Gut microbiome in colorectal adenoma, Latvia, case-control
136 fecal samples from adult patients undergoing colonoscopy in Latvia, including those with and without colorectal adenomas, analyzed by shotgun metagenomic sequencing in a case-control study of gut microbiome composition and function. machine-written summary
136 samples · 136 runs · LV · Age unknown · 2025 · 6.76 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 680 sample values (collection date, country, health condition, health condition detail, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 272 sample values (location locality, subject id) · PMC12978465 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 136 sample values (antibiotic exposure) · from BugSigDB |
| – 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 | 136 | 100% | ||||
| country | 136 | 100% | 136 | |||
| health_condition | 136 | 100% | 136 | |||
| subject_id | 136 | 100% | 136 | |||
| antibiotic_exposure | 136 | 100% | 136 | |||
| collection_date | 136 | 100% | 136 | |||
| detailed_location | 136 | 100% | ||||
| health_condition_detail | 136 | 100% | 136 | |||
| location_locality | 136 | 100% | 136 | |||
| sex | 136 | 100% | 136 |
- Colorectal adenoma presence is associated with decreased menaquinone pathway functions in the gut microbiome of patients undergoing routine colonoscopy. 2026 PMID 41811805 PMC12978465 own_data
Archive description
Our study aimed to examine the differences in gut microbiome compositions and functional implications between patients with and without colorectal adenomas. We employed shotgun metagenome sequencing of fecal samples collected a day before bowel preparation for a colonoscopy procedure using the DNBSEQ-G400RS sequencing platform and DNBSEQ-G400RS High-throughput Sequencing Set (FCL PE150). Microbial DNA was extracted from fecal samples using the FastDNA Spin Kit for Soil (MP Biomedicals), and libraries were prepared using the MGIEasy Universal DNA Library Prep Kit (MGI Tech Co., Ltd.). In addition, to characterize the miRNAs associated with colorectal adenomas and to assess the interaction between host miRNAs and gut microbiome in the background of the adenomas, intestinal miRNA sequencing was performed on a subset of patients using the Illumina Miseq platform and MiSeq Reagent Kit v3 (150 cycles). Intestinal biopsy samples were collected by trained medical personnel during the colonoscopy procedure. Total RNA, including miRNAs from intestinal biopsies, was extracted using AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN). Libraries were prepared using the QIAseq miRNA Library Kit (QIAGEN).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.60. Assay shotgun_dna.
- host study.title · “patients with colorectal adenomas”
- body site study.description · “shotgun metagenome sequencing of fecal samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA120468342 | antibiotic_exposure | no | R2 | 0.60 | external.bugsigdb source | Antibiotics exclusion: 1 month |
| SAMEA120468342 | collection_date | 2020 | R1 | 0.90 | biosample.attribute:collection_date | 2020 |
| SAMEA120468342 | country | LV | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | Latvia |
| SAMEA120468342 | health_condition | colorectal_adenoma | R1 | 0.80 | biosample_attr | ad |
| SAMEA120468345 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:colorectal_adenoma_status | colorectal_adenoma_status: co |
| SAMEA120468342 | health_condition_detail | ad | R1 | 0.90 | sample.attr.colorectal_adenoma_status | ad |
| SAMEA120468342 | location_locality | Riga | R3 | 0.70 | paper.fulltext.methods | outpatient endoscopy unit of Health Center 4 in Riga |
| SAMEA120468342 | sex | male | R1 | 0.90 | sample.attr.sex | M |
| SAMEA120468342 | subject_id | SAMEA120468342 | R3 | 0.75 | design.one_sample_per_subject:fulltext | This was an exploratory cross-sectional case– control study |
Sequencing
136 runs over 136 samples · mean 7.13 Gbp per run (median 6.76 Gbp, total 969.16 Gbp; 136 runs with a base count) · layout PAIRED 136 · platform DNBSEQ 136 · models DNBSEQ-G400 (136) · 0% of runs with a Sandpiper profile · first public 2025-11-05 – 2025-11-06
Authors (10)
Vilkoite I first · Silamiķelis I · Kloviņš J · Tolmanis I · Lejnieks A · Runce E · Cēbere K · Margole K · Sjomina O · Silamiķele L last
Downloads
PRJEB79034.csv.gz (4.4 KB) · parquet (76.0 KB) — all 136 samples, every field with route and confidence · PRJEB79034_determinations.csv.gz (6.9 KB) — 1,088 evidence rows