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PRJNA356225 SRP095060

Gut metagenome in VKH disease patients vs controls, China

human gut metagenome Metagenome

149 stool samples from Chinese provinces (e.g., Chongqing, Sichuan, Henan), comparing gut microbiome in Vogt-Koyanagi-Harada disease patients (94 samples) to healthy controls (54 samples) in a case-control design. machine-written summary

150 samples · 150 runs · CN · Adult · 2016 · 5.71 Gbp / sample · cohort A metagenomic study of the gut microbiome in Behce

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 866✓Abstract / description 1○Full text○Supplementary tables✓External resources 629–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive866 sample values (age, collection date, country, health condition, health condition detail, latitude, location locality, location region)
✓ Abstract / description1 sample values (health condition detail)
○ Full textread; no usable statement or table · PMC12274573, PMC7524263
○ Supplementary tablesfiles read; no table could be matched to the samples
✓ External resources629 sample values (antibiotic exposure, bmi, health condition, health condition detail, sex) · from BugSigDB, curatedMetagenomicData 3 (cMD 3), GMrepo v3
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 sampling locations · 1 country
Age
adult135
elderly12
adolescent3
Condition
autoimmune_inflammatory94
healthy_control1
other_disease1
Sex
male82
female36
Country
CN150
Body site
primary150
Collected 2014–2016
2014: 18 samples2015: 100 samples2016: 32 samples20142016
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)all projects, 0.3–1 Gbp: 47,044 samples (8 %)all projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 1 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 144 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 5 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 5.71 Gbp per sample0130Gbp
! Self-contradictory metadata

age: sequence archive and curatedMetagenomicData disagree for 67 samples (e.g. 16791.5 vs 21915.0) — withheld; health condition: curatedMetagenomicData and GMrepo disagree for 53 samples (e.g. healthy_control vs autoimmune_inflammatory) — withheld.

