Gut and Oral Microbiome in Rheumatoid Arthritis, China
530 fecal, dental and salivary samples from China compared autoimmune/inflammatory (rheumatoid arthritis) cases (n=135) with healthy controls (n=97) in a case-control design. machine-written summary
530 samples · 530 runs · CN · Adult · 2015 · 5.72 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,107 sample values (collection date, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10276029, PMC10318035, PMC10590964, PMC10609127, PMC10704812, PMC10773633, PMC11064737, PMC11418011, PMC11659515, PMC12297358, PMC12340149, PMC12764784, PMC12807719, PMC5907152, PMC6424576, PMC7157763, PMC7702799, PMC7707550, PMC8201803, PMC8262883, PMC8352958, PMC8485520, PMC8511818, PMC8528855, PMC9024311, PMC9051138, PMC9096808, PMC9426582, PMC9603985, PMC9663839, PMC9684161, PMC9975273 |
| ✓ Supplementary tables | 993 sample values (health condition, health condition detail, sex, subject id) |
| ✓ External resources | 1,381 sample values (age, antibiotic exposure, bmi, health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
sex differs between samples of the same subject id (1 subjects, 2 samples) — sex withheld; subject ids shared by samples of both sexes (1 ids, 2 samples) — ids withheld.
The sources disagree on 2 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 (4)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA2737678 | sex | male (curatedMetagenomicData) | subject D29: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA2737679 | sex | female (curatedMetagenomicData) | subject D29: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA2737678 | subject id | D29 | male (curatedMetagenomicData) | subject id withheld (samples of both sexes share it) |
| SAMEA2737679 | subject id | D29 | female (curatedMetagenomicData) | subject id withheld (samples of both sexes share it) |
Genera, mean relative abundance over 209 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 530 | 100% | ||||
| country | 530 | 100% | 530 | |||
| health_condition | 497 | 94% | 497 | |||
| subject_id | 528 | 100% | 330 | 198 | ||
| health_condition_detail | 497 | 94% | 497 | |||
| sex | 494 | 93% | 494 | |||
| collection_date | 247 | 47% | 247 | |||
| antibiotic_exposure | 232 | 44% | 232 | |||
| age_at_collection_days | 231 | 44% | 231 | |||
| bmi | 225 | 42% | 225 |
- A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases. 2021 PMID 34083435 PMC8201803 own_data
- Dysbiotic Oral and Gut Viromes in Untreated and Treated Rheumatoid Arthritis Patients. 2022 PMID 36040159 PMC9603985 own_data
- CXCL10 as a shared specific marker in rheumatoid arthritis and inflammatory bowel disease and a clue involved in the mechanism of intestinal flora in rheumatoid arthritis. 2023 PMID 37328529 PMC10276029 own_data
- A catalog of bacterial reference genomes from cultivated human oral bacteria. 2023 PMID 37400465 PMC10318035 own_data
- Prediction of BMI traits in the Chinese population based on the gut metagenome. 2023 PMID 38066544 PMC10704812 own_data
27 more
- Distinct oral DNA viral signatures in rheumatoid arthritis: a Pilot study. 2024 PMID 38698892 PMC11064737
- Revealing an unprecedented diversity of episymbiotic Saccharibacteria in a high-quality genome collection. 2024 PMID 39702451 PMC11659515
- KDiamend: a package for detecting key drivers in a molecular ecological network of disease. 2018 PMID 29671403 PMC5907152
- Extensive transmission of microbes along the gastrointestinal tract. 2019 PMID 30747106 PMC6424576
- Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides. 2020 PMID 32265336 PMC7157763
- Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on <i>Streptococcus mutans</i> and <i>Streptococcus sobrinus</i>. 2020 PMID 33012228 PMC7702799
- Perturbation of the human gastrointestinal tract microbial ecosystem by oral drugs to treat chronic disease results in a spectrum of individual specific patterns of extinction and persistence of dominant microbial strains. 2020 PMID 33259474 PMC7707550
- Human Gut Faecalibacterium prausnitzii Deploys a Highly Efficient Conserved System To Cross-Feed on β-Mannan-Derived Oligosaccharides. 2021 PMID 34061597 PMC8262883
- Compositional and genetic alterations in Graves' disease gut microbiome reveal specific diagnostic biomarkers. 2021 PMID 34079079 PMC8528855
- Metagenomic analysis revealed the potential role of gut microbiome in gout. 2021 PMID 34373464 PMC8352958
- Over 50,000 Metagenomically Assembled Draft Genomes for the Human Oral Microbiome Reveal New Taxa. 2022 PMID 34492339 PMC9684161
- MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen. 2021 PMID 34592929 PMC8485520
- Characterizing Enterotypes in Human Metagenomics: A Viral Perspective. 2021 PMID 34659174 PMC8511818
- Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria. 2022 PMID 35240043 PMC9096808
- The Potential of Gut Microbiota Metabolic Capability to Detect Drug Response in Rheumatoid Arthritis Patients. 2022 PMID 35464950 PMC9024311
