BIOME-Preserve storage medium for anaerobe culture recovery, USA
119 stool culture samples from 3 adult USA donors, comparing anaerobic bacteria recovered fresh versus after storage in BIOME-Preserve transport medium for up to 120 hours. machine-written summary
119 samples · 119 runs · US · Adult · 2021 · 0.37 Gbp / sample · cohort BIOME-Preserve: A novel storage and transport medi
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 476 sample values (collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8782539 |
| ○ 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
4 of 4 people sampled more than once (119 samples; median 33, up to 50 per person) · follow-up median 10 d (max 10 d) · median interval between samples 2 d (time from collection dates).
Each row is one person (3 shown of 4); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 15 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 | 119 | 100% | ||||
| country | 119 | 100% | 119 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 119 | 100% | 119 | |||
| collection_date | 119 | 100% | 119 | |||
| timepoint_label | 119 | 100% | 119 |
- BIOME-Preserve: A novel storage and transport medium for preserving anaerobic microbiota samples for culture recovery. 2022 PMID 35061732 PMC8782539 unsure
Archive description
To fully leverage the microbiome, culture-based techniques are necessary. However, gold-standard collection and transport methods consider only the preservation of DNA and RNA, rather than organisms for future culture recovery. Here we present a novel product that can preserve anaerobes in human stool for culture recovery. Here we collect stool samples from three adult human donors, and through WGS sequencing of culture material, determine which anaerobic bacteria are preserved and culturable from BIOME-Preserve after 72 hours and 120 hours compared to culturable bacteria from fresh stool.
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 study.description · “human donors”
- body site run.scientific_name · “human gut metagenome”
- life stage study.description · “three adult human donors”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA7501945 | collection_date | 2020-02-23 | R1 | 0.90 | biosample.attribute:collection_date | 2020-02-23 |
| SAMEA7501945 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA7501945 | subject_id | D1 | R1 | 0.50 | sample.attr.donor | D1 |
| SAMEA7501945 | timepoint_label | 0 | R1 | 0.85 | sample.attr.timepoint | 0 |
Sequencing
119 runs over 119 samples · mean 0.52 Gbp per run (median 0.37 Gbp, total 61.82 Gbp; 119 runs with a base count) · layout PAIRED 119 · platform ILLUMINA 119 · models Illumina NovaSeq 6000 (119) · 13% of runs with a Sandpiper profile · first public 2021-01-05
Downloads
PRJEB40933.csv.gz (3.4 KB) · parquet (73.4 KB) — all 119 samples, every field with route and confidence · PRJEB40933_determinations.csv.gz (2.5 KB) — 476 evidence rows