Gut metagenomes of infants and adults in Gimbichu, Ethiopia
50 stool samples from a longitudinal cohort of infants and adults in Gimbichu, Oromia Region, Ethiopia, mostly healthy with one malnutrition case, sequenced on Illumina HiSeq 2500. machine-written summary
50 samples · 52 runs · ET · Infant / toddler · 2018 · 5.17 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 143 sample values (country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 100 sample values (location locality, location region) · PMC10234599, PMC10769871, PMC10902438, PMC11019788, PMC12963580, PMC13083862, PMC6349461 |
| ✓ Supplementary tables | 50 sample values (age, delivery mode, health condition, sex, timepoint) |
| ✓ External resources | 140 sample values (age, health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
age: supplementary table and curatedMetagenomicData disagree for 17 samples (e.g. 274 vs 0.0) — withheld; health condition: supplementary table and curatedMetagenomicData disagree for 1 sample (e.g. malnutrition vs healthy_control) — withheld; sex: supplementary table and curatedMetagenomicData disagree for 3 samples (e.g. male vs female) — withheld.
The sources disagree on 21 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 (21)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN11252254 | age | 274 (supplementary table) | 0.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252256 | age | 61 (supplementary table) | 0.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252257 | age | 182 (supplementary table) | 0.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252261 | age | 182 (supplementary table) | 0.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252262 | age | 61 (supplementary table) | 0.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252263 | age | 213 (supplementary table) | 0.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252265 | age | 243 (supplementary table) | 0.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252267 | age | 548 (supplementary table) | 365.28 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252269 | age | 152 (supplementary table) | 0.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252272 | age | 213 (supplementary table) | 0.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252274 | age | 243 (supplementary table) | 0.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252275 | age | 304 (supplementary table) | 0.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252281 | age | 639 (supplementary table) | 365.28 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252282 | age | 973 (supplementary table) | 730.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252287 | age | 578 (supplementary table) | 365.28 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252291 | age | 517 (supplementary table) | 365.28 (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252297 | age | 91 (supplementary table) | 0.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN10407349 | health condition | malnutrition (supplementary table) | healthy_control (curatedMetagenomicData) | withheld: neither value published |
| SAMN10407346 | sex | male (supplementary table) | female (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252253 | sex | male (supplementary table) | female (curatedMetagenomicData) | withheld: neither value published |
| SAMN11252255 | sex | female (supplementary table) | male (curatedMetagenomicData) | withheld: neither value published |
Genera, mean relative abundance over 45 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 | 49 | 98% | ||||
| country | 50 | 100% | 50 | |||
| health_condition | 49 | 98% | 49 | |||
| subject_id | 50 | 100% | 50 | |||
| detailed_location | 50 | 100% | ||||
| health_condition_detail | 50 | 100% | 50 | |||
| location_locality | 50 | 100% | 50 | |||
| location_region | 50 | 100% | 50 | |||
| timepoint_label | 50 | 100% | 43 | 7 | ||
| sex | 45 | 90% | 45 | |||
| age_at_collection_days | 32 | 64% | 32 | |||
| delivery_mode | 7 | 14% | 7 |
- Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. PMID 30661755 PMC6349461 curated
- (no title) curated
- (no title) curated
- (no title) curated
- (no title) curated
15 more
- (no title)
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- Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population. PMID 37116481 PMC10234599
- (no title)
- (no title)
- BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. PMID 38172624 PMC10769871
- Genomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota. PMID 38426063 PMC10902438
- Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032 PMC11019788
- (no title)
- (no title)
- (no title)
- Gut microbial signatures expose the westernized lifestyle of urban Ethiopian children. PMID 41620544 PMC12963580
- Distinct infant resistome trajectories shaped by country income and geography revealed through global metagenomics reanalysis. PMID 41986657 PMC13083862
- (no title)
Archive description
Stool samples from a cohort of individuals in Gimbichu (Ethiopia, Oromia Region). 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 Ethiopian”
- body site study.description · “Stool samples from 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 |
|---|---|---|---|---|---|---|
| SAMN10407345 | age_at_collection_days | 9131.25 | R2 | 0.75 | external.cmd source | age: 25; age_unit: Year; age_group: Adult |
| SAMN11252255 | age_at_collection_days | 365 | R2 | 0.75 | paper.supp.table | Age (day)=365 |
| SAMN10407345 | country | ET | R1 | 0.90 | biosample_attr | Ethiopia |
| SAMN10407346 | delivery_mode | vaginal | R2 | 0.75 | paper.supp.table | Delivery_mode_factor=SPO |
| SAMN10407345 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN10407346 | health_condition | healthy_control | R2 | 0.80 | paper.supp.table | Wasting_factor=Normal |
| SAMN10407345 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN10407345 | location_locality | Gimbichu | R3 | 0.70 | paper.fulltext.methods | cohort in Gimbichu (Ethiopia, Oromia Region) |
| SAMN10407345 | location_region | Oromia Region | R3 | 0.70 | paper.fulltext.methods | cohort in Gimbichu (Ethiopia, Oromia Region) |
| SAMN10407345 | sex | female | R2 | 0.75 | paper.supp.table | Sex=F |
| SAMN11252257 | sex | male | R2 | 0.75 | external.cmd source | sex: Male |
| SAMN10407345 | subject_id | 1 | R1 | 0.85 | biosample_attr | 1 |
| SAMN10407345 | timepoint_label | D24 | R1 | 0.70 | run.library_name | CM_D24_M0_18 |
| SAMN11252254 | timepoint_label | 6 months - 1 yr | R2 | 0.75 | paper.supp.table | AGE GROUP G12=6 months - 1 yr |
Sequencing
52 runs over 50 samples · mean 6.25 Gbp per run (median 5.17 Gbp, total 325.17 Gbp; 52 runs with a base count) · layout PAIRED 52 · platform ILLUMINA 52 · models Illumina HiSeq 2500 (52) · 90% of runs with a Sandpiper profile · first public 2018-11-10 – 2022-04-04
Authors (225)
Pasolli E first · Asnicar F · Manara S · Zolfo M · Karcher N · Armanini F · Beghini F · Manghi P · Tett A · Ghensi P · Collado MC · Rice BL · DuLong C · Morgan XC · Golden CD · Quince C · Huttenhower C · Segata N last · Huang KD · Fehlner-Peach H · Bonham K · De Filippis F · Magnabosco C · Bonneau R · Lusingu J · Amuasi J · Reinhard K · Rattei T · Boulund F · Engstrand L · Zink A · Littman DR · Eibach D · Ercolini D · Rota-Stabelli O · Maixner F · Nazeen S first · Yu YW · Berger B last · Thomas AM · Mengoni C · Zhu Q · Bolzan M · Cumbo F · May U · Sanders JG · Kopylova E · Knight R · Mirarab S · Tisza MJ first · Buck CB last · Pan S first · Zhu C · Zhao XM · Coelho LP last · Lai S first · Sun C · Chen WH · Cohen Y first · Borenstein E 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 · Selma-Royo M · Blanco-Miguez A · 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 · Candeliere F first · Musmeci E · Amaretti A · Sola L · Raimondi S · Rossi M last · Hall B first · Levy S · Dufault-Thompson K · Arp G · Zhong A · Ndjite GM · Weiss A · Braccia D · Jenkins C · Grant MR · Abeysinghe S · Yang Y · Jermain MD · Wu CH · Ma B · Jiang X 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 · Herazo-Álvarez J first · Mora M · Cuadros-Orellana S · Vilches-Ponce K · Hernández-García R last · 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 · Jacoby C first · Scorza K · Ecker L · Nol Bernardino P · Little AS · McMillin M · Ramaswamy R · Sundararajan A · Sidebottom AM · Lin H · Light SH last · Kirsche L first · Leary P · Blaser MJ · Scharl M · Negussie A · Müller A last · Luchen CC first · Piedade GJ · Chibuye M · Simuyandi M · Chisenga CC · Chilengi R · Bosomprah S · Schultsz C · Mende DR · Harris VC last · Busi E
Downloads
PRJNA504891.csv.gz (2.8 KB) · parquet (72.7 KB) — all 50 samples, every field with route and confidence · PRJNA504891_determinations.csv.gz (5.2 KB) — 433 evidence rows