Gut microbiota in Lynch syndrome, Druze community, Israel
Case-control fecal metagenome study of 28 samples from Druze community members in Israel, comparing Lynch syndrome and non-Lynch individuals with and without cancer history. machine-written summary
28 samples · 28 runs · IL · Adult · 2023 · 28.56 Gbp / sample · cohort <i>Fusobacterium</i> species are disti
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 244 sample values (age, bmi, collection date, country, health condition, health condition detail, latitude, location region) |
| ✓ Abstract / description | 28 sample values (location site) |
| ✓ Full text | 28 sample values (subject id) · PMC10673896, PMC11237946 |
| ✓ Supplementary tables | 83 sample values (age, bmi, family id, family role, sex, shared setting id, shared setting type) |
| – 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 |
familieshouseholdsparent–childpartners / couplessiblings
Druze Lynch-syndrome carriers and family members: 4 multi-member families (A,B,D,E), 6 households (HH1–HH6), 4 partner, 2 sibling, 2 mother–child pairs · 4 families with 14 sampled people · 6 shared settings.
motherpartnerchildsiblingother relativemember · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 6 linked groups from explicit relations · 1 family · 6 shared settings. 28 people in the project overall.
Families (4)
| family | members | samples |
|---|---|---|
| B | partner + sibling×2 + other_relative×2 + unknown×3 | SAMN34358377 · SAMN34358378 · SAMN34358379 · SAMN34358385 · SAMN34358387 · SAMN34358388 · SAMN34358389 · SAMN34358392 · SAMN34358393 |
| A | partner + unknown | SAMN34358370 · SAMN34358390 |
| D | other_relative + unknown | SAMN34358384 · SAMN34358394 |
| E | partner + unknown | SAMN34358374 · SAMN34358386 |
Genera, mean relative abundance over 23 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 | 28 | 100% | ||||
| country | 28 | 100% | 28 | |||
| health_condition | 28 | 100% | 28 | |||
| subject_id | 28 | 100% | 28 | |||
| age_at_collection_days | 28 | 100% | 27 | 1 | ||
| collection_date | 28 | 100% | 28 | |||
| detailed_location | 28 | 100% | ||||
| health_condition_detail | 28 | 100% | 28 | |||
| latitude | 28 | 100% | 28 | |||
| location_region | 28 | 100% | 28 | |||
| location_site | 28 | 100% | 28 | |||
| longitude | 28 | 100% | 28 | |||
| sex | 28 | 100% | 28 | |||
| bmi | 23 | 82% | 21 | 2 | ||
| family_id | 15 | 54% | 15 | |||
| shared_setting_id | 14 | 50% | 14 | |||
| shared_setting_type | 14 | 50% | 14 | |||
| family_role | 9 | 32% | 9 |
- Gut microbial signatures are associated with Lynch syndrome (LS) and cancer history in Druze communities in Israel. 2023 PMID 38001152 PMC10673896 own_data
- <i>Fusobacterium</i> species are distinctly associated with patients with Lynch syndrome colorectal cancer. 2024 PMID 38993678 PMC11237946 unsure
Archive description
Fecal metagenomics analysis reveals signatures of gut microbiota associated with Lynch syndrome in Druze communities in Israel
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.65. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “Fecal metagenomics analysis”
- life stage study.title · “Lynch syndrome in Druze communities”
- life stage sample.attr.host_age · “64 (n=3/28)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN33454823 | age_at_collection_days | 22980.8 | R1 | 0.85 | sample.attr.host_age | 63 |
| SAMN34358387 | age_at_collection_days | 12784 | R2 | 0.80 | paper.supp.41598_2023_47723_MOESM2_ESM.xlsx[S1!Age] | 35 |
| SAMN33454823 | bmi | 26.3 | R1 | 0.90 | sample.attr.host_body_mass_index | 26.29757785 |
| SAMN34358378 | bmi | 26.5 | R2 | 0.80 | paper.supp.41598_2023_47723_MOESM2_ESM.xlsx[S1!BMI] | 26.5 |
| SAMN33454823 | collection_date | 2020-10-20 | R1 | 0.90 | biosample.attribute:collection_date | 2020-10-20 |
| SAMN33454823 | country | IL | R1 | 0.90 | sample.attr.geo_loc_name | Israel |
| SAMN34358370 | family_id | A | R2 | 0.85 | paper.supp.41598_2023_47723_MOESM2_ESM.xlsx[S1!Family] | number 7: Family A |
| SAMN34358385 | family_role | sibling | R2 | 0.85 | paper.supp.41598_2023_47723_MOESM2_ESM.xlsx[S1!Family_relations_ of_controls_to_LS] | Brother of 16 |
| SAMN33454823 | health_condition | other_disease | R1 | 0.60 | biosample_attr | Lynch syndrom |
| SAMN33454823 | health_condition_detail | Lynch syndrom | R1 | 0.90 | sample.attr.host_disease | Lynch syndrom |
| SAMN33454823 | latitude | 32.8330 | R1 | 0.90 | biosample.attribute:lat_lon | 32.833049 N 34.985710 E |
| SAMN33454823 | location_region | Haifa | R1 | 0.60 | biosample.attribute:lat_lon | 32.833049 N 34.985710 E |
| SAMN33454823 | location_site | Druze ethnoreligious community in Israel | R4 | 0.50 | paper.abstract | Druze ethnoreligious community in Israel |
| SAMN33454823 | longitude | 34.9857 | R1 | 0.90 | biosample.attribute:lat_lon | 32.833049 N 34.985710 E |
| SAMN33454823 | sex | male | R2 | 0.80 | paper.supp.41598_2023_47723_MOESM2_ESM.xlsx[S1!Sex] | M |
| SAMN34358370 | shared_setting_id | HH2 | R2 | 0.85 | paper.supp.41598_2023_47723_MOESM2_ESM.xlsx[S1!Household] | number 7: Household HH2 |
| SAMN34358370 | shared_setting_type | household | R2 | 0.85 | paper.supp.41598_2023_47723_MOESM2_ESM.xlsx[S1!Household] | number 7: Household HH2 |
| SAMN33454823 | subject_id | SAMN33454823 | R3 | 0.70 | design.one_sample_per_subject:fulltext | Our cohort consisted of 28 Druze individuals (54% females) |
Sequencing
28 runs over 28 samples · mean 30.28 Gbp per run (median 28.56 Gbp, total 847.92 Gbp; 28 runs with a base count) · layout PAIRED 28 · platform ILLUMINA 28 · models Illumina MiSeq (28) · 82% of runs with a Sandpiper profile · first public 2023-12-24
Authors (21)
Naddaf R first · Carasso S · Reznick-Levi G · Hasnis E · Qarawani A · Maza I · Gefen T · Half EE · Geva-Zatorsky N last · Salim F first · Mizutani S · Shiba S · Takamaru H · Yamada M · Nakajima T · Yachida T · Soga T · Saito Y · Fukuda S · Yachida S · Yamada T last
Downloads
PRJNA939026.csv.gz (2.3 KB) · parquet (73.5 KB) — all 28 samples, every field with route and confidence · PRJNA939026_determinations.csv.gz (4.5 KB) — 383 evidence rows