JP7317821B2 - ディスバイオシスを診断する方法 - Google Patents
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Description
i)被検者由来の試料中の核酸の配列を、細菌16S rRNA配列のデータベースに対してアラインメントすることと、
ii)ステップi)でのアラインメントを用いて、試料に存在する1種以上の細菌の同一性及び相対存在量を決定することと、
iii)試料中の1種以上の細菌の存在量を、健康な個体の参照集団における1種以上の細菌の存在量と比較することと、を含み、
参照集団に対する、試料中の細菌種の存在量の増加又は減少は、ディスバイオシスを示す。
i)被検者由来の試料中の核酸の配列を細菌16S rRNA配列のデータベースに対してアラインメントすることと、
ii)ステップi)のアライメントを用いて、試料に存在する1種以上の細菌の同一性及び相対存在量を決定することにより、試料データセットを得ることと、
iii)試料データセットに機械学習アルゴリズムを適用して、被検者におけるディスバイオシスを診断することと、を含み、
機械学習アルゴリズムは、ディスバイオシスを有する個体を含む参照集団由来の細菌種の同一性及び存在量を含むトレーニングデータセットによりトレーニングを行っている。
・生リード数。この数は、試料毎に30,000を超えることが予想された。
・第1のリードの品質。これは、分析した配列の280塩基以降に開始するQuality Value(QV)ビンフラグを渡すか、又は有する必要がある。これは、phredクオリティの中央値又は配列決定品質が、最初の280塩基の前に20未満に低下しなかったことを意味する。
・第1のリードの品質。これは、分析した配列の250塩基以降に開始するQVビンフラグを渡すか、又は有する必要がある。これは、phredクオリティの中央値又配列決定品質が、最初の250塩基の前に20未満に低下しなかったことを意味する。
・ライブラリGC含有量は、50乃至60%の範囲となるべきである。
・max-overlap:150
・max-mismatch-density:0.33
・リードは、長さが150bp未満の場合に除去し、
・残りの設定は、デフォルトの閾値のままとした。
・乳児:3歳まで、
・小児:3歳乃至12歳、
・大人:12乃至60歳、
・年配:60歳以上。
・IBS-D(下痢)、n=78
・IBS-M(混合)、n=22
・IBS-C(便秘)、n=78
Corynebacterium、Lachnobacterium、Propionibacterium、Kytococcus、Fusobacterium、Veillonella、Prevotella、Anaerofustis、Arthrobacter、Dysgonomonas、Calothrix、Atopobium、Brevibacterium、Micrococcus、Burkholderia、Veillonella、Pelotomaculum、Acidaminococcus、Mitsuokella、Allisonella、Odoribacter、Bacteroides、Coprobacter、Alistipes、Ruminococcus、Ferrimonas、Alkaliphilus、及びLautropia。
Corynebacterium minutissimum、Prevotella oulora、Fusobacterium naviforme、Prevotella ruminicola、Bifidobacterium thermacidophilum、Dysgonomonas wimpennyi、Propionibacterium acnes、Corynebacterium tuberculostearicum、Brevibacterium casei、Lachnobacterium bovis、Prevotella dentasini、Prevotella albensis、Veillonella atypica 、Kytococcus schroeteri、Prevotella copri、Bacteroides barnesiae、Prevotella conceptionensis、Anaerofustis stercorihominis、Bifidobacterium thermophilum、Prevotella brevis、Roseburia intestinalis、Clostridium symbiosum、Barnesiella intestinihominis、Bacteroides fragilis、Anaerostipes rhamnosus、Collinsella aerofaciens、Clostridium bolteae、Arthrobacter creatinolyticus、Atopobium fossor、Prevotella paludivivens、及びPelotomaculum isophthalicicum。
Christensenella minuta、Soleaferrea massiliensis、Papillibacter cinnamivorans、Oscillibacter valericigenes、Ruminococcus bromii、Gemmiger formicilis、Desulfitobacterium frappieri、Alistipes obesi、Anaerofilum pentosovorans、Akkermansia muciniphila、Alkaliphilus crotonatoxidans、Eubacterium sulci、Bdellovibrio exovorus、Curtobacterium pusillum、Flavonifractor plautii、Ruminococcus lactaris、Mogibacterium neglectum、Roseburia inulinivorans、Butyricimonas virosa、Intestinimonas butyriciproducens、Butyrivibrio crossotus、Barnesiella intestinihominis、Flavobacterium resistens、Flavobacterium cauense、Clostridium glycyrrhizinilyticum、Anaerostipes hadrus、Prevotella ruminicola、Blautia wexlerae、及びAnaerostipes coli。
