Fecal collection method comparison, adults, Minnesota
148 fecal samples from healthy adults in Rochester, Minnesota, comparing FOBT cards, FIT tubes, ethanol, and RNAlater storage methods against immediately-frozen samples for shotgun metagenomic microbiome profiling; cross-sectional design. machine-written summary
148 samples · 148 runs · US · Adult · 2020 · 3.67 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,184 sample values (collection date, country, latitude, location locality, location region, longitude, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 444 sample values (health condition, health condition detail, location site) · PMC7045388 |
| ○ 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
15 of 15 people sampled more than once (148 samples; median 10, up to 11 per person) · follow-up median 4 d (max 4 d) · median interval between samples 4 d (time from timepoint labels).
Each row is one person (15 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 138 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 | 148 | 100% | ||||
| country | 148 | 100% | 148 | |||
| health_condition | 148 | 100% | 148 | |||
| subject_id | 148 | 100% | 148 | |||
| collection_date | 148 | 100% | 148 | |||
| detailed_location | 148 | 100% | ||||
| health_condition_detail | 148 | 100% | 148 | |||
| latitude | 148 | 100% | 148 | |||
| location_locality | 148 | 100% | 148 | |||
| location_region | 148 | 100% | 148 | |||
| location_site | 148 | 100% | 148 | |||
| longitude | 148 | 100% | 148 | |||
| timepoint_label | 148 | 100% | 148 |
- Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing. 2020 PMID 32250964 PMC7045388 own_data
Archive description
Few previous studies have assessed stability and "gold-standard" concordance of fecal sample collection methods for whole genome shotgun metagenomic sequencing (WGSS), an increasingly popular method for studying the gut microbiome. We used WGSS data to investigate ambient temperature stability and putative gold-standard concordance of microbial profiles in fecal samples collected and stored using fecal occult blood test (FOBT) cards, fecal immunochemical tests (FIT) tubes, 95% ethanol, or RNAlater. Among 15 Mayo Clinic employees, for each collection method, we calculated intraclass correlation coefficients (ICCs) to estimate stability of fecal microbial profiles after storage for 4 days at ambient temperature and concordance with immediately-frozen, no-solution samples (i.e., the putative gold-standard). ICCs were estimated for multiple metrics including relative abundance of select phyla, species, KEGG k-genes, KEGG modules, KEGG pathways, species and k-gene alpha diversity, and Bray-Curtis and Jaccard species beta diversity. ICCs for microbial profile stability were excellent for fecal samples collected via most of the collection methods, except those preserved in 95% ethanol. Concordance with the immediately-frozen, no-solution samples varied for all collection methods, but the number of observed species and the beta diversity metrics tended to have higher concordance than other metrics. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT cards, FIT tubes, and RNAlater are acceptable choices for fecal sample collection methods in future WGSS studies.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “methods to collect fecal samples for microbiome”
- body site study.description · “"gold-standard" concordance of fecal sample collection methods”
- body site study.description · “using fecal occult blood test (FOBT) cards,”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN14087305 | collection_date | 2014-11-24 | R1 | 0.90 | biosample.attribute:collection_date | 2014-11-24 |
| SAMN14087305 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Rochester, Minnesota |
| SAMN14087305 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | 52 healthy volunteers were recruited |
| SAMN14087305 | health_condition_detail | healthy volunteers | R3 | 0.70 | paper.fulltext.methods | 52 healthy volunteers were recruited |
| SAMN14087305 | latitude | 44.0164 | R1 | 0.90 | biosample.attribute:lat_lon | 44.016369 N 92.475395 W |
| SAMN14087305 | location_locality | Rochester | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Rochester, Minnesota |
| SAMN14087305 | location_region | Minnesota | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Rochester, Minnesota |
| SAMN14087305 | location_site | Mayo Clinic | R3 | 0.70 | paper.fulltext.methods | Mayo Clinic employees in Rochester, MN |
| SAMN14087305 | longitude | -92.4754 | R1 | 0.90 | biosample.attribute:lat_lon | 44.016369 N 92.475395 W |
| SAMN14087305 | subject_id | 1004 | R1 | 0.70 | sample.name_rule:alias | 1004-0452 |
| SAMN14087305 | timepoint_label | Day4 | R1 | 0.85 | biosample.attribute:description | Day4 |
Sequencing
148 runs over 148 samples · mean 3.68 Gbp per run (median 3.67 Gbp, total 544.21 Gbp; 148 runs with a base count) · layout PAIRED 148 · platform ILLUMINA 148 · models Illumina HiSeq 2000 (148) · 93% of runs with a Sandpiper profile · first public 2020-02-18
Authors (16)
Byrd DA first · Sinha R · Hoffman KL · Chen J · Hua X · Shi J · Chia N · Petrosino J · Vogtmann E last · Tarracchini C first · Lugli GA · Mancabelli L · van Sinderen D · Turroni F · Ventura M · Milani C last
Downloads
PRJNA606198.csv.gz (4.3 KB) · parquet (75.8 KB) — all 148 samples, every field with route and confidence · PRJNA606198_determinations.csv.gz (10.6 KB) — 1,628 evidence rows