Microbiota & B12 genes in parasite-infected children
Cross-sectional study of 37 stool samples from children/infants in Argentina, comparing Giardia, helminth, and co-infection groups to examine effects on gut microbiota diversity and cobalamin (vitamin B12) synthesis genes. machine-written summary
37 samples · 37 runs · AR · Adult · 2020 · 3.87 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 259 sample values (age, collection date, country, latitude, location region, longitude, sex) |
| ✓ Abstract / description | 2 sample values (health condition detail) |
| ✓ Full text | 39 sample values (antibiotic exposure, subject id) · PMC7168842 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 105 sample values (antibiotic exposure, 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 |
Genera, mean relative abundance over 30 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 | 37 | 100% | ||||
| country | 37 | 100% | 37 | |||
| health_condition | 35 | 95% | 35 | |||
| subject_id | 37 | 100% | 37 | |||
| age_at_collection_days | 37 | 100% | 37 | |||
| antibiotic_exposure | 37 | 100% | 35 | 2 | ||
| collection_date | 37 | 100% | 37 | |||
| detailed_location | 37 | 100% | ||||
| health_condition_detail | 37 | 100% | 35 | 2 | ||
| latitude | 37 | 100% | 37 | |||
| location_region | 37 | 100% | 37 | |||
| longitude | 37 | 100% | 37 | |||
| sex | 37 | 100% | 37 |
- Impact of intestinal parasites on microbiota and cobalamin gene sequences: a pilot study. 2020 PMID 32306993 PMC7168842 own_data
Archive description
Study the parasite impact on vitamin B12 synthesis genes. - Rojelio Mejia, Ashish Damania, Rebecca Jeun, Patricia Bryan, Paola Vargas, Marisa Juarez, Pamela Cajal, Julio Nasser, Alejandro Krolewiecki, Emilie Lefoulon, Courtney Long, Evan Drake, Ruben Ciminio, Barton Slatko
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and child 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 · “Impact of Intestinal Parasites on Microbiota”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage sample.attr.age_in_years · “7 (n=37/37)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN14366065 | age_at_collection_days | 2922.0 | R1 | 0.90 | sample.attr.age_in_years | 8 |
| SAMN14366065 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN14366081 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | No previous antiparasitics or antibiotics were administered 3 months prior |
| SAMN14366065 | collection_date | 2012-12 | R1 | 0.90 | biosample.attribute:collection_date | 2012-12 |
| SAMN14366065 | country | AR | R1 | 0.90 | sample.attr.geo_loc_name | Argentina |
| SAMN14366065 | health_condition | other_infection | R2 | 0.75 | external.cmd source | disease: giardiasis;Helminthiasis |
| SAMN14366065 | health_condition_detail | giardiasis;Helminthiasis | R2 | 0.75 | external.cmd source | disease: giardiasis;Helminthiasis |
| SAMN14366081 | health_condition_detail | mixed_case_control: Study includes uninfected children (healthy controls) and children with various parasitic infections | R4 | 0.50 | paper.abstract | uninfected, Giardia-only, Giardia + helminth co-infections, and helminth-only groups |
| SAMN14366065 | latitude | -24.4700 | R1 | 0.90 | biosample.attribute:lat_lon | 24.47 S 65.25 W |
| SAMN14366065 | location_region | Jujuy | R1 | 0.60 | biosample.attribute:lat_lon | 24.47 S 65.25 W |
| SAMN14366065 | longitude | -65.2500 | R1 | 0.90 | biosample.attribute:lat_lon | 24.47 S 65.25 W |
| SAMN14366065 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN14366065 | subject_id | SAMN14366065 | R3 | 0.70 | design.one_sample_per_subject:fulltext | Stool samples were collected from 37 asymptomatic children from a previous cross-sectional Argentinian study |
Sequencing
37 runs over 37 samples · mean 4.23 Gbp per run (median 3.87 Gbp, total 156.54 Gbp; 37 runs with a base count) · layout SINGLE 25, PAIRED 12 · platform ILLUMINA 37 · models NextSeq 500 (37) · 81% of runs with a Sandpiper profile · first public 2020-03-23
Authors (14)
Mejia R first · Damania A · Jeun R · Bryan PE · Vargas P · Juarez M · Cajal PS · Nasser J · Krolewiecki A · Lefoulon E · Long C · Drake E · Cimino RO · Slatko B last
Downloads
PRJNA612291.csv.gz (2.1 KB) · parquet (72.5 KB) — all 37 samples, every field with route and confidence · PRJNA612291_determinations.csv.gz (4.5 KB) — 405 evidence rows