Library prep method comparison, 6 adult gut samples
6 adult samples (4 healthy controls) were sequenced to study how library preparation and sequencing protocol affect taxonomic and functional predictions in human microbiome analysis. machine-written summary
4 samples · 41 runs · ES · Adult · 2015 · 9.90 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 26 sample values (age, antibiotic exposure, collection date, intervention, sex, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC4653211, PMC5390407 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 12 sample values (country, health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
1 of 1 people sampled more than once (4 samples; median 4, up to 4 per person) · follow-up median 56 d (max 56 d) · median interval between samples 4 d (time from collection dates). Schedule stated by the source: “Single subject (CA21) sampled at day 0, day 3, day 7, and week 8 during 7-day amoxicillin treatment” (time origin: intervention_start).
Each row is one person (1 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 4 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 | 4 | 100% | ||||
| country | 4 | 100% | 4 | |||
| health_condition | 4 | 100% | 4 | |||
| subject_id | 4 | 100% | 4 | |||
| age_at_collection_days | 4 | 100% | 4 | |||
| antibiotic_exposure | 4 | 100% | 4 | |||
| collection_date | 4 | 100% | 4 | |||
| health_condition_detail | 4 | 100% | 4 | |||
| sex | 4 | 100% | 4 | |||
| timepoint_label | 4 | 100% | 4 | |||
| intervention | 2 | 50% | 2 |
- Library preparation methodology can influence genomic and functional predictions in human microbiome research. 2015 PMID 26512100 PMC4653211 own_data
- Utilization of defined microbial communities enables effective evaluation of meta-genomic assemblies. 2017 PMID 28407798 PMC5390407 own_data
- Quantifying and Cataloguing Unknown Sequences within Human Microbiomes. 2022 PMID 35258340 PMC9052204 unsure
Archive description
This project investigates how library preparation and sequencing protocol influence the taxonomy and function analysis of microbial species in human microbiome research.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
- life stage sample.attr.host_age · “22 (n=4/6)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN04168656 | age_at_collection_days | 8035.5 | R1 | 0.85 | sample.attr.host_age | 22 |
| SAMN04168656 | antibiotic_exposure | yes | R1 | 0.85 | biosample.attribute:chem_administration | antibiotics |
| SAMN04168656 | collection_date | 2014-03-17 | R1 | 0.90 | biosample.attribute:collection_date | 2014-03-17 |
| SAMN04168656 | country | ES | R2 | 0.75 | external.gmrepo source | country: Spain |
| SAMN04168656 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN04168656 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN04168657 | intervention | antibiotic | R1 | 0.85 | biosample.attribute:DESCRIPTION | Amoxicillin 7 day treatment, day 3 |
| SAMN04168656 | sex | female | R1 | 0.90 | sample.attr.host_sex | female |
| SAMN04168656 | subject_id | CA21 | R1 | 0.85 | biosample.attribute:host_subject_id | CA21 |
| SAMN04168656 | timepoint_label | day 0 | R1 | 0.70 | sample.name_rule:attr:description | Amoxicillin 7 day treatment, day 0 |
Sequencing
41 runs over 4 samples · mean 10.16 Gbp per run (median 9.48 Gbp, total 416.51 Gbp; 41 runs with a base count) · layout PAIRED 41 · platform ILLUMINA 41 · models Illumina HiSeq 2500 (41) · 83% of runs with a Sandpiper profile · first public 2015-10-18 – 2017-02-28
Authors (20)
Jones MB first · Highlander SK · Anderson EL · Li W · Dayrit M · Klitgord N · Fabani MM · Seguritan V · Green J · Pride DT · Yooseph S · Biggs W · Nelson KE · Venter JC last · Greenwald WW first · Garner C · Modha S first · Robertson DL · Hughes J · Orton RJ last
Downloads
PRJNA298489.csv.gz (1.0 KB) · parquet (70.3 KB) — all 4 samples, every field with route and confidence · PRJNA298489_determinations.csv.gz (1.2 KB) — 38 evidence rows