Antibiotics and infant/neonate gut microbiome, cohort study
64 stool samples from infants, neonates, and mothers comparing an antibiotics treatment group with a control group, examining gut microbial diversity, taxonomy, and antibiotic resistance genes; longitudinal cohort/case-control design. machine-written summary
64 samples · 64 runs · FI · Infant / toddler · 2019 · 1.46 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 64 sample values (collection date) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 199 sample values (country, delivery mode, location locality, preterm status) · PMC10904392, PMC11019788, PMC11322291, PMC11494892, PMC12769767, PMC6650395, PMC8514186, PMC9437082, PMC9512645 |
| ✓ Supplementary tables | 287 sample values (age, country, delivery mode, family id, family role, subject id, timepoint) |
| – 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 |
longitudinalmother–infant
14 of 40 people sampled more than once (28 samples; median 2, up to 2 per person) · follow-up median 12 mo (max 12 mo) · median interval between samples 12 mo (time from age at collection). Schedule stated by the source: “Infants: before discharge (3-7 days after birth) and at 12 months (or 6 months in related study); mothers: once after birth” (time origin: birth); stated follow-up 12 mo.
Each row is one person (14 shown); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother, father, child, twin).
20 mother–infant pairs (Table S1b family id); infants sampled at 3–7 days and 12 months; vertical transmission study · 20 families with 40 sampled people (20 with a parent and a child).
motherchild · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 20 families. 40 people in the project overall.
Families (20)
Genera, mean relative abundance over 57 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 | 64 | 100% | ||||
| country | 64 | 100% | 34 | 30 | ||
| health_condition | 0 | 0% | ||||
| subject_id | 54 | 84% | 54 | |||
| collection_date | 64 | 100% | 64 | |||
| delivery_mode | 64 | 100% | 23 | 41 | ||
| detailed_location | 64 | 100% | ||||
| location_locality | 64 | 100% | 64 | |||
| preterm_status | 64 | 100% | 64 | |||
| family_id | 54 | 84% | 54 | |||
| family_role | 54 | 84% | 54 | |||
| age_at_collection_days | 34 | 53% | 34 | |||
| timepoint_label | 34 | 53% | 34 |
- Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants. PMID 31337807 PMC6650395 curated
- Vertical Transmission of Gut Microbiome and Antimicrobial Resistance Genes in Infants Exposed to Antibiotics at Birth. PMID 32239170 PMC8514186 curated
- A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. PMID 36050292 PMC9437082 curated
- Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645 curated
- A metagenomic catalog of the early-life human gut virome. PMID 38424077 PMC10904392 curated
4 more
- Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032 PMC11019788
- Insights into the ecology of the infant gut plasmidome. PMID 39138199 PMC11322291
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767
Archive description
The stool microbiome samples of infants and mothers from an antibiotics treatment group and a control group were studied using metagenomic sequencing approach. The microbial diversity, taxonomy composition and antibiotics resistance genes were compared between the two groups and significantly differentially abundant species and genes were identified.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “antibiotics on the gut microbiome and emergence”
- body site study.description · “The stool microbiome samples of”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “antimicrobial resistance in infants”
- life stage study.description · “of infants and mothers from an antibiotics”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11761733 | age_at_collection_days | 5 | R2 | 0.75 | paper.supp.table | Age (day)=5 |
| SAMN11761733 | collection_date | 2014-04-12 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2014-04-12 |
| SAMN11761733 | country | FI | R2 | 0.75 | paper.supp.table | Nation=Finland |
| SAMN11761743 | country | FI | R3 | 0.80 | paper.fulltext.methods | Oulu University Hospital, Oulu, Finland |
| SAMN11761734 | delivery_mode | vaginal | R2 | 0.75 | paper.supp.table | Delivery Mode=Vaginal |
| SAMN11761733 | delivery_mode | vaginal | R3 | 0.80 | paper.fulltext.methods | term, vaginally delivered infants followed from birth |
| SAMN11761733 | family_id | 6 | R2 | 0.85 | paper.supp.jiaa155_suppl_supplementary_table_s1.docx[Table S1b!Family id] | OULU-49 Antibiotic infant 5 6 |
| SAMN11761733 | family_role | child | R2 | 0.85 | paper.supp.jiaa155_suppl_supplementary_table_s1.docx[Table S1b!Infant / mother] | OULU-49 Antibiotic infant 5 6 |
| SAMN11761733 | location_locality | Oulu | R3 | 0.70 | paper.fulltext.methods | Oulu University Hospital, Oulu, Finland from February 2014 |
| SAMN11761733 | preterm_status | term | R3 | 0.80 | paper.fulltext.methods | term, vaginally delivered infants followed from birth |
| SAMN11761733 | subject_id | family6_infant | R2 | 0.80 | paper.supp.jiaa155_suppl_supplementary_table_s1.docx[table2!Family id] | OULU-49 infant family 6 |
| SAMN11761733 | timepoint_label | 0 - 1 month | R2 | 0.75 | paper.supp.table | AGE GROUP G12=0 - 1 month |
Sequencing
64 runs over 64 samples · mean 2.00 Gbp per run (median 1.46 Gbp, total 127.70 Gbp; 64 runs with a base count) · layout PAIRED 64 · platform ILLUMINA 64 · models NextSeq 500 (64) · 89% of runs with a Sandpiper profile · first public 2019-07-27 – 2019-11-27
Authors (56)
Tapiainen T first · Koivusaari P · Brinkac L · Lorenzi HA · Salo J · Renko M · Pruikkonen H · Pokka T · Li W · Nelson K · Pirttilä AM · Tejesvi MV last · Moncera K · Nelson KE last · Zeng S first · Patangia D · Almeida A · Zhou Z · Mu D · Paul Ross R · Stanton C · Wang S last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Li S · Ying J · Wang H · Qu Y · Niu X · De Biase R · Bocchio F · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · van Sinderen D · Longhi G · Gennaioli E · Muscò A · Rizzo SM · Vitale SG · Angioni S
Downloads
PRJNA543520.csv.gz (3.3 KB) · parquet (74.3 KB) — all 64 samples, every field with route and confidence · PRJNA543520_determinations.csv.gz (6.0 KB) — 550 evidence rows