organism: Homo sapiens
description: 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.
attributes.tag: ENA first public
attributes.value: 2017-06-09
attributes.tag: ENA last update
attributes.value: 2017-06-08
attributes.tag: External Id
attributes.value: SAMEA104118158
attributes.tag: INSDC center alias
attributes.value: MPIEVB
attributes.tag: INSDC center name
attributes.value: Max-Planck-Institute for Evolutionary Biology
attributes.tag: INSDC first public
attributes.value: 2017-06-09T17:02:09Z
attributes.tag: INSDC last update
attributes.value: 2017-06-08T13:34:42Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: new_103
attributes.tag: age (years)
attributes.value: 26
attributes.tag: collection date
attributes.value: 2008-02-08
attributes.tag: common name
attributes.value: human
attributes.tag: environment (biome)
attributes.value: organism-associated habitat
attributes.tag: environment (feature)
attributes.value: organism-associated habitat
attributes.tag: environment (material)
attributes.value: mucus
attributes.tag: experimental factor
attributes.value: sex,sampling site,inflammatory bowel disease,clinical treatment,population,human gut metagenome,health trait
attributes.tag: gastrointestinal tract disorder
attributes.value: Healthy
attributes.tag: geographic location (country and/or sea)
attributes.value: Germany
attributes.tag: geographic location (latitude)
attributes.value: 10.142841
attributes.tag: geographic location (longitude)
attributes.value: 54.330532
attributes.tag: height (cm)
attributes.value: 166
attributes.tag: host body product
attributes.value: mucus
attributes.tag: host body site
attributes.value: sigmoid colon
attributes.tag: host disease status
attributes.value: healthy
attributes.tag: host sex
attributes.value: female
attributes.tag: host subject id
attributes.value: 1A
attributes.tag: human gut environmental package
attributes.value: human-gut
attributes.tag: investigation type
attributes.value: metagenome
attributes.tag: library screening strategy
attributes.value: PCR
attributes.tag: medication
attributes.value: no medication
attributes.tag: multiplex identifiers
attributes.value: TCACGTACTA
attributes.tag: nucleic acid amplification
attributes.value: PMID: 22068912
attributes.tag: nucleic acid extraction
attributes.value: Qiagen Allprep DNA/RNA (PMID: 20522625)
attributes.tag: pcr conditions
attributes.value: initial denaturation: 98degC_0.5min;30cycles denaturation=98degC_9sec,annealing=55degC_0.5min,extension=72degC_0.5min;final extension:72degC_10min
attributes.tag: pcr primers
attributes.value: 27F-338R
attributes.tag: project name
attributes.value: BMRP
attributes.tag: sample collection device or method
attributes.value: biopsy
attributes.tag: sample name
attributes.value: new_103
attributes.tag: sequencing method
attributes.value: pyrosequencing
attributes.tag: sequencing template
attributes.value: cDNA
attributes.tag: target gene
attributes.value: 16S rRNA
attributes.tag: target subfragment
attributes.value: V1V2
attributes.tag: weight (kg)
attributes.value: 63