Culturomics vs metagenomics in human gut microbiome
13 fecal samples from children were analyzed by comparing culture-dependent (colony picking, culture-enriched metagenomics) and culture-independent metagenomic sequencing to characterize gut microbiota; cross-sectional design. machine-written summary
13 samples · 13 runs · CN · Age unknown · 2024 · 6.70 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 52 sample values (collection date, latitude, location region, longitude) |
| ✓ Abstract / description | 13 sample values (subject id) |
| ✓ Full text | 39 sample values (antibiotic exposure, country, lifestyle) · PMC12039119 |
| ○ 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 |
intervention — arms not resolved
design observational_with_procedure
Genera, mean relative abundance over 12 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 | 13 | 100% | ||||
| country | 13 | 100% | 13 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 13 | 100% | 13 | |||
| antibiotic_exposure | 13 | 100% | 13 | |||
| collection_date | 13 | 100% | 13 | |||
| detailed_location | 13 | 100% | ||||
| latitude | 13 | 100% | 13 | |||
| lifestyle | 13 | 100% | 13 | |||
| location_region | 13 | 100% | 13 | |||
| longitude | 13 | 100% | 13 |
- Comparative analysis of three experimental methods for revealing human fecal microbial diversity. 2025 PMID 40301726 PMC12039119 own_data
Archive description
This study showed that a combination of culturomics and sequencing approaches can more effectively characterise the gut microbiota than either method alone. Culture restored some low-abundance bacterial species in the gut the CEMP approach provides a basis for the design of culture media to produce new microorganisms, and for the targeted screening of bacterial strains. CEMP will also allow for functional characterisation of bacterial populations, which will contribute to elucidation of their biological activity during host_bacteria and bacterial interactions in of the context of healthy and diseased states, and facilitate faecal transplantation. We also found that ECP missed most of the bacterial species present in culture media, therefore, the number of colonies collected during ECP should be expanded in future studies.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host study.title · “human gut microbiome”
- host run.host_tax_id · “9606”
- body site study.title · “human gut microbiome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN29590851 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | not used antibiotics or probiotics within 6 months |
| SAMN29590851 | collection_date | 2019-08-01/2019-08-30 | R1 | 0.90 | biosample.attribute:collection_date | 2019-08-01/2019-08-30 |
| SAMN29590851 | country | CN | R3 | 0.70 | paper.fulltext.methods | Hulunbuir Ewenki Banner, Inner Mongolia |
| SAMN29590851 | latitude | 49.1400 | R1 | 0.90 | biosample.attribute:lat_lon | 49.14 N 119.76 E |
| SAMN29590851 | lifestyle | pastoralist | R3 | 0.90 | paper.fulltext.methods | traditional animal husbandry village |
| SAMN29590851 | location_region | Inner Mongolia | R1 | 0.60 | biosample.attribute:lat_lon | 49.14 N 119.76 E |
| SAMN29590851 | longitude | 119.7600 | R1 | 0.90 | biosample.attribute:lat_lon | 49.14 N 119.76 E |
| SAMN29590851 | subject_id | PRJNA856821 | R4 | 0.65 | design.single_subject:abstract | In this study, one fresh fecal sample was cultured using 12 commercial or modified media |
Sequencing
13 runs over 13 samples · mean 6.73 Gbp per run (median 6.70 Gbp, total 87.44 Gbp; 13 runs with a base count) · layout PAIRED 13 · platform ILLUMINA 13 · models Illumina HiSeq 2500 (13) · 92% of runs with a Sandpiper profile · first public 2024-06-30
Downloads
PRJNA856821.csv.gz (1.2 KB) · parquet (70.3 KB) — all 13 samples, every field with route and confidence · PRJNA856821_determinations.csv.gz (1.6 KB) — 104 evidence rows