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PRJNA638405 SRP267134

Graves' disease gut microbiome in Haikou, China adults

Ecological and evolutionary alteration in the GD intestinal microbiome part07 Metagenome

Cross-sectional study of 34 gut microbiome samples from adults (and a few elderly) in Haikou, China, most with autoimmune/inflammatory (Graves') disease, part of a larger study comparing GD patients to healthy controls. machine-written summary

34 samples · 34 runs · CN · Age unknown · 2020 · 7.50 Gbp / sample

One study deposited as 6 BioProjects (164 catalog samples together): PRJNA602729 · PRJNA602731 · PRJNA602732 · PRJNA638403 · PRJNA638404 · PRJNA638405 · show together

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 220○Abstract / description○Full text–Supplementary tables✓External resources 99–User contribution–Human verified

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

what each source gave
✓ Sequence archive220 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude)
○ Abstract / descriptionread; no usable statement
○ Full textread; no usable statement or table
– Supplementary tablesno supplementary tables available (or none open access)
✓ External resources99 sample values (age, bmi, sex) · from Meta2DB (LLNL)
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
2 sampling locations · 1 country
Age
adult30
elderly3
unknown1
Condition
healthy_control1
Sex
female19
male14
Country
CN34
Body site
primary34
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 %)all projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 26 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 8 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 7.50 Gbp per sample0130Gbp
! Self-contradictory metadata

health condition: sequence archive and Meta2DB disagree for 33 samples (e.g. healthy_control vs autoimmune_inflammatory) — withheld.

The sources disagree on 33 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 (33)
samplefieldvalueother valuehandling
SAMN15195542health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195543health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195544health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195545health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195546health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195547health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195548health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195549health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195550health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195551health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195552health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195553health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195554health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195555health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195556health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195557health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195558health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195559health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195560health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195561health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195563health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195564health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195565health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195566health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195567health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195568health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195569health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195570health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195571health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195572health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195573health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195574health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195575health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
Community composition
Phocaeicola 12.2%Prevotella 10.4%Bacteroides 7.4%Roseburia 7.2%Faecalibacterium 6.9%Megamonas 4.0%Bifidobacterium 4.0%Lachnospira 3.3%Escherichia 3.0%Streptococcus 2.8%Mediterraneibacter 2.2%Collinsella 1.8%not assigned to a genus 3.4%other genera 31.4%

Genera, mean relative abundance over 30 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category33 97%
country34 100%34
health_condition1 3%1
subject_id0 0%
collection_date34 100%34
detailed_location34 100%
health_condition_detail34 100%34
latitude34 100%34
location_locality34 100%34
longitude34 100%34
age_at_collection_days33 97%33
bmi33 97%33
sex33 97%33
location_region15 44%15
Papers (3)
  • Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers. 2021 PMID 34079079 PMC8528855 unsure
  • Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach. 2023 PMID 37905808 PMC10734426 unsure
  • Modeling microbiome-trait associations with taxonomy-adaptive neural networks. 2025 PMID 40158141 PMC11954268 unsure
Details
Archive description

Ecological and evolutionary alteration in the GD intestinal microbiome part06

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN15195542age_at_collection_days18262.5R20.70external.meta2db sourcehost_age: 50
SAMN15195542bmi21.03R20.70external.meta2db sourcehost_body_mass_index: 21.03 kilogram per meter squared
SAMN15195542collection_date2018-09R10.90biosample.attribute:collection_date2018-09
SAMN15195542countryCNR10.90sample.attr.geo_loc_nameChina: Haikou
SAMN15195562health_conditionhealthy_controlR10.85biosample.attribute:TITLEHC metagenome
SAMN15195542health_condition_detailHC metagenomeR10.85biosample.attribute:TITLEHC metagenome
SAMN15195542latitude20.0300R10.90biosample.attribute:lat_lon20.03 N 110.10 E
SAMN15195542location_localityHaikouR10.85biosample.attribute:geo_loc_nameChina: Haikou
SAMN15195550location_regionHainanR10.60biosample.attribute:lat_lon20.03 N 110.18 E
SAMN15195542longitude110.1000R10.90biosample.attribute:lat_lon20.03 N 110.10 E
SAMN15195542sexfemaleR20.70external.meta2db sourcehost_sex: female
Sequencing

34 runs over 34 samples · mean 8.01 Gbp per run (median 7.50 Gbp, total 272.46 Gbp; 34 runs with a base count) · layout PAIRED 34 · platform ILLUMINA 34 · models Illumina HiSeq 4000 (34) · 88% of runs with a Sandpiper profile · first public 2020-06-13 – 2020-10-02

Authors (22)

Zhu Q first · Hou Q · Huang S · Ou Q · Huo D · Vázquez-Baeza Y · Cen C · Cantu V · Estaki M · Chang H · Belda-Ferre P · Kim HC · Chen K · Knight R · Zhang J last · Ma C first · Zhang Y · Jiang S · Teng F · Jiang Y first · Aton M · Lu YY last

Downloads

PRJNA638405.csv.gz (2.1 KB) · parquet (72.2 KB) — all 34 samples, every field with route and confidence · PRJNA638405_determinations.csv.gz (4.3 KB) — 319 evidence rows

Samples (34 · every field this project has values for · hover a cell for its source)
Loading the sample table…