Gut microbiota in hospitalized patients, Montreal
229 fecal samples from hospitalized patients in Montreal, Canada, studied longitudinally for gut microbiota changes related to Clostridium difficile colonization/infection, antibiotic use, and laxative exposure. machine-written summary
229 samples · 253 runs · CA · Adult · 2015 · 2.30 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,409 sample values (age, antibiotic exposure, collection date, country, health condition, health condition detail, latitude, location locality) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 229 sample values (location site) · PMC10154212, PMC13269251, PMC4791782, PMC6132499, PMC6833257 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 408 sample values (health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
antibiotic exposure: sequence archive and Meta2DB disagree for 36 samples (e.g. no vs yes) — withheld.
The sources disagree on 36 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 (36)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN04126100 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126101 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126103 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126104 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126121 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126138 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126141 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126152 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126154 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126155 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126156 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126219 | antibiotic exposure | no (sequence archive) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMN04126225 | antibiotic exposure | yes (sequence archive) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN04126226 | antibiotic exposure | yes (sequence archive) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN04126227 | antibiotic exposure | yes (sequence archive) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMN04126228 | antibiotic exposure | no (sequence archive) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMN04126229 | antibiotic exposure | no (sequence archive) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMN04126230 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126231 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126236 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126240 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126258 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126259 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126262 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126263 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126270 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126273 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126274 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126275 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126279 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126280 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126281 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126285 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126289 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126290 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
| SAMN04126291 | antibiotic exposure | no (sequence archive) | yes (Meta2DB) | withheld: neither value published |
longitudinal
69 of 98 people sampled more than once (200 samples; median 2, up to 15 per person) · follow-up median 4 d (max 2 mo) · median interval between samples 3 d (time from collection dates). Schedule stated by the source: “Fecal specimens at study enrollment, every 3 days during hospitalization, at onset of diarrhea (if applicable), and at discharge” (time origin: enrolment); stated follow-up 2 mo.
Each row is one person (36 shown of 69); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 208 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 | 229 | 100% | ||||
| country | 229 | 100% | 229 | |||
| health_condition | 229 | 100% | 25 | 204 | ||
| subject_id | 229 | 100% | 229 | |||
| age_at_collection_days | 229 | 100% | 229 | |||
| collection_date | 229 | 100% | 229 | |||
| detailed_location | 229 | 100% | ||||
| health_condition_detail | 229 | 100% | 25 | 204 | ||
| latitude | 229 | 100% | 229 | |||
| location_locality | 229 | 100% | 229 | |||
| location_site | 229 | 100% | 229 | |||
| longitude | 229 | 100% | 229 | |||
| sex | 229 | 100% | 229 | |||
| timepoint_label | 200 | 87% | 200 | |||
| antibiotic_exposure | 193 | 84% | 193 | |||
| medication | 134 | 59% | 134 |
- Bloom and bust: intestinal microbiota dynamics in response to hospital exposures and Clostridium difficile colonization or infection. 2016 PMID 26975510 PMC4791782 own_data
- Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes. 2018 PMID 29445826 PMC6132499 unsure
- Mash Screen: high-throughput sequence containment estimation for genome discovery. 2019 PMID 31690338 PMC6833257 unsure
- Toward an improved definition of a healthy microbiome for healthy aging. 2022 PMID 37118093 PMC10154212 unsure
- Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals. 2026 PMID 42312244 PMC13269251 unsure
Archive description
Using whole-metagenome shotgun sequencing, we examined the diversity and composition of the fecal microbiota in a prospective cohort study of 98 hospitalized patients.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Intestinal microbiota dynamics in”
- body site study.description · “composition of the fecal microbiota in a”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage sample.attr.host_age · “66 (n=186/229)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN04126092 | age_at_collection_days | 29220.0 | R1 | 0.70 | sample.attr.host_age | 80 |
| SAMN04126092 | antibiotic_exposure | yes | R1 | 0.90 | biosample_attr | 1 |
| SAMN04126092 | collection_date | 2009-10-29 | R1 | 0.90 | biosample.attribute:collection_date | 2009-10-29 |
| SAMN04126092 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada:Montreal |
| SAMN04126105 | health_condition | healthy_control | R1 | 0.80 | biosample_attr | Control |
| SAMN04126092 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN04126105 | health_condition_detail | Control | R1 | 0.85 | biosample.attribute:status | Control |
| SAMN04126092 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN04126092 | latitude | 45.5000 | R1 | 0.90 | biosample.attribute:lat_lon | 45.50 N 73.63 W |
| SAMN04126092 | location_locality | Montreal | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada:Montreal |
| SAMN04126092 | location_site | Jewish General Hospital | R3 | 0.70 | paper.fulltext.methods | conducted at the Jewish General Hospital (JGH) in Montréal |
| SAMN04126092 | longitude | -73.6300 | R1 | 0.90 | biosample.attribute:lat_lon | 45.50 N 73.63 W |
| SAMN04126094 | medication | nsaid_or_aspirin | R1 | 0.90 | biosample.attribute:nsaid | 1To3Days |
| SAMN04126098 | medication | ppi | R1 | 0.90 | biosample.attribute:ppi | 1To3Days |
| SAMN04126258 | medication | chemotherapy | R1 | 0.90 | biosample.attribute:chemo | 4To14Days |
| SAMN04126092 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN04126092 | subject_id | MM001 | R1 | 0.85 | sample.attr.host_subject_id | MM001 |
| SAMN04126092 | timepoint_label | 1 | R1 | 0.70 | sample.name_rule:alias | MM001.1 |
Sequencing
253 runs over 229 samples · mean 2.61 Gbp per run (median 2.25 Gbp, total 661.48 Gbp; 253 runs with a base count) · layout SINGLE 253 · platform ILLUMINA 253 · models Illumina HiSeq 2000 (247), Illumina HiSeq 2500 (6) · 90% of runs with a Sandpiper profile · first public 2015-10-08 – 2015-10-09
Authors (50)
Vincent C first · Miller MA · Edens TJ · Mehrotra S · Dewar K · Manges AR last · Cabal A first · Jun SR · Jenjaroenpun P · Wanchai V · Nookaew I · Wongsurawat T · Burgess MJ · Kothari A · Wassenaar TM · Ussery DW last · Ondov BD first · Starrett GJ · Sappington A · Kostic A · Koren S · Buck CB · Phillippy AM last · Ghosh TS first · Shanahan F · O'Toole PW last · Tarracchini C first · Lugli GA · Mancabelli L · van Sinderen D · Turroni F · Ventura M · Milani C last · Heidrich V first · Fackelmann G · Ricci L · Spadazzi R · Baldanzi G · Punčochář M · Catassi G · Marchi P · Modesto M · Piccinno G · Porcari S · Rondinella D · Asnicar F · Valles-Colomer M · Mattarelli P · Ianiro G · Segata N last
Downloads
PRJNA297252.csv.gz (8.8 KB) · parquet (82.7 KB) — all 229 samples, every field with route and confidence · PRJNA297252_determinations.csv.gz (25.6 KB) — 3,046 evidence rows