PRJNA1225421 SRP573961
ECoMiD longitudinal gut microbiome cohort in Ecuador
Microbiome data from the ECoMiD cohort study in Ecuador
210 samples from the ECoMiD longitudinal cohort study in Ecuador. No health conditions, interventions, or demographic details are specified in the available sources. machine-written summary
210 samples · 210 runs · EC · Infant / toddler · 2025 · 2.76 Gbp / sample
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Sources
✓ Sequence archive 416 ○ Abstract / description✓ Full text 420 ✓ Supplementary tables 1,336 – External resources– User contribution– Human verified
Checked this project's papers and archive records yourself? Mark it human-verified .
what each source gave ✓ Sequence archive416 sample values (country, subject id) ○ Abstract / descriptionread; no usable statement ✓ Full text420 sample values (collection date, health condition) · PMC12764814 ✓ Supplementary tables1,336 sample values (age, family id, family role, sex, shared setting id, shared setting type, timepoint) – External resourcesnot covered by the external resources we ingest – User contributionnothing uploaded yet – Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
Age
infant 100
unknown 57
neonate 53
Condition
healthy_control 210
Sequencing depth per sample ·
all projects, 0–0.03 Gbp: 25,080 samples (4 %) all projects, 0.03–0.1 Gbp: 17,066 samples (3 %) all projects, 0.1–0.3 Gbp: 29,179 samples (5 %) all projects, 0.3–1 Gbp: 47,044 samples (8 %) this project, 0.3–1 Gbp: 2 samples all projects, 1–3 Gbp: 124,983 samples (22 %) this project, 1–3 Gbp: 131 samples all projects, 3–10 Gbp: 253,728 samples (44 %) this project, 3–10 Gbp: 73 samples all projects, 10–30 Gbp: 72,533 samples (13 %) this project, 10–30 Gbp: 4 samples all projects, 30–100 Gbp: 3,024 samples (1 %) all projects, 100–300 Gbp: 106 samples (0 %) all projects, ≥ 300 Gbp: 9 samples (0 %) project median 2.76 Gbp per sample 0 1 30 Gbp
Sampling design and relatedness
longitudinal households mother–infant
32 of 137 people sampled more than once (101 samples; median 4, up to 4 per person) · follow-up median 18 mo (max 18 mo) · median interval between samples 3 mo (time from age at collection) .
Schedule stated by the source: “Children sampled at 1 week, 3 months, 6 months, and 18 months; mothers sampled once at week 37 of pregnancy.” (time origin: birth).
EB1001 EB1001 (child): day 0 EB1001 (child): day 83 EB1001 (child): day 173 EB1001 (child): day 533 EB1002 EB1002 (child): day 0 EB1002 (child): day 83 EB1002 (child): day 173 EB1002 (child): day 533 EB1003 EB1003 (child): day 0 EB1003 (child): day 83 EB1003 (child): day 173 EB1003 (child): day 533 EB1004 EB1004 (child): day 0 EB1004 (child): day 83 EB1004 (child): day 173 EB1004 (child): day 533 EB1007 EB1007 (child): day 0 EB1007 (child): day 533 EB1101 EB1101 (child): day 0 EB1101 (child): day 83 EB1101 (child): day 173 EB1101 (child): day 533 EB1102 EB1102 (child): day 0 EB1102 (child): day 83 EB1102 (child): day 173 EB1102 (child): day 533 EB1103 EB1103 (child): day 0 EB1103 (child): day 83 EB1103 (child): day 173 EB1103 (child): day 533 EB1104 EB1104 (child): day 0 EB1104 (child): day 83 EB1104 (child): day 173 EB1104 (child): day 533 EB1106 EB1106 (child): day 0 EB1106 (child): day 83 EB1106 (child): day 173 EB1106 (child): day 533 EB1107 EB1107 (child): day 0 EB1107 (child): day 533 BB2002 BB2002 (child): day 0 BB2002 (child): day 83 BB2002 (child): day 173 BB2002 (child): day 533 BB2003 BB2003 (child): day 0 BB2003 (child): day 83 BB2003 (child): day 173 BB2003 (child): day 533 BB2009 BB2009 (child): day 0 BB2009 (child): day 533 BB2101 BB2101 (child): day 0 BB2101 (child): day 533 BB2202 BB2202 (child): day 0 