Gut microbiome and social networks in rural Honduras
Cross-sectional study of 1,889 gut microbiome samples from isolated villages in Copan, Honduras, examining how social network structure relates to species- and strain-level microbiome composition and sharing among adults. machine-written summary
1,889 samples · 1,889 runs · HN · Age unknown · 2023 · 12.09 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 5,667 sample values (collection date, country, location locality) |
| ✓ Abstract / description | 3,778 sample values (lifestyle, lifestyle detail) |
| ○ Full text | read; no usable statement or table · PMC10645880, PMC11290354, PMC11666459, PMC12534905, PMC12636519, PMC12867399 |
| ○ 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 |
community — not resolved
1,889 adults sampled across multiple isolated villages in Copan, Honduras; study examines social-network-linked microbiome sharing..
Genera, mean relative abundance over 1,719 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 | 1,889 | 100% | 1,889 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 1,889 | 100% | 1,889 | |||
| detailed_location | 1,889 | 100% | ||||
| lifestyle | 1,889 | 100% | 1,889 | |||
| lifestyle_detail | 1,889 | 100% | 1,889 | |||
| location_locality | 1,889 | 100% | 1,889 |
- Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages. 2024 PMID 38968070 PMC11290354 own_data
- Gut microbiome strain-sharing within isolated village social networks. 2025 PMID 39567691 PMC11666459 own_data
- Enhancing genome recovery across metagenomic samples using MAGmax. 2025 PMID 41002272 PMC12534905 own_data
- Evaluation of metagenome binning: advances and challenges. 2025 PMID 41269281 PMC12636519 own_data
- Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide. 2023 PMID 37963868 PMC10645880 unsure
1 more
- Socioeconomic position and the gut microbiota: a narrative synthesis of the association and recommendations. 2026 PMID 41620643 PMC12867399
Archive description
Gut Microbiome of isolated villages in rural Honduras
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Gut Microbiome of isolated villages”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN36744534 | collection_date | 2020-02-21 | R1 | 0.90 | biosample.attribute:collection_date | 2020-02-21 |
| SAMN36744534 | country | HN | R1 | 0.90 | sample.attr.geo_loc_name | Honduras:Copan |
| SAMN36744534 | lifestyle | rural_non_industrialized | R4 | 0.50 | paper.abstract | 19 isolated villages in the Mesoamerican highlands |
| SAMN36744534 | lifestyle_detail | isolated villages, Mesoamerican highlands, western Honduras | R4 | 0.50 | paper.abstract | 19 isolated villages in the Mesoamerican highlands |
| SAMN36744534 | location_locality | Copan | R1 | 0.85 | biosample.attribute:geo_loc_name | Honduras:Copan |
Sequencing
1,889 runs over 1,889 samples · mean 12.45 Gbp per run (median 12.09 Gbp, total 23,520.07 Gbp; 1,889 runs with a base count) · layout PAIRED 1,889 · platform ILLUMINA 1,889 · models Illumina NovaSeq 6000 (1,889) · 91% of runs with a Sandpiper profile · first public 2023-10-02 – 2025-12-21
Authors (31)
Diebold PJ first · Rhee MW · Shi Q · Trung NV · Umrani F · Ahmed S · Kulkarni V · Deshpande P · Alexander M · Thi Hoa N · Christakis NA · Iqbal NT · Ali SA · Mathad JS · Brito IL last · Shridhar SV first · Beghini F · Singh A · Juárez RM · Yazhini A first · Söding J last · Morice · Jochheim A · Lieser B · Ratcliff JS first · Kumari M · Varga-Weisz P · O'Gorman R last · Schroer HW first · Raygoza Garay JA · Bosch DE last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJNA999635.csv.gz (44.4 KB) · parquet (135.7 KB) — all 1,889 samples, every field with route and confidence · PRJNA999635_determinations.csv.gz (49.5 KB) — 9,445 evidence rows