Microeukaryote enrichment method in UK human faecal samples
156 faecal samples from the United Kingdom were used to benchmark a bacterial-depletion SOP for enriching microeukaryotic cells before metagenomic sequencing, testing eight individuals with three technical replicates each. machine-written summary
156 samples · 156 runs · GB · Age unknown · 2026 · 3.06 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 780 sample values (collection date, country, latitude, location region, longitude) |
| ○ 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 · 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 | 156 | 100% | 156 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 156 | 100% | 156 | |||
| detailed_location | 156 | 100% | ||||
| latitude | 156 | 100% | 156 | |||
| location_region | 156 | 100% | 156 | |||
| longitude | 156 | 100% | 156 |
- Enriching the Human Stool Microeukaryotes for Shotgun Sequencing 2026 own_data
Archive description
The human gut microbiome harbours a diverse community of microeukaryotes, predominantly fungi, which may potentially play important roles in gut ecology and homeostasis. Despite their potential, the study of gut microeukaryotes has been hampered by the limited sensitivity of standard sequencing approaches, which struggle to capture DNA from low-abundance microorganisms against the overwhelming background of bacterial biomass. To address this, we developed a method to selectively enrich for microeukaryotic cells in human faecal samples by depleting bacterial cells prior to metagenomic sequencing. Through systematic comparison and optimisation at each processing step, we established a robust standard operating procedure (SOP) for microeukaryotic cell enrichment. By benchmarking this SOP across eight human faecal samples with three technical replicates each, we showed that it consistently increased microeukaryote representation in metagenomic libraries, greater microeukaryotic taxonomic diversity, and a reduced proportion of unclassified taxa. Together, these improvements enabled substantially deeper characterisation of the microeukaryotic fraction of the human gut microbiome.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.scientific_name · “human feces metagenome”
- body site study.description · “human faecal samples by depleting bacterial cells”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA123369398 | collection_date | 2023 | R1 | 0.90 | biosample.attribute:collection_date | 2023 |
| SAMEA123369398 | country | GB | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | United Kingdom |
| SAMEA123369398 | latitude | 52.6200 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.62 1.22 |
| SAMEA123369398 | location_region | England | R1 | 0.60 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.62 1.22 |
| SAMEA123369398 | longitude | 1.2200 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 52.62 1.22 |
Sequencing
156 runs over 156 samples · mean 6.95 Gbp per run (median 3.06 Gbp, total 1,084.08 Gbp; 156 runs with a base count) · layout PAIRED 156 · platform ILLUMINA 156 · models NextSeq 500 (156) · 0% of runs with a Sandpiper profile · first public 2026-09-04
Authors (0)
No author record.
Help complete this project
3 of the 4 core fields are below 50% coverage: age_category, health_condition, subject_id. Share metadata
Downloads
PRJEB123560.csv.gz (4.3 KB) · parquet (75.1 KB) — all 156 samples, every field with route and confidence · PRJEB123560_determinations.csv.gz (4.7 KB) — 780 evidence rows