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PRJNA375935 SRP100575

Microbiome case-control study, ankylosing spondylitis, China

human gut Metagenome

211 fecal samples from Chinese individuals (97 with ankylosing spondylitis and healthy controls) analyzed by deep shotgun metagenomic sequencing in a case-control study. machine-written summary

211 samples · 211 runs · CN · Adult · 2017 · 3.64 Gbp / sample · cohort Quantitative metagenomics reveals unique gut micro

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Sources
✓Sequence archive 1,494✓Abstract / description 211–Full text–Supplementary tables✓External resources 385–User contribution–Human verified

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

what each source gave
✓ Sequence archive1,494 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude)
✓ Abstract / description211 sample values (subject id)
– Full textno open-access full text linked
– Supplementary tablesno supplementary tables available (or none open access)
✓ External resources385 sample values (age, antibiotic exposure, bmi, sex) · from curatedMetagenomicData 3 (cMD 3)
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
4 sampling locations · 1 country
Age
adult208
adolescent2
elderly1
Condition
healthy_control114
autoimmune_inflammatory97
Sex
male56
female41
Country
CN211
Body site
primary211
Collected 2013–2015
2013: 114 samples2015: 97 samples20132015
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 %)this project, 0.1–0.3 Gbp: 2 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 2 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 59 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 143 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 3.64 Gbp per sample0130Gbp
Community composition
Phocaeicola 20.8%Bacteroides 13.0%Prevotella 10.8%Faecalibacterium 7.9%Lachnospira 5.3%Roseburia 3.7%Alistipes 3.0%Acetatifactor 1.3%Ruminococcoides 1.3%Megamonas 1.2%Bifidobacterium 1.1%Parabacteroides 1.1%not assigned to a genus 6.2%other genera 23.2%

Genera, mean relative abundance over 193 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category211 100%
country211 100%211
health_condition211 100%211
subject_id211 100%211
collection_date211 100%211
health_condition_detail211 100%211
latitude211 100%211
longitude211 100%211
detailed_location114 54%
location_locality114 54%114
location_region114 54%114
age_at_collection_days97 46%97
antibiotic_exposure97 46%97
sex97 46%97
bmi94 45%94
Papers (11)
  • Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis. 2017 PMID 28750650 PMC5530561 unsure
  • Human Gut Microbiome Aging Clock Based on Taxonomic Profiling and Deep Learning. 2020 PMID 32534441 PMC7298543 unsure
  • Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers. 2021 PMID 34079079 PMC8528855 unsure
  • Metagenomic analysis revealed the potential role of gut microbiome in gout. 2021 PMID 34373464 PMC8352958 unsure
  • MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen. 2021 PMID 34592929 PMC8485520 unsure
6 more
  • Characterizing Enterotypes in Human Metagenomics: A Viral Perspective. 2021 PMID 34659174 PMC8511818
  • Identification and Characterization of Major Bile Acid 7α-Dehydroxylating Bacteria in the Human Gut. 2022 PMID 35736002 PMC9426597
  • Four functional profiles for fibre and mucin metabolism in the human gut microbiome. 2023 PMID 37858269 PMC10588041
  • Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach. 2023 PMID 37905808 PMC10734426
  • Microbes with higher metabolic independence are enriched in human gut microbiomes under stress. 2025 PMID 40377187 PMC12084026
  • A genomic atlas of gut clostridia: phylogeny, butyrate, and propionate production. 2026 PMID 42039832 PMC13106387
Details
Archive description

To reveal the relationship between the gut microbiome and ankylosing spondylitis, a quantitative metagenomics study that was based on deep shotgun sequencing of the gut microbial DNA from 211 Chinese individuals (97 patients and 104 healthy controls) was carried out. A total of 23,709 genes and 16 metagenomic species that were differentially abundant in the two groups were identified.

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”
  • body site study.description · “relationship between the gut microbiome and ankylosing”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN06348104age_at_collection_days14975.25R20.75external.cmd sourceage: 41; age_unit: Year; age_group: Adult
SAMN06348104antibiotic_exposureyesR20.75external.cmd sourceantibiotics_current_use: Yes
SAMN06348104bmi19.72R20.75external.cmd sourcebmi: 19.7210369679802
SAMN06348104collection_date2015-10R10.90biosample.attribute:collection_date2015-10
SAMN06348104countryCNR10.90sample.attr.geo_loc_nameChina
SAMN06348104health_conditionautoimmune_inflammatoryR10.70sample.name_rule:aliasAS100raw
SAMN06348104health_condition_detailAutoimmune / inflammatory (RA (name token 'AS')R10.70sample.name_rule:aliasAS100raw
SAMN06348104latitude30.3000R10.90biosample.attribute:lat_lon30.3 N 120.2 E
SAMN08357915location_localityHangzhouR10.85biosample.attribute:geo_loc_nameChina:Zhejiang, Hangzhou
SAMN08357915location_regionZhejiangR10.85biosample.attribute:geo_loc_nameChina:Zhejiang, Hangzhou
SAMN06348104longitude120.2000R10.90biosample.attribute:lat_lon30.3 N 120.2 E
SAMN06348104sexmaleR20.75external.cmd sourcesex: Male
SAMN06348104subject_idSAMN06348104R40.60design.one_sample_per_subject:descriptiondeep shotgun sequencing of the gut microbial DNA from 211 Chinese individuals (97 patients and 104 healthy controls)
Sequencing

211 runs over 211 samples · mean 3.82 Gbp per run (median 3.64 Gbp, total 806.93 Gbp; 211 runs with a base count) · layout PAIRED 211 · platform ILLUMINA 211 · models Illumina HiSeq 2000 (211) · 91% of runs with a Sandpiper profile · first public 2017-03-01 – 2018-01-16

Authors (34)

Shao L first · Liao J · Qian J · Chen W · Fan X last · Kim KH first · Park D · Jia B · Baek JH · Hahn Y · Jeon CO last · Ormaasen I first · Rudi K · Diep DB · Snipen L last · Labarthe S first · Plancade S · Raguideau S · Plaza Oñate F · Le Chatelier E · Leclerc M · Laroche B last · Ma C first · Zhang Y · Jiang S · Teng F · Huang S · Zhang J last · Sola L first · Candeliere F · Busi E · Raimondi S · Amaretti A · Rossi M last

Downloads

PRJNA375935.csv.gz (7.4 KB) · parquet (81.7 KB) — all 211 samples, every field with route and confidence · PRJNA375935_determinations.csv.gz (19.9 KB) — 2,090 evidence rows

Samples (211 · every field this project has values for · hover a cell for its source)
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