Gut microbiome in obese and lean female twins
18 fecal samples from adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers; a case-control design comparing microbial community composition between obese and lean states. machine-written summary
18 samples · 18 runs · US · Adult · 2010 · 0.11 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ✓ Abstract / description | 18 sample values (health condition detail) |
| ✓ Full text | 18 sample values (subject id) · PMC2677729 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 18 sample values (country) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
families — not resolvedtwins — not resolved
Adult female MZ/DZ twin pairs and their mothers (Turnbaugh 2009); TS sample ids not linkable to families from accessible sources.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 18 | 100% | ||||
| country | 18 | 100% | 18 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 18 | 100% | 18 | |||
| health_condition_detail | 18 | 100% | 18 |
- A core gut microbiome in obese and lean twins. 2009 PMID 19043404 PMC2677729 own_data
- CD-HIT: accelerated for clustering the next-generation sequencing data. 2012 PMID 23060610 PMC3516142 own_data
- The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences. 2012 PMID 23320832 PMC3426808 own_data
- ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time. 2017 PMID 28437450 PMC5421816 own_data
- Bacterial bile metabolising gene abundance in Crohn's, ulcerative colitis and type 2 diabetes metagenomes. 2014 PMID 25517115 PMC4269443 unsure
1 more
- Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome. 2018 PMID 29668682 PMC5927471
Archive description
Total community DNA was isolated from the feces of monozygotic and dizygotic twins and their mothers. <p> We have characterized the fecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers. The results demonstrate that a diversity of organismal assemblages can nonetheless yield a core microbiome at a functional level, and that deviations from this core are associated with different physiologic states (obese versus lean). <p> <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=&db=Nucleotide&cmd=search&term=FJ362604:FJ372382 [accn]">FJ362604-FJ372382 </a> correspond to 16S ribosomal RNA sequences isolated from this study. <p> 454 sequence data is available from the Short Read Archive (SRA): <a href="ftp://ftp.ncbi.nih.gov/sra/Submissions/SRA002/SRA002775/ ">SRA002775</a>.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “A core gut microbiome in obese”
- body site study.description · “isolated from the feces of monozygotic and”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “twins and their mothers . <p> We”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN00000682 | country | US | R2 | 0.75 | external.gmrepo source | country: United States of America |
| SAMN00000682 | health_condition_detail | mixed_case_control: obese vs lean twin pairs and their mothers | R4 | 0.50 | paper.abstract | twin pairs concordant for leanness or obesity |
| SAMN00000682 | subject_id | SAMN00000682 | R3 | 0.70 | design.one_sample_per_subject:fulltext | the fecal microbiomes of 18 individuals representing 6 of the families |
Sequencing
18 runs over 18 samples · mean 0.12 Gbp per run (median 0.11 Gbp, total 2.20 Gbp; 18 runs with a base count) · layout SINGLE 18 · platform LS454 18 · models 454 GS FLX (18) · 0% of runs with a Sandpiper profile · first public 2010-02-26
Authors (46)
Turnbaugh PJ first · Hamady M · Yatsunenko T · Cantarel BL · Duncan A · Ley RE · Sogin ML · Jones WJ · Roe BA · Affourtit JP · Egholm M · Henrissat B · Heath AC · Knight R · Gordon JI last · Fu L first · Niu B · Zhu Z · Wu S · Li W last · Labbé A first · Ganopolsky JG · Martoni CJ · Prakash S · Jones ML last · Cai Y first · Zheng W · Yao J · Yang Y · Mai V · Mao Q · Sun Y last · Hannigan GD first · Duhaime MB · Koutra D · Schloss PD last · Huang S first · Chaudhari DS · Shukla R · Kanani P · Zeidan RS · Lin Y · Burrow W · Mankowski RT · Jain S · Yadav H last
Downloads
PRJNA32089.csv.gz (1.3 KB) · parquet (69.5 KB) — all 18 samples, every field with route and confidence · PRJNA32089_determinations.csv.gz (1.1 KB) — 54 evidence rows