PRJNA698223 SRP304988
Gut microbiome in international travelers, Cusco, Peru
TD Cusco travelers study
993 longitudinal stool samples from international travelers in Cusco, Peru, studying effects of travel and diarrhea/GI infection on gut microbiome and resistome dynamics. machine-written summary
993 samples · 993 runs · PE · Adult · 2022 · 1.36 Gbp / sample
Sources
✓Sequence archive 8,036✓Abstract / description 735✓Full text 993✓Supplementary tables 1,812✓External resources 394–User contribution–Human verified
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 8,036 sample values (age, antibiotic exposure, collection date, country, health condition, health condition detail, latitude, location locality) |
| ✓ Abstract / description | 735 sample values (health condition detail) |
| ✓ Full text | 993 sample values (location site) · PMC9722912 |
| ✓ Supplementary tables | 1,812 sample values (antibiotic exposure, health condition, health condition detail, medication, timepoint) |
| ✓ External resources | 394 sample values (health condition, health condition detail) · from Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Samples at a glance
1 sampling locations · 1 country
Age
adult989
elderly4
Condition
healthy_control191
gi_infection_or_diarrhoea138
other_disease107
Sex
female446
male264
Country
PE384
Body site
primary993
Collected 2012–2016
Sequencing depth per sample · this project all projects
! Self-contradictory metadata
country: sequence archive and supplementary table disagree for 609 samples (e.g. PE vs US) — withheld.
The sources disagree on 609 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 (40 of 609)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN17772725 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772726 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772727 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772728 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772729 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772730 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772731 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772732 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772733 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772734 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772735 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772736 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772737 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772738 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772739 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772740 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772741 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772742 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772743 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772744 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772745 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772746 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772747 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772748 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772749 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772750 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772751 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772752 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772753 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772754 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772755 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772756 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772757 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772758 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772759 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772760 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772761 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772762 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772763 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
| SAMN17772764 | country | PE (sequence archive) | US (supplementary table) | withheld: neither value published |
Sampling design and relatedness
longitudinal
148 of 159 people sampled more than once (699 samples; median 4, up to 22 per person) · follow-up median 24 d (max 5 mo) · median interval between samples 7 d (time from collection dates).
Each row is one person (36 shown of 148); dots are samples at days since that person's first sample.
Community composition
Blautia_A 11.5%Roseburia 9.3%Faecalibacterium 5.9%Bifidobacterium 4.5%Mediterraneibacter 4.1%Ruminococcoides 3.7%Fusicatenibacter 3.5%Gemmiger 2.8%Anaerostipes 2.7%Collinsella 2.1%Bacteroides 2.1%Dorea_A 1.9%not assigned to a genus 11.3%other genera 34.7%
Genera, mean relative abundance over 641 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Field coverage
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 993 | 100% | ||||
| country | 384 | 39% | 384 | |||
| health_condition | 436 | 44% | 137 | 299 | ||
| subject_id | 710 | 72% | 710 | |||
| collection_date | 993 | 100% | 993 | |||
| detailed_location | 993 | 100% | ||||
| health_condition_detail | 993 | 100% | 137 | 121 | 735 | |
| latitude | 993 | 100% | 993 | |||
| location_locality | 993 | 100% | 993 | |||
| location_region | 993 | 100% | 993 | |||
| location_site | 993 | 100% | 993 | |||
| longitude | 993 | 100% | 993 | |||
| antibiotic_exposure | 961 | 97% | 283 | 678 | ||
| age_at_collection_days | 710 | 72% | 710 | |||
| sex | 710 | 72% | 710 | |||
| medication | 674 | 68% | 674 | |||
| timepoint_label | 434 | 44% | 434 |
Papers (1)
- Impact of international travel and diarrhea on gut microbiome and resistome dynamics. 2022 PMID 36470885 PMC9722912 own_data
Details
Archive description
Understand the impact of international travel and diarrhea on gut microbiomes and resistomes dynamics
How this project entered the registry
Classified as human gut / stool mixed assays of adult by sonnet_x2 with confidence 0.60. Assay mixed.
