Gut microbiota in community-acquired pneumonia, Zibo China
68 fecal samples from adult and elderly subjects in Zibo, China, comparing CAP patients and healthy controls using metagenomic and metabolomic profiling in a case-control design. machine-written summary
68 samples · 68 runs · CN · Age unknown · 2024 · 11.76 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 340 sample values (age, collection date, country, location locality, sex) |
| ✓ Abstract / description | 68 sample values (health condition detail) |
| ✓ Full text | 68 sample values (subject id) · PMC11960049 |
| ✓ Supplementary tables | 32 sample values (health condition) |
| – 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 |
Genera, mean relative abundance over 59 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 | 68 | 100% | ||||
| country | 68 | 100% | 68 | |||
| health_condition | 32 | 47% | 32 | |||
| subject_id | 68 | 100% | 68 | |||
| age_at_collection_days | 68 | 100% | 68 | |||
| collection_date | 68 | 100% | 68 | |||
| detailed_location | 68 | 100% | ||||
| health_condition_detail | 68 | 100% | 68 | |||
| location_locality | 68 | 100% | 68 | |||
| sex | 68 | 100% | 68 |
- Altered gut microbiota and metabolite profiles in community-acquired pneumonia: a metagenomic and metabolomic study. 2025 PMID 40062854 PMC11960049 own_data
Archive description
Although emerging evidences suggest an association between the altered gut microbiota and community-acquired pneumonia (CAP), little is known about the potential mechanisms that linked the dysbiosis of the gut microbiota and the development of CAP. In this study, we performed a metagenome-wide association study of 32 CAP patients and 36 health controls, which identified significant alterations in gut microbiota and dysbiosis-related metabolomics associated with CAP occurrence. We identified gut microbial alterations associated with CAP and linked to the changes in stool metabolites. Fecal metabolite profiles revealed that CAP patients exhibited a notable increase in Arachidonic acid, but a decrease in deoxycholic acid, lithocholic acid, ursodeoxycholic acid compared to control groups. Short-chain fatty acid-producing genera, including Faecalibacterium, Ruminococcus, and Eubacterium, and species Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, Prevotella copri, and Ruminococcus bromii, were significantly delepleted in CAP patients relative to those in control groups. Bacterial co-occurrence network analysis revealed that pro-inflammatory bacteria were over-represented and became to the core gut microbiome in CAP patients. These microbial and metabolic signatures are closely associated in CAP patients and control group. In conclusion, we identified bile acids (BAs) insufficiency, imbalanced production of short chain fatty acids (SCFAs), and excessive metabolic inflammation as gut microbiota-driven mechanisms linked to CAP. This work might explain in part the mechanistic link between altered gut microbiota and CAP pathogenesis.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of elderly and adult by opus_adjudicated with confidence 0.80. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “32 CAP patients and 36 health controls”
- body site study.description · “changes in stool metabolites”
- life stage sample.attr.age · “70 (n=34/68)”
- life stage sample.attr.age · “61 (n=34/68)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN43380229 | age_at_collection_days | 24471.8 | R1 | 0.70 | sample.attr.age | 67 |
| SAMN43380229 | collection_date | 2023-02-25 | R1 | 0.90 | biosample.attribute:collection_date | 2023-02-25T08:10:05Z |
| SAMN43380229 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China: zibo |
| SAMN43380265 | health_condition | other_infection | R2 | 0.85 | paper.supp.spectrum.02639-24-s0006.docx[table1!Group] | CAP patients |
| SAMN43380229 | health_condition_detail | mixed_case_control: community-acquired pneumonia patients vs healthy controls | R4 | 0.50 | study.description | 32 CAP patients and 36 health controls |
| SAMN43380229 | location_locality | Zibo | R1 | 0.85 | biosample.attribute:geo_loc_name | China: zibo |
| SAMN43380229 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN43380229 | subject_id | SAMN43380229 | R3 | 0.70 | design.one_sample_per_subject:fulltext | This study enrolled 32 CAP patients and 36 matched non-infectious healthy controls. |
Sequencing
68 runs over 68 samples · mean 11.72 Gbp per run (median 11.76 Gbp, total 797.04 Gbp; 68 runs with a base count) · layout PAIRED 68 · platform ILLUMINA 68 · models Illumina NovaSeq 6000 (68) · 87% of runs with a Sandpiper profile · first public 2024-12-29
Authors (10)
Zhang F first · Luan J · Suo L · Wang H · Zhao Y · Sun T · Ni Y · Cao H · Zou X · Liu B last
Downloads
PRJNA1152927.csv.gz (3.1 KB) · parquet (74.0 KB) — all 68 samples, every field with route and confidence · PRJNA1152927_determinations.csv.gz (5.0 KB) — 508 evidence rows