Gut Microbiome in Hadza, Nepali, and Californian Populations
Cross-sectional study of 439 fecal samples from Tanzania (Hadza), Nepal, and California, USA, spanning age groups from neonate to adult, comparing non-industrialized and industrialized gut microbiomes. machine-written summary
439 samples · 457 runs · TZ, NP, US · Infant / toddler · 2022 · 19.06 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,050 sample values (age, bmi, collection date, country, diet, diet detail, health condition detail, intervention) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10330870, PMC9894631 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
longitudinalcommunitytribe
72 of 228 people sampled more than once (261 samples; median 3, up to 11 per person) · follow-up median 3 mo (max 12 mo) · median interval between samples 2 d (time from collection dates). Schedule stated by the source: “Published timepoint_label field lists irregular day points (D_2,5,7,10,12,14,19,21,23) and a month-24 point (M_24) for a subset of samples; only 12% of samples carry a timepoint label.”.
Each row is one person (36 shown of 72); dots are samples at days since that person's first sample.
Hadza bush camps (17 camps with >=2 sampled people, e.g. HUKAMAKO 50, SENGELI 47 people) and Nepali ethnic groups (Tharu, Chepang, Raute, Raji)18 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: 8 of 18 shared settings. 228 people in the project overall.
Genera, mean relative abundance over 382 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 | 386 | 88% | ||||
| country | 439 | 100% | 439 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 418 | 95% | 418 | |||
| collection_date | 412 | 94% | 412 | |||
| shared_setting_id | 405 | 92% | 405 | |||
| shared_setting_type | 405 | 92% | 405 | |||
| sex | 398 | 91% | 398 | |||
| age_at_collection_days | 386 | 88% | 386 | |||
| health_condition_detail | 54 | 12% | 54 | |||
| timepoint_label | 54 | 12% | 54 | |||
| detailed_location | 11 | 3% | ||||
| diet | 11 | 3% | 11 | |||
| diet_detail | 11 | 3% | 11 | |||
| intervention | 11 | 3% | 11 | |||
| intervention_detail | 11 | 3% | 11 | |||
| latitude | 11 | 3% | 11 | |||
| location_region | 11 | 3% | 11 | |||
| longitude | 11 | 3% | 11 | |||
| bmi | 2 | 0% | 2 |
- Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. 2017 PMID 28839072 PMC5891123 cites_accession
- Rapid species-level metagenome profiling and containment estimation with sylph. 2025 PMID 39379646 PMC12339375 cites_accession
- The physical biogeography of Fusobacterium nucleatum in health and disease. 2025 PMID 40062772 PMC11980382 cites_accession
- Functional archetypes in the human gut microbiome reveal metabolic diversity, stability, and influence disease-associated signatures. 2025 PMID 41299634 PMC12659530 cites_accession
- Early-life colonization with Clostridioides difficile remodels the developing gut. 2026 PMID 42691172 PMC13626140 cites_accession
4 more
- Laccase-mediated biotransformation potential for fluorinated compounds by geographically diverse human gut microbiota 2026
- Robust variation in infant gut microbiome assembly across a spectrum of lifestyles. 2022 PMID 35679413 PMC9894631
- Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. 2023 PMID 37348505 PMC10330870
- Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes 2022
Archive description
The gut microbiome has been identified as a key to immune and metabolic health, especially in industrialized populations. Non-industrialized individuals harbor more diverse microbiomes and distinct bacterial lineages, but systemic under-sampling has hindered insight into the extent and functional consequences of these differences. Here, we performed ultra-deep metagenomic sequencing and laboratory strain isolation on fecal samples from the Hadza, hunter-gatherers in Tanzania, and comparative populations in Nepal and California. We recover 94,971 total genomes of bacteria, archaea, bacteriophage, and eukaryotes, and find that 43% are novel upon aggregating with existing unified datasets. Analysis of in situ growth rates, genetic pN/pS signatures, and high-resolution strain tracking reveal dynamics in the hunter-gatherer gut microbiome that are distinct from industrialized populations. Industrialized versus Hadza gut microbes are enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. We use phylogenomics to reveal that global spread of the spirochaete Treponema succinifaciens parallels historic human migration prior to its extinction in industrialized populations. When combined with a detailed definition of gut-resident strains that are vanishing in industrialized populations, our data demonstrate extensive perturbation in many facets of the gut microbiome brought on by the industrialized lifestyle.
