Gut metagenomes of South African infants, Khula cohort
65 gut metagenome samples from infants in Cape Town, South Africa, collected longitudinally as part of the Khula cohort (Wellcome LEAP 1kD) to study the gut microbiome and developmental outcomes in the first 1000 days of life. machine-written summary
429 samples · 429 runs · ZA · Infant / toddler · 2025 · 2.44 Gbp / sample · cohort Early life microbial succession in the gut follows
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,696 sample values (age, collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 1,716 sample values (antibiotic exposure, location locality, location region, location site) · PMC11733223, PMC12345167, PMC13269231 |
| ✓ Supplementary tables | 436 sample values (age, 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
114 of 297 people sampled more than once (246 samples; median 2, up to 3 per person) · follow-up median 7 mo (max 13 mo) · median interval between samples 5 mo (time from age at collection). Schedule stated by the source: “Up to three stool visits per infant labeled 3mo, 6mo, 12mo timepoints (samples per subject median 1, max 3).” (time origin: birth); stated follow-up 18 mo.
Each row is one person (36 shown of 114); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 60 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 | 426 | 99% | ||||
| country | 429 | 100% | 429 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 429 | 100% | 357 | 72 | ||
| antibiotic_exposure | 429 | 100% | 429 | |||
| collection_date | 429 | 100% | 429 | |||
| detailed_location | 429 | 100% | ||||
| location_locality | 429 | 100% | 429 | |||
| location_region | 429 | 100% | 429 | |||
| location_site | 429 | 100% | 429 | |||
| age_at_collection_days | 426 | 99% | 62 | 364 | ||
| timepoint_label | 419 | 98% | 419 |
- Early life microbial succession in the gut follows common patterns in humans across the globe. PMID 39809768 PMC11733223 curated
- Codevelopment of gut microbial metabolism and visual neural circuitry over human infancy. PMID 40586263 PMC12345167 curated
- Microbiome-behavior coupling shapes infant adaptation to early maternal unpredictability. PMID 42311381 PMC13269231 curated
- Early life microbial succession in the gut follows common patterns in humans across the globe. 2025 PMID 39809768 PMC11733223 own_data
- Codevelopment of gut microbial metabolism and visual neural circuitry over human infancy. 2025 PMID 40586263 PMC12345167 own_data
1 more
- Microbiome-behavior coupling shapes infant adaptation to early maternal unpredictability. 2026 PMID 42311381 PMC13269231
Archive description
Infant gut metagenomes collected by the Khula cohort (South Africa) as part of the Wellcome LEAP 1kD grant to investigate relationships between the gut microbiome and developmental outcomes in the first 1000 days of life
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and neonate 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 metagenomes of South”
- body site study.description · “Infant gut metagenomes collected by”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “of South African infants”
- life stage study.description · “the first 1000 days of life”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN43292793 | age_at_collection_days | 91 | R1 | 0.85 | sample.title | 3mo |
| SAMN43038866 | age_at_collection_days | 111 | R2 | 0.75 | paper.supp.table | ageMonths=3.64 |
| SAMN43038866 | antibiotic_exposure | no | R3 | 0.70 | paper.body.methods_results | Stool samples were not collected if the participant had taken antibiotics within the 2 weeks prior to sampling |
| SAMN43038866 | collection_date | 2022-06-07 | R1 | 0.85 | biosample.attribute:collection_date | 2022-06-07 |
| SAMN43038866 | country | ZA | R1 | 0.90 | biosample_attr | South Africa: Cape Town |
| SAMN43038868 | country | ZA | R1 | 0.90 | sample.attr.geo_loc_name | South Africa: Cape Town |
| SAMN43038866 | location_locality | Gugulethu, Cape Town | R3 | 0.70 | paper.body.methods_results | longitudinal community sample of 194 infants from Gugulethu in Cape Town, South Africa |
| SAMN43038866 | location_region | Western Cape | R3 | 0.70 | paper.fulltext.methods | Gugulethu, an informal settlement in Cape Town, South Africa |
| SAMN43038866 | location_site | local community clinics, Gugulethu | R3 | 0.70 | paper.fulltext.methods | recruited from local community clinics in Gugulethu |
| SAMN43292786 | subject_id | 2mod8j52e9i80 | R1 | 0.70 | sample.name_rule:TITLE | Infant stool sample: subject 2mod8j52e9i80, timepoint 3mo |
| SAMN43038866 | subject_id | khula-191-69114318 | R2 | 0.75 | paper.supp.table | subject_id=khula-191-69114318 |
| SAMN43292786 | timepoint_label | 3mo | R1 | 0.70 | sample.name_rule:TITLE | Infant stool sample: subject 2mod8j52e9i80, timepoint 3mo |
| SAMN43292793 | timepoint_label | 3mo | R1 | 0.70 | sample.title | Infant stool sample: subject tx81m5jbp2u7, timepoint 3mo |
Sequencing
429 runs over 429 samples · mean 2.72 Gbp per run (median 2.44 Gbp, total 1,168.51 Gbp; 429 runs with a base count) · layout PAIRED 429 · platform ILLUMINA 429 · models NextSeq 2000 (429) · 89% of runs with a Sandpiper profile · first public 2025-01-04
Authors (47)
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 · Margolis ET · Sobrino AC · Zieff MR · Miles M · Herr D · Davel L · Bosco C · Khula South African Data Collection Team · Pini N · Alexander DC · Jones DK · Williams SCR · Amso D · Gladstone M · Fifer WP · Gabard-Durnam LJ · Forest TT · Khula South Africa Data Collection Team · Espinoza-Heredia C · D'Amato CL · Ren J · Mbale E
Downloads
PRJNA1128723.csv.gz (19.5 KB) · parquet (97.6 KB) — all 429 samples, every field with route and confidence · PRJNA1128723_determinations.csv.gz (44.7 KB) — 3,848 evidence rows