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PRJNA701480 SRP305943

Vaginal seeding after C-section birth, Auckland trial

Vaginal seeding in babies born by caesarean section (ECOBABe trial) - shotgun metagenomics data

116 shotgun metagenomic samples from CS-born infants (seeded or placebo), vaginally born infant controls, and CS mothers' vaginal samples in Auckland, New Zealand, from a randomised placebo-controlled pilot trial of vaginal seeding. machine-written summary

116 samples · 116 runs · NZ · Infant / toddler · 2021 · 5.69 Gbp / sample

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Sources
✓Sequence archive 1,207○Abstract / description✓Full text 348○Supplementary tables–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive1,207 sample values (age, country, delivery mode, family id, family role, health condition, health condition detail, intervention)
○ Abstract / descriptionread; no usable statement
✓ Full text348 sample values (collection date, location region, preterm status) · PMC8254083, PMC9467569
○ Supplementary tablesfiles read; no table could be matched to the samples
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet
– Human verifiednot yet checked by a person · I checked this project — verify it
Interventions

intervention — arms not resolved

Faecal microbiota transplantation design randomized_controlled_trial · population healthy_control · Vaginal seeding: maternal vaginal microbes vs sterile water placebo at birth

“randomised to receive a 3 ml solution” — abstract:34186487 (study level; per-sample arms are in the intervention column below)

Samples at a glance
1 country
Age
infant77
adult25
neonate14
Condition
healthy_control91
Sex
female70
male46
Country
NZ116
Body site
primary116
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)all projects, 0.03–0.1 Gbp: 17,066 samples (3 %)all projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 6 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 17 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 8 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 85 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)all projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 5.69 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinalmother–infant

44 of 72 people sampled more than once (88 samples; median 2, up to 2 per person) · follow-up median 56 d (max 3 mo) · median interval between samples 56 d (time from age at collection). Schedule stated by the source: “Infant stool collected at 1 month and 3 months of age; maternal vaginal sample collected around time of CS delivery”; stated follow-up 3 mo.

QT8QT8 (child): day 0QT8 (child): day 56MJ9MJ9 (child): day 0MJ9 (child): day 62GK9GK9 (child): day 0GK9 (child): day 63UW5UW5 (child): day 0UW5 (child): day 56FQ4FQ4 (child): day 0FQ4 (child): day 56UV5UV5 (child): day 0UV5 (child): day 58ZZ9ZZ9 (child): day 0ZZ9 (child): day 57MI7MI7 (child): day 0MI7 (child): day 65RR3RR3 (child): day 0RR3 (child): day 61FB2FB2 (child): day 0FB2 (child): day 89BO4BO4 (child): day 0BO4 (child): day 52OZ4OZ4 (child): day 0OZ4 (child): day 60DK2DK2 (child): day 0DK2 (child): day 50FU0FU0 (child): day 0FU0 (child): day 62KC9KC9 (child): day 0KC9 (child): day 55VX8VX8 (child): day 0VX8 (child): day 62VB1VB1 (child): day 0VB1 (child): day 56GT5GT5 (child): day 0GT5 (child): day 63WY9WY9 (child): day 0WY9 (child): day 49GS0GS0 (child): day 0GS0 (child): day 27YM5YM5 (child): day 0YM5 (child): day 62ON6ON6 (child): day 0ON6 (child): day 53FH1FH1 (child): day 0FH1 (child): day 56LX9LX9 (child): day 0LX9 (child): day 57EU1EU1 (child): day 0EU1 (child): day 40LD1LD1 (child): day 0LD1 (child): day 56OY3OY3 (child): day 0OY3 (child): day 57CR3CR3 (child): day 0CR3 (child): day 52WV9WV9 (child): day 0WV9 (child): day 61SS7SS7 (child): day 0SS7 (child): day 58WK0WK0 (child): day 0WK0 (child): day 62SO9SO9 (child): day 0SO9 (child): day 59MD2MD2 (child): day 0MD2 (child): day 44WM9WM9 (child): day 0WM9 (child): day 51ER3ER3 (child): day 0ER3 (child): day 40MD1MD1 (child): day 0MD1 (child): day 340 d22 d44 d2 mo3 mo

Each row is one person (36 shown of 44); 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).

