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PRJNA948840 SRP430581

Gut/respiratory microbiome in SARS-CoV-2 youth, NC

Upper respiratory and gut microbiomes of children and adolescents with SARS-CoV-2 infection (BRAVE Kids study)

Cross-sectional study of 727 samples from children, adolescents, and young adults in Durham, NC, examining upper respiratory and gut microbiomes in relation to SARS-CoV-2 susceptibility and severity. machine-written summary

727 samples · 727 runs · US · Child · 2025 · 0.20 Gbp / sample

ENABioProjectSample sheetRegistryDownloadFlag an issue

Sources
✓Sequence archive 6,371✓Abstract / description 727○Full text–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 archive6,371 sample values (age, collection date, country, latitude, location locality, location region, longitude, sex)
✓ Abstract / description727 sample values (health condition)
○ Full textread; no usable statement or table
– Supplementary tablesno supplementary tables available (or none open access)
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 sampling locations · 1 country
Age
unknown298
child177
adolescent119
infant66
adult65
neonate2
Condition
gi_infection_or_diarrhoea727
Sex
female228
male201
Country
US727
Body site
excluded428
primary295
unknown4
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 213 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 103 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 71 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 35 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 9 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 67 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 227 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)this project, 30–100 Gbp: 2 samplesall projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 0.20 Gbp per sample0130Gbp
! Self-contradictory metadata

age: two sequence archives disagree for 14 samples (e.g. 82.0 vs 825.5) — withheld.

The sources disagree on 14 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).

Contradicted values (14)
samplefieldvalueother valuehandling
SAMN43688693age82.0 (sequence archive)825.5 (sequence archive)withheld: neither value published
SAMN43688763age18.5 (sequence archive)6746.2 (sequence archive)withheld: neither value published
SAMN43688822age27.7 (sequence archive)277.6 (sequence archive)withheld: neither value published
SAMN43688827age9.0 (sequence archive)3305.5 (sequence archive)withheld: neither value published
SAMN43688911age210.0 (sequence archive)2118.4 (sequence archive)withheld: neither value published
SAMN43688915age264.0 (sequence archive)2640.8 (sequence archive)withheld: neither value published
SAMN43688933age39.0 (sequence archive)390.8 (sequence archive)withheld: neither value published
SAMN43688954age77.0 (sequence archive)924.1 (sequence archive)withheld: neither value published
SAMN43688958age82.0 (sequence archive)825.5 (sequence archive)withheld: neither value published
SAMN43688974age27.7 (sequence archive)277.6 (sequence archive)withheld: neither value published
SAMN43688985age103.0 (sequence archive)1030.0 (sequence archive)withheld: neither value published
SAMN43689036age103.0 (sequence archive)1030.0 (sequence archive)withheld: neither value published
SAMN43689057age39.0 (sequence archive)390.8 (sequence archive)withheld: neither value published
SAMN43689062age25.2 (sequence archive)252.0 (sequence archive)withheld: neither value published
Community composition
Prevotella 11.5%Faecalibacterium 10.8%Bifidobacterium 9.5%Bacteroides 6.6%Phocaeicola 5.8%Blautia_A 5.1%Roseburia 3.7%Alistipes 3.3%Mediterraneibacter 2.3%Collinsella 2.2%Ruminococcoides 2.1%Gemmiger 1.8%not assigned to a genus 3.2%other genera 32.0%

Genera, mean relative abundance over 287 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category429 59%
country727 100%727
health_condition727 100%727
subject_id727 100%727
collection_date727 100%727
detailed_location727 100%
location_locality727 100%727
location_region727 100%727
timepoint_label720 99%720
latitude586 81%586
longitude586 81%586
sex429 59%429
age_at_collection_days415 57%415
Papers (1)
Details
Archive description

This study explored the extent to which the upper respiratory and gut microbiomes influence susceptibility to and severity of SARS-CoV-2 infection among children, adolescents, and young adults.

How this project entered the registry

Classified as human gut / stool / nasal / nasopharyngeal shotgun DNA metagenome of child and adolescent and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.

  • host external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
  • body site study.title · “Upper respiratory and gut microbiomes of children”
  • body site study.description · “upper respiratory and gut microbiomes influence susceptibility”
  • body site run.scientific_name · “human nasopharyngeal metagenome”
  • life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
  • life stage study.title · “gut microbiomes of children and adolescents with”
  • life stage study.title · “of children and adolescents with SARS-CoV-2 infection”
  • life stage study.description · “infection among children, adolescents , and young”
  • life stage study.description · “adolescents, and young adults .”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN43688655age_at_collection_days2530.0R10.85sample.attr.host_age6.93
SAMN34037640collection_date2020-04-01/2022-07-28R10.90biosample.attribute:collection_date2020-04-01/2022-07-28
SAMN34037640countryUSR10.90sample.attr.geo_loc_nameUSA: Durham, NC
SAMN34037640health_conditiongi_infection_or_diarrhoeaR40.50study.descriptionSARS-CoV-2 infection
SAMN34037640latitude35.9900R10.90biosample.attribute:lat_lon35.99 N 78.90 W
SAMN34037640location_localityDurhamR10.85biosample.attribute:geo_loc_nameUSA: Durham, NC
SAMN34037640location_regionNorth CarolinaR10.75biosample.attribute:geo_loc_nameUSA: Durham, NC
SAMN34037640longitude-78.9000R10.90biosample.attribute:lat_lon35.99 N 78.90 W
SAMN43688655sexfemaleR10.90sample.attr.host_sexfemale
SAMN34037640subject_idAC1525R10.85sample.attr.patient_codeAC1525
SAMN34037640timepoint_labelM0R10.70sample.name_rule:aliasAC1525.M0.STOOL
Sequencing

727 runs over 727 samples · mean 4.79 Gbp per run (median 0.20 Gbp, total 3,482.78 Gbp; 727 runs with a base count) · layout PAIRED 727 · platform ILLUMINA 727 · models Illumina NovaSeq X Plus (432), Illumina NovaSeq 6000 (295) · 41% of runs with a Sandpiper profile · first public 2025-06-18

Authors (24)

Jiang D first · Soo N · Tan CY · Dankwa S · Wang HY · Theriot BS · Xue K · Hill D · Ardeshir A · Bain JR · Heston SM · Hurst JH · Siddiqui NY · Van Rompay KKA · Cervantes-Barragan L · Smith JP · Song R · Roper J · Kelly MS · Hudgens MG · De Paris K · Permar SR · Goswami R · Surana NK last

Downloads

PRJNA948840.csv.gz (25.0 KB) · parquet (103.3 KB) — all 727 samples, every field with route and confidence · PRJNA948840_determinations.csv.gz (55.8 KB) — 7,098 evidence rows

Samples (727 · every field this project has values for · hover a cell for its source)
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