Peptoniphilus coxii、Clostridium clariflavum、Bacteroides thetaiotaomicron、Bacteroides coprocola、Oscillibacter valericigenes、Clostridium hveragerdense、Ruminiclostridium clariflavum、Bacteroides xylanisolvens、Clostridium chauvoei、Clostridium tepidiprofundi、Papillibacter cinnamivorans、Lactococcus fujiensis、Bacteroides uniformis、Bacillus thuringiensis、Johnsonella ignava、Pseudoflavonifractor capillosus、Christensenella minuta、Enterococcus azikeevi、Intestinimonas butyriciproducens、Eubacterium sulci、Flavobacterium resistens、Anaerotruncus colihominis、Pseudoflavonifractor capillosus、Bacteroides fluxus、Ruminococcus lactaris、Butyrivibrio crossotus、Eubacterium rectale、Prevotella ruminicola、Gemmiger formicilis、Ruminococcus flavefaciens、及びFaecalibacterium prausnitzii。
Eubacterium hallii、Eubacterium rectale、Lachnobacterium bovis、Lachnoclostridium glycyrrhizinilyticum、Blautia glucerasea、Eubacterium desmolans、Anoxystipes fissicatena、Blautia coccoides、Faecalibacterium prausnitzii、Clostridium symbiosum、Roseburia inulinivorans、Anaerostipes coli、Coprococcus comes、Lachnospira pectinoschiza、Arthrobacter creatinolyticus、Clostridium nexile、Bifidobacterium thermacidophilum、Anaerostipes rhamnosus、Clostridium clariflavum、Blautia wexlerae、Fusicatenibacter saccharivorans、Tolumonas auensis、Ruminococcus gnavus、Peptococcus niger、Dorea formicigenerans、Roseburia intestinalis、Blautia wexlerae、Clostridium populeti、Dorea massiliensis、及びEubacterium eligens。
Pseudobutyrivibrio xylanivorans、Dorea massiliensis、Blautia glucerasea、Lachnoclostridium herbivorans、Faecalibacterium prausnitzii、Romboutsia lituseburense、Peptoniphilus methioninivorax、Blautia coccoides、Megamonas funiformis、Eubacterium rectale、Clostridium bifermentans、Roseburia intestinalis、Clostridium populeti、Clostridium hiranonis、Peptoclostridium difficile、Lactonifactor longoviformis、Clostridium caliptrosporum、Asaccharospora irregulare、Clostridium malenominatum、Clostridium symbiosum、Clostridium thermoalcaliphilum、Lachnoclostridium glycyrrhizinilyticum、Ruminococcus faecis、Blautia schinkii、Pseudoflavonifractor capillosus、Clostridium chromoreductans、Clostridium ghonii、Clostridium innocuum、Christensenella minuta、Dorea formicigenerans、及びClostridium tertium。
Core analysis with QIIME: QIIMEによるコア解析
Report: レポート
A. Checksums: A. チェックサム
B. FASTQC (QV): B. FASTQC (QV):
C. Combining the paired reads: C. ペアリードの結合
D. Quality trimming: D. クオリティトリミング
E. OTU clustering: E. OTUクラスタリング
F. Picking representative sequence: F. 代表配列のピッキング
G. Assigning taxonomy -alignment to database: G. データベースへのタクソノミアラインメントの割り当て
H. Convert taxonomy table (.biome -> .txt ): H. タクソノミテーブルの変換(.biome -> .txt )
I. Beta diversity within control populations (Bray Curtis): I. 対照集団内でのベータ多様性(Bray-Curtis)
J. PDF file with figures: J. 図付きのPDFファイル
K. Krona chart: K. Kronaチャート
[図2]
Controls: 対照
[図3]
Before treatment: 治療前
After first treatment: 第1の治療後
After second treatment: 第2の治療後
Claims (17)
