Phage isolation methods in healthy adult faeces, France
33 faecal samples from healthy French adults, used to compare five phage isolation techniques, MDA amplification reproducibility, and sequencing depth effects on phage diversity; cross-sectional design. machine-written summary
33 samples · 33 runs · FR · Adult · 2019 · 0.33 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 192 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 66 sample values (health condition, health condition detail) · PMC6683287 |
| ○ 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
Other administered intervention (see intervention_detail) design observational_with_procedure · population healthy_control · Methodological comparison of phage isolation/extraction techniques from faeces, incl. MDA
“five different techniques to isolate phages” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
3 of 3 people sampled more than once (27 samples; median 9, up to 9 per person).
Genera, mean relative abundance over 2 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 | 33 | 100% | ||||
| country | 33 | 100% | 33 | |||
| health_condition | 33 | 100% | 33 | |||
| subject_id | 27 | 82% | 27 | |||
| collection_date | 33 | 100% | 33 | |||
| detailed_location | 33 | 100% | ||||
| health_condition_detail | 33 | 100% | 33 | |||
| latitude | 33 | 100% | 33 | |||
| location_region | 33 | 100% | 33 | |||
| longitude | 33 | 100% | 33 |
- A simple, reproducible and cost-effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach. 2019 PMID 31383878 PMC6683287 own_data
Archive description
The microbiota of the human gut is a complex and rich community where bacteria and their viruses, the phages, are numerically dominant. While the bacterial components have been extensively studied, there are fewer studies on the phage community and no clear standard for isolating the phages and sequencing and analysing their genomes. Since this makes comparisons between studies difficult, we aimed at defining an easy, low-cost, and reproducible methodology for each of these three steps. We analysed five different techniques to isolate phages from human adult faeces and developed a pipeline to analyse their genomes in order to quantify contamination and classify phage contigs in terms of taxonomy and lifestyle. Among the five techniques, we chose the polyethylene glycol concentration method to isolate phages because of its simplicity, low cost, reproducibility, and high number and diversity of phage sequences. We also tested the reproducibility of this method with multiple displacement amplification (MDA) and showed that MDA severely decreases the phage genetic diversity of the samples and the reproducibility of the method. Lastly, we studied the influence of depth sequencing on phage diversity and observed the beginning of a plateau for phage contigs at 20,000,000 reads. This work contributes for the development of methods to the isolation of phages in faeces and of their comparative analysis.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_unknown_no_evidence”
- body site study.title · “from human adult faeces”
- body site study.description · “of the human gut is a complex”
- life stage study.title · “phages from human adult faeces”
- life stage study.description · “phages from human adult faeces and developed”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA5376168 | collection_date | 2015-10 | R1 | 0.90 | biosample.attribute:collection_date | 2015-10 |
| SAMEA5376168 | country | FR | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | France |
| SAMEA5376168 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | three unrelated healthy adult volunteers (AA, BB and CC) |
| SAMEA5376168 | health_condition_detail | healthy adult volunteer(s) | R3 | 0.70 | paper.fulltext.methods | three unrelated healthy adult volunteers (AA, BB and CC) |
| SAMEA5376168 | latitude | 48.8534 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.85341 2.3488 |
| SAMEA5376168 | location_region | Ile-de-France | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.85341 2.3488 |
| SAMEA5376168 | longitude | 2.3488 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 48.85341 2.3488 |
| SAMEA5376174 | subject_id | AA | R1 | 0.70 | sample.name_rule:alias | alias=AA1_S; |
Sequencing
33 runs over 33 samples · mean 1.03 Gbp per run (median 0.33 Gbp, total 33.90 Gbp; 33 runs with a base count) · layout PAIRED 33 · platform ILLUMINA 33 · models Illumina MiSeq (32), Illumina HiSeq 2500 (1) · 6% of runs with a Sandpiper profile · first public 2019-02-26
Authors (10)
d'Humières C first · Touchon M · Dion S · Cury J · Ghozlane A · Garcia-Garcera M · Bouchier C · Ma L · Denamur E · P C Rocha E last
Downloads
PRJEB30796.csv.gz (1.6 KB) · parquet (70.9 KB) — all 33 samples, every field with route and confidence · PRJEB30796_determinations.csv.gz (2.5 KB) — 258 evidence rows