研 |
| 21 | Bifidobacterium scardovii JCM 12489 | Complete | 2,635,669 nt | commensal | in preparation | 麻布大 |
| 22 | Bifidobacterium pseudocatenulatum JCM 1200 | Complete | 2,313,752 nt | commensal | in preparation | 麻布大 |
| 23 | Bifidobacterium kashiwanohense JCM 15439 | Complete | 2,337,234 nt | commensal | IJSEM (2011) | 麻布大 |
| 24 | Bifidobacterium sp. JCM 16039 | Complete | 2,345,793 nt | commensal | in preparation | 麻布大 |
| 25 | Bradyrhizobium betae S23321 | Complete | 7,231,841 nt | soil | in preparation | 東北大 |
| 26 | Buchnera aphidicola str.APS | Complete | 640,681nt | insect symbiont | Nature (2000) | 東京大/理研 |
| 27 | Burkholderia multivorans ATCC 17616 | Complete | 6,841,388 nt | pathogen | 東北大 | |
| 28 | Candidatus Arthromitus sp. SFB-mouse-Japan | Complete | 1,620,005 nt | mouse commensal | DNA Res (2011) | 香川大/宮崎大/麻布大 |
| 29 | Candidatus Arthromitus sp. SFB-mouse-Yit | Complete | 1,586,397 nt | mouse commensal | Cell MH (2011) | 理研/ヤクルト/麻布大 |
| 30 | Candidatus Arthromitus sp. SFB-rat-Yit | Complete | 1,515,556 nt | rat commensal | Cell MH (2011) | 理研/ヤクルト/麻布大 |
| 31 | Canditatus Carsonella ruddii PV | Complete | 159,662 nt | insect symbiont | Science (2006) | 理研/Arizona-U |
| 32 | Candidatus Ishikawaella capsulata Mpkobe | Complete | 745,590 nt | insect symbiont | Genome Biol Evol (2011) | 放送大/産総研 |
| 33 | Chlamydophila caviae | Complete | 1,173,387 nt | pathogen | in preparation | 岡山大 |
| 34 | Chlamydophila felis Fe/C-56 | Complete | 1,166,239 nt | pathogen | DNA Res (2006) | 山口大 |
| 35 | Chlamydophila pneumoniae J138 | Complete | 1,226,565 nt | pathogen | Nucleic Acids Res (2000) | 山口大 |
| 36 | Clostridium acetobutylicum | Draft | 4.0 M | industrial use | 九州大 | |
| 37 | Clostridium chauvoei | Draft | 3.0 M | pathogen | 金沢大 | |
| 38 | Clostridium cluster group XIVa SY8519 | Complete | 3,031,430 nt | probaiotics | J Bacteriol (2011) | 岐阜大 |
| 39 | Clostridium clostridioforme JCM 1291 | Incomplete | 5.3 M | calf rumen | 徳島大/理研 | |
| 40 | Clostridium innocuum JCM 1292 | Draft | 3.0 M | commensal | 徳島大/理研 | |
| 41 | Clostridium paraputrificum JCM 1293 | Complete | 3,515,907 nt | commensal | in preparation | 徳島大/理研 |
| 42 | Clostridium perfringens str.13 | Complete | 3,031,430 nt | pathogen | PNAS (2002) | 筑波大 |
| 43 | Clostridium ramosum JCM 1298 | Complete | 3,240,990 nt | commensal | in preparation | 徳島大/理研 |
| 44 | Clostridium septicum | Draft | 3.0 M | pathogen | 金沢大 | |
| 45 | Corynebacterium glutamicum ATCC 13032 | Complete | 3,309,401 nt | industrial use | Appl Microbiol Biotech (2003) | 協和発酵 |
| 46 | Corynebacterium macginleyi TBS-13 | Complete | 2,695,463 nt | pathogen | in preparation | 徳島大 |
| 47 | Cyanothece sp. TU126 | Draft | 6.0 M | marine | RITE | |
| 48 | Cycloclasticus sp. SUSI-4 | Complete | 2,338,755 nt | industrial use | in preparation | 日本大 |
| 49 | Eggerthella sp. YY7918 | Complete | 3,123,671 nt | industrial use | J Bacteriol (2011) | 岐阜大 |
| 50 | Escherichia coli O103 strain12009 | Complete | 5,449,314 nt | pathogen | PNAS (2009) | 宮崎大 |
| 51 | Escherichia coli O111 strain11128 | Complete | 5,371,077 nt | pathogen | PNAS (2009) | 宮崎大 |
| 52 | Escherichia coli O26 strain11044 | Complete | 5,697,240 nt | pathogen | PNAS (2009) | 宮崎大 |
| 53 | Escherichia coli O157:H7 sakai | Complete | 5,498,450 nt | pathogen | DNA Res (2001) | 宮崎大/大阪大 |
| 54 | Escherichia coli SE11 (JCM 16574) | Complete | 4,887,515 nt | commensal | DNA Res (2008) | 宮崎大 |
| 55 | Escherichia coli SE15 (JCM 16575) | Complete | 4,717,338 nt | commensal | J Bacteriol (2010) | 宮崎大/理研 |
| 56 | Finegoldia magna ATCC 29328 | Complete | 1,797,577 nt | pathogen | DNA Res (2008) | 和歌山医大 |
| 57 | Gardnerella vaginalis JCM 11026T | Complete | 1,667,406 nt | pathogen | in preparation | 麻布大 |
| 58 | Halomonas elongata | Complete | 4,066,209 nt | pathogen | in preparation | 大阪大/RITE |
| 59 | Helicobacter pyroli F16 | Complete | 1,575,399 nt | pathgen | PNAS (2011) | 東京大/神戸大 |
| 60 | Helicobacter pyroli F30 | Complete | 1,5705,64 nt | pathgen | PNAS (2011) | 東京大/神戸大 |
