16S and metagenomic study of microbiota in IBD
12 samples were analyzed using integrated 16S rRNA sequencing and metagenomics to examine microbial dysbiosis and virulence factors in inflammatory bowel disease; no further sample details are given. machine-written summary
12 samples · 12 runs · CN · Age unknown · 2026 · 7.36 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 24 sample values (collection date, health condition, health condition detail) |
| ✓ Abstract / description | 12 sample values (subject id) |
| ✓ Full text | 36 sample values (country, location locality, location region) · PMC10999624 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 12 | 100% | 12 | |||
| health_condition | 6 | 50% | 6 | |||
| subject_id | 12 | 100% | 12 | |||
| collection_date | 12 | 100% | 12 | |||
| detailed_location | 12 | 100% | ||||
| location_locality | 12 | 100% | 12 | |||
| location_region | 12 | 100% | 12 | |||
| health_condition_detail | 6 | 50% | 6 |
- Integrated 16S rRNA sequencing and metagenomics insights into microbial dysbiosis and distinct virulence factors in inflammatory bowel disease. 2024 PMID 38591039 PMC10999624 own_data
Archive description
With the rapid pace of urbanization, there has been an observed increase in the prevalence and incidence of Inflammatory Bowel Disease (IBD). Here, 16S rRNA and metagenomic sequencing have been utilized to investigate the gut microbiota profiles in a case-control study of IBD patients, to decipher the microbial underpinnings of these diseases. Notably, the phylum Proteobacteria, particularly the genus Escherichia-Shigella, was found to be significantly elevated in Crohn's Disease (CD) patients, while the genus Enterococcus showed a marked increase in Ulcerative Colitis (UC) patients. Core gut microbiota such as Christensenellaceae R-7 group, Fusicatenibacter, and Holdemanella were identified in healthy individuals. This study also highlighted significant interactions between the microbiome and virulence factors, specifically the role of Chu (VF0227) in CD patients. Additionally, functional analysis suggested that oxidative stress might play a significant role in the pathological processes of IBD. These comprehensive insights into the gut microbiota of IBD patients enhanced our understanding of the pathogenesis, highlighted the complex interplay between the microbiome.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host study.title · “inflammatory bowel disease”
- body site study.description · “gut microbiota profiles in a case-control study”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMD02002982 | collection_date | 2020-12-21 | R1 | 0.85 | biosample.attribute:collection_date | 2020-12-21 |
| SAMD02002982 | country | CN | R3 | 0.70 | paper.body.text | at Xining in Qinghai Province, China, from 2020. |
| SAMD02002988 | health_condition | ulcerative_colitis | R1 | 0.70 | sample.name_rule:sample_name | SAMC3400719_UC1 |
| SAMD02002988 | health_condition_detail | UC | R1 | 0.70 | sample.name_rule:sample_name | SAMC3400719_UC1 |
| SAMD02002982 | location_locality | Xining | R3 | 0.70 | paper.body.text | at Xining in Qinghai Province, China, from 2020. |
| SAMD02002982 | location_region | Qinghai | R3 | 0.70 | paper.body.text | at Xining in Qinghai Province, China, from 2020. |
| SAMD02002982 | subject_id | SAMD02002982 | R4 | 0.60 | design.one_sample_per_subject:abstract | 16S rRNA gene sequencing (n = 36) and metagenomic sequencing (n = 12) to analyze the gut microbiota of newly diagnosed IBD patients |
Sequencing
12 runs over 12 samples · mean 7.16 Gbp per run (median 7.36 Gbp, total 85.95 Gbp; 12 runs with a base count) · layout PAIRED 12 · platform ILLUMINA 12 · models Illumina NovaSeq 6000 (11), Illumina MiSeq (1) · 0% of runs with a Sandpiper profile · first public 2026-09-27
Authors (0)
No author record.
Downloads
PRJDB43252.csv.gz (1.3 KB) · parquet (70.1 KB) — all 12 samples, every field with route and confidence · PRJDB43252_determinations.csv.gz (1.3 KB) — 72 evidence rows