Longitudinal gut metagenome in HIV-1 infection, Mozambique
54 fecal metagenome samples from subjects in Manhiça/Maputo, Mozambique, studied longitudinally in relation to HIV-1 infection status. machine-written summary
54 samples · 54 runs · MZ · Age unknown · 2019 · 1.79 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 432 sample values (collection date, country, latitude, location locality, location site, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11892071, PMC6511141 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 108 sample values (health condition, health condition detail) · from African Human Microbiome Portal (H3ABioNet) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
21 of 21 people sampled more than once (54 samples; median 3, up to 3 per person) · follow-up median 7 mo (max 17 mo) · median interval between samples 4 mo (time from collection dates). Schedule stated by the source: “Subjects sampled longitudinally at timepoints 1, 4, and 9 (months) over a 9-18 month follow-up period.” (time origin: diagnosis); stated follow-up 18 mo.
Each row is one person (21 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 52 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 | 54 | 100% | 54 | |||
| health_condition | 54 | 100% | 54 | |||
| subject_id | 54 | 100% | 54 | |||
| collection_date | 54 | 100% | 54 | |||
| detailed_location | 54 | 100% | ||||
| health_condition_detail | 54 | 100% | 54 | |||
| latitude | 54 | 100% | 54 | |||
| location_locality | 54 | 100% | 54 | |||
| location_site | 54 | 100% | 54 | |||
| longitude | 54 | 100% | 54 | |||
| timepoint_label | 54 | 100% | 54 |
- Evolution of the gut microbiome following acute HIV-1 infection. 2019 PMID 31078141 PMC6511141 own_data
- Decreased intestinal abundance of <i>Akkermansia muciniphila</i> is associated with metabolic disorders among people living with HIV. 2025 PMID 40052450 PMC11892071 unsure
Archive description
Human Fecal Metagenome from primarily and chronically HIV infected and non-infected subjects was sequenced using both illumina(MiSeq) sequencing and 16s V3-V4 region and shotgun
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.50. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “Human Fecal Metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09355485 | collection_date | 2013-05-23 | R1 | 0.90 | biosample.attribute:collection_date | 2013-05-23 |
| SAMN09355485 | country | MZ | R1 | 0.90 | sample.attr.geo_loc_name | Mozambique: Manhica, Maputo |
| SAMN09355485 | health_condition | other_infection | R2 | 0.70 | external.ahmp source | DISEASE: Hiv |
| SAMN09355485 | health_condition_detail | Hiv | R2 | 0.70 | external.ahmp source | DISEASE: Hiv |
| SAMN09355485 | latitude | -25.4000 | R1 | 0.90 | biosample.attribute:lat_lon | 25.4 S 32.8 E |
| SAMN09355485 | location_locality | Maputo | R1 | 0.85 | biosample.attribute:geo_loc_name | Mozambique: Manhica, Maputo |
| SAMN09355485 | location_site | Manhica | R1 | 0.85 | biosample.attribute:geo_loc_name | Mozambique: Manhica, Maputo |
| SAMN09355485 | longitude | 32.8000 | R1 | 0.90 | biosample.attribute:lat_lon | 25.4 S 32.8 E |
| SAMN09355485 | subject_id | 0333 | R1 | 0.85 | sample.attr.subjectid | 0333 |
| SAMN09355485 | timepoint_label | 1 | R1 | 0.85 | sample.attr.timepoint | 1 |
Sequencing
54 runs over 54 samples · mean 1.80 Gbp per run (median 1.79 Gbp, total 97.44 Gbp; 54 runs with a base count) · layout PAIRED 54 · platform ILLUMINA 54 · models Illumina HiSeq 2500 (54) · 96% of runs with a Sandpiper profile · first public 2019-01-02
Authors (29)
Rocafort M first · Noguera-Julian M · Rivera J · Pastor L · Guillén Y · Langhorst J · Parera M · Mandomando I · Carrillo J · Urrea V · Rodríguez C · Casadellà M · Calle ML · Clotet B · Blanco J · Naniche D · Paredes R last · Qian Z first · Chen S · Liao X · Xie J · Xu Y · Zhong H · Ou L · Zuo X · Xu X · Peng J · Wu J · Cai S last
Downloads
PRJNA450025.csv.gz (2.5 KB) · parquet (72.5 KB) — all 54 samples, every field with route and confidence · PRJNA450025_determinations.csv.gz (4.8 KB) — 540 evidence rows