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PRJNA638403 SRP266848

Gut microbiome in T2DM, Haikou, China, case-control

Ecological and evolutionary alteration in the GD intestinal microbiome part05 Metagenome

34 fecal metagenome samples from Haikou, China, comparing gut microbiomes of type 2 diabetes mellitus subjects and controls using a case-control design, with MAG-based analysis of microbial signatures linked to T2DM. machine-written summary

34 samples · 34 runs · CN · Age unknown · 2020 · 7.87 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 219○Abstract / description○Full text✓Supplementary tables 68✓External resources 102–User contribution–Human verified

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

what each source gave
✓ Sequence archive219 sample values (collection date, country, health condition detail, latitude, location locality, location region, longitude)
○ Abstract / descriptionread; no usable statement
○ Full textread; no usable statement or table · PMC10734426, PMC11954268, PMC13067670, PMC8528855
✓ Supplementary tables68 sample values (smoking status, subject id)
✓ External resources102 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
adult32
elderly2
Sex
female21
male13
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: 28 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 6 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 7.87 Gbp per sample0130Gbp
! Self-contradictory metadata

health condition: sequence archive and Meta2DB disagree for 34 samples (e.g. healthy_control vs autoimmune_inflammatory) — withheld.

The sources disagree on 34 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 (34)
samplefieldvalueother valuehandling
SAMN15195486health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195487health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195488health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195489health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195490health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195491health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195492health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195493health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195494health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195495health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195496health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195497health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195498health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195499health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195500health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195501health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195502health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195503health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195504health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195505health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195506health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195507health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195508health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195509health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195510health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195511health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195512health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195513health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195514health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195515health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195516health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195517health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195518health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
SAMN15195519health conditionhealthy_control (sequence archive)autoimmune_inflammatory (Meta2DB)withheld: neither value published
Community composition
Phocaeicola 13.8%Bacteroides 9.6%Prevotella 9.1%Roseburia 7.3%Faecalibacterium 6.5%Megamonas 3.7%Streptococcus 2.8%Lachnospira 2.8%Bifidobacterium 2.6%Mediterraneibacter 2.5%Escherichia 2.5%Alistipes 2.0%not assigned to a genus 3.4%other genera 31.5%

Genera, mean relative abundance over 31 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category34 100%
country34 100%34
health_condition0 0%
subject_id34 100%34
age_at_collection_days34 100%34
bmi34 100%34
collection_date34 100%34
detailed_location34 100%
health_condition_detail34 100%34
latitude34 100%34
location_locality34 100%34
longitude34 100%34
sex34 100%34
smoking_status34 100%34
location_region15 44%15
Papers (4)
  • 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
  • Metagenome-assembled genomes from the gut microbiome of spontaneous diabetic macaques provide insights into microbes associated with type 2 diabetes mellitus. 2026 PMID 41781883 PMC13067670 unsure
Details
Archive description

Ecological and evolutionary alteration in the GD intestinal microbiome part05

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.57. Assay shotgun_dna.

  • host run.host_tax_id · “9606”
  • host run.scientific_name · “human gut metagenome”
  • body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN15195486age_at_collection_days13879.5R20.70external.meta2db sourcehost_age: 38
SAMN15195486bmi18.15R20.70external.meta2db sourcehost_body_mass_index: 18.15 kilogram per meter squared
SAMN15195486collection_date2018-08R10.90biosample.attribute:collection_date2018-08
SAMN15195486countryCNR10.90sample.attr.geo_loc_nameChina: Haikou
SAMN15195486health_condition_detailHC metagenomeR10.85biosample.attribute:titletitle: HC metagenome
SAMN15195486latitude20.0300R10.90biosample.attribute:lat_lon20.03 N 110.10 E
SAMN15195486location_localityHaikouR10.85biosample.attribute:geo_loc_nameChina: Haikou
SAMN15195494location_regionHainanR10.60biosample.attribute:lat_lon20.03 N 110.18 E
SAMN15195486longitude110.1000R10.90biosample.attribute:lat_lon20.03 N 110.10 E
SAMN15195486sexmaleR20.70external.meta2db sourcehost_sex: male
SAMN15195486smoking_statuscurrentR20.85paper.supp.41396_2021_1016_MOESM2_ESM.xlsx[Table_S1!Smoking]GA01 | Smoking: Y
SAMN15195486subject_idG001R20.85paper.supp.41396_2021_1016_MOESM2_ESM.xlsx[Table_S1!col0]GA01 | col0: G001
Sequencing

34 runs over 34 samples · mean 8.13 Gbp per run (median 7.87 Gbp, total 276.34 Gbp; 34 runs with a base count) · layout PAIRED 34 · platform ILLUMINA 34 · models Illumina HiSeq 4000 (34) · 91% of runs with a Sandpiper profile · first public 2020-06-12 – 2020-10-02

Authors (31)

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 · Xie Y first · Wang R · Liu X · Du Q · Mo S · Liu Q · Yang G · Fan Z · Li J last

Downloads

PRJNA638403.csv.gz (2.2 KB) · parquet (72.5 KB) — all 34 samples, every field with route and confidence · PRJNA638403_determinations.csv.gz (5.4 KB) — 389 evidence rows

Samples (34 · every field this project has values for · hover a cell for its source)
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