Long COVID gut/oral microbiome, Shanghai, longitudinal
2 samples from adults in Shanghai, China, studying gastrointestinal symptoms of long COVID and oral-gut microbial ectopic colonization, using a longitudinal design. machine-written summary
128 samples · 128 runs · Adult · 2023 · 15.16 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
longitudinal — not resolved
Schedule stated by the source: “Fecal (and saliva) samples collected during hospitalization (baseline) and again at a 3-month follow-up postdischarge” (time origin: other:discharge); stated follow-up 3 mo.
Genera, mean relative abundance over 2 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 | 128 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% |
- Gastrointestinal symptoms of long COVID-19 related to the ectopic colonization of specific bacteria that move between the upper and lower alimentary tract and alterations in serum metabolites. 2023 PMID 37468867 PMC10355065 unsure
Archive description
We prospectively collected oral, fecal, and serum samples from 983 antibiotic treatment-naive patients with mild COVID-19 and performed a 3-month follow-up postdischarge. Forty five and 25 paired fecal and saliva samples were collected from these patients at the 3 month follow up and from healthy controls, respectively. Shotgun metagenomic sequencing of fecal samples and 2bRAD sequencing for Microbiome (2bRAD-M) analysis of saliva samples collected from the 45 patients during hospitalization and after 3 months and from healthy controls were performed.
How this project entered the registry
Classified as human gut / stool / oral cavity / blood / tissue / internal fluids shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Gastrointestinal symptoms of long”
- body site study.description · “prospectively collected oral, fecal , and serum”
- body site study.description · “We prospectively collected oral , fecal, and”
- body site study.description · “oral, fecal, and serum samples from 983”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Sequencing
128 runs over 128 samples · mean 15.78 Gbp per run (median 15.16 Gbp, total 2,019.35 Gbp; 128 runs with a base count) · layout PAIRED 128 · platform ILLUMINA 128 · models Illumina NovaSeq 6000 (128) · 91% of runs with a Sandpiper profile · first public 2023-06-25 – 2023-07-02
Authors (23)
Zhang D first · Weng S · Xia C · Ren Y · Liu Z · Xu Y · Yang X · Wu R · Peng L · Sun L · Zhu J · Liang X · Jia Y · Wang H · Chen Q · Liu D · Chen Y · Guo H · Han X · Jin Z · Chen C · Li Z · Huang H last
Help complete this project
3 of the 4 core fields are below 50% coverage: country, health_condition, subject_id. Share metadata
Downloads
PRJNA908301.csv.gz (3.3 KB) · parquet (72.1 KB) — all 128 samples, every field with route and confidence · PRJNA908301_determinations.csv.gz (168 B) — 0 evidence rows