Pediatric Fecal Metagenome for Antibiotic Resistance
22 fecal metagenome samples from healthy children (infants, children, adolescents) in Seattle, WA, used in a case series of functional metagenomic selections to identify antibiotic resistance genes via E. coli library screening. machine-written summary
22 samples · 169 runs · US · Infant / toddler · 2014 · 1.37 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 88 sample values (age, collection date, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10269646, PMC11494892, PMC12769767, PMC3827270, PMC9512645 |
| ✓ Supplementary tables | 10 sample values (timepoint) |
| ✓ External resources | 44 sample values (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 |
Genera, mean relative abundance over 1 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 | 22 | 100% | ||||
| country | 22 | 100% | 22 | |||
| health_condition | 22 | 100% | 22 | |||
| subject_id | 22 | 100% | 22 | |||
| age_at_collection_days | 22 | 100% | 22 | |||
| collection_date | 22 | 100% | 22 | |||
| health_condition_detail | 22 | 100% | 22 | |||
| timepoint_label | 10 | 45% | 10 |
- Pediatric fecal microbiota harbor diverse and novel antibiotic resistance genes. PMID 24236055 PMC3827270 curated
- Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645 curated
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646 curated
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892 curated
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767 curated
Archive description
Functional metagenomic selections were performed from various pediatric fecal metagenomes, enriched for children in the first two years of life. A major goal was to understand how antibiotic resistance genes establish and propagate among developing intestinal microbiomes. Fecal metagenomic DNA was cloned into an E. coli library and subjected to selections for antibiotic resistance. After selection, resistance-conferring fragments (the only fragments conferring survival to E. coli in the presence of the drugs) were PCR-amplified, sequenced, and assembled.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “Pediatric Fecal Metagenome”
- life stage study.description · “children in the first two years of life”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN02317157 | age_at_collection_days | 3105 | R1 | 0.90 | sample.attr.host_age | 8.5 y |
| SAMN02317158 | age_at_collection_days | 548 | R1 | 0.90 | biosample_attr | 1.5 y |
| SAMN02317157 | collection_date | 2001 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2001 |
| SAMN02317157 | country | US | R1 | 0.90 | biosample_attr | USA: Seattle,WA |
| SAMN02317157 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN02317157 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN02317157 | subject_id | F04 | R1 | 0.85 | biosample.attribute:misc_param | misc_param: F04 |
| SAMN02317158 | timepoint_label | post-weaning | R2 | 0.75 | paper.supp.table | Time Group=post-weaning |
Sequencing
169 runs over 22 samples · mean 0.23 Gbp per run (median 0.16 Gbp, total 39.52 Gbp; 169 runs with a base count) · layout PAIRED 169 · platform ILLUMINA 169 · models Illumina Genome Analyzer IIx (169) · 1% of runs with a Sandpiper profile · first public 2014-04-15
Authors (27)
Moore AM first · Patel S · Forsberg KJ · Wang B · Bentley G · Razia Y · Qin X · Tarr PI · Dantas G last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Rizzo SM first · Viappiani A · Bianchi MG · Bussolati O · van Sinderen D · Longhi G · Gennaioli E · Muscò A · Vitale SG · Angioni S
Downloads
PRJNA215106.csv.gz (1.6 KB) · parquet (70.7 KB) — all 22 samples, every field with route and confidence · PRJNA215106_determinations.csv.gz (2.2 KB) — 142 evidence rows