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text: The knowledge of species composition and functional aspects of the human microbiome is steadily increasing; but still limited information regarding its variation on a global scale is available. Due to the microbial involvement in inflammatory bowel diseases and their increase in global frequency; shared patterns across populations may hold important clinical relevance. In this study; we analyze a set of 89 mucosal biopsies sampled from individuals of German; Lithuanian and Indian origins; using bacterial community profiling of a roughly equal number of healthy controls; Crohn Disease and Ulcerative Colitis patients from each location. From each individual sample 16S rDNA and rRNA are analyzed as proxies for standing and active microbial community structure; respectively. We find pronounced regional as well as global disease patterns in the major phyla and patterns of diversity; which differ when investigated in the standing or active community. Geography appears to dominate patterns of beta diversity; with European samples being more similar to each other; which is more pronounced in the active microbial community. However; when geographic influence is accounted for; some universal patterns of disease become apparent. In particular; two genera belonging to the Clostridium leptum subgroup; Faecalibacteria and Papillibacter; display consistent patterns with respect to disease status and may thus serve as reliable ?microbiomarkers?. These analyses reveal the importance of the interaction of geography and disease in the interpretation of disease-associated changes in microbial communities and highlight the added value of analyzing communities on both the rDNA and rRNA level.

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text: Regional patterns of the standing and active human gut microbiome in health and inflammatory bowel diseases

characteristic: title

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characteristic: INSDC center name

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text: human

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characteristic: geographic location (latitude)

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characteristic: geographic location (country and/or sea)

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characteristic: geographic location (longitude)

text: not provided

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characteristic: organism

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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

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characteristic: SRA accession

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text: human

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text: organism-associated habitat

text: organism-associated habitat

text: mucus

text: Crohn's Disease

text: India

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text: sigmoid colon

text: remission

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characteristic: host sex

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

text: PCR

characteristic: library screening strategy

text: ASA,Antibiotics

characteristic: medication

text: AGCACTGTAG

characteristic: multiplex identifiers

text: PMID: 22068912

characteristic: nucleic acid amplification

text: Qiagen Allprep DNA/RNA (PMID: 20522625)

characteristic: nucleic acid extraction

text: Homo sapiens

characteristic: pcr conditions

characteristic: pcr primers

text: BMRP

characteristic: project name

text: biopsy

characteristic: sample collection device or method

text: Homo sapiens

text: pyrosequencing

text: cDNA

characteristic: sequencing template

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

characteristic: weight (kg)


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

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characteristic: SRA accession

characteristic: Submitter Id

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characteristic: collection date

text: human

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text: organism-associated habitat

characteristic: environment (biome)

text: organism-associated habitat

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text: mucus

characteristic: environment (material)

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text: Healthy

characteristic: gastrointestinal tract disorder

text: India

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: height (cm)

text: mucus

characteristic: host body product

text: sigmoid colon

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text: healthy

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text: PMID: 22068912

text: Qiagen Allprep DNA/RNA (PMID: 20522625)

text: Homo sapiens

characteristic: organism

text: BMRP

text: biopsy

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text: pyrosequencing

characteristic: sequencing method

text: cDNA

text: 16S rRNA

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

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text: human

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text: organism-associated habitat

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text: mucus

text: sigmoid colon

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characteristic: host sex

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text: metagenome

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text: AGCACTGTAG

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text: PMID: 22068912

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text: Qiagen Allprep DNA/RNA (PMID: 20522625)

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characteristic: pcr primers

text: BMRP

characteristic: project name

text: biopsy

characteristic: sample collection device or method

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text: pyrosequencing

text: cDNA

characteristic: sequencing template

text: 16S rRNA

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characteristic: target subfragment

text: not provided

characteristic: weight (kg)