47 mother-infant pairs (CS mothers' vaginal samples linked to their CS-born infants' stool samples via mum_ID/baby_ID) · 25 families with 50 sampled people (25 with a parent and a child).

motherMchildC
25 × mother + child
family M06M06 — mother · 1 sampleMM06GK9 — child · 2 samplesCGK9
family M09M09 — mother · 1 sampleMM09UW5 — child · 2 samplesCUW5
family M11M11 — mother · 1 sampleMM11FQ4 — child · 2 samplesCFQ4
family M15M15 — mother · 1 sampleMM15UV5 — child · 2 samplesCUV5
family M16M16 — mother · 1 sampleMM16ZZ9 — child · 2 samplesCZZ9
family M18M18 — mother · 1 sampleMM18MI7 — child · 2 samplesCMI7
family M19M19 — mother · 1 sampleMM19RR3 — child · 2 samplesCRR3
family M24M24 — mother · 1 sampleMM24DK2 — child · 2 samplesCDK2
family M26M26 — mother · 1 sampleMM26FU0 — child · 2 samplesCFU0
family M27M27 — mother · 1 sampleMM27KC9 — child · 2 samplesCKC9
family M28M28 — mother · 1 sampleMM28VX8 — child · 2 samplesCVX8
family M39M39 — mother · 1 sampleMM39YM5 — child · 2 samplesCYM5
family M41M41 — mother · 1 sampleMM41ON6 — child · 2 samplesCON6
family M53M53 — mother · 1 sampleMM53LD1 — child · 2 samplesCLD1
family M56M56 — mother · 1 sampleMM56CR3 — child · 2 samplesCCR3
family M57M57 — mother · 1 sampleMM57WV9 — child · 2 samplesCWV9
family M58M58 — mother · 1 sampleMM58SS7 — child · 2 samplesCSS7
family M69M69 — mother · 1 sampleMM69MD1 — child · 2 samplesCMD1
family M72M72 — mother · 1 sampleMM72FX4 — child · 2 samplesCFX4
family M75M75 — mother · 1 sampleMM75UV1 — child · 2 samplesCUV1
family M77M77 — mother · 1 sampleMM77PN5 — child · 2 samplesCPN5
family M83M83 — mother · 1 sampleMM83RP0 — child · 2 samplesCRP0
family M89M89 — mother · 1 sampleMM89DP7 — child · 2 samplesCDP7
family M90M90 — mother · 1 sampleMM90XY8 — child · 2 samplesCXY8

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: 24 of 25 families (one per family structure, then more). 72 people in the project overall.

Families (25)
familymemberssamples
M06mother + childSAMN17884030 · SAMN17884078 · SAMN17884115
M53mother + childSAMN17884043 · SAMN17884056 · SAMN17884119
M90mother + childSAMN17884053 · SAMN17884103 · SAMN17884143
M89mother + childSAMN17884052 · SAMN17884061 · SAMN17884071
M83mother + childSAMN17884051 · SAMN17884092 · SAMN17884131
M77mother + childSAMN17884050 · SAMN17884090 · SAMN17884128
M75mother + childSAMN17884049 · SAMN17884059 · SAMN17884134
M72mother + childSAMN17884048 · SAMN17884063 · SAMN17884077
M69mother + childSAMN17884047 · SAMN17884083 · SAMN17884121
M58mother + childSAMN17884046 · SAMN17884058 · SAMN17884064
M57mother + childSAMN17884045 · SAMN17884100 · SAMN17884141
M56mother + childSAMN17884044 · SAMN17884069 · SAMN17884108
M41mother + childSAMN17884042 · SAMN17884087 · SAMN17884125
M09mother + childSAMN17884031 · SAMN17884095 · SAMN17884136
M39mother + childSAMN17884041 · SAMN17884060 · SAMN17884144
M28mother + childSAMN17884040 · SAMN17884097 · SAMN17884138
M27mother + childSAMN17884039 · SAMN17884081 · SAMN17884118
M26mother + childSAMN17884038 · SAMN17884076 · SAMN17884114
M24mother + childSAMN17884037 · SAMN17884070 · SAMN17884109
M19mother + childSAMN17884036 · SAMN17884057 · SAMN17884132
M18mother + childSAMN17884035 · SAMN17884085 · SAMN17884123
M16mother + childSAMN17884034 · SAMN17884104 · SAMN17884145
M15mother + childSAMN17884033 · SAMN17884094 · SAMN17884135
M11mother + childSAMN17884032 · SAMN17884075 · SAMN17884113
M93mother + childSAMN17884054 · SAMN17884066 · SAMN17884105

