Gut microbiome in HIV, subclinical atherosclerosis, Montreal
16 fecal samples from adults in Montreal, Canada, comparing gut microbiome in people living with HIV and HIV-negative controls, with or without subclinical atherosclerosis, in a case-control design. machine-written summary
16 samples · 16 runs · CA · Adult · 2021 · 12.79 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 88 sample values (collection date, country, health condition, health condition detail, latitude, location locality, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8083984 |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 13 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 | 16 | 100% | ||||
| country | 16 | 100% | 16 | |||
| health_condition | 4 | 25% | 4 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 16 | 100% | 16 | |||
| detailed_location | 16 | 100% | ||||
| latitude | 16 | 100% | 16 | |||
| location_locality | 16 | 100% | 16 | |||
| longitude | 16 | 100% | 16 | |||
| health_condition_detail | 4 | 25% | 4 |
- Upregulated IL-32 Expression And Reduced Gut Short Chain Fatty Acid Caproic Acid in People Living With HIV With Subclinical Atherosclerosis. 2021 PMID 33936102 PMC8083984 own_data
Archive description
16 fecal samples were collected from n=90 PLWH and HIVneg individuals, with or without subclinical atherosclerosis
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.title · “human stool Metagenome”
- body site study.title · “human stool Metagenome”
- life stage study.description · “PLWH and HIVneg individuals, with or without subclinical atherosclerosis”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN18239573 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMN18239573 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada: Montreal |
| SAMN18239573 | health_condition | cardiometabolic_other | R1 | 0.70 | sample.name_rule:description | TPV |
| SAMN18239573 | health_condition_detail | TPV | R1 | 0.70 | sample.name_rule:description | TPV |
| SAMN18239573 | latitude | 45.5000 | R1 | 0.90 | biosample.attribute:lat_lon | 45.50 N 75.57 W |
| SAMN18239573 | location_locality | Montreal | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada: Montreal |
| SAMN18239573 | longitude | -75.5700 | R1 | 0.90 | biosample.attribute:lat_lon | 45.50 N 75.57 W |
Sequencing
16 runs over 16 samples · mean 12.53 Gbp per run (median 12.79 Gbp, total 200.44 Gbp; 16 runs with a base count) · layout PAIRED 16 · platform ILLUMINA 16 · models Illumina NovaSeq 6000 (16) · 81% of runs with a Sandpiper profile · first public 2021-03-13
Authors (32)
El-Far M first · Durand M · Turcotte I · Larouche-Anctil E · Sylla M · Zaidan S · Chartrand-Lefebvre C · Bunet R · Ramani H · Sadouni M · Boldeanu I · Chamberland A · Lesage S · Baril JG · Trottier B · Thomas R · Gonzalez E · Filali-Mouhim A · Goulet JP · Martinson JA · Kassaye S · Karim R · Kizer JR · French AL · Gange SJ · Ancuta P · Routy JP · Hanna DB · Kaplan RC · Chomont N · Landay AL · Tremblay CL last
Downloads
PRJNA713013.csv.gz (1.3 KB) · parquet (70.1 KB) — all 16 samples, every field with route and confidence · PRJNA713013_determinations.csv.gz (1.1 KB) — 88 evidence rows