Human gut microbiome in healthy adults, cross-sectional
3 gut samples from healthy adult controls (country not reported), collected in a cross-sectional design; part of a study describing a new candidate bacterial phylum found in human gut and groundwater. machine-written summary
3 samples · 3 runs · GB · Adult · 2016 · 5.48 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 9 sample values (health condition, health condition detail, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 3 sample values (country) · PMC3787301, PMC5538567 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 3 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 3 | 100% | ||||
| country | 3 | 100% | 3 | |||
| health_condition | 3 | 100% | 3 | |||
| subject_id | 3 | 100% | 3 | |||
| health_condition_detail | 3 | 100% | 3 |
- The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. 2013 PMID 24137540 PMC3787301 own_data
- Measurement of bacterial replication rates in microbial communities. 2016 PMID 27819664 PMC5538567 own_data
Archive description
S. C. Di Rienzi, I. Sharon, K. C. Wrighton, O. Koren, L. A. Hug, B. C. Thomas, J. K. Goodrich, J. T. Bell, T. D. Spector, J. F. Banfield, and R. E. Ley, “The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria.,” Elife, vol. 2, pp. e01102–e01102, Jan. 2013.
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 · “human gut and groundwater harbor”
- body site study.description · “Ley, “The human gut and groundwater harbor”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN04978191 | country | GB | R3 | 0.70 | paper.fulltext.methods | United Kingdom Adult Twin Registry (TwinsUK) |
| SAMN04978191 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:alias | alias: fecal sample 1 from healthy adult A |
| SAMN04978191 | health_condition_detail | fecal sample 1 from healthy adult A | R1 | 0.85 | biosample.attribute:alias | alias: fecal sample 1 from healthy adult A |
| SAMN04978191 | subject_id | adult A | R1 | 0.85 | biosample.attribute:DESCRIPTION | sample from healthy adult A |
Sequencing
3 runs over 3 samples · mean 5.57 Gbp per run (median 5.48 Gbp, total 16.70 Gbp; 3 runs with a base count) · layout PAIRED 3 · platform ILLUMINA 3 · models Illumina HiSeq 2000 (3) · 100% of runs with a Sandpiper profile · first public 2016-05-17
Authors (33)
Di Rienzi SC first · Sharon I · Wrighton KC · Koren O · Hug LA · Thomas BC · Goodrich JK · Bell JT · Spector TD · Banfield JF · Ley RE last · Brown CT first · Olm MR · Fontana F first · Alessandri G · Tarracchini C · Bianchi MG · Rizzo SM · Mancabelli L · Lugli GA · Argentini C · Vergna LM · Anzalone R · Longhi G · Viappiani A · Taurino G · Chiu M · Turroni F · Bussolati O · van Sinderen D · Milani C · Ventura M last · Angelini L
Downloads
PRJNA321218.csv.gz (954 B) · parquet (69.0 KB) — all 3 samples, every field with route and confidence · PRJNA321218_determinations.csv.gz (720 B) — 12 evidence rows