Gut/oropharyngeal microbiome in COVID-19 vs controls, Berlin
192 samples (stool, oropharyngeal swabs, tracheobronchial secretions) from hospitalized adult and elderly COVID-19 patients and non-infected controls in Berlin, Germany, in a case-control study of microbiome alterations linked to COVID-19 severity. machine-written summary
192 samples · 192 runs · DE · Age unknown · 2024 · 3.50 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,911 sample values (age, bmi, collection date, country, latitude, location locality, location region, longitude) |
| ✓ Abstract / description | 192 sample values (health condition detail) |
| ✓ Full text | 192 sample values (location site) · PMC11291933 |
| ○ 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 |
longitudinal
27 of 41 people sampled more than once (67 samples; median 2, up to 6 per person) · follow-up median 6 d (max 29 d) · median interval between samples 6 d (time from collection dates). Schedule stated by the source: “Controls sampled day 1 and again 3–7 days later; patients classified early (≤10d) or late (>10d) post symptom onset, repeated stool/OP/TBS sampling” (time origin: other).
Each row is one person (27 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 75 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 | 192 | 100% | ||||
| country | 192 | 100% | 192 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 192 | 100% | 192 | |||
| age_at_collection_days | 192 | 100% | 192 | |||
| collection_date | 192 | 100% | 192 | |||
| detailed_location | 192 | 100% | ||||
| health_condition_detail | 192 | 100% | 192 | |||
| latitude | 192 | 100% | 192 | |||
| location_locality | 192 | 100% | 192 | |||
| location_region | 192 | 100% | 192 | |||
| location_site | 192 | 100% | 192 | |||
| longitude | 192 | 100% | 192 | |||
| sex | 192 | 100% | 192 | |||
| bmi | 183 | 95% | 183 |
- Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19. 2024 PMID 39085233 PMC11291933 own_data
Archive description
The clinical course of the 2019 coronavirus disease (COVID-19) is variable and largely unpredictable, especially in persons who have neither been vaccinated nor recovered from previous infection. We hypothesized that disease progression and inflammatory responses were associated with alterations in the microbiome. To test this, we characterized the metagenome of longitudinally collected stool samples and oropharyngeal swabs from hospitalized COVID-19 patients and non-infected controls, as well as tracheobronchial secretions from ventilated patients with COVID-19. Severe COVID-19 was directly associated with a depletion of potentially beneficial intestinal microbes mainly belonging to Clostridiales, whereas oropharyngeal microbiota disturbance appeared to be mainly driven by antibiotic use. Collectively, our study identifies microbiome alterations in severe COVID-19.
How this project entered the registry
Classified as human gut / stool / oral cavity / lower respiratory / multiple sites / nasal / nasopharyngeal shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human metagenome”
- body site study.description · “stool samples and oropharyngeal swabs”
- body site study.description · “tracheobronchial secretions from ventilated patients”
- body site sample.attr.env_medium · “oropharyngeal (OP) swabs [UBERON:0001729] (n=93/192)”
- life stage sample.attr.host_age · “63 (n=108/192)”
- life stage sample.attr.host_age · “76 (n=74/192)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN32072363 | age_at_collection_days | 13504.0 | R1 | 0.85 | sample.attr.host_age | 37 |
| SAMN32072363 | bmi | 41.52 | R1 | 0.90 | sample.attr.host_body_mass_index | 41.52 |
| SAMN32072363 | collection_date | 2020-04-01 | R1 | 0.90 | biosample.attribute:collection_date | 2020-04-01 |
| SAMN32072363 | country | DE | R1 | 0.90 | sample.attr.geo_loc_name | Germany: Berlin |
| SAMN32072363 | health_condition_detail | mixed_case_control: severe COVID-19 patients vs healthy controls | R4 | 0.40 | study.description | hospitalized COVID-19 patients and non-infected controls |
| SAMN32072363 | latitude | 52.4422 | R1 | 0.90 | biosample.attribute:lat_lon | 52.4422263 N 13.3211978 E |
| SAMN32072363 | location_locality | Berlin | R1 | 0.85 | biosample.attribute:geo_loc_name | Germany: Berlin |
| SAMN32072363 | location_region | Berlin | R1 | 0.60 | biosample.attribute:lat_lon | 52.4422263 N 13.3211978 E |
| SAMN32072363 | location_site | Charité-Universitätsmedizin Berlin | R3 | 0.70 | paper.fulltext.methods | treated at Charité-Universitätsmedizin Berlin |
| SAMN32072363 | longitude | 13.3212 | R1 | 0.90 | biosample.attribute:lat_lon | 52.4422263 N 13.3211978 E |
| SAMN32072363 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN32072363 | subject_id | C19-CB-43 | R1 | 0.70 | sample.name_rule:title | title: C19-CB-43 |
Sequencing
192 runs over 192 samples · mean 4.26 Gbp per run (median 3.50 Gbp, total 818.18 Gbp; 192 runs with a base count) · layout PAIRED 192 · platform ILLUMINA 192 · models Illumina NovaSeq 6000 (192) · 66% of runs with a Sandpiper profile · first public 2024-06-10
Authors (29)
Essex M first · Millet Pascual-Leone B · Löber U · Kuhring M · Zhang B · Brüning U · Fritsche-Guenther R · Krzanowski M · Fiocca Vernengo F · Brumhard S · Röwekamp I · Anna Bielecka A · Lesker TR · Wyler E · Landthaler M · Mantei A · Meisel C · Caesar S · Thibeault C · Corman VM · Marko L · Suttorp N · Strowig T · Kurth F · Sander LE · Li Y · Kirwan JA · Forslund SK · Opitz B last
Downloads
PRJNA909223.csv.gz (7.0 KB) · parquet (79.9 KB) — all 192 samples, every field with route and confidence · PRJNA909223_determinations.csv.gz (18.3 KB) — 2,295 evidence rows