Gut metagenomes of healthy individuals from Ghana
44 stool metagenome samples from healthy individuals in the Asante Akim North district, Ghana, spanning age groups from neonates to adults, sequenced on Illumina HiSeq 2500. machine-written summary
44 samples · 44 runs · GH · Infant / toddler · 2019 · 4.85 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 44 sample values (country) |
| ✓ Abstract / description | 44 sample values (location locality) |
| ○ Full text | read; no usable statement or table · PMC10234599, PMC10902438, PMC11019788 |
| ✓ Supplementary tables | 27 sample values (subject id) |
| ✓ External resources | 131 sample values (age, health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 41 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 | 43 | 98% | ||||
| country | 44 | 100% | 44 | |||
| health_condition | 44 | 100% | 44 | |||
| subject_id | 27 | 61% | 27 | |||
| detailed_location | 44 | 100% | ||||
| health_condition_detail | 44 | 100% | 44 | |||
| location_locality | 44 | 100% | 44 | |||
| age_at_collection_days | 43 | 98% | 43 |
- (no title) curated
- (no title) curated
- Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population. PMID 37116481 PMC10234599 curated
- (no title) curated
- Genomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota. PMID 38426063 PMC10902438 curated
3 more
- Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032 PMC11019788
- (no title)
- (no title)
Archive description
Stool samples of a cohort of individuals from Ghana (Asante Akim North district). Samples were sequenced with Illumina HiSeq 2500 using NexteraXT library preparation.
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 · “Metagenomic sequencing of stool samples from Ghanaian”
- body site study.description · “Stool samples of a”
- 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 |
|---|---|---|---|---|---|---|
| SAMN11265215 | age_at_collection_days | 12418.5 | R2 | 0.75 | external.cmd source | age: 34; age_unit: Year; age_group: Adult |
| SAMN11265215 | country | GH | R1 | 0.90 | biosample_attr | Ghana |
| SAMN11265215 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN11265215 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN11265215 | location_locality | Asante Akim North district | R4 | 0.45 | ena.study_description | Ghana (Asante Akim North district) |
| SAMN11265215 | subject_id | C16-10022-GH_M | R2 | 0.80 | paper.supp.mmc7.xlsx[A!subjectID] | sample=C16-20005-GH; subjectID=C16-10022-GH_M |
Sequencing
44 runs over 44 samples · mean 4.97 Gbp per run (median 4.85 Gbp, total 218.81 Gbp; 44 runs with a base count) · layout PAIRED 44 · platform ILLUMINA 44 · models Illumina HiSeq 2000 (44) · 93% of runs with a Sandpiper profile · first public 2019-03-28
Authors (146)
Tett A first · Huang KD · Asnicar F · Fehlner-Peach H · Pasolli E · Karcher N · Armanini F · Manghi P · Bonham K · Zolfo M · De Filippis F · Magnabosco C · Bonneau R · Lusingu J · Amuasi J · Reinhard K · Rattei T · Boulund F · Engstrand L · Zink A · Collado MC · Littman DR · Eibach D · Ercolini D · Rota-Stabelli O · Huttenhower C · Maixner F · Segata N last · Tomofuji Y first · Kishikawa T · Maeda Y · Ogawa K · Otake-Kasamoto Y · Kawabata S · Nii T · Okuno T · Oguro-Igashira E · Kinoshita M · Takagaki M · Oyama N · Todo K · Yamamoto K · Sonehara K · Yagita M · Hosokawa A · Motooka D · Matsumoto Y · Matsuoka H · Yoshimura M · Ohshima S · Shinzaki S · Nakamura S · Iijima H · Inohara H · Kishima H · Takehara T · Mochizuki H · Takeda K · Kumanogoh A · Okada Y last · Manara S first · Selma-Royo M · Blanco-Miguez A · Cumbo F · Golzato D · Pinto F · Valles-Colomer M · Amoroso L · Corrias MV · Ponzoni M · Raffaetà R · Cabrera-Rubio R · Olcina M · Zhu J first · Xie H · Yang Z · Chen J · Yin J · Tian P · Wang H · Zhao J · Zhang H · Lu W · Chen W last · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last · De Biase R · Bocchio F · De Conto F · Nouvenne A · Ticinesi A · Meschi T · Cecchi R · Lin NY first · Fukuoka S · Koyama S · Tourlousse DM · Shigeno Y · Yamano H · Murotomi K · Tamaki H · Irie T · Sugiyama E · Kumagai S · Itahashi K · Tanegashima T · Fujimaki K · Ito S · Shindo M · Tsuji T · Wake H · Watanabe K · Enokida T · Tahara M · Yamashita R · Fujisawa T · Nomura M · Kawazoe A · Goto K · Doi T · Shitara K · Mano H · Sekiguchi Y · Benno Y · Nishikawa H last · Sola L first · Candeliere F · Busi E · Raimondi S · Amaretti A · Rossi M last
Downloads
PRJNA529124.csv.gz (2.4 KB) · parquet (71.8 KB) — all 44 samples, every field with route and confidence · PRJNA529124_determinations.csv.gz (3.5 KB) — 246 evidence rows