Faecal preservation method comparison, healthy adults, Australia
420 faecal samples from healthy participants in Australia comparing room-temperature preservation methods (FLOQSwab-ADT, RNAlater, OMNIgene-GUT, LifeGuard, BBL swab) against flash-freezing, using shotgun metagenomics to assess species and functional reproducibility. machine-written summary
420 samples · 420 runs · AU · Age unknown · 2021 · 3.77 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,100 sample values (collection date, country, latitude, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 1,500 sample values (health condition, health condition detail, location locality, location site) · PMC9645250 |
| ✓ Supplementary tables | 840 sample values (health condition detail, subject id, timepoint) |
| – 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
15 of 15 people sampled more than once (420 samples; median 24, up to 36 per person) · follow-up median 28 d (max 28 d) · median interval between samples 28 d (time from timepoint labels).
Each row is one person (10 shown of 15); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 388 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 | 420 | 100% | 420 | |||
| health_condition | 420 | 100% | 420 | |||
| subject_id | 420 | 100% | 420 | |||
| collection_date | 420 | 100% | 420 | |||
| detailed_location | 420 | 100% | ||||
| health_condition_detail | 420 | 100% | 180 | 240 | ||
| latitude | 420 | 100% | 420 | |||
| location_locality | 420 | 100% | 420 | |||
| location_region | 420 | 100% | 420 | |||
| location_site | 420 | 100% | 420 | |||
| longitude | 420 | 100% | 420 | |||
| timepoint_label | 240 | 57% | 240 |
- Critical evaluation of faecal microbiome preservation using metagenomic analysis. 2021 PMID 37938632 PMC9645250 own_data
Archive description
Objective The ability to preserve microbial communities [DP1] in faecal samples is essential as increasing numbers of studies seek to use the gut microbiome to identify biomarkers of disease. Here we rigorously evaluate five room temperature (RT) preservation methods to accurately represent species and functional profiles from faecal metagenomes compared to the commonly accepted best practice of flash-freezing.Design The methods evaluated were OMNIgene-GUT, RNAlater, LifeGuard, BBL CultureSwab, and the Copan FLOQSwab in an active drying tube (FLOQSwab-ADT) for the maximum recommended storage time at RT, then at -20ᵒC until four weeks[DP2] [AP3] [AP4] . Each [DP5] method was assessed using six replicate faecal samples from five participants, totalling 180 samples. We further evaluated 240 samples across ten participants with the FLOQSwab-ADT to determine community stability after storage at -20ᵒC, RT, and 50ᵒC for four weeks compared to fresh controls. All samples were sequenced using shotgun metagenomics and gut microbiome profiles were assessed for technical and compositional (species and functional) reproducibility. Results FLOQSwab-ADT had the best combined performance followed by RNAlater and OMNIgene-GUT. LifeGuard and the BBL swab had unpredictable outgrowth of Escherichia species in at least one replicate from each participant. Additionally, FLOQSwab-ADT accurately preserved species and functional profiles at all temperatures tested relative to fresh controls. Conclusions FLOQSwab-ADT is a simple and robust liquid-free sampling method well-suited for direct-to-consumer and research-focused faecal sample preservation. BBL swab and LifeGuard are not recommended for RT preservation of faecal samples.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “metagenomic analysis of faecal microbiomes”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA7609822 | collection_date | 2018 | R1 | 0.90 | biosample.attribute:collection_date | 2018 |
| SAMEA7609822 | country | AU | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Australia |
| SAMEA7609822 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | five participants with no major medical conditions |
| SAMEA7610183 | health_condition_detail | Baseline | R2 | 0.85 | paper.supp.43705_2021_14_MOESM4_ESM.xlsx[Method comparison!Condition] | Baseline |
| SAMEA7609822 | health_condition_detail | participants with no major medical conditions | R3 | 0.70 | paper.fulltext.methods | five participants with no major medical conditions |
| SAMEA7609822 | latitude | -27.4660 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | -27.465979 153.029768 |
| SAMEA7609822 | location_locality | Woolloongabba | R3 | 0.70 | paper.fulltext.methods | collected on-site at the Translational Research Institute (Woolloongabba, QLD, AU) |
| SAMEA7609822 | location_region | Queensland | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | -27.465979 153.029768 |
| SAMEA7609822 | location_site | Translational Research Institute | R3 | 0.70 | paper.fulltext.methods | collected on-site at the Translational Research Institute |
| SAMEA7609822 | longitude | 153.0298 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | -27.465979 153.029768 |
| SAMEA7609822 | subject_id | 1 | R2 | 0.85 | paper.supp.43705_2021_14_MOESM4_ESM.xlsx[Temp comparison!Participant] | 1 |
| SAMEA7609822 | timepoint_label | T0 | R2 | 0.80 | paper.supp.43705_2021_14_MOESM4_ESM.xlsx[Temp comparison!Time] | Time: T0 |
Sequencing
420 runs over 420 samples · mean 4.35 Gbp per run (median 3.77 Gbp, total 1,828.34 Gbp; 420 runs with a base count) · layout PAIRED 420 · platform ILLUMINA 420 · models Illumina NovaSeq 6000 (420) · 92% of runs with a Sandpiper profile · first public 2021-01-22
Authors (12)
Pribyl AL first · Parks DH · Angel NZ · Boyd JA · Hasson AG · Fang L · MacDonald SL · Wills BA · Wood DLA · Krause L · Tyson GW · Hugenholtz P last
Downloads
PRJEB41481.csv.gz (10.2 KB) · parquet (84.0 KB) — all 420 samples, every field with route and confidence · PRJEB41481_determinations.csv.gz (24.8 KB) — 4,440 evidence rows