Gut microbiome and immunity in rural/urban Tanzanians
Cross-sectional study of 320 stool samples from healthy adults (and one elderly individual) in Tanzania, comparing rural and urban populations to examine gut microbiome composition and its association with immune (cytokine) responses. machine-written summary
320 samples · 320 runs · TZ · Adult · 2021 · 5.09 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 960 sample values (age, country, sex) |
| ✓ Abstract / description | 640 sample values (health condition, health condition detail) |
| ✓ Full text | 640 sample values (collection date, location region) · PMC10808065, PMC8357928 |
| ✓ Supplementary tables | 316 sample values (bmi) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 294 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 | 320 | 100% | ||||
| country | 320 | 100% | 320 | |||
| health_condition | 320 | 100% | 320 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 320 | 100% | 320 | |||
| collection_date | 320 | 100% | 320 | |||
| detailed_location | 320 | 100% | ||||
| health_condition_detail | 320 | 100% | 320 | |||
| location_region | 320 | 100% | 320 | |||
| sex | 320 | 100% | 320 | |||
| bmi | 316 | 99% | 316 |
- Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations. 2021 PMID 34381036 PMC8357928 own_data
- Host genetic regulation of human gut microbial structural variation. 2024 PMID 38172637 PMC10808065 unsure
Archive description
The human gut microbiota is increasingly recognized as an important factor in modulating innate and adaptive immunity through release of ligands and metabolites that translocate into circulation. Urbanizing African populations harbor large intestinal diversity due to a range of lifestyles, providing the necessary variation to gauge immunomodulatory factors. Stool metagenomics uncovers a gradient of intestinal microbial compositions from rural through urban Tanzania, towards European samples, manifested both in relative abundance and genomic variation. The rural population shows increase Bacteroidetes, led by Prevotella copri, but also presence of fungi. Measured ex vivo cytokine responses were significantly associated with 34 significant microbes. Pathway effects on cytokines, notably TNF-alpha and IFN-gamma, differential metabolome analysis and enzyme copy number enrichment converge on histidine and arginine metabolism as potential immunomodulatory pathways mediated by Bifidobacterium longum and Akkermansia muciniphila.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host study.description · “The human gut microbiota is increasingly recognized”
- body site study.description · “Stool metagenomics uncovers a gradient”
- life stage sample.attr.age · “20 (n=310/320)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17126948 | age_at_collection_days | 13149.0 | R1 | 0.85 | sample.attr.age | 36 |
| SAMN17126948 | bmi | 32.27 | R2 | 0.85 | paper.supp.41467_2021_25213_MOESM3_ESM.xlsx[300FG Tanzania Metadata!BMI] | 32.2707877657858 |
| SAMN17126948 | collection_date | 2017-03/2017-12 | R3 | 0.70 | paper.fulltext.methods | enrolled between March and December 2017 |
| SAMN17126948 | country | TZ | R1 | 0.90 | sample.attr.geo_loc_name | Tanzania: Africa |
| SAMN17126948 | health_condition | healthy_control | R4 | 0.50 | study.description | Urbanizing African populations |
| SAMN17126948 | health_condition_detail | Rural and urban African populations; no disease stated | R4 | 0.50 | study.description | Urbanizing African populations |
| SAMN17126948 | location_region | Kilimanjaro region | R3 | 0.70 | paper.fulltext.methods | living in the Kilimanjaro region in Northern Tanzania |
| SAMN17126948 | sex | male | R1 | 0.90 | sample.attr.sex | male |
Sequencing
320 runs over 320 samples · mean 5.01 Gbp per run (median 5.09 Gbp, total 1,603.90 Gbp; 320 runs with a base count) · layout PAIRED 320 · platform ILLUMINA 320 · models Illumina NovaSeq 6000 (320) · 92% of runs with a Sandpiper profile · first public 2021-06-24
Authors (49)
Stražar M first · Temba GS · Vlamakis H · Kullaya VI · Lyamuya F · Mmbaga BT · Joosten LAB · van der Ven AJAM · Netea MG · de Mast Q · Xavier RJ last · Zhernakova DV first · Wang D · Liu L · Andreu-Sánchez S · Zhang Y · Ruiz-Moreno AJ · Peng H · Plomp N · Del Castillo-Izquierdo · Gacesa R · Lopera-Maya EA · van Leeuwen SS · Lifelines Cohort Study · Riksen NP · Rutten JHW · Sanna S · Wijmenga C · Weersma RK · Zhernakova A · Harmsen HJM · Fu J 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
Downloads
PRJNA686265.csv.gz (10.4 KB) · parquet (84.3 KB) — all 320 samples, every field with route and confidence · PRJNA686265_determinations.csv.gz (18.2 KB) — 2,556 evidence rows