Tunisian newborn gut microbiota by delivery mode
33 stool samples from Tunisian neonates/infants (Zaghouan) born via elective cesarean or vaginal delivery, collected at Day0, Day15, and Day30; a longitudinal cohort comparing gut microbiota by delivery mode. machine-written summary
33 samples · 33 runs · TN · Infant / toddler · 2022 · 2.72 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 115 sample values (collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 210 sample values (age, antibiotic exposure, birth weight grams, delivery mode, gestational age weeks, maternal antibiotics, preterm status) · PMC9083410 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 87 sample values (age, health condition, health condition detail) · from African Human Microbiome Portal (H3ABioNet) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
10 of 10 people sampled more than once (33 samples; median 3, up to 4 per person) · follow-up median 30 d (max 30 d) · median interval between samples 15 d (time from age at collection). Schedule stated by the source: “stool at Day0, Day15, and Day30” (time origin: birth); stated follow-up 30 d.
Each row is one person (10 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 17 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 | 33 | 100% | ||||
| country | 33 | 100% | 33 | |||
| health_condition | 33 | 100% | 33 | |||
| subject_id | 33 | 100% | 33 | |||
| age_at_collection_days | 33 | 100% | 21 | 12 | ||
| antibiotic_exposure | 33 | 100% | 33 | |||
| birth_weight_grams | 33 | 100% | 33 | |||
| collection_date | 33 | 100% | 33 | |||
| delivery_mode | 33 | 100% | 33 | |||
| gestational_age_weeks | 33 | 100% | 33 | |||
| health_condition_detail | 33 | 100% | 33 | |||
| maternal_antibiotics | 33 | 100% | 33 | |||
| preterm_status | 33 | 100% | 33 | |||
| timepoint_label | 16 | 48% | 16 |
- Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode. PMID 35547149 PMC9083410 curated
Archive description
Profiling of the early bacterial microbiota composition from stool samples of Tunisian newborns using shotgun metagenomic sequencing. Samples were collected from 5 neonates born by elective cesareans and 5 others vaginally delivered at Day0, Day15, and Day30.
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 · “of Tunisian newborns gut microbiota according to”
- body site study.description · “microbiota composition from stool samples of Tunisian”
- life stage study.title · “analysis of Tunisian newborns gut microbiota according”
- life stage study.description · “samples of Tunisian newborns using shotgun metagenomic”
- 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 |
|---|---|---|---|---|---|---|
| SAMN21400407 | age_at_collection_days | 15.0 | R2 | 0.70 | external.ahmp source | participant_feature: …at day 15 |
| SAMN21400395 | age_at_collection_days | 0 | R3 | 0.60 | paper.fulltext.results | collected on the birthday (Day 0) |
| SAMN21400395 | antibiotic_exposure | no | R3 | 0.80 | paper.fulltext.methods | did not receive any antibiotic treatment |
| SAMN21400395 | birth_weight_grams | 3430 | R3 | 0.40 | paper.fulltext.results | birth weight [3.43 kg (SD ± 0.34)] |
| SAMN21400395 | collection_date | 2019-04-29 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2019-04-29 |
| SAMN21400395 | country | TN | R1 | 0.90 | biosample_attr | Tunisia:Zaghouan |
| SAMN21400395 | delivery_mode | c_section_elective | R3 | 0.40 | paper.fulltext.abstract | 5 elective cesarean section (ECS) |
| SAMN21400395 | gestational_age_weeks | 38.5 | R3 | 0.40 | paper.fulltext.results | mean gestational age of 38.5 weeks |
| SAMN21400395 | health_condition | healthy_control | R2 | 0.70 | external.ahmp source | DISEASE: Healthy |
| SAMN21400395 | health_condition_detail | Healthy | R2 | 0.70 | external.ahmp source | DISEASE: Healthy |
| SAMN21400395 | maternal_antibiotics | no | R3 | 0.80 | paper.fulltext.methods | did not receive antibiotics, anti-inflammatory drugs |
| SAMN21400395 | preterm_status | term | R3 | 0.40 | paper.fulltext.results | Full-term newborns (5 from vaginal delivery and 5 from ECS delivery) |
| SAMN21400395 | subject_id | T1 | R1 | 0.85 | biosample.attribute:title | title: T1 |
| SAMN21400395 | timepoint_label | T1 | R1 | 0.70 | sample.title | T1 |
Sequencing
33 runs over 33 samples · mean 2.15 Gbp per run (median 2.72 Gbp, total 70.86 Gbp; 33 runs with a base count) · layout PAIRED 33 · platform ILLUMINA 33 · models Illumina NovaSeq 6000 (33) · 52% of runs with a Sandpiper profile · first public 2022-04-08
Authors (12)
Hanachi M first · Maghrebi O · Bichiou H · Trabelsi F · Bouyahia NM · Zhioua F · Belghith M · Harigua-Souiai E · Baouendi M · Guizani-Tabbane L · Benkahla A · Souiai O last
Downloads
PRJNA762668.csv.gz (2.0 KB) · parquet (71.7 KB) — all 33 samples, every field with route and confidence · PRJNA762668_determinations.csv.gz (4.6 KB) — 412 evidence rows