crAss001 phage-Bacteroides intestinalis persistence, Cork
101 samples from Cork, Ireland, including an intervention cohort of 29, studying persistence of crAss-like phage crAss001 in Bacteroides intestinalis cultures in vitro and in vivo; design listed as other. machine-written summary
101 samples · 101 runs · IE · Age unknown · 2021 · 1.06 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 666 sample values (collection date, country, health condition, intervention, latitude, location region, longitude, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8375218 |
| ○ 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 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 101 | 100% | 101 | |||
| health_condition | 29 | 29% | 29 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 101 | 100% | 101 | |||
| detailed_location | 101 | 100% | ||||
| latitude | 101 | 100% | 101 | |||
| location_region | 101 | 100% | 101 | |||
| longitude | 101 | 100% | 101 | |||
| timepoint_label | 101 | 100% | 101 | |||
| intervention | 31 | 31% | 31 |
- Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis. 2021 PMID 34407825 PMC8375218 own_data
Archive description
The crAss-like phages are ubiquitous and highly abundant members of the human gut virome that infect commensal bacteria of the order Bacteroidales. Although incapable of classical lysogeny, these viruses demonstrate long-term persistence in the human gut microbiome, dominating the virome in some individuals. Here we employ a combination of genomic and transcriptomic approaches to investigate persistence mechanisms of phage crAss001 in cultures of its host Bacteroides intestinalis both in vitro and in vivo.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.45. Assay shotgun_dna.
- host study.description · “human gut microbiome”
- body site study.description · “human gut virome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN16802447 | collection_date | 2020 | R1 | 0.90 | biosample.attribute:collection_date | 2020 |
| SAMN16802447 | country | IE | R1 | 0.90 | sample.attr.geo_loc_name | Ireland:Cork |
| SAMN16802462 | health_condition | intervention_cohort | R1 | 0.80 | biosample_attr | phage |
| SAMN16802494 | intervention | no_intervention | R1 | 0.85 | biosample.attribute:experimental_group | no phage |
| SAMN16802447 | latitude | 51.8900 | R1 | 0.90 | biosample.attribute:lat_lon | 51.89 N 8.47 W |
| SAMN16802447 | location_region | Cork | R1 | 0.85 | biosample.attribute:geo_loc_name | Ireland:Cork |
| SAMN16802447 | longitude | -8.4700 | R1 | 0.90 | biosample.attribute:lat_lon | 51.89 N 8.47 W |
| SAMN16802447 | timepoint_label | 0 | R1 | 0.85 | sample.attr.time_point | 0 |
Sequencing
101 runs over 101 samples · mean 1.08 Gbp per run (median 1.06 Gbp, total 108.82 Gbp; 101 runs with a base count) · layout PAIRED 101 · platform ILLUMINA 101 · models Illumina NovaSeq 6000 (101) · 92% of runs with a Sandpiper profile · first public 2021-05-25
Authors (9)
Shkoporov AN first · Khokhlova EV · Stephens N · Hueston C · Seymour S · Hryckowian AJ · Scholz D · Ross RP · Hill C last
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJNA678472.csv.gz (3.2 KB) · parquet (74.1 KB) — all 101 samples, every field with route and confidence · PRJNA678472_determinations.csv.gz (4.3 KB) — 666 evidence rows