- A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments. 2022 PMID 35484115 PMC9051138
- Phage Cocktails Constrain the Growth of Enterococcus. 2022 PMID 35762793 PMC9426582
- Alternation of the gut microbiota in metabolically healthy obesity: An integrated multiomics analysis. 2022 PMID 36389176 PMC9663839
- Enrichment of oral-derived bacteria in inflamed colorectal tumors and distinct associations of Fusobacterium in the mesenchymal subtype. 2023 PMID 36706753 PMC9975273
- NCRD: A non-redundant comprehensive database for detecting antibiotic resistance genes. 2023 PMID 37876810 PMC10590964
- A Pipeline for Constructing Reference Genomes for Large Cohort-Specific Metagenome Compression. 2023 PMID 37894218 PMC10609127
- Isolation and characterization of a novel lytic Parabacteroides distasonis bacteriophage φPDS1 from the human gut. 2024 PMID 38178369 PMC10773633
- The molecular basis of cereal mixed-linkage β-glucan utilization by the human gut bacterium Segatella copri. 2024 PMID 39122003 PMC11418011
- Integrating metagenomics and cultivation unveils oral phage diversity and potential impact on hosts. 2025 PMID 40715125 PMC12297358
- Giant extrachromosomal element "Inocle" potentially expands the adaptive capacity of the human oral microbiome. 2025 PMID 40790024 PMC12340149
- The gut methanotroph Methylocystis intestini modulates intestinal peristalsis and fat metabolism via reducing methane levels. 2025 PMID 41331251 PMC12764784
- gutMSNP: a comprehensive database for human gut microbial single-nucleotide polymorphisms. 2026 PMID 41359024 PMC12807719
Archive description
Bacterial infection has long been implicated with rheumatoid arthritis (RA), but a systematic analysis of the probiotic and pathogenic microbiome in RA has been lacking. It is not clear whether and how the gut or oral microbial community is compositionally and functionally altered in RA, and whether and how the microbiota at different body sites overlap. Here we perform whole-genome shotgun sequencing for fecal, dental and salivary samples from a large cohort of RA patients, analyze metagenomic linkage groups to construct an RA classifier.
How this project entered the registry
Classified as human gut / stool / oral cavity shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “human oral metagenome”
- body site study.description · “fecal, dental and salivary samples”
- life stage study.description · “large cohort of RA patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA2737649 | age_at_collection_days | 17897.25 | R2 | 0.75 | external.cmd source | age: 49; age_unit: (empty); age_group: Adult |
| SAMEA2737649 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMEA2737649 | bmi | 20.8 | R2 | 0.75 | external.cmd source | bmi: 20.8 |
| SAMEA2737649 | collection_date | 2012 | R1 | 0.90 | biosample.attribute:collection_date | 2012 |
| SAMEA2737649 | country | CN | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | China |
| SAMEA2737649 | health_condition | autoimmune_inflammatory | R2 | 0.75 | external.cmd source | disease: Rheumatoid Arthritis |
| SAMEA2737881 | health_condition | healthy_control | R2 | 0.85 | paper.supp.spectrum.00348-22-s0002.xlsx[ST1][Subject type] | Control |
| SAMEA2737649 | health_condition_detail | Rheumatoid Arthritis | R2 | 0.75 | external.cmd source | disease: Rheumatoid Arthritis |
| SAMEA2737881 | health_condition_detail | Control | R2 | 0.85 | paper.supp.spectrum.00348-22-s0002.xlsx[ST1][Subject type] | Control |
| SAMEA2737649 | sex | male | R2 | 0.75 | external.cmd source | sex: Male |
| SAMEA2737881 | sex | female | R2 | 0.85 | paper.supp.spectrum.00348-22-s0002.xlsx[ST1][Sex (F/M)] | F |
| SAMEA2737650 | subject_id | D69_G | R1 | 0.85 | sample.attr.individual_name | D69_G |
| SAMEA2737649 | subject_id | D201_GM | R2 | 0.85 | paper.supp.spectrum.00348-22-s0002.xlsx[ST1!Sample ID] | f.D201_GM ERR589440 SAMEA2737649 feces Treated |
Sequencing
530 runs over 530 samples · mean 5.29 Gbp per run (median 5.72 Gbp, total 2,804.20 Gbp; 530 runs with a base count) · layout PAIRED 530 · platform ILLUMINA 530 · models Illumina HiSeq 2000 (530) · 88% of runs with a Sandpiper profile · first public 2015-07-16
Authors (38)
Tisza MJ first · Buck CB last · Guan Y first · Zhang Y · Zhu Y · Wang Y last · Liang Y first · Dou S · Zhao G · Shen J · Fu G · Fu L · Li S · Cong B · Dong C last · Ghorbani M first · Khoshdoozmasouleh N last · Tarracchini C first · Lugli GA · Mancabelli L · van Sinderen D · Turroni F · Ventura M · Milani C last · Qian K first · Du M · Tan S · Ding M · Song M · Lu M · Qi C · Cheng L · Zhang X last · Schroer HW first · Beghini F · Raygoza Garay JA · Christakis NA · Bosch DE last
Downloads
PRJEB6997.csv.gz (16.7 KB) · parquet (94.0 KB) — all 530 samples, every field with route and confidence · PRJEB6997_determinations.csv.gz (34.9 KB) — 3,481 evidence rows