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

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characteristic: environment (biome)

text: organism-associated habitat

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characteristic: environment (material)

characteristic: experimental factor

text: Ulcerative Colitis

characteristic: gastrointestinal tract disorder

text: India

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: not provided

characteristic: height (cm)

text: mucus

characteristic: host body product

text: sigmoid colon

characteristic: host body site

text: remission

characteristic: host disease status

text: male

text: human-gut

text: metagenome

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text: ASA,Antibiotics,Probiotics

text: TCACGTACTA

text: PMID: 22068912

text: Qiagen Allprep DNA/RNA (PMID: 20522625)

text: Homo sapiens

characteristic: organism

text: BMRP

text: biopsy

text: Homo sapiens

text: pyrosequencing

characteristic: sequencing method

text: cDNA

text: 16S rRNA

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text: not provided


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characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

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text: MPIEVB

characteristic: INSDC center name

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text: public

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text: human

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text: not provided

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characteristic: host sex

characteristic: host subject id

text: human-gut

characteristic: human gut environmental package

text: metagenome

text: PCR

characteristic: library screening strategy

text: ASA,Probiotics

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text: CGTCTAGTAC

characteristic: multiplex identifiers

text: PMID: 22068912

characteristic: nucleic acid amplification

text: Qiagen Allprep DNA/RNA (PMID: 20522625)

characteristic: nucleic acid extraction

text: Homo sapiens

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characteristic: pcr primers

text: BMRP

characteristic: project name

text: biopsy

characteristic: sample collection device or method

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text: pyrosequencing

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characteristic: sequencing template

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characteristic: target subfragment

text: not provided

characteristic: weight (kg)


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

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text: MPIEVB

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

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text: human

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characteristic: environment (biome)

text: organism-associated habitat

characteristic: environment (feature)

text: mucus

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text: Healthy

characteristic: gastrointestinal tract disorder

text: India

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: not provided

characteristic: height (cm)

text: mucus

characteristic: host body product

text: sigmoid colon

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text: healthy

characteristic: host disease status

text: female

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characteristic: organism

text: BMRP

text: biopsy

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text: pyrosequencing

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text: cDNA

text: 16S rRNA

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text: not provided


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characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

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text: public

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text: human

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text: organism-associated habitat

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text: Germany

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characteristic: host sex

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text: human-gut

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text: metagenome

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text: BMRP

characteristic: project name

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text: cDNA

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characteristic: target gene

characteristic: target subfragment

characteristic: weight (kg)


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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

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characteristic: SRA accession

characteristic: Submitter Id

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characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: organism-associated habitat

characteristic: environment (biome)

text: organism-associated habitat

characteristic: environment (feature)

text: mucus

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characteristic: experimental factor

text: Ulcerative Colitis

characteristic: gastrointestinal tract disorder

text: India

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: not provided

characteristic: height (cm)

text: mucus

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text: sigmoid colon

characteristic: host body site

text: remission

characteristic: host disease status

text: male

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text: ASA,Antibiotics,Cortisone,AZA

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text: PMID: 22068912

text: Qiagen Allprep DNA/RNA (PMID: 20522625)

text: Homo sapiens

characteristic: organism

text: BMRP

text: biopsy

text: Homo sapiens

text: pyrosequencing

characteristic: sequencing method

text: cDNA

text: 16S rRNA

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text: not provided


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characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MPIEVB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

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text: human

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text: organism-associated habitat

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text: Healthy

text: Germany

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text: healthy

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text: metagenome

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characteristic: library screening strategy

text: no medication

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text: TCACGTACTA

characteristic: multiplex identifiers

text: PMID: 22068912

characteristic: nucleic acid amplification

text: Qiagen Allprep DNA/RNA (PMID: 20522625)

characteristic: nucleic acid extraction

text: Homo sapiens

characteristic: pcr conditions

characteristic: pcr primers

text: BMRP

characteristic: project name

text: biopsy

characteristic: sample collection device or method

text: Homo sapiens

text: pyrosequencing

text: cDNA

characteristic: sequencing template

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

characteristic: weight (kg)