Childhood malnutrition gut microbiome in Shenzhen, China
126 gut metagenome samples from Shenzhen, China, comparing malnutrition (65 samples) and healthy control (61 samples) groups; most samples lack age category data, with 3 labeled infant. machine-written summary
126 samples · 126 runs · CN · Infant / toddler · 2020 · 5.30 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 252 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 126 sample values (subject id) · PMC11019788, PMC11494892, PMC12769767, PMC9512645 |
| ✓ Supplementary tables | 92 sample values (age, feeding mode, sex, timepoint) |
| ✓ External resources | 252 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 110 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 | 29 | 23% | ||||
| country | 126 | 100% | 126 | |||
| health_condition | 126 | 100% | 126 | |||
| subject_id | 126 | 100% | 126 | |||
| collection_date | 126 | 100% | 126 | |||
| health_condition_detail | 126 | 100% | 126 | |||
| age_at_collection_days | 29 | 23% | 29 | |||
| sex | 29 | 23% | 29 | |||
| timepoint_label | 29 | 23% | 29 | |||
| feeding_mode | 5 | 4% | 5 |
- Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645 curated
- Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032 PMC11019788 curated
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892 curated
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767 curated
Archive description
Childhood Malnutrition and the Intestinal Microbiome
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.title · “human gut metagenome Metagenome”
- body site study.description · “Malnutrition and the Intestinal Microbiome”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “Childhood Malnutrition and the”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN12011382 | age_at_collection_days | 2555.0 | R2 | 0.85 | paper.supp.msystems.01294-23-s0004.xlsx[Sheet1!Age (day)] | Sample=SRR9264580; Age (day)=2555 |
| SAMN12011381 | collection_date | 2017 | R1 | 0.85 | biosample.attribute:collection_date | 2017 |
| SAMN12011381 | country | CN | R1 | 0.90 | biosample_attr | China:Shenzhen |
| SAMN12011382 | feeding_mode | exclusive_breast | R2 | 0.75 | paper.supp.table | -=Breast milk |
| SAMN12011381 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN12011381 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN12011382 | sex | female | R2 | 0.75 | paper.supp.table | Sex=F |
| SAMN12011381 | subject_id | SAMN12011381 | R3 | 0.70 | design.one_sample_per_subject:fulltext | a total of 768 gigabases (Gb) of data was obtained for the 126 participants |
| SAMN12011382 | timepoint_label | 5 yr - 10 yr | R2 | 0.75 | paper.supp.table | AGE GROUP G12=5 yr - 10 yr |
Sequencing
126 runs over 126 samples · mean 5.27 Gbp per run (median 5.30 Gbp, total 664.21 Gbp; 126 runs with a base count) · layout PAIRED 126 · platform ILLUMINA 126 · models Illumina HiSeq 2000 (126) · 87% of runs with a Sandpiper profile · first public 2020-06-21
Authors (24)
Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · De Biase R · Bocchio F · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · van Sinderen D · Longhi G · Gennaioli E · Muscò A · Rizzo SM · Vitale SG · Angioni S
Downloads
PRJNA543967.csv.gz (4.6 KB) · parquet (76.9 KB) — all 126 samples, every field with route and confidence · PRJNA543967_determinations.csv.gz (6.7 KB) — 722 evidence rows