Pooled gut microbiome standards, omnivore vs vegan diet
PacBio HiFi sequencing of 4 pooled human gut microbiome standard samples (fecal material from four adults each), produced by The BioCollective and NIST; two samples represent an omnivore diet and two a vegan diet. machine-written summary
4 samples · 4 runs · Adult · 2021 · 17.01 Gbp / sample · cohort HiFi metagenomic sequencing enables assembly of ac
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 16 sample values (collection date, diet, diet detail, lifestyle, lifestyle detail) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 4 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 4 | 100% | 4 | |||
| diet | 4 | 100% | 4 | |||
| diet_detail | 4 | 100% | 4 | |||
| lifestyle | 2 | 50% | 2 | |||
| lifestyle_detail | 2 | 50% | 2 |
- HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota. 2022 PMID 36289209 PMC9606305 unsure
- BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis. 2024 PMID 38467684 PMC10928208 unsure
Archive description
Sequencing of pooled human gut microbiome standards. These samples are provided to allow evaluation of long-read shotgun metagenomics in empirical samples (vs. mock communities). These samples are standardized controls produced and provided by The BioCollective, in conjunction with the National Institute of Standard and Technology (NIST). Each sample contains fecal material from four human adults. The pooled samples were lyophilized, homogenized, and processed with TruMatrix technology to ensure long-term stability of the microbial community. Samples 138274 and 138390 represent an omnivore diet, whereas samples 139369 and 139445 represent a vegan diet.</p><p>For each sample, high molecular weight DNA was extracted using the Qiagen PowerSoil Pro kit. Size selection was performed using 3.7X Diluted AMPure. Library prep was performed using the SMRTbell Express Template Prep Kit 2.0 and Enzyme Clean Up Kit 2.0. Each sample was sequenced on one SMRT Cell 8M on the Sequel IIe System with Sequel II Binding Kit 2.2 chemistry 2.0, with a 30hr movie time with a 2 hr pre-extension. HiFi reads (>Q20, >99% accurate CCS reads) were generated using CCS v6.0.0 in SMRT Link v10.1.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host study.description · “fecal material from four human adults”
- body site run.scientific_name · “human gut metagenome”
- life stage study.description · “fecal material from four human adults”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN20443128 | collection_date | 2020 | R1 | 0.90 | biosample.attribute:collection_date | 2020 |
| SAMN20443128 | diet | omnivore | R1 | 0.90 | biosample.attribute:host_diet | omnivore |
| SAMN20443128 | diet_detail | omnivore | R1 | 0.90 | biosample.attribute:host_diet | omnivore |
| SAMN20443130 | lifestyle | vegetarian_or_vegan | R1 | 0.85 | biosample.attribute:host_diet | vegan |
| SAMN20443130 | lifestyle_detail | vegan | R1 | 0.85 | biosample.attribute:host_diet | vegan |
Sequencing
4 runs over 4 samples · mean 17.02 Gbp per run (median 17.01 Gbp, total 68.08 Gbp; 4 runs with a base count) · layout SINGLE 4 · platform PACBIO_SMRT 4 · models Sequel II (4) · 0% of runs with a Sandpiper profile · first public 2021-08-25
Authors (28)
Kim CY first · Ma J · Lee I last · Qiu Z first · Yuan L · Lian CA · Lin B · Chen J · Mu R · Qiao X · Zhang L · Xu Z · Fan L · Zhang Y · Wang S · Li J · Cao H · Li B · Chen B · Song C · Liu Y · Shi L · Tian Y · Ni J · Zhang T · Zhou J · Zhuang WQ · Yu K last
Downloads
PRJNA750084.csv.gz (973 B) · parquet (69.1 KB) — all 4 samples, every field with route and confidence · PRJNA750084_determinations.csv.gz (515 B) — 16 evidence rows