| 61 | Helicobacter pyroli F32 | Complete | 1,578,824 nt | pathgen | PNAS (2011) | 東京大/神戸大 |
| 62 | Helicobacter pyroli F57 | Complete | 1,609,006 nt | pathgen | PNAS (2011) | 東京大/神戸大 |
| 63 | Lactobacillus brevis KB290 | Complete | 2,395,134 nt | probiotics | in preparation | カゴメ |
| 64 | Lactobacillus casei ATCC 393 | Complete | 2,924,929 nt | probiotics | in preparation | 麻布大/NIHS |
| 65 | Lactobacillus fermentum IFO 3956 | Complete | 2,098,685 nt | others | DNA Res (2008) | 麻布大 |
| 66 | Lactobacillus helveticus CM4 | Complete | 2,028,493 nt | probiotics | カルピス | |
| 67 | Lactobacillus paracasei JCM 8130T | Complete | 2,995,875 nt | commensal | in preparation | 麻布大 |
| 68 | Lactobacillus reuteri JCM 1112 | Complete | 2,039,414 nt | commensal | DNA Res (2008) | 麻布大 |
| 69 | Lactobacillus rhamnosus ATCC 53103 | Complete | 3,005,051 nt | commensal | J Bacteriol (2009) | 麻布大/NIHS |
| 70 | Lactococcus garviae ATCC 49156 | Complete | 1,950,135 nt | marine | PLoS ONE (2011) | 麻布大 |
| 71 | Lactococcus garviae Lg2 | Complete | 1,963,964 nt | fish pathogen | PLoS ONE (2011) | 麻布大 |
| 72 | Lactococcus lactis IO-1 | Complete | 2,421,471 nt | probaiotics | in preparation | 東京農大 |
| 73 | Micromonospora olivasterospor | Draft | 8.0 M | Industrial use | 東京大/北里大 | |
| 74 | Mycoplasma penetrans HF-2 | Complete | 1,358,633 nt | pathogen | Nucleic Acids Res (2002) | 感染研 |
| 75 | Nocardia farcinica IFM10152 | Complete | 6,021,225 nt | pathogen | PNAS (2004) | 感染研 |
| 76 | Orientia tsutsugamushi IKEDA | Complete | 2,008,987 nt | pathogen | DNA Res (2008) | 宮崎大 |
| 77 | Parascardovia denticolens JCM 12538T | Complete | 1,890,857 nt | pathogen | in preparation | 麻布大 |
| 78 | Porphyromonas gingivalis ATCC 33277 | Complete | 2,354,886 nt | pathogen | DNA Res (2008) | 長崎大 |
| 79 | Porphyromonas gingivalis TDC60 | Complete | 2,354,886 nt | pathogen | J Bacteriol (2011) | 東工大/日医歯大 |
| 80 | Pseudogulbenkiania sp. NH8B | Complete | 4,332,995 nt | soil | J Bacteriol (2011) | 東京大 |
| 81 | Raoultella ornithinolytica AA097 | Complete | 5,470,207 nt | commensal | in preparation | 宮崎大/理研 |
| 82 | Rickettsia japonica YH | Complete | 1,283,087 nt | pathogen | 山口大 | |
| 83 | Ruminococcus gnavus TBH11 | Complete | 3,953,418 nt | commensal | in preparation | 徳島大 |
| 84 | Scardovia inopinata JCM 12537T | Complete | 1,797,862 nt | pathogen | in preparation | 麻布大 |
| 85 | Serratia marcescens SM28 | Complete | 5,225,987 nt | pathogen | in preparation | 京薬大 |
| 86 | Sodalis glossinidius str.'morsitans' | Complete | 4,171,146 nt | insect symbiont | Genome Res (2006) | Yale-U |
| 87 | Staphylococcus aureus subsp. aureus Mu50 | Complete | 2,878,529 nt | pathogen | Lancet (2001) | 筑波大 |
| 88 | Staphylococcus hyicus | Complete | 2.5 M | pathogen | in preparation | 広島大 |
| 89 | Staphylococcus pseudintermedius MS5134 | Complete | 2,532,333 nt | pathogen | in preparation | 広島大 |
| 90 | Staphylococcus saprophyticus ATCC15305 | Complete | 2,516,575 nt | pathogen | PNAS (2005) | 筑波大 |
| 91 | Streptococcus mutans NN2025 | Complete | 2,013,587 nt | pathogen | BMC Genomics (2009) | 東京医歯大 |
| 92 | Streptococcus pyogenes SSI-1 | Complete | 1,894,275 nt | pathogen | Genome Res (2003) | 大阪大 |
| 93 | Streptomyces avermitilis MA-4680 | Complete | 9,025,608 nt | soil, industrial use | PNAS (2001) | 北里大/NITE |
| 94 | Streptomyces griseus IFO 13350 | Complete | 8,545,929 nt | soil, industrial use | J Bacteriol (2008) | 東京大 |
| 95 | Symbiobacterium thermophilum IAM14863 | Complete | 3,566,135 nt | soil, symbiont | Nucleic Acids Res (2004) | 日本大 |
| 96 | Treponema phagedenis YG3903R | Complete | 3,558,565 nt | animal pathogen | in preparation | 宮崎大 |
| 97 | Vibrio parahaemolyticus RIMD2210633 | Complete | 5,165,770 nt | pathogen | Lancet (2003) | 大阪大 |
| 98 | Wigglesworthia glossinidia endosymbiont of G.brevipalpis | Complete | 697,724 nt | insect symbiont | Nature Genet (2002) | Yale-U/理研 |
| 99 | Wigglesworthia morsitans | Complete | 719,535 nt | insect symbiont | in preparation | Yale-U |
