Multi-omic gut microbiome in Japanese UC and Crohn's disease
654 fecal samples from a Japanese cohort (4D study), comparing ulcerative colitis and Crohn's disease patients with healthy controls using shotgun metagenomics of bacteria, phages, and fungi; case-control design. machine-written summary
654 samples · 654 runs · Age unknown · 2024 · 1.20 Gbp / sample · cohort Multi-biome analysis identifies distinct gut micro
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what each source gave
| ✓ Sequence archive | 654 sample values (subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11603027 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 586 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 | 0 | 0% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 654 | 100% | 654 |
- Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn's disease. 2024 PMID 39604394 PMC11603027 unsure
Archive description
Gut microbial dysbiosis has been implicated in the pathogenesis of Inflammatory bowel disease. However, comprehensive analyses of the interactions between various components of the gut microbiome, including the bacteriome, virome, and mycobiome, in ulcerative colitis (UC) and Crohn's disease (CD) remain fully understood. Here, we performed shotgun metagenomic sequencing of feces from patients with UC and CD, and healthy controls in the Japanese 4D cohort, and profiled bacterial taxa, gene functions, and antibacterial genes, bacteriophages, and fungi. External metagenomic datasets from the US, Spain, the Netherlands, and China were analyzed to validate our multi-biome findings. Our analysis showed that Enterococcus faecium and Bifidobacterium spp. were enriched in both diseases. Enriched Escherichia coli was particularly characteristic of CD and was significantly linked to numerous antibiotic-resistance genes involved in efflux pumps and adherent-invasive Escherichia coli virulence factors. Changes in the virome were correlated with the shifts in the bacteriome, including the increased abundance of phages encoding pathogenic genes. Saccharomyces paradoxus and Saccharomyces cerevisiae were significantly enriched in UC and CD, respectively. Saccharomyces cerevisiae and Escherichia coli had specific negative associations with SCFA-producing bacteria in CD. Multi-biome signatures and their interactions in UC and CD showed high similarities between Japan and other countries. Since several bacteria, phages, and fungi formed a hub of an intra- or trans-kingdom network with SCFA producers as well as pathobionts in UC and CD, an approach targeting the interaction network may hold therapeutic promise.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “shotgun metagenomic sequencing of feces”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN44682188 | subject_id | JP4D_11 | R1 | 0.85 | sample.attr.host_subject_id | JP4D_11 |
Sequencing
654 runs over 654 samples · mean 1.23 Gbp per run (median 1.20 Gbp, total 801.20 Gbp; 654 runs with a base count) · layout PAIRED 654 · platform ILLUMINA 654 · models Illumina HiSeq 4000 (654) · 90% of runs with a Sandpiper profile · first public 2024-11-16
Authors (13)
Akiyama S first · Nishijima S · Kojima Y · Kimura M · Ohsugi M · Ueki K · Mizokami M · Hattori M · Tsuchiya K · Uemura N · Kawai T · Bork P · Nagata N last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, country, health_condition. Share metadata
Downloads
PRJNA1169537.csv.gz (16.5 KB) · parquet (95.3 KB) — all 654 samples, every field with route and confidence · PRJNA1169537_determinations.csv.gz (7.5 KB) — 654 evidence rows