Resistome of gut microbiota in El Salvador and Lima, Peru
Cross-sectional study of 191 fecal microbiome/resistome samples from healthy individuals (spanning infant to elderly age groups) in rural El Salvador and peri-urban Lima, Peru, examining antibiotic resistance exchange between microbiota. machine-written summary
191 samples · 570 runs · SV, PE · Infant / toddler · 2016 · 0.73 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,077 sample values (age, collection date, country, lifestyle, sex, subject id, timepoint) |
| ✓ Abstract / description | 191 sample values (preterm status) |
| ○ Full text | read; no usable statement or table · PMC10269646, PMC11494892, PMC11733223, PMC12769767, PMC9512645 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 382 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 |
longitudinal
59 of 93 people sampled more than once (157 samples; median 3, up to 4 per person) · follow-up median 12 mo (max 12 mo) · median interval between samples 12 mo (time from age at collection). Schedule stated by the source: “Catalog shows 7 distinct timepoint_label values (e.g. 01D,03D,04D,05D,07D,08D,09D) suggesting day-labeled repeated sampling; exact schedule not stated in text.”.
Each row is one person (36 shown of 59); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 179 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 | 191 | 100% | ||||
| country | 191 | 100% | 191 | |||
| health_condition | 191 | 100% | 191 | |||
| subject_id | 191 | 100% | 191 | |||
| age_at_collection_days | 191 | 100% | 191 | |||
| collection_date | 191 | 100% | 191 | |||
| health_condition_detail | 191 | 100% | 191 | |||
| preterm_status | 191 | 100% | 191 | |||
| sex | 188 | 98% | 188 | |||
| lifestyle | 114 | 60% | 114 | |||
| timepoint_label | 11 | 6% | 11 |
- (no title) curated
- (no title) curated
- Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645 curated
- (no title) curated
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646 curated
5 more
- (no title)
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892
- Early life microbial succession in the gut follows common patterns in humans across the globe. PMID 39809768 PMC11733223
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767
- (no title)
Archive description
Microbiome and resistome of human fecal and environmental microbiota from rural El Salvador and peri-urban Lima, Peru
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “resistome of human fecal and environmental microbiota”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN04261143 | age_at_collection_days | 26663 | R1 | 0.85 | sample.attr.host_age | 73 |
| SAMN04261143 | collection_date | 2013-01-07 | R1 | 0.85 | biosample.attribute:collection_date | 2013-01-07 |
| SAMN04261143 | country | SV | R1 | 0.90 | biosample_attr | El Salvador |
| SAMN04261143 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN04261143 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN04261143 | lifestyle | rural_non_industrialized | R1 | 0.85 | biosample.attribute:env_biome | rural village |
| SAMN04261143 | preterm_status | term | R4 | 0.45 | paper.abstract | healthy, full-term infants across various geographical |
| SAMN04261143 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMN04261143 | subject_id | 1_1 | R1 | 0.85 | biosample_attr | 1_1 |
| SAMN04261324 | timepoint_label | 01D | R1 | 0.70 | run.library_name | WGS_paired_01D_013 |
Sequencing
570 runs over 191 samples · mean 0.59 Gbp per run (median 0.37 Gbp, total 336.25 Gbp; 570 runs with a base count) · layout PAIRED 285, SINGLE 285 · platform ILLUMINA 570 · models Illumina HiSeq 2500 (430), NextSeq 500 (140) · 77% of runs with a Sandpiper profile · first public 2016-03-12
Authors (91)
Pehrsson EC first · Tsukayama P · Patel S · Mejía-Bautista M · Sosa-Soto G · Navarrete KM · Calderon M · Cabrera L · Hoyos-Arango W · Bertoli MT · Berg DE · Gilman RH · Dantas G last · Tisza MJ first · Buck CB last · Pan S first · Zhu C · Zhao XM · Coelho LP last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Ghosh TS first · Shanahan F · O'Toole PW last · Rizzo SM first · Viappiani A · Bianchi MG · Bussolati O · van Sinderen D · Yersin S first · Garneau JR · Schneeberger PHH · Osman KA · Cercamondi CI · Muhummed AM · Tschopp R · Zinsstag J · Vonaesch P last · Fahur Bottino G first · Bonham KS · Patel F · McCann S · Zieff M · Naspolini N · Ho D · Portlock T · Joos R · Midani FS · Schüroff P · Das A · Shennon I · Wilson BC · O'Sullivan JM · Britton RA · Murray DM · Kiely ME · Taddei CR · Beltrão-Braga PCB · Campos AC · Polanczyk GV · Huttenhower C · Donald KA · Klepac-Ceraj V last · Longhi G · Gennaioli E · Muscò A · Vitale SG · Angioni S · 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
PRJNA300541.csv.gz (7.3 KB) · parquet (79.9 KB) — all 191 samples, every field with route and confidence · PRJNA300541_determinations.csv.gz (13.7 KB) — 1,650 evidence rows