Seasonal gut microbiome dynamics in Hadza hunter-gatherers
Longitudinal study of 40 gut microbiome samples from healthy Hadza hunter-gatherers (adults, adolescents, and children) in Tanzania, examining seasonal cycling of the gut microbiome. machine-written summary
40 samples · 40 runs · TZ · Adult · 2017 · 0.57 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 160 sample values (collection date, country, latitude, longitude) |
| ✓ Abstract / description | 80 sample values (lifestyle, lifestyle detail) |
| ○ Full text | read; no usable statement or table · PMC10773633, PMC10993611, PMC11418011, PMC5891123, PMC6546328, PMC6781418, PMC6879853, PMC6961876, PMC7157763, PMC7671402, PMC7972227, PMC8095712, PMC8262883, PMC8497558, PMC8763029, PMC9040266, PMC9096808, PMC9721016 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 175 sample values (age, antibiotic exposure, 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 |
longitudinal — not resolved
Schedule stated by the source: “Stool samples collected longitudinally over more than a year; no explicit per-subject timepoints given in this 40-sample subset”.
Genera, mean relative abundance over 32 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 | 40 | 100% | ||||
| country | 40 | 100% | 40 | |||
| health_condition | 40 | 100% | 40 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 40 | 100% | 40 | |||
| collection_date | 40 | 100% | 40 | |||
| health_condition_detail | 40 | 100% | 40 | |||
| latitude | 40 | 100% | 40 | |||
| lifestyle | 40 | 100% | 40 | |||
| lifestyle_detail | 40 | 100% | 40 | |||
| longitude | 40 | 100% | 40 | |||
| sex | 28 | 70% | 28 | |||
| age_at_collection_days | 27 | 68% | 27 |
- Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. 2017 PMID 28839072 PMC5891123 own_data
- Links between environment, diet, and the hunter-gatherer microbiome. 2019 PMID 30118385 PMC6546328 own_data
- Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates. 2019 PMID 31548686 PMC6879853 own_data
- Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny. 2019 PMID 31590679 PMC6781418 own_data
- Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology. 2020 PMID 33575595 PMC7671402 own_data
13 more
- ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries. 2021 PMID 33731016 PMC7972227
- Butyrate Production Pathway Abundances Are Similar in Human and Nonhuman Primate Gut Microbiomes. 2022 PMID 34542625 PMC8763029
- Ontology-aware deep learning enables ultrafast and interpretable source tracking among sub-million microbial community samples from hundreds of niches. 2022 PMID 35473941 PMC9040266
- A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments. 2024 PMID 38576042 PMC10993611
- Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion. 2020 PMID 31940321 PMC6961876
- Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides. 2020 PMID 32265336 PMC7157763
- Inter-Individual Diversity Scaling Analysis of the Human Virome With Classic Diversity-Area Relationship (DAR) Modeling. 2021 PMID 33959147 PMC8095712
- Human Gut Faecalibacterium prausnitzii Deploys a Highly Efficient Conserved System To Cross-Feed on β-Mannan-Derived Oligosaccharides. 2021 PMID 34061597 PMC8262883
- Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth-gut axis. 2021 PMID 34620880 PMC8497558
- Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria. 2022 PMID 35240043 PMC9096808
- The microbiome's fiber degradation profile and its relationship with the host diet. 2022 PMID 36464700 PMC9721016
- Isolation and characterization of a novel lytic Parabacteroides distasonis bacteriophage φPDS1 from the human gut. 2024 PMID 38178369 PMC10773633
- The molecular basis of cereal mixed-linkage β-glucan utilization by the human gut bacterium Segatella copri. 2024 PMID 39122003 PMC11418011
Archive description
Seasonal Cycling in the Gut Microbiome of the Hadza Hunter-Gatherers of Tanzania
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult 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 · “Cycling in the Gut Microbiome of the”
- body site study.description · “Cycling in the Gut Microbiome of the”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07284951 | age_at_collection_days | 12783.75 | R2 | 0.75 | external.cmd source | age: 35; age_unit: Year; age_group: Adult |
| SAMN07284950 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMN07284950 | collection_date | 2013-09-07 | R1 | 0.90 | biosample.attribute:collection_date | 2013-09-07 |
| SAMN07284950 | country | TZ | R1 | 0.90 | sample.attr.geo_loc_name | Tanzania |
| SAMN07284950 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN07284950 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN07284950 | latitude | -3.5500 | R1 | 0.90 | biosample.attribute:lat_lon | 3.55 S 34.58 E |
| SAMN07284950 | lifestyle | hunter_gatherer | R4 | 0.40 | ena.study_title | Hadza Hunter-Gatherers of Tanzania |
| SAMN07284950 | lifestyle_detail | Hadza hunter-gatherers | R4 | 0.40 | ena.study_title | Hadza Hunter-Gatherers of Tanzania |
| SAMN07284950 | longitude | 34.5800 | R1 | 0.90 | biosample.attribute:lat_lon | 3.55 S 34.58 E |
| SAMN07284951 | sex | male | R2 | 0.75 | external.cmd source | sex: Male |
Sequencing
40 runs over 40 samples · mean 0.78 Gbp per run (median 0.57 Gbp, total 31.24 Gbp; 40 runs with a base count) · layout SINGLE 40 · platform ILLUMINA 40 · models Illumina HiSeq 4000 (40) · 80% of runs with a Sandpiper profile · first public 2017-11-09
Authors (59)
Xiao W first · Ma ZS last · Mallott EK first · Amato KR last · Zha Y first · Chong H · Qiu H · Kang K · Dun Y · Chen Z · Cui X · Ning K last · Auchtung TA first · Stewart CJ · Smith DP · Triplett EW · Agardh D · Hagopian WA · Ziegler AG · Rewers MJ · She JX · Toppari J · Lernmark Å · Akolkar B · Krischer JP · Vehik K · Auchtung JM · Ajami NJ · Petrosino JF last · Cohen Y first · Borenstein E last · Ormaasen I first · Rudi K · Diep DB · Snipen L last · Mancabelli L first · Milani C · De Biase R · Bocchio F · Fontana F · Lugli GA · Alessandri G · Tarracchini C · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · Turroni F · Ventura M last · Golisch B first · Cordeiro RL · Fraser ASC · Briggs J · Stewart WA · Van Petegem F · Brumer H last
Downloads
PRJNA392180.csv.gz (2.1 KB) · parquet (72.0 KB) — all 40 samples, every field with route and confidence · PRJNA392180_determinations.csv.gz (4.5 KB) — 415 evidence rows