Cameroon gut microbiome, GI infection vs healthy
Cross-sectional study of 180 fecal samples from Cameroon, profiled by 16S rRNA V4 amplicon and shotgun metagenomic sequencing, comparing samples with GI infection or diarrhoea (89) to healthy controls (91) across adult, child, adolescent, and elderly age groups. machine-written summary
180 samples · 180 runs · CM · Child · 2020 · 2.11 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 900 sample values (collection date, country, latitude, location region, longitude) |
| ✓ Abstract / description | 5 sample values (health condition) |
| ✓ Full text | 175 sample values (subject id) · PMC12051316, PMC7249393 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 1,050 sample values (age, antibiotic exposure, bmi, 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 |
Genera, mean relative abundance over 157 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 | 180 | 100% | ||||
| country | 180 | 100% | 180 | |||
| health_condition | 180 | 100% | 175 | 5 | ||
| subject_id | 175 | 97% | 175 | |||
| collection_date | 180 | 100% | 180 | |||
| detailed_location | 180 | 100% | ||||
| latitude | 180 | 100% | 180 | |||
| location_region | 180 | 100% | 180 | |||
| longitude | 180 | 100% | 180 | |||
| age_at_collection_days | 175 | 97% | 175 | |||
| antibiotic_exposure | 175 | 97% | 175 | |||
| bmi | 175 | 97% | 175 | |||
| health_condition_detail | 175 | 97% | 175 | |||
| sex | 175 | 97% | 175 |
- Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians. 2020 PMID 32450885 PMC7249393 own_data
- The altitudinal patterns of global human gut microbial diversity. 2025 PMID 40320537 PMC12051316 own_data
- Nanopore-based analysis unravels the genetic landscape and phylogenetic relationships of human-infecting Trichuris incognita and Trichuris trichiura in Côte d’Ivoire, Uganda, Tanzania, and Laos 2024 own_data
- Toward an improved definition of a healthy microbiome for healthy aging. 2022 PMID 37118093 PMC10154212 unsure
- Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits. 2023 PMID 38049420 PMC10696028 unsure
Archive description
Fecal shotgun metagenomic data and V4 targeted amplicon sequencing of the bacterial 16S rRNA gene for Cameroonians and U.S. samples
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- body site study.title · “Cameroon, U.S. fecal V4 amplicon sequencing”
- body site study.description · “Fecal shotgun metagenomic data”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11977739 | age_at_collection_days | 13514.25 | R2 | 0.75 | external.cmd source | age: 37; age_unit: Year; age_group: Adult |
| SAMN11977739 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN11977739 | bmi | 24.7 | R2 | 0.75 | external.cmd source | bmi: 24.7 |
| SAMN11977733 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMN11977733 | country | CM | R1 | 0.90 | sample.attr.geo_loc_name | Cameroon |
| SAMN11977739 | health_condition | gi_infection_or_diarrhoea | R2 | 0.70 | external.cmd source | disease: Parasite Present |
| SAMN11977733 | health_condition | healthy_control | R4 | 0.50 | paper.abstract | healthy human gut microbiota |
| SAMN11977739 | health_condition_detail | Parasite Present | R2 | 0.75 | external.cmd source | disease: Parasite Present |
| SAMN11977733 | latitude | 3.8480 | R1 | 0.90 | biosample.attribute:lat_lon | 3.8480 N 11.5021 E |
| SAMN11977733 | location_region | Centre | R1 | 0.60 | biosample.attribute:lat_lon | 3.8480 N 11.5021 E |
| SAMN11977733 | longitude | 11.5021 | R1 | 0.90 | biosample.attribute:lat_lon | 3.8480 N 11.5021 E |
| SAMN11977739 | sex | female | R2 | 0.75 | external.cmd source | sex: Female |
| SAMN11977739 | subject_id | SAMN11977739 | R3 | 0.65 | design.one_sample_per_subject:fulltext | We performed shotgun metagenomic sequencing on a subset of 175 Cameroonian fecal samples (94 Bantu, 37 Baka, 22 Bagyeli, 22 Fulani) |
Sequencing
180 runs over 180 samples · mean 2.25 Gbp per run (median 2.11 Gbp, total 404.20 Gbp; 180 runs with a base count) · layout PAIRED 180 · platform ILLUMINA 180 · models Illumina HiSeq 2500 (180) · 87% of runs with a Sandpiper profile · first public 2020-03-27
Authors (58)
Rubel MA first · Abbas A · Taylor LJ · Connell A · Tanes C · Bittinger K · Ndze VN · Fonsah JY · Ngwang E · Essiane A · Fokunang C · Njamnshi AK · Bushman FD · Tishkoff SA last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Ghosh TS first · Shanahan F · O'Toole PW last · Yersin S first · Garneau JR · Schneeberger PHH · Osman KA · Cercamondi CI · Muhummed AM · Tschopp R · Zinsstag J · Vonaesch P last · De Biase R · Bocchio F · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · van Sinderen D · Peng LL first · Qi FL · Tan K · Xiao W last · Rahman N first · Bär MA · Dommann J · Hürlimann E · Coulibaly JT · Ali S · Sayasone S · Beinamaryo P · Keiser J · Schneeberger PH last
Downloads
PRJNA547591.csv.gz (6.7 KB) · parquet (80.0 KB) — all 180 samples, every field with route and confidence · PRJNA547591_determinations.csv.gz (21.9 KB) — 2,130 evidence rows