Longitudinal infant gut microbiome development in Kazakhstan
183 samples from a longitudinal cohort in Kazakhstan, spanning neonate, infant, and adult age categories, studying gut microbiome development from birth through 12 months of age. machine-written summary
183 samples · 183 runs · KZ · Infant / toddler · 2023 · 6.41 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,439 sample values (age, collection date, country, family id, family role, health condition, health condition detail, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 326 sample values (delivery mode, location locality) · PMC10261102, PMC12024737, PMC12095471 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 |
sex differs between samples of the same subject id (1 subjects, 2 samples) — sex withheld; subject ids shared by samples of both sexes (1 ids, 2 samples) — ids withheld.
The sources disagree on 2 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (4)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN33944789 | sex | female (sequence archive) | subject 74P: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMN33944883 | sex | male (sequence archive) | subject 74P: female in 1 sample, male in 1 sample | withheld: neither value published |
| SAMN33944789 | subject id | 74P | female (sequence archive) | subject id withheld (samples of both sexes share it) |
| SAMN33944883 | subject id | 74P | male (sequence archive) | subject id withheld (samples of both sexes share it) |
longitudinalmother–infant
39 of 60 people sampled more than once (120 samples; median 3, up to 5 per person) · follow-up median 5 mo (max 12 mo) · median interval between samples 3 mo (time from age at collection). Schedule stated by the source: “Infants sampled at 0, 1, 3, 6, and 12 months of age” (time origin: birth); stated follow-up 12 mo.
Each row is one person (36 shown of 39); 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).
66 mother–infant families by library-name number (35 with mother and infant sampled; 40 maternal, 143 infant samples) · 36 families with 72 sampled people (35 with a parent and a child).
motherchild · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 24 of 36 families (one per family structure, then more). 60 people in the project overall.
Families (25 of 36)
Genera, mean relative abundance over 131 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 | 183 | 100% | ||||
| country | 183 | 100% | 183 | |||
| health_condition | 40 | 22% | 40 | |||
| subject_id | 181 | 99% | 181 | |||
| age_at_collection_days | 183 | 100% | 183 | |||
| collection_date | 183 | 100% | 183 | |||
| detailed_location | 183 | 100% | ||||
| family_id | 183 | 100% | 183 | |||
| family_role | 183 | 100% | 183 | |||
| location_locality | 183 | 100% | 183 | |||
| delivery_mode | 143 | 78% | 143 | |||
| sex | 137 | 75% | 137 | |||
| timepoint_label | 126 | 69% | 126 | |||
| health_condition_detail | 40 | 22% | 40 |
- Compositional and functional variability of the gut microbiome in children with infantile colic. PMID 37308527 PMC10261102 curated
- Alterations in Gut Microbiota of Infants Born to Mothers with Obesity. PMID 40299456 PMC12024737 curated
- Parity influences postpartum adaptations in the maternal gut microbiota. PMID 40399402 PMC12095471 curated
Archive description
We are studying the diversity and composition of the gut metagenome isolated from children immediately after birth and up to 12 months of age in Kazakhstan in order to deepen our understanding of the development of the microflora in early life and look for possible factors influencing the change in the developmental trajectory of the microbiome of children.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “composition of the gut metagenome isolated from”
- 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)”
- life stage study.title · “evolution of the infants microbiome”
- life stage study.description · “metagenome isolated from children immediately after birth”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN33944788 | age_at_collection_days | 30 | R1 | 0.90 | biosample_attr | 1 month |
| SAMN33944932 | age_at_collection_days | 12053 | R1 | 0.90 | sample.attr.host_age | 33 |
| SAMN33944788 | collection_date | 2021-09-11 | R1 | 0.85 | biosample.attribute:collection_date | 2021-09-11 |
| SAMN33944788 | country | KZ | R1 | 0.90 | biosample_attr | Kazakhstan |
| SAMN33944788 | delivery_mode | vaginal | R3 | 0.80 | paper.fulltext.abstract | Colic and control groups were vaginally born |
| SAMN33944788 | family_id | 89 | R1 | 0.70 | sample.name_rule:library_name | SBM0089P2 |
| SAMN33944788 | family_role | child | R1 | 0.80 | sample.name_rule:sample_title | infant |
| SAMN33944932 | health_condition | pregnancy_postpartum | R1 | 0.85 | biosample.attribute:title | mother |
| SAMN33944932 | health_condition_detail | mother | R1 | 0.85 | biosample.attribute:title | mother |
| SAMN33944788 | location_locality | Astana | R3 | 0.70 | paper.fulltext.methods | Perinatal center no. 2, Astana city (Kazakhstan) |
| SAMN33944788 | sex | female | R1 | 0.90 | biosample_attr | female |
| SAMN33944788 | subject_id | 89P | R1 | 0.70 | sample.name_rule:library_name | SBM0089P2 |
| SAMN33944799 | subject_id | 86P | R1 | 0.70 | sample.name_rule:library_names | BM086P2 |
| SAMN33944788 | timepoint_label | visit 2 | R1 | 0.70 | sample.name_rule:library_name | SBM0089P2 |
Sequencing
183 runs over 183 samples · mean 6.57 Gbp per run (median 6.41 Gbp, total 1,202.26 Gbp; 183 runs with a base count) · layout PAIRED 183 · platform ILLUMINA 183 · models Illumina NovaSeq 6000 (183) · 92% of runs with a Sandpiper profile · first public 2023-04-01 – 2023-06-05
Authors (14)
Kozhakhmetov S first · Meiirmanova Z · Mukhanbetzhanov N · Jarmukhanov Z · Vinogradova E · Mureyev S · Kozhakhmetova S · Morenko M · Shnaider K · Duisbayeva A · Kushugulova A last · Duisebayeva A · Poddighe D · Khassenbekova D
Downloads
PRJNA949528.csv.gz (7.6 KB) · parquet (80.8 KB) — all 183 samples, every field with route and confidence · PRJNA949528_determinations.csv.gz (16.0 KB) — 1,765 evidence rows