Methods optimization for gut metagenome profiling (Poland)
39 samples from Poland, including fecal samples from healthy adult volunteers and bacterial mock mixes, comparing homogenization times and library preparation kits (KAPA, Nextera, Qiagen) to assess bias in microbiome community profiling. machine-written summary
39 samples · 39 runs · PL · Adult · 2022 · 3.18 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 234 sample values (collection date, country, latitude, location region, longitude, subject id) |
| ✓ Abstract / description | 39 sample values (health condition detail) |
| ✓ Full text | 39 sample values (health condition) · PMC9120454 |
| ○ 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 — not resolved
5 of 5 people sampled more than once (39 samples; median 9, up to 9 per person).
Genera, mean relative abundance over 33 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 | 39 | 100% | ||||
| country | 39 | 100% | 39 | |||
| health_condition | 39 | 100% | 39 | |||
| subject_id | 39 | 100% | 39 | |||
| collection_date | 39 | 100% | 39 | |||
| detailed_location | 39 | 100% | ||||
| health_condition_detail | 39 | 100% | 39 | |||
| latitude | 39 | 100% | 39 | |||
| location_region | 39 | 100% | 39 | |||
| longitude | 39 | 100% | 39 |
- The standardisation of the approach to metagenomic human gut analysis: from sample collection to microbiome profiling. 2022 PMID 35589762 PMC9120454 own_data
Archive description
In this study, we intended to establish an optimized approach to investigating the metagenomes of fecal samples. We checked how experimental procedures on different stages of the analyses influenced community profiling and investigated the bias caused by subsequent bioinformatics procedures.We designed a test experiment that allowed us to scrutinize each part of the investigation procedure of fecal samples metagenomes. We started with the DNA isolation procedure and finished with computational methods for microbial communities profiling. For this study, we used: three fecal samples obtained from healthy volunteers (S1, S2, S3) and two commercially available bacterial mixes (ATCC Bacterial Mix MSA-2006 - a mix of 12 known bacteria and ATCC Genomic DNA MSA-1003 - a mix of 20 bacterial DNA). We tested three different times of homogenization: 10 min., 15 min., 20 min. We prepared DNA libraries using three sets of reagents from leading manufacturers - KAPA, Nextera, and Qiagen, obtaining 36 libraries. Additionally, we also introduced ATCC Genomic Mix DNA isolate sample to imitate the perfect isolation serve, giving three additional libraries (for KAPA, Nextera, and Qiagen). In total, we prepared 39 libraries - 13 libraries with each kit.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.57. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.description · “fecal samples metagenomes”
- life stage study.description · “healthy volunteers”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN20425676 | collection_date | 2019-09-15 | R1 | 0.90 | biosample.attribute:collection_date | 2019-09-15 |
| SAMN20425676 | country | PL | R1 | 0.90 | sample.attr.geo_loc_name | Poland |
| SAMN20425676 | health_condition | healthy_control | R3 | 0.70 | paper.fulltext.methods | three faecal samples obtained from healthy volunteers |
| SAMN20425676 | health_condition_detail | healthy volunteers | R4 | 0.50 | study.description | three fecal samples obtained from healthy volunteers |
| SAMN20425676 | latitude | 52.4064 | R1 | 0.90 | biosample.attribute:lat_lon | 52.4064 N 16.9252 E |
| SAMN20425676 | location_region | Greater Poland Voivodeship | R1 | 0.60 | biosample.attribute:lat_lon | 52.4064 N 16.9252 E |
| SAMN20425676 | longitude | 16.9252 | R1 | 0.90 | biosample.attribute:lat_lon | 52.4064 N 16.9252 E |
| SAMN20425676 | subject_id | GD | R1 | 0.85 | biosample.attribute:isolation_source | GD |
Sequencing
39 runs over 39 samples · mean 3.55 Gbp per run (median 3.18 Gbp, total 138.33 Gbp; 39 runs with a base count) · layout PAIRED 39 · platform ILLUMINA 39 · models NextSeq 550 (39) · 85% of runs with a Sandpiper profile · first public 2022-05-26
Authors (12)
Szóstak N first · Szymanek A · Havránek J · Tomela K · Rakoczy M · Samelak-Czajka A · Schmidt M · Figlerowicz M · Majta J · Milanowska-Zabel K · Handschuh L · Philips A last
Downloads
PRJNA749919.csv.gz (1.8 KB) · parquet (71.1 KB) — all 39 samples, every field with route and confidence · PRJNA749919_determinations.csv.gz (2.5 KB) — 312 evidence rows