Gut metagenomes of rural Cameroonian adults by subsistence mode
Cross-sectional study of 57 fecal metagenome samples from healthy adult and elderly individuals in Cameroon (hunter-gatherers, farmers, and fishers), examining gut eukaryotic-prokaryotic interactions and protozoan symbiont prevalence across subsistence modes. machine-written summary
57 samples · 57 runs · CM · Adult · 2019 · 5.09 Gbp / sample · cohort A plasmid network from the gut microbiome of semi-
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 495 sample values (age, bmi, collection date, country, location locality, sex, shared setting id, shared setting type) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11685674, PMC12089645, PMC6364966 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 114 sample values (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 |
country: sequence archive and microbeatlas disagree for 17 samples (e.g. CM vs GQ) — withheld.
The sources disagree on 17 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 (17)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA4719781 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
| SAMEA4719782 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
| SAMEA4719783 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
| SAMEA4719784 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
| SAMEA4719785 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
| SAMEA4719786 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
| SAMEA4719787 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
| SAMEA4719788 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
| SAMEA4719789 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
| SAMEA4719790 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
| SAMEA4719791 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
| SAMEA4719792 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
| SAMEA4719793 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
| SAMEA4719794 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
| SAMEA4719795 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
| SAMEA4719796 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
| SAMEA4719797 | country | CM (sequence archive) | GQ (microbeatlas) | withheld: neither value published |
communitytribe
58 adults from seven villages in Southwest Cameroon (2–19 per village); Bantu and Bagyeli (Pygmy) ethnic groups7 shared settings.
member · 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: 7 shared settings. 57 people in the project overall.
Genera, mean relative abundance over 51 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 | 57 | 100% | ||||
| country | 40 | 70% | 40 | |||
| health_condition | 57 | 100% | 57 | |||
| subject_id | 57 | 100% | 57 | |||
| age_at_collection_days | 57 | 100% | 57 | |||
| collection_date | 57 | 100% | 57 | |||
| detailed_location | 57 | 100% | ||||
| health_condition_detail | 57 | 100% | 57 | |||
| location_locality | 57 | 100% | 57 | |||
| sex | 57 | 100% | 57 | |||
| shared_setting_id | 57 | 100% | 57 | |||
| shared_setting_type | 57 | 100% | 57 | |||
| bmi | 56 | 98% | 56 |
- Use of shotgun metagenomics for the identification of protozoa in the gut microbiota of healthy individuals from worldwide populations with various industrialization levels. 2019 PMID 30726303 PMC6364966 own_data
- Codiversification of gut microbiota with humans. 2022 PMID 36108023 PMC10777373 unsure
- Toward an improved definition of a healthy microbiome for healthy aging. 2022 PMID 37118093 PMC10154212 unsure
- Statistical modeling of gut microbiota for personalized health status monitoring. 2023 PMID 37596617 PMC10436630 unsure
- DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction. 2024 PMID 39738309 PMC11685674 unsure
3 more
- PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2. 2025 PMID 40293718 PMC12089645
- Microbiota-driven antitumour immunity mediated by dendritic cell migration. 2025 PMID 40659786 PMC12390848
- Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery. 2026 PMID 41980943 PMC13079874
Archive description
In order to examine how the subsistence mode affects the human gut microbiome, we analyzed faecal metagenomes of 58 healthy adults from Cameroon (hunter-gatherers, farmers and fishers).Our aim is to describe taxonomical and functional diversity, as well as to unveil the interactions between the eukaryotic and prokaryotic componenet of the gut microbiome.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Gut metagenomes of rural”
- body site study.description · “affects the human gut microbiome, we analyzed”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage study.description · “of 58 healthy adults from Cameroon (hunter-gatherers,”
- life stage sample.attr.host_age · “68 (n=8/57)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA4719760 | age_at_collection_days | 22280.2 | R1 | 0.70 | sample.attr.host_age | 61 |
| SAMEA4719760 | bmi | 19.06 | R1 | 0.90 | sample.attr.host_body_mass_index | 19.06 |
| SAMEA4719760 | collection_date | 2013-10 | R1 | 0.90 | biosample.attribute:collection_date | 2013-10 |
| SAMEA4719760 | country | CM | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Cameroon |
| SAMEA4719760 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA4719760 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA4719760 | location_locality | Bandevouri | R1 | 0.85 | biosample.attribute:geographic_location_region_and_locality | Cameroon: Bandevouri |
| SAMEA4719760 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMEA4719760 | shared_setting_id | Bandevouri | R1 | 0.85 | biosample.attribute:geographic_location_region_and_locality | Cameroon: Bandevouri |
| SAMEA4719760 | shared_setting_type | village_or_community | R1 | 0.85 | biosample.attribute:geographic_location_region_and_locality | Cameroon: Bandevouri |
| SAMEA4719760 | subject_id | BAB01 | R1 | 0.85 | sample.attr.host_subject_id | BAB01 |
Sequencing
57 runs over 57 samples · mean 5.18 Gbp per run (median 5.09 Gbp, total 295.36 Gbp; 57 runs with a base count) · layout PAIRED 57 · platform ILLUMINA 57 · models Illumina HiSeq 2000 (57) · 89% of runs with a Sandpiper profile · first public 2019-01-30
Authors (81)
Lokmer A first · Cian A · Froment A · Gantois N · Viscogliosi E · Chabé M · Ségurel L last · Suzuki TA first · Fitzstevens JL · Schmidt VT · Enav H · Huus KE · Mbong Ngwese M · Grießhammer A · Pfleiderer A · Adegbite BR · Zinsou JF · Esen M · Velavan TP · Adegnika AA · Song LH · Spector TD · Muehlbauer AL · Marchi N · Kang H · Maier L · Blekhman R · Ko G · Youngblut ND · Kremsner P · Ley RE last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Ormaasen I first · Rudi K · Diep DB · Snipen L last · De Biase R · Bocchio F · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · van Sinderen D · Tawfiq R first · Niu K · Hoehndorf R · Kulmanov M last · Nooij S first · Plomp N · Sanders IMJG · Schout L · van der Meulen AE · Terveer EM · Norman JM · Karcher N · Larralde MF · Vossen RHAM · Kloet SL · Faber KN · Harmsen HJM · Zeller GF · Kuijper EJ · Smits WK · Ducarmon QR last · Wright RJ first · Langille MGI last · Kim J first · Kim N · Cha JH · Ma J · Lee I last
Downloads
PRJEB27005.csv.gz (3.1 KB) · parquet (73.6 KB) — all 57 samples, every field with route and confidence · PRJEB27005_determinations.csv.gz (6.3 KB) — 609 evidence rows