The sources disagree on 88 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 (40 of 120)
samplefieldvalueother valuehandling
SAMN06115402age16791.5 (sequence archive)21915.0 (curatedMetagenomicData)withheld: neither value published
SAMN06115407age8391.0 (sequence archive)22645.5 (curatedMetagenomicData)withheld: neither value published
SAMN06115425age13504.0 (sequence archive)7670.25 (curatedMetagenomicData)withheld: neither value published
SAMN06115426age21915.0 (sequence archive)4748.25 (curatedMetagenomicData)withheld: neither value published
SAMN06115427age7670.2 (sequence archive)18262.5 (curatedMetagenomicData)withheld: neither value published
SAMN06115428age4748.2 (sequence archive)14975.25 (curatedMetagenomicData)withheld: neither value published
SAMN06115433age12783.8 (sequence archive)8035.5 (curatedMetagenomicData)withheld: neither value published
SAMN06115434age15330.0 (sequence archive)21184.5 (curatedMetagenomicData)withheld: neither value published
SAMN06115435age8035.5 (sequence archive)10957.5 (curatedMetagenomicData)withheld: neither value published
SAMN06115436age21177.0 (sequence archive)14610.0 (curatedMetagenomicData)withheld: neither value published
SAMN06115437age10957.5 (sequence archive)27028.5 (curatedMetagenomicData)withheld: neither value published
SAMN06115438age14610.0 (sequence archive)8766.0 (curatedMetagenomicData)withheld: neither value published
SAMN06115439age8766.0 (sequence archive)18993.0 (curatedMetagenomicData)withheld: neither value published
SAMN06115440age27028.5 (sequence archive)18993.0 (curatedMetagenomicData)withheld: neither value published
SAMN06115442age8766.0 (sequence archive)12053.25 (curatedMetagenomicData)withheld: neither value published
SAMN06115443age18993.0 (sequence archive)7305.0 (curatedMetagenomicData)withheld: neither value published
SAMN06115444age18993.0 (sequence archive)9131.25 (curatedMetagenomicData)withheld: neither value published
SAMN06115446age7670.2 (sequence archive)10592.25 (curatedMetagenomicData)withheld: neither value published
SAMN06115448age9131.0 (sequence archive)17532.0 (curatedMetagenomicData)withheld: neither value published
SAMN06115449age16069.0 (sequence archive)10592.25 (curatedMetagenomicData)withheld: neither value published
SAMN06115452age17532.0 (sequence archive)11688.0 (curatedMetagenomicData)withheld: neither value published
SAMN06115454age17532.0 (sequence archive)28124.25 (curatedMetagenomicData)withheld: neither value published
SAMN06115456age10601.0 (sequence archive)23376.0 (curatedMetagenomicData)withheld: neither value published
SAMN06115457age11688.0 (sequence archive)21184.5 (curatedMetagenomicData)withheld: neither value published
SAMN06115459age9496.5 (sequence archive)16071.0 (curatedMetagenomicData)withheld: neither value published
SAMN06115468age8391.0 (sequence archive)16801.5 (curatedMetagenomicData)withheld: neither value published
SAMN06115477age17532.0 (sequence archive)12053.25 (curatedMetagenomicData)withheld: neither value published
SAMN06115478age9857.0 (sequence archive)13149.0 (curatedMetagenomicData)withheld: neither value published
SAMN06115482age13878.5 (sequence archive)9131.25 (curatedMetagenomicData)withheld: neither value published
SAMN06115484age12783.8 (sequence archive)10227.0 (curatedMetagenomicData)withheld: neither value published
SAMN06115486age9496.5 (sequence archive)13149.0 (curatedMetagenomicData)withheld: neither value published
SAMN06115487age9131.0 (sequence archive)16801.5 (curatedMetagenomicData)withheld: neither value published
SAMN06115488age9857.0 (sequence archive)16436.25 (curatedMetagenomicData)withheld: neither value published
SAMN06115489age10234.0 (sequence archive)18627.75 (curatedMetagenomicData)withheld: neither value published
SAMN06115490age10234.0 (sequence archive)14610.0 (curatedMetagenomicData)withheld: neither value published
SAMN06115491age13149.0 (sequence archive)17532.0 (curatedMetagenomicData)withheld: neither value published
SAMN06115492age16791.5 (sequence archive)6939.75 (curatedMetagenomicData)withheld: neither value published
SAMN06115493age16436.2 (sequence archive)11322.75 (curatedMetagenomicData)withheld: neither value published
SAMN06115495age18627.8 (sequence archive)13879.5 (curatedMetagenomicData)withheld: neither value published
SAMN06115497age17532.0 (sequence archive)9131.25 (curatedMetagenomicData)withheld: neither value published
Community composition
Prevotella 25.2%Phocaeicola 16.0%Bacteroides 11.4%Alistipes 8.8%Faecalibacterium 5.4%Roseburia 1.6%Parabacteroides 1.3%Escherichia 1.1%Acetatifactor 1.0%Oscillibacter 1.0%Sutterella 0.9%Ruminococcoides 0.9%not assigned to a genus 4.8%other genera 20.6%

Genera, mean relative abundance over 138 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category150 100%
country150 100%150
health_condition96 64%195
subject_id0 0%
antibiotic_exposure150 100%150
collection_date150 100%150
health_condition_detail150 100%11481
detailed_location149 99%
latitude149 99%149
location_region149 99%149
longitude149 99%149
bmi118 79%118
sex118 79%118
age_at_collection_days83 55%83
location_locality34 23%34
Papers (4)
  • Altered gut microbiome composition in patients with Vogt-Koyanagi-Harada disease. 2020 PMID 31928124 PMC7524263 own_data
  • A metagenomic study of the gut microbiome in Behcet's disease. 2018 PMID 30077182 PMC6091101 unsure
  • Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation. 2025 PMID 40681522 PMC12274573 unsure
  • The porphyran degradation system is complete, phylogenetically and geographically diverse across the gut microbiota of East Asian populations. 2025 PMID 40748897 PMC12316285 unsure
Details
Archive description

