PRJNA808806 SRP361099
Healthy control gut metagenomes, Xi'an China, case-control
human gut metagenome Raw sequence reads
48 gut metagenome samples from healthy control adults in Xi'an, China, collected as part of a case-control study examining gut microbiota in heroin use disorder. machine-written summary
48 samples · 48 runs · CN · Adult · 2023 · 7.10 Gbp / sample
Sources
✓Sequence archive 408○Abstract / description✓Full text 12○Supplementary tables–External resources–User contribution–Human verified
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 408 sample values (collection date, country, health condition, health condition detail, intervention, latitude, location locality, location region) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 12 sample values (sex) · PMC10635210 |
| ○ 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 |
Interventions
intervention — arms not resolved
design observational_with_procedure
Samples at a glance
3 sampling locations · 1 country
Age
adult48
Condition
healthy_control12
Sex
male48
Country
CN48
Body site
primary48
Sequencing depth per sample · this project all projects
! Self-contradictory metadata
health condition: sample names and GMrepo disagree for 36 samples (e.g. neurological_psychiatric vs healthy_control) — withheld.
The sources disagree on 36 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (36)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN26106945 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106946 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106947 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106948 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106949 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106950 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106951 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106952 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106953 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106954 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106955 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106956 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106957 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106958 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106959 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106960 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106961 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106962 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106963 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106964 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106965 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106966 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106967 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106968 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106969 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106970 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106971 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106972 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106973 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106974 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106975 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106976 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106977 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106978 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106979 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
| SAMN26106980 | health condition | neurological_psychiatric (sample names) | healthy_control (GMrepo) | withheld: neither value published |
Community composition
Bifidobacterium 12.1%Escherichia 8.2%Streptococcus 4.6%Pediococcus 4.3%Blautia_A 3.3%Faecalibacterium 3.1%Phocaeicola 2.9%Lacticaseibacillus 2.5%Fimenecus 2.2%Collinsella 2.2%Levilactobacillus 2.1%Prevotella 1.9%not assigned to a genus 4.7%other genera 46.0%
Genera, mean relative abundance over 44 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Field coverage
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 48 | 100% | ||||
| country | 48 | 100% | 48 | |||
| health_condition | 12 | 25% | 12 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 48 | 100% | 48 | |||
| detailed_location | 48 | 100% | ||||
| health_condition_detail | 48 | 100% | 48 | |||
| latitude | 48 | 100% | 48 | |||
| location_locality | 48 | 100% | 48 | |||
| location_region | 48 | 100% | 48 | |||
| longitude | 48 | 100% | 48 | |||
| sex | 48 | 100% | 36 | 12 | ||
| intervention | 12 | 25% | 12 | |||
| medication | 12 | 25% | 12 |
Papers (1)
- Methadone maintenance treatment is more effective than compulsory detoxification in addressing gut microbiota dysbiosis caused by heroin abuse. 2023 PMID 37954240 PMC10635210 own_data
Details
Archive description
normal metagenome of human gut
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 metagenome Raw sequence”
- body site study.description · “metagenome of human gut”
- 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 |
|---|---|---|---|---|---|---|
| SAMN26106933 | collection_date | 2017-11-14 | R1 | 0.90 | biosample.attribute:collection_date | 2017-11-14 |
| SAMN26106933 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: Xi'an |
| SAMN26106933 | health_condition | healthy_control | R1 | 0.70 | sample.name_rule:description | health control replicate 1 |
| SAMN26106933 | health_condition_detail | health control | R1 | 0.70 | sample.name_rule:description | health control replicate 1 |
| SAMN26106969 | intervention | drug_therapy | R1 | 0.70 | sample.name_rule:description | methadone replicate 1 |
| SAMN26106933 | latitude | 34.2587 | R1 | 0.90 | biosample.attribute:lat_lon | 34.258698 N 108.887016 E |
| SAMN26106933 | location_locality | Xi'an | R1 | 0.85 | biosample.attribute:geo_loc_name | China: Xi'an |
| SAMN26106933 | location_region | Shaanxi | R1 | 0.60 | biosample.attribute:lat_lon | 34.258698 N 108.887016 E |
| SAMN26106933 | longitude | 108.8870 | R1 | 0.90 | biosample.attribute:lat_lon | 34.258698 N 108.887016 E |
| SAMN26106969 | medication | other_medication | R1 | 0.70 | sample.name_rule:description | methadone replicate 1 |
| SAMN26106945 | sex | male | R1 | 0.70 | sample.name_rule:description | heroin addiction replicate 1 |
| SAMN26106933 | sex | male | R3 | 0.70 | paper.fulltext.methods | Males were selected because they comprise a much higher proportion |
Sequencing
48 runs over 48 samples · mean 7.05 Gbp per run (median 7.10 Gbp, total 338.34 Gbp; 48 runs with a base count) · layout SINGLE 48 · platform ILLUMINA 48 · models Illumina MiSeq (48) · 92% of runs with a Sandpiper profile · first public 2023-03-03
Downloads
PRJNA808806.csv.gz (2.1 KB) · parquet (72.0 KB) — all 48 samples, every field with route and confidence · PRJNA808806_determinations.csv.gz (3.8 KB) — 420 evidence rows
Samples (48 · every field this project has values for · hover a cell for its source)
Loading the sample table…