Capsid-packaged DNA in healthy adult gut viromes, Cork, Ireland
Cross-sectional study of 10 faecal virome samples from healthy adult donors in Cork, Ireland, using nanopore sequencing to study capsid-mediated packaging and mobilisation of bacterial DNA by phages and gene transfer agents. machine-written summary
10 samples · 22 runs · IE · Adult · 2024 · 15.49 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 66 sample values (collection date, country, latitude, location region, longitude, sex, subject id) |
| ✓ Abstract / description | 20 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC12946183 |
| ○ 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 — not resolved
3 of 3 people sampled more than once (9 samples; median 3, up to 3 per person). Schedule stated by the source: “Single faecal collection per donor, fractionated into total community DNA and two VLP fractions (T/B); no repeat timepoints stated.”.
Genera, mean relative abundance over 9 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 | 10 | 100% | ||||
| country | 10 | 100% | 10 | |||
| health_condition | 10 | 100% | 10 | |||
| subject_id | 9 | 90% | 9 | |||
| collection_date | 10 | 100% | 10 | |||
| detailed_location | 10 | 100% | ||||
| health_condition_detail | 10 | 100% | 10 | |||
| location_region | 10 | 100% | 10 | |||
| latitude | 9 | 90% | 9 | |||
| longitude | 9 | 90% | 9 | |||
| sex | 9 | 90% | 9 |
- Large-scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome. 2026 PMID 41593069 PMC12946183 own_data
Archive description
Here, we present a novel approach to study packaging and mobilisation of bacterial DNA in complex microbial communities, such as the human gut microbiome, by viral or virus-like capsids.</p><p>Defective bacteriophage (phage) particles and gene transfer agents (GTAs) are constrained by their capsids structural properties in the length of host DNA they can package. This results in a narrow distribution of DNA fragment lengths associated with a given viral carrier. Oxford Nanopore long read sequencing of intact capsid-packaged single DNA molecules can be used to measure their lengths and identify read lengths peaks associated with specific viral carrier agents. The methodology developed in this study was validated using a selection of well-characterised transducing phages and a GTA-like element, and then applied to study bacterial DNA encapsidation and mobilisation in the faecal microbiomes from three healthy human donors.</p><p>Bacterial DNA encapsidation and mobilisation appears to be widespread in the microbiome with up to 4% of capsid-packaged DNA in he gut virome being of bacterial (non-prophage) origin. Generalised transduction and GTA activity is especially prevalent in the family Ospillospiraceae (genera Faecalibacterium, Gemmiger, Onthomonas), whereas examples of lateral transduction were observed in genus Bacteroides. In addition to that induction of prophages in a variety of highly prevalent anaerobic bacteria was observed.</p><p>Further work will be needed to understand biological significance of capsid mediated DNA packaging in the gut microbiome and its role in community structure, evolution on ecological timescales, spread of beneficial and detrimental genes, as well as its possible role in gastrointestinal disease.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “faecal microbiomes from three healthy human donors”
- life stage study.description · “three healthy human donors”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN42497252 | collection_date | 2019-12 | R1 | 0.90 | biosample.attribute:collection_date | 2019-12 |
| SAMN42497252 | country | IE | R1 | 0.90 | sample.attr.geo_loc_name | Ireland: Cork |
| SAMN42497252 | health_condition | healthy_control | R4 | 0.50 | study.description | three healthy human donors |
| SAMN42497252 | health_condition_detail | Healthy | R4 | 0.50 | study.description | three healthy human donors |
| SAMN42497252 | latitude | 51.8900 | R1 | 0.90 | biosample.attribute:lat_lon | 51.89 N 8.47 W |
| SAMN42497252 | location_region | Cork | R1 | 0.85 | biosample.attribute:geo_loc_name | Ireland: Cork |
| SAMN42497252 | longitude | -8.4700 | R1 | 0.90 | biosample.attribute:lat_lon | 51.89 N 8.47 W |
| SAMN42497252 | sex | female | R1 | 0.70 | sample.name_rule:host_subject_id | 925 |
| SAMN42497252 | subject_id | 925 | R1 | 0.85 | sample.attr.host_subject_id | 925 |
Sequencing
22 runs over 10 samples · mean 5.85 Gbp per run (median 2.58 Gbp, total 128.68 Gbp; 22 runs with a base count) · layout PAIRED 12, SINGLE 10 · platform ILLUMINA 12, OXFORD_NANOPORE 10 · models Illumina NovaSeq 6000 (12), MinION (10) · 50% of runs with a Sandpiper profile · first public 2024-12-01
Authors (11)
Borodovich T first · Buttimer C · Wilson JS · Bardy P · Smith M · Hill C · Khokhlova EV · Harte M · Govi B · Fogg PCM · Shkoporov AN last
Downloads
PRJNA1135972.csv.gz (1.2 KB) · parquet (70.3 KB) — all 10 samples, every field with route and confidence · PRJNA1135972_determinations.csv.gz (1.2 KB) — 86 evidence rows