Antibiotic-associated gut microbiota and pneumonia risk, Berlin
95 gut metagenome samples from hospitalized patients in Berlin, Germany, examining how antibiotic-induced microbiome perturbations (via fecal transplant) affect pulmonary defense against Klebsiella pneumoniae; case-control design. machine-written summary
70 samples · 99 runs · DE · Age unknown · 2024 · 3.77 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 280 sample values (collection date, country, health condition, health condition detail, location locality) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 70 sample values (location site) · PMC10981692 |
| ○ 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 |
intervention — arms not resolved
Faecal microbiota transplantation design observational_with_procedure · population other_infection · FMT from antibiotic-treated hospitalized patients into mice
“mice transplanted with patient fecal material reveal that” — abstract:38555356 (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 82 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 | 0 | 0% | ||||
| country | 70 | 100% | 70 | |||
| health_condition | 35 | 50% | 35 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 70 | 100% | 70 | |||
| detailed_location | 70 | 100% | ||||
| location_locality | 70 | 100% | 70 | |||
| location_site | 70 | 100% | 70 | |||
| health_condition_detail | 35 | 50% | 35 |
- Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung. 2024 PMID 38555356 PMC10981692 own_data
Archive description
Hospital-acquired pneumonia (HAP) is associated with high mortality and costs, and frequently caused by multidrug-resistant (MDR) bacteria. Although prior antimicrobial therapy is a major risk factor for HAP, the underlying mechanism remains incompletely understood. Here, we demonstrate that antibiotic therapy in hospitalized patients is associated with decreased diversity of the gut microbiome and depletion of short-chain fatty acid (SCFA) producers. Infection experiments with mice transplanted with patient fecal material reveal that these antibiotic-induced microbiota perturbations impair pulmonary defense against MDR Klebsiella pneumoniae. This was dependent on inflammatory monocytes (IMs), whose fatty acid receptor (FFAR)2/3-controlled and phagolysosome-dependent antibacterial activity was compromed in mice transplanted with antibiotic-associated patient microbiota. Collectively, we characterize how clinically relevant antibiotics affect antimicrobial defense in the context of human microbiota, and reveal a critical impairment of IM's antimicrobial activity. Our study provides additional arguments for the rational use of antibiotics and offers mechanistic insights for the development of novel prophylactic strategies to protect high-risk patients from HAP.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.55. Assay shotgun_dna.
- host run.scientific_name · “human feces metagenome”
- host run.scientific_name · “mouse gut metagenome”
- body site run.scientific_name · “human feces metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN39433709 | collection_date | 2021 | R1 | 0.90 | biosample.attribute:collection_date | 2021 |
| SAMN39433709 | country | DE | R1 | 0.90 | sample.attr.geo_loc_name | Germany: Berlin |
| SAMN39433709 | health_condition | healthy_control | R1 | 0.70 | biosample.name_rule:TITLE | H1H-Human_healthy |
| SAMN39433709 | health_condition_detail | healthy | R1 | 0.70 | biosample.name_rule:TITLE | H1H-Human_healthy |
| SAMN39433709 | location_locality | Berlin | R1 | 0.85 | biosample.attribute:geo_loc_name | Germany: Berlin |
| SAMN39433709 | location_site | Charité respiratory medicine wards | R3 | 0.70 | paper.fulltext.methods | recruited between 2020 and 2021 in respiratory medicine wards at Charité |
Sequencing
99 runs over 70 samples · mean 3.42 Gbp per run (median 3.71 Gbp, total 338.36 Gbp; 99 runs with a base count) · layout PAIRED 99 · platform ILLUMINA 99 · models Illumina NovaSeq X (99) · 87% of runs with a Sandpiper profile · first public 2024-01-18 – 2024-01-21
Authors (33)
Dörner PJ first · Anandakumar H · Röwekamp I · Fiocca Vernengo F · Millet Pascual-Leone B · Krzanowski M · Sellmaier J · Brüning U · Fritsche-Guenther R · Pfannkuch L · Kurth F · Milek M · Igbokwe V · Löber U · Gutbier B · Holstein M · Heinz GA · Mashreghi MF · Schulte LN · Klatt AB · Caesar S · Wienhold SM · Offermanns S · Mack M · Witzenrath M · Jordan S · Beule D · Kirwan JA · Forslund SK · Wilck N · Bartolomaeus H · Heimesaat MM · Opitz B last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJNA1064467.csv.gz (2.6 KB) · parquet (72.7 KB) — all 70 samples, every field with route and confidence · PRJNA1064467_determinations.csv.gz (2.9 KB) — 350 evidence rows