- 被検者の過敏性腸症候群(IBS)のサブタイプを決定する方法であって、前記被検者由来の試料中又は前記被検者の環境由来の試料中の少なくとも5種の細菌の存在量を決定することを含み、前記少なくとも5種の細菌は、Christensenella minuta、Papillibacter cinnamivorans、Bilophila wadsworthia、Ruminococcus bromii、及びSoleaferrea massiliensisを含む、方法。
- Akkermansia muciniphila、Oscillibacter valericigenes、Desulfitobacterium frappieri、Anaerofilum pentosovorans、Lactobacillus japonicas、Catabacter hongkongensis、Clostridium sporosphaeroides、及びFaecalibacterium prausnitziiから選択される少なくとも1種の細菌の存在量を決定することを更に含む、請求項1記載の方法。
- 少なくとも10種の細菌の前記存在量を決定する、請求項1記載の方法。
- 被検者のディスバイオシスを検出する方法であって、前記被検者由来の試料中の少なくとも5種の細菌の存在量を決定することを含み、前記少なくとも5種の細菌は、Corynebacterium minutissimum、Prevotella oulora、Fusobacterium naviforme、Prevotella ruminicola、及びBifidobacterium thermacidophilumを含む、方法。
- Dysgonomonas wimpennyi、Propionibacterium acnes、Corynebacterium tuberculostearicum、Brevibacterium casei、Lachnobacterium bovis、Prevotella dentasini、Prevotella albensis、Veillonella atypica 、Kytococcus schroeteri、Prevotella copri、Bacteroides barnesiae、Prevotella conceptionensis、Anaerofustis stercorihominis、Bifidobacterium thermophilum、Prevotella brevis、Roseburia intestinalis、Clostridium symbiosum、Barnesiella intestinihominis、Bacteroides fragilis、Anaerostipes rhamnosus、Collinsella aerofaciens、Clostridium bolteae、Arthrobacter creatinolyticus、Atopobium fossor、Prevotella paludivivens、及びPelotomaculum isophthalicicumから選択される少なくとも1種の細菌の存在量を決定することを更に含む、請求項4記載の方法。
- 少なくとも10種の細菌の前記存在量を決定する、請求項4記載の方法。
- 少なくとも20種の細菌の前記存在量を決定する、請求項4記載の方法。
- 前記ディスバイオシスは、IBSである、請求項4乃至7の何れかに記載の方法。
- 過敏性腸症候群(IBS)である被検者のIBSのサブタイプを決定する方法であって、前記被検者由来の試料中の少なくとも5種の細菌の存在量を決定することを含み、前記少なくとも5種の細菌は、Christensenella minuta、Soleaferrea massiliensis、Papillibacter cinnamivorans、Oscillibacter valericigenes、及びRuminococcus bromiiを含む、方法。
- Gemmiger formicilis、Desulfitobacterium frappieri、Alistipes obesi、Anaerofilum pentosovorans、Akkermansia muciniphila、Alkaliphilus crotonatoxidans、Eubacterium sulci、Bdellovibrio exovorus、Curtobacterium pusillum、Flavonifractor plautii、Ruminococcus lactaris、Mogibacterium neglectum、Roseburia inulinivorans、Butyricimonas virosa、Intestinimonas butyriciproducens、Butyrivibrio crossotus、Barnesiella intestinihominis、Flavobacterium resistens、Flavobacterium cauense、Clostridium glycyrrhizinilyticum、Anaerostipes hadrus、Prevotella ruminicola、Blautia wexlerae、及びAnaerostipes coliから選択される少なくとも1種の細菌の存在量を決定することを更に含む、請求項9記載の方法。
- 少なくとも10種の細菌の前記存在量を決定する、請求項9記載の方法。
- 少なくとも20種の細菌の前記存在量を決定する、請求項9記載の方法。
- 請求項8記載の方法により被検者の過敏性腸症候群(IBS)を検出することと、前記被検者のIBSが検出された場合、その後、請求項9乃至12記載の方法によりIBSのサブタイプを決定することと、を含む方法。
- ディスバイオシスを有する被検者に適切な治療の決定を補助する方法であって、請求項1乃至3又は9乃至13の何れかに記載の方法により過敏性腸症候群(IBS)のサブタイプを決定することと、IBSのサブタイプの決定の結果に基づいて、適切な治療の決定を補助することと、を含む方法。
- 被検者は、ヒトである、請求項1乃至14の何れかに記載の方法。
- 被検者は、以前に化学療法又は抗生物質投与を受けている、請求項1乃至14の何れかに記載の方法。
- 前記試料は、糞便試料である、請求項1乃至16の何れかに記載の方法。
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TW202214273A (zh) * | 2020-06-15 | 2022-04-16 | 香港中文大學 | 細菌在孩童發育評估和治療的應用 |
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