Longitudinal gut microbiome in rural Mexican infants
Shotgun metagenomics of 156 samples from a longitudinal cohort of ten rural infants in Morelos, Mexico, sampled monthly from birth to 18 months to study early-life gut microbial development. machine-written summary
156 samples · 156 runs · MX · Infant / toddler · 2026 · 0.81 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 321 sample values (collection date, country, subject id, timepoint) |
| ✓ Abstract / description | 156 sample values (lifestyle detail) |
| ✓ Full text | 623 sample values (collection date, lifestyle, location locality, location region) · PMC13317942 |
| ✓ Supplementary tables | 504 sample values (age, delivery mode, sex, subject id) |
| – 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 |
longitudinal
15 of 16 people sampled more than once (144 samples; median 11, up to 17 per person) · follow-up median 17 mo (max 17 mo) · median interval between samples 31 d (time from age at collection). Schedule stated by the source: “sampled monthly from birth to 18 months” (time origin: birth).
Each row is one person (10 shown of 15); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 156 | 100% | ||||
| country | 156 | 100% | 156 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 145 | 93% | 19 | 126 | ||
| collection_date | 156 | 100% | 1 | 155 | ||
| detailed_location | 156 | 100% | ||||
| lifestyle | 156 | 100% | 156 | |||
| lifestyle_detail | 156 | 100% | 156 | |||
| location_locality | 156 | 100% | 156 | |||
| location_region | 156 | 100% | 156 | |||
| timepoint_label | 145 | 93% | 145 | |||
| age_at_collection_days | 126 | 81% | 126 | |||
| delivery_mode | 126 | 81% | 126 | |||
| sex | 126 | 81% | 126 |
- Impact of maternal, infant, and household factors on early-life gut microbiome development in a rural setting. PMID 42127418 PMC13317942 curated
Archive description
Shotgun metagenomics data from a unique longitudinal study of ten rural infants in Morelos, Mexico, sampled monthly from birth to 18 months, profiling bacterial gut microbiomes to explore early-life microbial development in a rural environment.
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.title · “Human Gut Metagenome”
- body site study.description · “months, profiling bacterial gut microbiomes to explore”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “of ten rural infants in Morelos, Mexico,”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SRR33958015 | age_at_collection_days | 122 | R2 | 0.75 | paper.supp.table | Infant age (month)=4 |
| SRR33958170 | collection_date | 2016 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2016 |
| SRR33958015 | collection_date | 2015-03/2016-05 | R3 | 0.70 | paper.fulltext.methods | born between March 2015 and May 2016 |
| SRR33958015 | country | MX | R1 | 0.90 | sample.attr.geo_loc_name | Mexico |
| SRR33958015 | delivery_mode | vaginal | R2 | 0.75 | paper.supp.table | Mode of birth=Vaginal |
| SRR33958015 | lifestyle | rural_non_industrialized | R3 | 0.70 | paper.fulltext.methods | predominantly rural character |
| SRR33958015 | lifestyle_detail | rural community in Morelos, Mexico | R4 | 0.50 | paper.abstract | rural community in Morelos, Mexico |
| SRR33958015 | location_locality | Xoxocotla | R3 | 0.70 | paper.fulltext.methods | rural district in Xoxocotla |
| SRR33958015 | location_region | Morelos | R3 | 0.70 | paper.fulltext.methods | in the state of Morelos, central Mexico |
| SRR33958015 | sex | female | R2 | 0.75 | paper.supp.table | Sex=Female |
| SRR33958019 | subject_id | 07 | R1 | 0.70 | sample.name_rule:library_names | XC07-16-02 |
| SRR33958015 | subject_id | P09 | R2 | 0.75 | paper.supp.table | Infant ID=P09 |
| SRR33958015 | timepoint_label | 04 | R1 | 0.70 | sample.name_rule:library_names | XC09-04 |
Sequencing
156 runs over 156 samples · mean 0.82 Gbp per run (median 0.81 Gbp, total 128.28 Gbp; 156 runs with a base count) · layout PAIRED 156 · platform ILLUMINA 156 · models NextSeq 500 (156) · 0% of runs with a Sandpiper profile · first public 2026-06-21
Authors (8)
Parizadeh M first · Laforest-Lapointe I · Serrano-Vázquez A · Morán-Silva P · Rojas-Velázquez L · Torres J · Ximénez-García C · Arrieta MC last
Downloads
PRJNA1258733.csv.gz (5.0 KB) · parquet (75.7 KB) — all 156 samples, every field with route and confidence · PRJNA1258733_determinations.csv.gz (11.5 KB) — 1,604 evidence rows