DNA extraction kit comparison for neonatal gut microbiota
20 stool samples from neonates and infants in Kano, Nigeria, comparing three DNA extraction kits (QIAamp, PowerSoil Pro, ZymoBIOMICS) under varied storage conditions, sequenced with Oxford Nanopore long-read technology. machine-written summary
20 samples · 20 runs · NG · Infant / toddler · 2025 · 0.58 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 90 sample values (age, collection date, country, subject id, timepoint) |
| ✓ Abstract / description | 20 sample values (location locality) |
| – 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 |
longitudinal
5 of 5 people sampled more than once (20 samples; median 4, up to 4 per person) · follow-up median 42 d (max 42 d) · median interval between samples 42 d (time from timepoint labels). Schedule stated by the source: “Each of 5 infants sampled at Day 0 and Week 6, with two extraction kits (PowerSoil, ZymoBIOMICS) per timepoint.” (time origin: birth); stated follow-up 42 d.
Each row is one person (5 shown); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 20 | 100% | ||||
| country | 20 | 100% | 20 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 20 | 100% | 20 | |||
| collection_date | 20 | 100% | 20 | |||
| detailed_location | 20 | 100% | ||||
| location_locality | 20 | 100% | 20 | |||
| timepoint_label | 20 | 100% | 20 | |||
| age_at_collection_days | 10 | 50% | 10 |
Archive description
Accurate and reproducible gut microbiome profiling depends heavily on the DNA extraction method, particularly in low-biomass samples such as neonatal stool. In this study, we evaluated the performance of three commercially available DNA extraction kits - QIAamp Fast DNA Stool Mini, DNeasy PowerSoil Pro, and ZymoBIOMICS DNA Miniprep on neonatal stool samples collected in a resource-limited hospital in Kano, Nigeria. Samples were stored under various conditions (temperature and preservatives), and DNA was extracted and sequenced using Oxford Nanopore long-read technology. Our results showed that fresh, unpreserved samples yielded significantly higher DNA concentrations than stored or preserved samples. Kits incorporating mechanical lysis (PowerSoil and ZymoBIOMICS) outperformed the chemical lysis-based QIAamp kit in DNA yield and microbial recovery. While microbial diversity and taxonomic profiles were comparable between PowerSoil and ZymoBIOMICS, PowerSoil produced longer sequencing reads and required less processing time, making it more suitable for long-read metagenomics in field conditions. We conclude that same-day processing using bead-beating-based extraction kits improves yield and reduces bias in neonatal gut microbiome studies. These findings are especially relevant for low-resource settings, where equipment limitations and delayed sample processing can impact data quality and study scalability.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of neonate and infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “protocols for neonatal gut microbiota profiling in”
- body site study.description · “Accurate and reproducible gut microbiome profiling depends”
- life stage study.title · “extraction protocols for neonatal gut microbiota profiling”
- life stage study.description · “samples such as neonatal stool. In this”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN48451578 | age_at_collection_days | 0 | R1 | 0.80 | sample.title | D0 |
| SAMN48451578 | collection_date | 2023-02 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2023-02 |
| SAMN48451578 | country | NG | R1 | 0.90 | biosample_attr | Nigeria: Kano city |
| SAMN48451578 | location_locality | Kano | R4 | 0.45 | ena.study_description | resource-limited hospital in Kano, Nigeria |
| SAMN48451578 | subject_id | Sample1 | R1 | 0.50 | biosample_attr | Sample1 |
| SAMN48451578 | timepoint_label | D0 | R1 | 0.70 | sample.title | S1_PS_D0 |
Sequencing
20 runs over 20 samples · mean 0.71 Gbp per run (median 0.58 Gbp, total 14.13 Gbp; 20 runs with a base count) · layout SINGLE 20 · platform OXFORD_NANOPORE 20 · models GridION (20) · 0% of runs with a Sandpiper profile · first public 2025-05-28
Authors (0)
No author record.
Downloads
PRJNA1260441.csv.gz (1.4 KB) · parquet (70.3 KB) — all 20 samples, every field with route and confidence · PRJNA1260441_determinations.csv.gz (1.3 KB) — 110 evidence rows