BB2202 (child): day 90 BB2204 BB2204 (child): day 0 BB2204 (child): day 83 BB2204 (child): day 173 BB2204 (child): day 533 BB2205 BB2205 (child): day 0 BB2205 (child): day 533 BB2206 BB2206 (child): day 0 BB2206 (child): day 533 BB2301 BB2301 (child): day 0 BB2301 (child): day 83 BB2301 (child): day 173 BB2301 (child): day 533 BB2302 BB2302 (child): day 0 BB2302 (child): day 83 BB2302 (child): day 173 BB2302 (child): day 533 BB2306 BB2306 (child): day 0 BB2306 (child): day 533 MB3001 MB3001 (child): day 0 MB3001 (child): day 83 MB3001 (child): day 173 MB3001 (child): day 533 MB3004 MB3004 (child): day 0 MB3004 (child): day 533 MB3006 MB3006 (child): day 0 MB3006 (child): day 533 MB3101 MB3101 (child): day 0 MB3101 (child): day 83 MB3101 (child): day 173 MB3101 (child): day 533 MB3102 MB3102 (child): day 0 MB3102 (child): day 533 MB3201 MB3201 (child): day 0 MB3201 (child): day 83 MB3201 (child): day 173 MB3201 (child): day 533 TB6001 TB6001 (child): day 0 TB6001 (child): day 533 TB6006 TB6006 (child): day 0 TB6006 (child): day 533 ZB7001 ZB7001 (child): day 0 ZB7001 (child): day 83 ZB7001 (child): day 173 ZB7001 (child): day 533 ZB7002 ZB7002 (child): day 0 ZB7002 (child): day 83 ZB7002 (child): day 173 0 d 4 mo 9 mo 13 mo 18 mo
Each row is one person (32 shown); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother , father , child , twin ).
84 households: 53 mother–child pairs (mother at ~37 wk pregnancy, child 1 wk–18 mo) and 31 child-only households · 53 families with 106 sampled people (53 with a parent and a child) · 53 shared settings.
mother M child C 53 × mother + child
family 1002 EB1002 — child · 4 samples C EB1002 EM1002 — mother · 1 sample M EM1002 family 1003 EB1003 — child · 4 samples C EB1003 EM1003 — mother · 1 sample M EM1003 family 1004 EB1004 — child · 4 samples C EB1004 EM1004 — mother · 1 sample M EM1004 family 1005 EB1005 — child · 1 sample C EB1005 EM1005 — mother · 1 sample M EM1005 family 1006 EB1006 — child · 1 sample C EB1006 EM1006 — mother · 1 sample M EM1006 family 1007 EB1007 — child · 2 samples C EB1007 EM1007 — mother · 1 sample M EM1007 family 1011 EB1011 — child · 1 sample C EB1011 EM1011 — mother · 1 sample M EM1011 family 1012 EB1012 — child · 1 sample C EB1012 EM1012 — mother · 1 sample M EM1012 family 1101 EB1101 — child · 4 samples C EB1101 EM1101 — mother · 1 sample M EM1101 family 1102 EB1102 — child · 4 samples C EB1102 EM1102 — mother · 1 sample M EM1102 family 1103 EB1103 — child · 4 samples C EB1103 EM1103 — mother · 1 sample M EM1103 family 1104 EB1104 — child · 4 samples C EB1104 EM1104 — mother · 1 sample M EM1104 family 1106 EB1106 — child · 4 samples C EB1106 EM1106 — mother · 1 sample M EM1106 family 1107 EB1107 — child · 2 samples C EB1107 EM1107 — mother · 1 sample M EM1107 family 2001 BB2001 — child · 1 sample C BB2001 BM2001 — mother · 1 sample M BM2001 family 2002 BB2002 — child · 4 samples C BB2002 BM2002 — mother · 1 sample M BM2002 family 2003 BB2003 — child · 4 samples C BB2003 BM2003 — mother · 1 sample M BM2003 family 2004 BB2004 — child · 1 sample C BB2004 BM2004 — mother · 1 sample M BM2004 family 2008 BB2008 — child · 1 sample C BB2008 BM2008 — mother · 1 sample M BM2008 family 2009 BB2009 — child · 2 samples C BB2009 BM2009 — mother · 1 sample M BM2009 family 2101 BB2101 — child · 2 samples C BB2101 BM2101 — mother · 1 sample M BM2101 family 2102 BB2102 — child · 1 sample C BB2102 BM2102 — mother · 1 sample M BM2102 family 2103 BB2103 — child · 1 sample C BB2103 BM2103 — mother · 1 sample M BM2103 family 2201 BB2201 — child · 1 sample C BB2201 BM2201 — mother · 1 sample M BM2201 household 1002 · 2 people household 1002 EB1002 — member · 4 samples EB1002 EM1002 — member · 1 sample EM1002 household 2206 · 2 people household 2206 BB2206 — member · 2 samples BB2206 BM2206 — member · 1 sample BM2206 household 2302 · 2 people household 2302 BB2302 — member · 4 samples BB2302 BM2302 — member · 1 sample BM2302 household 2304 · 2 people household 2304 BB2304 — member · 1 sample BB2304 BM2304 — member · 1 sample BM2304 household 2305 · 2 people household 2305 BB2305 — member · 1 sample BB2305 BM2305 — member · 1 sample BM2305 household 2306 · 2 people household 2306 BB2306 — member · 2 samples BB2306 BM2306 — member · 1 sample BM2306 household 2308 · 2 people household 2308 BB2308 — member · 1 sample BB2308 BM2308 — member · 1 sample BM2308 household 2311 · 2 people household 2311 BB2311 — member · 1 sample BB2311 BM2311 — member · 1 sample BM2311
Families (25 of 53) How longitudinal and relatedness information is derived
Community composition
Bifidobacterium 28.5%Prevotella 14.2%Bacteroides 4.5%Faecalibacterium 4.1%Streptococcus 3.7%Escherichia 3.6%Klebsiella 2.2%Roseburia 1.8%Succinivibrio 1.3%Phocaeicola 1.3%Mediterraneibacter 1.2%Blautia_A 1.1%
Genera, mean relative abundance over 209 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Papers (1)
Environmental exposures associated with the gut microbiome and resistome of pregnant women and children in Northwest Ecuador. 2025 PMID 41390665 PMC12764814 own_data
Details
Archive description Microbiome sequencing data from the ECoMiD cohort study.
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 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
SAMN47621659 age_at_collection_days 540.0 R2 0.75 paper.supp.41467_2025_66567_MOESM3_ESM.xlsx[Analysis data!Age] 2002 18m SAMN47621659 collection_date 2019-05/2024-12 R3 0.70 paper.fulltext.methods ECoMiD study commenced enrollment in May 2019 SAMN47621659 country EC R1 0.90 biosample_attr Ecuador SAMN47621659 family_id 2002 R2 0.85 paper.supp.41467_2025_66567_MOESM3_ESM.xlsx[No. of reads per metagenome!Household ID] 2002 | 18m | BB200218mHN1e3_S11_R1_001.fastq.gz SAMN47621659 family_role child R2 0.60 paper.supp.41467_2025_66567_MOESM3_ESM.xlsx[No. of reads per metagenome!Age] 2002 | 18m | BB200218mHN1e3_S11_R1_001.fastq.gz SAMN47621659 health_condition healthy_control R3 0.70 paper.fulltext.methods investigate the gut microbiome’s interactions with enteric infections and environmental conditions SAMN47621659 sex female R2 0.80 paper.supp.41467_2025_66567_MOESM3_ESM.xlsx[Analysis data!Children sex] 2002 18m Female SAMN47621659 shared_setting_id 2002 R2 0.85 paper.supp.41467_2025_66567_MOESM3_ESM.xlsx[No. of reads per metagenome!Household ID] Household ID 2002 | BB200218mHN1e3_S11_R1_001.fastq.gz SAMN47621659 shared_setting_type household R2 0.85 paper.supp.41467_2025_66567_MOESM3_ESM.xlsx[No. of reads per metagenome!Household ID] Household ID 2002 | BB200218mHN1e3_S11_R1_001.fastq.gz SAMN47621659 subject_id BB2002 R1 0.70 sample.name_rule:library_name BB200218m SAMN47621659 timepoint_label month 18 R2 0.80 paper.supp.41467_2025_66567_MOESM3_ESM.xlsx[Analysis data!Age] 2002 18m
Sequencing 210 runs over 210 samples · mean 3.55 Gbp per run (median 2.76 Gbp, total 745.00 Gbp; 210 runs with a base count) · layout PAIRED 210 · platform ILLUMINA 210 · models Illumina NovaSeq 6000 (150), NextSeq 2000 (60) · 100% of runs with a Sandpiper profile · first public 2025-11-23
Authors (0) No author record.
Downloads PRJNA1225421.csv.gz (8.4 KB) · parquet (81.7 KB) — all 210 samples, every field with route and confidence · PRJNA1225421_determinations.csv.gz (21.0 KB) — 2,172 evidence rows
Samples (210 · every field this project has values for · hover a cell for its source)
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