Read-cloud assembly of healthy adult gut microbiomes
5 samples from healthy adults, used to test Athena, a read-cloud de novo assembler for metagenomic assembly, alongside marine sediment and synthetic (ATCC MSA-1003) validation samples. machine-written summary
4 samples · 5 runs · US · Age unknown · 2018 · 36.52 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 16 sample values (collection date, health condition, health condition detail, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 12 sample values (antibiotic exposure, country, location site) · PMC6465186 |
| ○ 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 |
longitudinal — not resolved
2 of 2 people sampled more than once (4 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 4 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 | 4 | 100% | ||||
| country | 4 | 100% | 4 | |||
| health_condition | 4 | 100% | 4 | |||
| subject_id | 4 | 100% | 4 | |||
| antibiotic_exposure | 4 | 100% | 4 | |||
| collection_date | 4 | 100% | 4 | |||
| detailed_location | 4 | 100% | ||||
| health_condition_detail | 4 | 100% | 4 | |||
| location_site | 4 | 100% | 4 |
- High-quality genome sequences of uncultured microbes by assembly of read clouds. 2018 PMID 30320765 PMC6465186 own_data
Archive description
Read cloud sequencing and assembly of the human gut microbiome One marine sediment metagenome and one synthetic metagenome were included as validation and proof-of-concept of a new assembly approach in a project primarily focused on assembly within the human gut metagenome. The synthetic metagenome is a mixture of DNA from 20 different ATCC organisms and is available in ATCC:MSA-1003.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.55. Assay shotgun_dna.
- host study.title · “Human gut metagenome, marine sediment metagenome”
- host run.scientific_name · “marine sediment metagenome”
- body site study.description · “assembly of the human gut microbiome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN08533508 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | no gastrointestinal disease or antibiotic use in the 6 months |
| SAMN08533508 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMN08533508 | country | US | R3 | 0.70 | paper.fulltext.methods | recruited at Stanford University |
| SAMN08533508 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:alias | participant_1_10x |
| SAMN08533508 | health_condition_detail | participant | R1 | 0.70 | sample.name_rule:alias | participant_1_10x |
| SAMN08533508 | location_site | Stanford University | R3 | 0.70 | paper.fulltext.methods | Two healthy adult volunteers were recruited at Stanford University |
| SAMN08533508 | subject_id | participant_1 | R1 | 0.70 | sample.name_rule:alias | participant_1_10x |
Sequencing
5 runs over 4 samples · mean 41.93 Gbp per run (median 36.52 Gbp, total 209.66 Gbp; 5 runs with a base count) · layout SINGLE 5 · platform ILLUMINA 5 · models Illumina HiSeq 4000 (5) · 80% of runs with a Sandpiper profile · first public 2018-08-04
Authors (9)
Bishara A first · Moss EL · Kolmogorov M · Parada AE · Weng Z · Sidow A · Dekas AE · Batzoglou S · Bhatt AS last
Downloads
PRJNA380276.csv.gz (1000 B) · parquet (69.8 KB) — all 4 samples, every field with route and confidence · PRJNA380276_determinations.csv.gz (893 B) — 28 evidence rows