Microbiome of wild/captive apes & humans, Congo & US zoos
Cross-sectional study of 160 gut samples comparing wild chimpanzees and gorillas near Nouabale-Ndoki National Park (Republic of the Congo) and nearby humans with captive apes at two US zoos (Lincoln Park, St. Louis). machine-written summary
81 samples · 160 runs · Age unknown · 2019 · 1.19 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 162 sample values (collection date, location site) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10770139, PMC11406404, PMC12573826, PMC7242348 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
country: sequence archive and hmgdb disagree for 81 samples (e.g. CG vs CD) — withheld.
The sources disagree on 81 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 (40 of 81)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN11515082 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515083 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515084 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515085 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515086 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515087 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515088 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515089 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515090 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515091 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515092 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515093 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515094 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515095 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515096 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515097 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515098 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515099 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515100 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515101 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515102 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515103 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515104 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515105 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515106 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515107 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515108 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515109 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515110 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515111 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515112 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515113 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515114 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515115 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515116 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515117 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515118 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515119 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515120 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
| SAMN11515121 | country | CG (sequence archive) | CD (hmgdb) | withheld: neither value published |
Genera, mean relative abundance over 146 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 | 0 | 0% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 81 | 100% | 81 | |||
| detailed_location | 81 | 100% | ||||
| location_site | 81 | 100% | 81 |
- The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography. 2020 PMID 32203121 PMC7242348 own_data
- Multiomics characterisation of the zoo-housed gorilla gut microbiome reveals bacterial community compositions shifts, fungal cellulose-degrading, and archaeal methanogenic activity. 2023 PMID 39295898 PMC11406404 own_data
- Functional host-specific adaptation of the intestinal microbiome in hominids. 2024 PMID 38182626 PMC10770139 unsure
- Comprehensive metagenomic analysis of the giant panda's oral microbiome reveals distinct taxonomic and functional characteristics. 2025 PMID 41163128 PMC12573826 unsure
Archive description
The aims of this project were to compare the gut microbiome and resistome between sympatric wild chimpanzees and gorillas in the Republic of the Congo, captive apes living in zoos in the United States, and humans living near the wild apes in the Congo.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host study.title · “Gut microbiome of humans and wild and captive chimpanzees and gorillas”
- host run.host_tax_id · “9606”
- body site run.scientific_name · “feces metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11515082 | collection_date | 2014-05-21 | R1 | 0.90 | biosample.attribute:collection_date | 2014-05-21 |
| SAMN11515082 | location_site | Nouabale-Ndoki National park | R1 | 0.85 | biosample.attribute:geo_loc_name | Republic of the Congo: near Nouabale-Ndoki National park |
Sequencing
160 runs over 81 samples · mean 1.27 Gbp per run (median 1.19 Gbp, total 202.64 Gbp; 160 runs with a base count) · layout PAIRED 160 · platform ILLUMINA 160 · models NextSeq 500 (160) · 91% of runs with a Sandpiper profile · first public 2019-05-18
Authors (43)
Campbell TP first · Sun X · Patel VH · Sanz C · Morgan D · Dantas G last · Rühlemann MC first · Bang C · Gogarten JF · Hermes BM · Groussin M · Waschina S · Poyet M · Ulrich M · Akoua-Koffi C · Deschner T · Muyembe-Tamfum JJ · Robbins MM · Surbeck M · Wittig RM · Zuberbühler K · Baines JF · Leendertz FH · Franke A last · Houtkamp IM first · van Zijll Langhout M · Bessem M · Pirovano W · Kort R last · Xiao LF first · Li Y · Lian H · Liu X · Wen Y · Chen X · Huang W · Li B · Luo L · Wang X · Tutt C · Zheng J · Wang VY · Shao NY last
Help complete this project
4 of the 4 core fields are below 50% coverage: age_category, country, health_condition, subject_id. Share metadata
Downloads
PRJNA539933.csv.gz (2.7 KB) · parquet (72.3 KB) — all 81 samples, every field with route and confidence · PRJNA539933_determinations.csv.gz (1.5 KB) — 162 evidence rows