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PRJNA819232 SRP365600

Gut/oral microbiome in HIV patients on INSTIs, Spain

Impact of Integrase Inhibitors on gut and oral microbiome

59 samples from La Rioja, Spain, comparing HIV-infected patients (naïve or on integrase inhibitor therapy) with uninfected controls, in a case-control study of gut/oral microbiome and inflammation. machine-written summary

59 samples · 59 runs · ES · Age unknown · 2022 · 1.67 Gbp / sample

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Sources

✓Sequence archive 478○Abstract / description✓Full text 63○Supplementary tables–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave

✓ Sequence archive	478 sample values (country, health condition, health condition detail, intervention, intervention detail, latitude, location region, longitude)
○ Abstract / description	read; no usable statement
✓ Full text	63 sample values (collection date, location region) · PMC9334516
○ 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

Interventions

intervention · arms resolved

exposed vs. not exposed (observational)

design observational_with_procedure

Samples at a glance

1 sampling locations · 1 country

Age

unknown59

Condition

other_infection29

healthy_control26

Country

ES55

Body site

primary55

unknown4

Sequencing depth per sample · this project all projects

Community composition

Prevotella 18.2%Faecalibacterium 6.7%Ruminococcoides 3.6%Alistipes 3.4%Ruminococcus_C 2.8%CAG-217 2.7%Bacteroides 1.8%Phocaeicola 1.5%Romboutsia 1.4%Vescimonas 1.3%CAG-611 1.2%CAZU01 1.2%not assigned to a genus 30.6%other genera 23.7%

Genera, mean relative abundance over 43 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage

field	samples	coverage	R1	R3
age_category	0	0%
country	55	93%	55
health_condition	55	93%	55
subject_id	0	0%
collection_date	59	100%		59
detailed_location	59	100%
health_condition_detail	59	100%	59
intervention	59	100%	59
location_region	59	100%	55	4
intervention_detail	55	93%	55
latitude	55	93%	55
longitude	55	93%	55
medication	15	25%	15
medication_detail	15	25%	15

Papers (1)

Integrase Inhibitors Partially Restore Bacterial Translocation, Inflammation and Gut Permeability Induced by HIV Infection: Impact on Gut Microbiota. 2022 PMID 35618952 PMC9334516 own_data

Details

Archive description

To characterizate the gut microbiota (both bacteriome and virome) and the oral bacteriome of HIV-infected patients, to investigate their relationship with their inflammatory state and cardiovascular risk and to analyze the effects of the current integrase strand transfer inhibitors (INSTIs)

How this project entered the registry

Classified as human gut / stool / oral cavity shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.70. Assay shotgun_dna.

host run.host_tax_id · “9606”
host study.description · “HIV-infected patients”
body site study.title · “gut and oral microbiome”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN27030689	collection_date	2019-03/2021-02	R3	0.70	paper.fulltext.methods	from March 2019 to February 2021
SAMN27030689	country	ES	R1	0.90	sample.attr.geo_loc_name	Spain: La Rioja
SAMN27030689	health_condition	other_infection	R1	0.85	biosample_attr	HIV
SAMN27030689	health_condition_detail	HIV	R1	0.90	sample.attr.hiv_status	HIV
SAMN27030689	intervention	no_intervention	R1	0.80	biosample.attribute:treatment_status	treatment_status: Naive
SAMN27030689	intervention_detail	ART-naive HIV patient, pre-treatment	R1	0.80	biosample.attribute:treatment_status	treatment_status: Naive
SAMN27030689	latitude	42.4500	R1	0.90	biosample.attribute:lat_lon	42.45 N 2.43 W
SAMN27030689	location_region	La Rioja	R1	0.85	biosample.attribute:geo_loc_name	Spain: La Rioja
SAMN27030744	location_region	La Rioja	R3	0.70	paper.fulltext.methods	Ethics in Drug Research in La Rioja
SAMN27030689	longitude	-2.4300	R1	0.90	biosample.attribute:lat_lon	42.45 N 2.43 W
SAMN27030725	medication	antiretroviral	R1	0.90	biosample.attribute:treatment_status	ART
SAMN27030725	medication_detail	ART	R1	0.90	biosample.attribute:treatment_status	ART

Sequencing

59 runs over 59 samples · mean 1.54 Gbp per run (median 1.67 Gbp, total 91.07 Gbp; 59 runs with a base count) · layout PAIRED 59 · platform ILLUMINA 59 · models NextSeq 500 (59) · 73% of runs with a Sandpiper profile · first public 2022-05-26

Authors (10)

Villoslada-Blanco P first · Pérez-Matute P · Íñiguez M · Recio-Fernández E · Blanco-Navarrete P · Metola L · Ibarra V · Alba J · de Toro M · Oteo JA last

Help complete this project

2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata

Downloads

PRJNA819232.csv.gz (2.5 KB) · parquet (72.8 KB) — all 59 samples, every field with route and confidence · PRJNA819232_determinations.csv.gz (4.0 KB) — 541 evidence rows

Samples (59 · every field this project has values for · hover a cell for its source)

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