Effects of preservation and storage on fecal microbiome
1536 human and canine fecal samples exposed to preservation methods (freezing, ethanol, RNALater, Omni-gene gut, FTA cards) and temperature conditions; note: the attached paper abstract (American Gut Project, Boulder, CO) describes a different study and was not used. machine-written summary
1,076 samples · 4,221 runs · US · Adult · 2018 · 0.16 Gbp / sample · cohort American Gut: an Open Platform for Citizen Science
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 7,532 sample values (collection date, country, latitude, location locality, location region, longitude, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC5069758, PMC5954204, PMC6860998 |
| ○ 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
design observational_with_procedure
longitudinal — not resolved
23 of 56 people sampled more than once (1,043 samples; median 13, up to 97 per person).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 1,076 | 100% | ||||
| country | 1,076 | 100% | 1,076 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 1,076 | 100% | 1,076 | |||
| collection_date | 1,076 | 100% | 1,076 | |||
| detailed_location | 1,076 | 100% | ||||
| latitude | 1,076 | 100% | 1,076 | |||
| location_locality | 1,076 | 100% | 1,076 | |||
| location_region | 1,076 | 100% | 1,076 | |||
| longitude | 1,076 | 100% | 1,076 |
- Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies. 2016 PMID 27822526 PMC5069758 own_data
- American Gut: an Open Platform for Citizen Science Microbiome Research. 2018 PMID 29795809 PMC5954204 own_data
- Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations. 2019 PMID 31738775 PMC6860998 own_data
Archive description
Microbiome studies using fecal samples have allowed us to discover a lot about human health, animal evolution, and basic host-microbe interactions. In most studies, the workflow of conducting a microbiome study involves collecting and stabilizing a sample until it can be processed in a laboratory so that the community experiences little to no change until analysis. One widely used method is freezing at -20C or -80C. However, in scenarios were freezing is not a viable option, an alternative preservation method must used, but the effectiveness of commonly used preservatives is not well understood. To better understand the effects of different storage preservatives and storage conditions on the microbial community of fecal samples, we exposed human and canine fecal samples to a variety of commonly used preservation methods including freezing, using ethanol, RNALater, Omni-gene gut, and FTA cards, and a range of temperature conditions.
How this project entered the registry
Classified as human and non-human (mixed) gut / stool mixed assays of adult by sonnet_x2 with confidence 0.72. Assay mixed.
- host run.host_tax_id · “9606”
- host run.host_tax_id · “9615”
- host study.description · “we exposed human and canine fecal samples”
- body site run.scientific_name · “human gut metagenome”
- life stage sample.attr.host_life_stage · “adult (n=1411/1536)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104467936 | collection_date | 2014-10-13 | R1 | 0.85 | biosample.attribute:collection_timestamp | 2014-10-13 |
| SAMEA104467936 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:CO:Boulder |
| SAMEA104467936 | latitude | 40.0100 | R1 | 0.90 | biosample.attribute:latitude+longitude | 40.01 -105.25 |
| SAMEA104467936 | location_locality | Boulder | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:CO:Boulder |
| SAMEA104467936 | location_region | Colorado | R1 | 0.75 | biosample.attribute:geo_loc_name | USA:CO:Boulder |
| SAMEA104467936 | longitude | -105.2500 | R1 | 0.90 | biosample.attribute:latitude+longitude | 40.01 -105.25 |
| SAMEA104467936 | subject_id | BLANK.5.11.F | R1 | 0.85 | sample.attr.host_subject_id | BLANK.5.11.F |
Sequencing
4,221 runs over 1,076 samples · mean 0.12 Gbp per run (median 0.13 Gbp, total 499.82 Gbp; 4,221 runs with a base count) · layout PAIRED 3,070, SINGLE 1,151 · platform ILLUMINA 4,221 · models Illumina HiSeq 2500 (4,221) · 0% of runs with a Sandpiper profile · first public 2018-01-12 – 2020-12-24
Authors (72)
Song SJ first · Amir A · Metcalf JL · Amato KR · Xu ZZ · Humphrey G · Knight R last · McDonald D first · Hyde E · Debelius JW · Morton JT · Gonzalez A · Ackermann G · Aksenov AA · Behsaz B · Brennan C · Chen Y · DeRight Goldasich L · Dorrestein PC · Dunn RR · Fahimipour AK · Gaffney J · Gilbert JA · Gogul G · Green JL · Hugenholtz P · Huttenhower C · Jackson MA · Janssen S · Jeste DV · Jiang L · Kelley ST · Knights D · Kosciolek T · Ladau J · Leach J · Marotz C · Meleshko D · Melnik AV · Mohimani H · Montassier E · Navas-Molina J · Nguyen TT · Peddada S · Pevzner P · Pollard KS · Rahnavard G · Robbins-Pianka A · Sangwan N · Shorenstein J · Smarr L · Spector T · Swafford AD · Thackray VG · Thompson LR · Tripathi A · Vázquez-Baeza Y · Vrbanac A · Wischmeyer P · Wolfe E · Zhu Q · American Gut Consortium · Byrd DA first · Chen J · Vogtmann E · Hullings A · Kibriya MG · Ahsan H · Nelson H · Shi J · Chia N · Sinha R last
Downloads
PRJEB13595.csv.gz (21.4 KB) · parquet (102.5 KB) — all 1,076 samples, every field with route and confidence · PRJEB13595_determinations.csv.gz (38.3 KB) — 7,532 evidence rows