Single-cell viral tagging of gut phage-host pairs, Brisbane
560 fecal samples from healthy control subjects in Brisbane, Australia, analyzed in a cross-sectional study using single-cell viral tagging to identify bacteriophage-host pairings in the gut microbiome. machine-written summary
560 samples · 560 runs · AU · Age unknown · 2019 · 1.33 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 4,452 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| ✓ External resources | 1,032 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
28 of 28 people sampled more than once (560 samples; median 10, up to 108 per person).
Genera, mean relative abundance over 436 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 | 0 | 0% | ||||
| country | 560 | 100% | 560 | |||
| health_condition | 560 | 100% | 44 | 516 | ||
| subject_id | 560 | 100% | 560 | |||
| collection_date | 560 | 100% | 560 | |||
| detailed_location | 560 | 100% | ||||
| health_condition_detail | 560 | 100% | 44 | 516 | ||
| latitude | 560 | 100% | 560 | |||
| location_locality | 560 | 100% | 560 | |||
| location_region | 560 | 100% | 560 | |||
| longitude | 560 | 100% | 560 | |||
| timepoint_label | 240 | 43% | 240 | |||
| sex | 204 | 36% | 204 |
- Defining the human gut host-phage network through single-cell viral tagging. 2019 PMID 31384000 own_data
Archive description
Human fecal samples were collected to find links between bacteria and their bacteriophages
How this project entered the registry
Classified as human gut / stool mixed assays of age unknown by sonnet_x2 with confidence 0.60. Assay mixed.
- host run.host_tax_id · “9606”
- host study.description · “Human fecal samples were collected”
- body site study.title · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN10174413 | collection_date | 2017 | R1 | 0.90 | biosample.attribute:collection_date | 2017 |
| SAMN10174413 | country | AU | R1 | 0.90 | sample.attr.geo_loc_name | Australia: Brisbane |
| SAMN10174413 | health_condition | healthy_control | R1 | 0.90 | biosample_attr | healthy |
| SAMN10174458 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN10174413 | health_condition_detail | healthy | R1 | 0.90 | sample.attr.health_state | healthy |
| SAMN10174458 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN10174413 | latitude | -27.4698 | R1 | 0.90 | biosample.attribute:lat_lon | 27.4698 S 153.0251 E |
| SAMN10174413 | location_locality | Brisbane | R1 | 0.85 | biosample.attribute:geo_loc_name | Australia: Brisbane |
| SAMN10174413 | location_region | Queensland | R1 | 0.60 | biosample.attribute:lat_lon | 27.4698 S 153.0251 E |
| SAMN10174413 | longitude | 153.0251 | R1 | 0.90 | biosample.attribute:lat_lon | 27.4698 S 153.0251 E |
| SAMN10174413 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN10174413 | subject_id | S01 | R1 | 0.85 | sample.attr.host_subject_id | S01 |
| SAMN10174720 | subject_id | male | R1 | 0.85 | biosample.attribute:host_subject_id | male |
| SAMN11380905 | subject_id | S03 | R1 | 0.70 | sample.name_rule:alias | S03.t01.a |
| SAMN11380905 | timepoint_label | sample 01 | R1 | 0.70 | sample.name_rule:alias | S03.t01.a |
Sequencing
560 runs over 560 samples · mean 1.65 Gbp per run (median 1.33 Gbp, total 924.52 Gbp; 560 runs with a base count) · layout SINGLE 560 · platform ILLUMINA 560 · models NextSeq 500 (560) · 82% of runs with a Sandpiper profile · first public 2019-06-18
Authors (25)
Džunková M first · Low SJ · Daly JN · Deng L · Rinke C · Hugenholtz P last · Fontana F first · Alessandri G · Tarracchini C · Bianchi MG · Rizzo SM · Mancabelli L · Lugli GA · Argentini C · Vergna LM · Anzalone R · Longhi G · Viappiani A · Taurino G · Chiu M · Turroni F · Bussolati O · van Sinderen D · Milani C · Ventura M last
Downloads
PRJNA492716.csv.gz (12.7 KB) · parquet (87.9 KB) — all 560 samples, every field with route and confidence · PRJNA492716_determinations.csv.gz (35.0 KB) — 5,484 evidence rows