This study presented the bacterial diversity of human stool sample from the Vogt-Koyanagi-Harada disease patients in Chinese population

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.72. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • host run.scientific_name · “human gut metagenome”
  • body site study.description · “human stool sample from the Vogt-Koyanagi-Harada disease patients”
  • life stage sample.attr.host_age · “34 (n=133/150)”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN06115394age_at_collection_days10234.0R10.85sample.attr.host_age28
SAMN06115429age_at_collection_days18262.5R10.85biosample.attribute:host_agehost_age: 50
SAMN06115394antibiotic_exposurenoR20.60external.bugsigdb sourceAntibiotics exclusion: 1 month
SAMN06115400bmi23.2R20.75external.cmd sourcebmi: 23.2
SAMN06115394collection_date2016-04-27R10.90biosample.attribute:collection_date2016-04-27
SAMN06115394countryCNR10.90sample.attr.geo_loc_nameChina:Hubei
SAMN06115409health_conditionother_diseaseR10.70sample.name_rule:library_namesF-V-8
SAMN06115394health_conditionautoimmune_inflammatoryR20.75external.gmrepo sourcephenotype: Uveomeningoencephalitic Syndrome
SAMN06115400health_conditionautoimmune_inflammatoryR20.75external.cmd sourcedisease: Uveomeningoencephalitic Syndrome
SAMN06115409health_condition_detailOther disease / condition [sample-name token 'F-V']R10.70sample.name_rule:library_namesF-V-8
SAMN06115394health_condition_detailUveomeningoencephalitic SyndromeR20.75external.gmrepo sourcephenotype: Uveomeningoencephalitic Syndrome
SAMN06115400health_condition_detailUveomeningoencephalitic SyndromeR20.75external.cmd sourcedisease: Uveomeningoencephalitic Syndrome
SAMN06115429health_condition_detailmixed_case_control: VKH disease patients vs healthy controlsR40.50study.descriptionVogt-Koyanagi-Harada disease patients
SAMN06115394latitude29.3500R10.90biosample.attribute:lat_lon29.35 N 106.33 E
SAMN06115397location_localityChongqingR10.85biosample.attribute:geo_loc_nameChina:Chongqing
SAMN06115394location_regionHubeiR10.85biosample.attribute:geo_loc_nameChina:Hubei
SAMN06115397location_regionChongqing ShiR10.60biosample.attribute:lat_lon29.35 N 106.33 E
SAMN06115394longitude106.3300R10.90biosample.attribute:lat_lon29.35 N 106.33 E
SAMN06115400sexmaleR20.75external.cmd sourcesex: Male
Sequencing

150 runs over 150 samples · mean 6.07 Gbp per run (median 5.71 Gbp, total 910.55 Gbp; 150 runs with a base count) · layout PAIRED 150 · platform ILLUMINA 150 · models Illumina HiSeq 4000 (150) · 93% of runs with a Sandpiper profile · first public 2016-12-20

Authors (36)

Ye Z first · Zhang N · Wu C · Zhang X · Wang Q · Huang X · Du L · Cao Q · Tang J · Zhou C · Hou S · He Y · Xu Q · Xiong X · Kijlstra A · Qin N · Yang P last · Li F · Xiang X first · Li Y · Ye J · Li B · He G · Zhu M · Zhang J · Zhang B · Miao M · Yang Y last · Ségurel L first · Ulaganathan TS · Mathieu S · Loiodice M · Poulet L · Drouillard S · Cygler M · Helbert W last

Downloads

PRJNA356225.csv.gz (6.5 KB) · parquet (79.2 KB) — all 150 samples, every field with route and confidence · PRJNA356225_determinations.csv.gz (17.7 KB) — 1,496 evidence rows

Samples (150 · every field this project has values for · hover a cell for its source)
Loading the sample table…