Gut metagenome in Lynch syndrome CRC patients, France
Case-control study of 33 fecal metagenome samples from France, comparing Lynch syndrome colorectal cancer patients (19) to healthy first-degree relative controls (14) to assess bacterial network structures. machine-written summary
33 samples · 33 runs · FR · Adult · 2024 · 3.07 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 231 sample values (age, bmi, collection date, country, health condition, health condition detail, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 99 sample values (antibiotic exposure, location locality, location region) · PMC10876293, PMC13281578 |
| ○ 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 |
families — not resolved
19 Lynch-syndrome CRC patients and 15 first-degree relatives from 17 families; family membership not given per sample.
Genera, mean relative abundance over 28 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 | 33 | 100% | ||||
| country | 33 | 100% | 33 | |||
| health_condition | 33 | 100% | 33 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 33 | 100% | 33 | |||
| antibiotic_exposure | 33 | 100% | 33 | |||
| bmi | 33 | 100% | 33 | |||
| collection_date | 33 | 100% | 33 | |||
| detailed_location | 33 | 100% | ||||
| health_condition_detail | 33 | 100% | 33 | |||
| location_locality | 33 | 100% | 33 | |||
| location_region | 33 | 100% | 33 | |||
| sex | 33 | 100% | 33 |
- Loss of symbiotic and increase of virulent bacteria through microbial networks in Lynch syndrome colon carcinogenesis. 2023 PMID 38375206 PMC10876293 own_data
- Gut fungal signatures in colorectal cancer and their potential for supporting diagnosis: a multi-cohort metagenomic analysis. 2026 PMID 42271362 PMC13281578 unsure
Archive description
We performed whole gut metagenomic analysis in 17 Lynch syndrome (LS) families, including colorectal cancer (CRC) patients and their healthy first-degree relatives (Controls). Since bacteria are organized into different networks within the microbiota, we compared related network structures in patients and controls. Experimental Design: Fecal prokaryote DNA was extracted prior to colonoscopy for whole metagenome. We characterized bacteria taxonomy using the Diamond/MEGAN6 pipeline and performed differential abundances using the Shaman website. We constructed networks using SparCC inference tools and validated the construction's accuracy by performing qPCR on selected bacteria Results: Significant differences in bacterial communities in LS-CRC patients were identified, with an enrichment of virulent bacteria and a depletion of symbionts compared to their first-degree relatives. The main bacterial network structures, constructed based on bacteria-bacteria correlations in CRC (pilot study) and in precancerous patients (validation-study, data not deposited here), showed a different pattern than in controls. It was characterized by virulent/symbiotic co-exclusion in both studies and illustrated (validation study) by a higher Escherichia/Bifidobacterium ratio, as assessed by qPCR. Conclusions: Enhanced fecal virulent/symbiotic bacteria ratios influence bacterial network structures. As an early event in colon carcinogenesis, these ratios can be used to identify asymptomatic LS individual with a higher risk of CRC
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “Fecal prokaryote DNA was extracted”
- life stage sample.attr.age · “47 (n=26/33)”
- life stage sample.attr.age · “76 (n=7/33)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA114807790 | age_at_collection_days | 28489.5 | R1 | 0.70 | sample.attr.age | 78 |
| SAMEA114807790 | antibiotic_exposure | no | R3 | 0.60 | paper.fulltext.results | Antibiotic therapy was excluded |
| SAMEA114807790 | bmi | 24.0 | R1 | 0.90 | sample.attr.bmi | 24 |
| SAMEA114807790 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMEA114807790 | country | FR | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | France |
| SAMEA114807790 | health_condition | colorectal_cancer | R1 | 0.90 | biosample_attr | CRC |
| SAMEA114807790 | health_condition_detail | CRC | R1 | 0.85 | biosample.attribute:status | status: CRC |
| SAMEA114807790 | location_locality | Paris | R3 | 0.70 | paper.fulltext.methods | academic hospitals in the Paris area |
| SAMEA114807790 | location_region | Ile-de-France | R3 | 0.70 | paper.fulltext.methods | academic hospitals in the Paris area |
| SAMEA114807790 | sex | female | R1 | 0.90 | sample.attr.gender | F |
Sequencing
33 runs over 33 samples · mean 3.12 Gbp per run (median 3.07 Gbp, total 102.83 Gbp; 33 runs with a base count) · layout SINGLE 33 · platform ILLUMINA 33 · models Illumina HiSeq 2000 (33) · 85% of runs with a Sandpiper profile · first public 2024-01-09
Authors (23)
Sadeghi M first · Mestivier D · Carbonnelle E · Benamouzig R · Khazaie K · Sobhani I last · Zhang Z first · Lu T · Dong B · Liu J · Zhang Y · Li S · Liu H · Li X · Guan T · Guo H · Yan Q · Lei Z · Yu X · Wang L · Kang J · Li L · Zhao D last
Downloads
PRJEB70916.csv.gz (2.0 KB) · parquet (71.7 KB) — all 33 samples, every field with route and confidence · PRJEB70916_determinations.csv.gz (3.0 KB) — 330 evidence rows