Frozen storage effects on stool microbiota, Switzerland
55 stool suspension samples from a single donor in Switzerland, studied for changes in 16S rRNA bacterial taxonomic profiles over 18 months of frozen storage at -80°C, comparing two DNA extraction protocols. machine-written summary
55 samples · 55 runs · CH · Age unknown · 2020 · 68.6 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 329 sample values (collection date, country, latitude, location region, longitude, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 110 sample values (health condition, health condition detail) · PMC7058979 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 55 | 100% | 55 | |||
| health_condition | 55 | 100% | 55 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 55 | 100% | 55 | |||
| detailed_location | 55 | 100% | ||||
| health_condition_detail | 55 | 100% | 55 | |||
| latitude | 55 | 100% | 55 | |||
| location_region | 55 | 100% | 55 | |||
| longitude | 55 | 100% | 55 | |||
| timepoint_label | 54 | 98% | 54 |
- Changes in Microbiota Profiles After Prolonged Frozen Storage of Stool Suspensions. 2020 PMID 32185143 PMC7058979 own_data
Archive description
Introduction. Faecal microbiota transplantation is recommended as a more efficacious alternative to standard vancomycin treatment for recurrent C. difficile infections. Freezing a donor’s stool samples simplifies the process, allowing a single stool sample to be used across multiple receivers and over an extended period of time. The aim was to assess the effect of long-term frozen storage on bacterial taxonomic profiles of frozen stool sample suspension prepared according to the standardized protocol.Methods. DNA was extracted from a stool sample suspension before freezing and sequentially during storage at –80°C for 1 week, 1 month, and then every three months from month 3 to month 18. Two different protocols were used for DNA extraction. The first relied on a combined mechanical and chemical cell disruption to extract both intra- and extracellular DNA the second included specific pre-treatments aimed at removing DNA from human and damaged bacterial cells.Results. Taxonomic profiling of bacterial communities was performed by sequencing of V3–V4 16S rRNA gene amplicons. Microbiota similarity between fresh and frozen samples progressively decreased with longer frozen storage times when DNA extraction procedure included pre-treatments notably, Bacteroidetes and Spirochaetes, tended to decrease in the relative abundance in a storage-duration dependent manner. In contrast, microbiota profiles obtained by whole DNA extraction procedure remained relatively stable for different frozen storage periods.Conclusion. Our data show that metataxonomic analysis of frozen stool suspensions subjected to specific pre-treatments prior to DNA extractions may provide an indirect measure of bacterial viability and/or susceptibility to survive stress conditions.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host study.description · “DNA from human and damaged bacterial cells”
- body site study.title · “Frozen Storage of Stool Suspensions”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA5843221 | collection_date | 2016-05-26 | R1 | 0.90 | biosample.attribute:collection_date | 2016-05-26 |
| SAMEA5843221 | country | CH | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Switzerland |
| SAMEA5843221 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | Stool sample(s) collected from a healthy volunteer |
| SAMEA5843221 | health_condition_detail | healthy volunteer | R3 | 0.70 | paper.fulltext.methods | Stool sample(s) collected from a healthy volunteer |
| SAMEA5843221 | latitude | 46.1920 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.192038 6.147173 |
| SAMEA5843221 | location_region | Geneva | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.192038 6.147173 |
| SAMEA5843221 | longitude | 6.1472 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 46.192038 6.147173 |
| SAMEA5843221 | timepoint_label | T0 | R1 | 0.70 | sample.name_rule:sample_alias | T0 - Molzym 1 |
Sequencing
55 runs over 55 samples · mean 68.1 Mbp per run (median 68.6 Mbp, total 3.75 Gbp; 55 runs with a base count) · layout PAIRED 55 · platform ILLUMINA 55 · models Illumina MiSeq (55) · 0% of runs with a Sandpiper profile · first public 2020-02-26
Authors (9)
Dorsaz S first · Charretier Y · Girard M · Gaïa N · Leo S · Schrenzel J · Harbarth S · Huttner B · Lazarevic V last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJEB33794.csv.gz (2.1 KB) · parquet (71.6 KB) — all 55 samples, every field with route and confidence · PRJEB33794_determinations.csv.gz (3.6 KB) — 439 evidence rows