- host run.host_tax_id · “9606”
- body site study.description · “gut microbiomes and resistomes dynamics”
- life stage study.title · “TD Cusco travelers study”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17772725 | age_at_collection_days | 8035.5 | R1 | 0.85 | sample.attr.host_age | 22 |
| SAMN31371967 | antibiotic_exposure | yes | R1 | 0.95 | biosample_attr | Aztreonam |
| SAMN17772725 | antibiotic_exposure | no | R2 | 0.85 | paper.supp.41467_2022_34862_MOESM7_ESM.xlsx[SD06!Abx_dur_stay] | No |
| SAMN17772725 | collection_date | 2012-06-25 | R1 | 0.90 | biosample.attribute:collection_date | 2012-06-25 |
| SAMN17772836 | country | PE | R1 | 0.90 | sample.attr.geo_loc_name | Peru: Cusco |
| SAMN17772733 | health_condition | gi_infection_or_diarrhoea | R1 | 0.85 | biosample.attribute:sample_type | diarrhea |
| SAMN17772746 | health_condition | other_disease | R2 | 0.70 | external.meta2db source | gastroesophageal reflux disease |
| SAMN17772773 | health_condition | healthy_control | R2 | 0.85 | paper.supp.41467_2022_34862_MOESM7_ESM.xlsx[SD11!Sample_code(A=Non-diarrhea, D=Diarrhea)] | A |
| SAMN17772733 | health_condition_detail | diarrhea | R1 | 0.85 | biosample.attribute:sample_type | diarrhea |
| SAMN17772746 | health_condition_detail | gastroesophageal reflux disease | R2 | 0.70 | external.meta2db source | gastroesophageal reflux disease |
| SAMN17772773 | health_condition_detail | A | R2 | 0.85 | paper.supp.41467_2022_34862_MOESM7_ESM.xlsx[SD11!Sample_code(A=Non-diarrhea, D=Diarrhea)] | A |
| SAMN17772725 | health_condition_detail | mixed_case_control: Travelers with diarrhea vs travelers without diarrhea | R4 | 0.50 | paper.abstract | diarrheal and non-diarrheal samples |
| SAMN17772725 | latitude | -13.5188 | R1 | 0.90 | biosample.attribute:lat_lon | 13.518840 S 71.975040 W |
| SAMN17772725 | location_locality | Cusco | R1 | 0.85 | biosample.attribute:geo_loc_name | Peru: Cusco |
| SAMN17772725 | location_region | Cusco | R1 | 0.60 | biosample.attribute:lat_lon | 13.518840 S 71.975040 W |
| SAMN17772725 | location_site | Amauta Spanish School | R3 | 0.70 | paper.fulltext.methods | enrolled at the Amauta Spanish School in Cusco |
| SAMN17772725 | longitude | -71.9750 | R1 | 0.90 | biosample.attribute:lat_lon | 13.518840 S 71.975040 W |
| SAMN17772725 | medication | none_reported | R2 | 0.75 | paper.supp.41467_2022_34862_MOESM7_ESM.xlsx[SD01!Medication_type] | No |
| SAMN17772725 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN17772725 | subject_id | TD0002 | R1 | 0.85 | sample.attr.host_subject_id | TD0002 |
| SAMN17772725 | timepoint_label | 4 - 12 | R2 | 0.85 | paper.supp.41467_2022_34862_MOESM7_ESM.xlsx[SD22!days] | 4 - 12 |
Sequencing
993 runs over 993 samples · mean 1.23 Gbp per run (median 1.36 Gbp, total 1,218.40 Gbp; 993 runs with a base count) · layout PAIRED 993 · platform ILLUMINA 993 · models NextSeq 500 (993) · 65% of runs with a Sandpiper profile · first public 2022-10-25
Authors (13)
Boolchandani M first · Blake KS · Tilley DH · Cabada MM · Schwartz DJ · Patel S · Morales ML · Meza R · Soto G · Isidean SD · Porter CK · Simons MP · Dantas G last
Help complete this project
2 of the 4 core fields are below 50% coverage: country, health_condition. Share metadata
Downloads
PRJNA698223.csv.gz (31.6 KB) · parquet (114.0 KB) — all 993 samples, every field with route and confidence · PRJNA698223_determinations.csv.gz (89.3 KB) — 11,970 evidence rows
Samples (993 · every field this project has values for · hover a cell for its source)
Loading the sample table…