How this project entered the registry
Classified as human gut / stool / skin 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 · “Hadza and Nepali gut microbiome reveals how”
- body site study.description · “The gut microbiome has been”
- body site run.scientific_name · “human skin metagenome”
- 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 |
|---|---|---|---|---|---|---|
| SAMEA11460262 | age_at_collection_days | 12784 | R1 | 0.85 | sample.attr.host_age | 35 |
| SAMEA4765564 | age_at_collection_days | 1096 | R1 | 0.85 | biosample_attr | host_age=3 (years; U1_sibling_unit_attr) |
| SAMEA11460264 | bmi | 13.15 | R1 | 0.90 | biosample.attribute:host_body_mass_index | host_body_mass_index: 13.14924392 |
| SAMEA4765500 | collection_date | 2013-09-06 | R1 | 0.85 | biosample.attribute:collection_timestamp | collection_timestamp: 2013-09-06 |
| SAMN20031235 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMEA11460262 | country | TZ | R1 | 0.90 | biosample_attr | Tanzania |
| SAMN20031235 | diet | therapeutic_or_study_diet | R1 | 0.70 | biosample.attribute:host_diet | Fiber |
| SAMN20031235 | diet_detail | Fiber | R1 | 0.70 | biosample.attribute:host_diet | Fiber |
| SAMEA4969120 | health_condition_detail | OMNI | R1 | 0.90 | biosample.attribute:condition | condition: OMNI |
| SAMN20031235 | intervention | diet_intervention | R1 | 0.90 | biosample.attribute:host_diet | host_diet: Fiber |
| SAMN20031235 | intervention_detail | high fiber diet arm | R1 | 0.90 | biosample.attribute:host_diet | host_diet: Fiber |
| SAMN20031235 | latitude | 37.4275 | R1 | 0.90 | biosample.attribute:lat_lon | 37.4275 N 122.1697 W |
| SAMN20031235 | location_region | California | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: California |
| SAMN20031235 | longitude | -122.1697 | R1 | 0.90 | biosample.attribute:lat_lon | 37.4275 N 122.1697 W |
| SAMEA11460262 | sex | female | R1 | 0.90 | biosample_attr | female |
| SAMEA11460263 | shared_setting_id | HUKAMAKO | R1 | 0.85 | biosample.attribute:BUSH_CAMP | BUSH_CAMP: HUKAMAKO |
| SAMEA11460266 | shared_setting_id | Raji | R1 | 0.85 | biosample.attribute:Population | Population: Raji |
| SAMEA4765500 | shared_setting_id | MWAMUDU | R1 | 0.85 | biosample.attribute:bush_camp | bush_camp: MWAMUDU |
| SAMEA4969120 | shared_setting_id | Chepang | R1 | 0.85 | biosample.attribute:population | population: Chepang |
| SAMEA11460263 | shared_setting_type | village_or_community | R1 | 0.85 | biosample.attribute:BUSH_CAMP | BUSH_CAMP: HUKAMAKO |
| SAMEA11460266 | shared_setting_type | ethnic_group_or_tribe | R1 | 0.85 | biosample.attribute:Population | Population: Raji |
| SAMEA4765500 | shared_setting_type | village_or_community | R1 | 0.85 | biosample.attribute:bush_camp | bush_camp: MWAMUDU |
| SAMEA4969120 | shared_setting_type | ethnic_group_or_tribe | R1 | 0.85 | biosample.attribute:population | population: Chepang |
| SAMEA11460262 | subject_id | 194 | R1 | 0.85 | biosample_attr | 194 |
| SAMEA11460266 | subject_id | RAJ1013YZ | R1 | 0.70 | sample.name_rule:TITLE | 11947.RAJ1013YZ |
| SAMEA4765641 | timepoint_label | D_12 | R1 | 0.70 | run.library_name | Hadza_MoBio_hadza-I-L_D_12_1182 |
Sequencing
477 runs over 439 samples · mean 22.00 Gbp per run (median 17.35 Gbp, total 10,492.64 Gbp; 477 runs with a base count) · layout PAIRED 477 · platform ILLUMINA 477 · models Illumina NovaSeq 6000 (477) · 86% of runs with a Sandpiper profile · first public 2022-04-01 – 2022-04-20
Authors (24)
Smits SA first · Leach J · Sonnenburg ED · Gonzalez CG · Lichtman JS · Reid G · Knight R · Manjurano A · Changalucha J · Elias JE · Dominguez-Bello MG · Sonnenburg JL last · Fragiadakis GK first · Van Treuren W · Jha AR first · Davenport ER · Gautam Y · Bhandari D · Tandukar S · Ng KM · Holmes S · Gautam GP · Sherchand JB · Bustamante CD
Downloads
PRJEB49206.csv.gz (16.7 KB) · parquet (95.0 KB) — all 439 samples, every field with route and confidence · PRJEB49206_determinations.csv.gz (24.7 KB) — 3,050 evidence rows