Testing MACM preservation of stool anaerobes, USA
98 stool samples from healthy controls in the USA were used to evaluate BIOME-Preserve (MACM), a preservation medium for maintaining anaerobic bacteria viability for later culture recovery. machine-written summary
98 samples · 98 runs · US · Age unknown · 2021 · 0.63 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 | 294 sample values (collection date, country, timepoint) |
| ✓ Abstract / description | 196 sample values (health condition, health condition detail) |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 5 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 | 98 | 100% | 98 | |||
| health_condition | 98 | 100% | 98 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 98 | 100% | 98 | |||
| health_condition_detail | 98 | 100% | 98 | |||
| timepoint_label | 98 | 100% | 98 |
- BIOME-Preserve: A novel storage and transport medium for preserving anaerobic microbiota samples for culture recovery. 2022 PMID 35061732 PMC8782539 unsure
Archive description
An increasing number of microbiome studies are using culture-based methods to phenotype and study organisms of interest from the microbiome. A large number of these organisms are facultative anaerobes or obligate anaerobes, yet the field remains without a viable product that can maintain viability of organisms in whole microbiome samples. Here we perform a preliminary assessment of the ability of a new product, Microbiota Anaerobic Collection Medium (MACM), to preserve bacteria from human stool for later culture recovery.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host study.description · “preserve bacteria from human stool”
- body site study.description · “human stool for later culture recovery”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA8918122 | collection_date | 2019-09-20 | R1 | 0.90 | biosample.attribute:collection_date | 2019-09-20 |
| SAMEA8918122 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA8918122 | health_condition | healthy_control | R4 | 0.35 | paper.abstract | fresh human stool and from human stool |
| SAMEA8918122 | health_condition_detail | healthy donors (no disease stated; stool donors presumed healthy) | R4 | 0.35 | paper.abstract | fresh human stool and from human stool |
| SAMEA8918122 | timepoint_label | 0 | R1 | 0.85 | sample.attr.timepoint | 0 |
Sequencing
98 runs over 98 samples · mean 0.62 Gbp per run (median 0.63 Gbp, total 60.43 Gbp; 98 runs with a base count) · layout SINGLE 98 · platform ILLUMINA 98 · models Illumina NovaSeq 6000 (98) · 5% of runs with a Sandpiper profile · first public 2021-07-02 – 2021-07-05
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJEB45653.csv.gz (3.2 KB) · parquet (73.4 KB) — all 98 samples, every field with route and confidence · PRJEB45653_determinations.csv.gz (3.0 KB) — 490 evidence rows