Gut microbiome in hospitalized vs ER diarrhea patients, Colombia
41 fecal samples from adult and elderly diarrhea patients at a Bogotá, Colombia hospital, comparing hospitalized (n=24) and emergency room (n=17) groups in a case-control design. machine-written summary
41 samples · 41 runs · CO · Age unknown · 2024 · 7.30 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 82 sample values (collection date, country) |
| ✓ Abstract / description | 41 sample values (health condition) |
| ✓ Full text | 123 sample values (location locality, location site, subject id) · PMC12980963 |
| ✓ Supplementary tables | 117 sample values (age, health condition detail, sex) |
| – 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 41 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 | 41 | 100% | ||||
| country | 41 | 100% | 41 | |||
| health_condition | 41 | 100% | 41 | |||
| subject_id | 41 | 100% | 41 | |||
| collection_date | 41 | 100% | 41 | |||
| detailed_location | 41 | 100% | ||||
| health_condition_detail | 41 | 100% | 41 | |||
| location_locality | 41 | 100% | 41 | |||
| location_site | 41 | 100% | 41 | |||
| age_at_collection_days | 38 | 93% | 38 | |||
| sex | 38 | 93% | 38 |
- Contrasting the gut microbiome in Colombian patients with diarrhea: a comparative metagenomic study in hospitalization and emergency room services. 2026 PMID 41692795 PMC12980963 own_data
Archive description
Background: Hospital environments contain several factors that can alter the intestinal microbiome of patients. Among the most critical risk factors to patient health in these settings are the circulation of virulence factors (VFs) and antibiotic resistance markers (ARMs) from potentially pathogenic organisms. Shotgun metagenomics aids in describing the microbiome composition throughout microbial communities profiling while also providing functional profiling targeting crucial molecular markers associated with the risk of diseases, mainly at the hospital level. Thus, we characterized the intestinal microbiome of patients with diarrhea admitted to hospitalization (Hosp, n=24) and emergency departments (ER, n=17) at the Hospital Universitario Mayor Méderi in Bogotá, Colombia. The collected fecal samples were subjected to shotgun metagenomics for subsequent taxonomical profiling of bacterial and viral communities and identification of VFs and ARMs. Results: Our results showed a high abundance of species belonging to the Enterobacteriaceae family in the study groups, such as Klebsiella pneumoniae and Escherichia coli. Additionally, viral families such as Myoviridae, Siphoviridae, and Podoviridae displayed high abundance in both groups, being crAss-like viruses particularly notable. Interestingly, the differentially abundant members between the study groups were Escherichia-specific and Klebsiella-specific phages (p<0.05). Additionally, we identified virulence factors associated with Klebsiella pneumoniae capsule and secretion systems. Also, we highlighted the presence of different toxins of Clostridioides difficile and Clostridium perfringens in the study groups. Finally, Hosp patients exhibited many genomic and plasmid ARMs, with those conferring resistance to glycopeptides showing a differential abundance between groups. Conclusions: This study provides microbiome profiling performed in hospitalization and emergency patients in Colombia. Thus, this information can contribute to optimizing treatments and practices for managing patients in these facilities.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “characterized the intestinal microbiome of patients”
- body site study.description · “The collected fecal samples were subjected”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA115811451 | age_at_collection_days | 14245 | R2 | 0.85 | paper.supp.13099_2026_809_MOESM4_ESM.xlsx[Hoja1!Age] | 39 |
| SAMEA115811451 | collection_date | 2022-08-18/2023-05-08 | R1 | 0.90 | biosample.attribute:collection_date | 2022-08-18/2023-05-08 |
| SAMEA115811451 | country | CO | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Colombia |
| SAMEA115811451 | health_condition | gi_infection_or_diarrhoea | R4 | 0.50 | study.description | patients with diarrhea admitted to hospitalization |
| SAMEA115811451 | health_condition_detail | Hosp | R2 | 0.85 | paper.supp.13099_2026_809_MOESM5_ESM.xlsx[Hoja4!Group] | Hosp |
| SAMEA115811451 | location_locality | Bogotá | R3 | 0.70 | paper.fulltext.methods | Universitario Mayor Méderi in Bogotá, Colombia |
| SAMEA115811451 | location_site | Hospital Universitario Mayor Méderi | R3 | 0.70 | paper.fulltext.methods | attending the Universitario Mayor Méderi in Bogotá |
| SAMEA115811451 | sex | male | R2 | 0.85 | paper.supp.13099_2026_809_MOESM4_ESM.xlsx[Hoja1!Sex] | Male |
| SAMEA115811451 | subject_id | SAMEA115811451 | R3 | 0.70 | design.one_sample_per_subject:fulltext | Fecal samples from 41 patients (Hosp = 24; ER = 17) |
Sequencing
41 runs over 41 samples · mean 7.07 Gbp per run (median 7.30 Gbp, total 290.01 Gbp; 41 runs with a base count) · layout PAIRED 41 · platform ILLUMINA 41 · models Illumina NovaSeq 6000 (41) · 100% of runs with a Sandpiper profile · first public 2024-12-16
Authors (14)
Vega L first · Birchenall-Jiménez CI · Aponte A · Durán D · López C · Moreno-Matson MC · Perilla C · Pinilla D · Rodríguez-Leguizamón G · Sánchez E · Santana A · Herrera G · Ramírez JD · Muñoz M last
Downloads
PRJEB77410.csv.gz (2.4 KB) · parquet (72.5 KB) — all 41 samples, every field with route and confidence · PRJEB77410_determinations.csv.gz (3.6 KB) — 363 evidence rows