How longitudinal and relatedness information is derived

Community composition
Lactobacillus 18.5%Bifidobacterium 16.9%Escherichia 12.5%Clostridium 9.6%Klebsiella 8.9%Bacteroides 5.8%Veillonella 5.2%Phocaeicola 5.1%Parabacteroides 1.5%Streptococcus 1.4%Haemophilus_D 1.3%Veillonella_A 0.9%not assigned to a genus 2.3%other genera 10.1%

Genera, mean relative abundance over 103 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category116 100%
country116 100%116
health_condition91 78%91
subject_id116 100%116
age_at_collection_days116 100%116
collection_date116 100%116
delivery_mode116 100%116
detailed_location116 100%
family_role116 100%116
location_region116 100%116
preterm_status116 100%116
sex116 100%116
timepoint_label116 100%116
family_id113 97%113
health_condition_detail91 78%91
intervention50 43%50
probiotic_exposure50 43%50
Papers (2)
  • Oral administration of maternal vaginal microbes at birth to restore gut microbiome development in infants born by caesarean section: A pilot randomised placebo-controlled trial. PMID 34186487 PMC8254083 curated
  • Infant gut microbiota restoration: state of the art. PMID 36093611 PMC9467569 curated
Details
Archive description

The ECOBABe trial was a single-blinded randomised placebo-controlled pilot study to evaluate the efficacy of administration of maternal vaginal microbes (vaginal seeding) at birth to restore gut microbiome development in babies born by caesarean section (CS). The trial included 25 babies born by CS that were randomised to receive a 3ml solution of either maternal vaginal microbes (CS-seeded, n = 12) or sterile water (CS-placebo, n = 13). The trial also included a control group of vaginally born babies (VB, n = 22). Stool samples were collected from babies at 1 month and 3 months of age. Maternal vaginal samples were collected from CS mothers. Samples underwent shotgun metagenomic sequencing to assess microbiome composition and metabolic capacity . The primary outcome was a difference in gut microbiome composition at 1 month of age between CS-seeded and CS-placebo groups.

How this project entered the registry

Classified as human vaginal / urogenital / 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 · “Vaginal seeding in babies”
  • body site study.description · “administration of maternal vaginal microbes (vaginal seeding)”
  • body site study.description · “birth to restore gut microbiome development in”
  • body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
  • life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
  • life stage study.title · “Vaginal seeding in babies born by caesarean”
  • life stage study.description · “of administration of maternal vaginal microbes (vaginal”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN17884030age_at_collection_days10738R10.90sample.attr.host_age29.4 years
SAMN17884055age_at_collection_days29R10.90biosample_attr29 days
SAMN17884030collection_date2019-05/2020-03R30.70paper.fulltext.methodsvaginal birth (VB, reference group) were recruited
SAMN17884030countryNZR10.90biosample_attrNew Zealand: Auckland
SAMN17884030delivery_modec_sectionR10.90biosample_attrCS
SAMN17884030family_idM06R10.85biosample.attribute:mum_IDM06
SAMN17884030family_rolemotherR10.85biosample.attribute:groupMaternal
SAMN17884055health_conditionhealthy_controlR10.85biosample.attribute:groupgroup: VB
SAMN17884055health_condition_detailVBR10.85biosample.attribute:groupgroup: VB
SAMN17884056interventionplaceboR10.85biosample.attribute:groupgroup: CS-placebo
SAMN17884030location_regionAuckland RegionR30.70paper.fulltext.methodsrecruited from three hospitals in the Auckland region
SAMN17884030preterm_statustermR30.75paper.fulltext.methodsexcluded if they delivered preterm (<37 weeks of gestation)
SAMN17884056probiotic_exposurenoR10.60biosample_attrCS-placebo
SAMN17884030sexfemaleR10.90biosample_attrfemale
SAMN17884030subject_idM06R10.85biosample_attrM06
SAMN17884030timepoint_labelMaternalR10.80biosample_attrMaternal
Sequencing

116 runs over 116 samples · mean 4.43 Gbp per run (median 5.69 Gbp, total 514.17 Gbp; 116 runs with a base count) · layout PAIRED 116 · platform ILLUMINA 116 · models Illumina NovaSeq 6000 (116) · 89% of runs with a Sandpiper profile · first public 2021-06-16

Authors (14)

Wilson BC first · Butler ÉM · Grigg CP · Derraik JGB · Chiavaroli V · Walker N · Thampi S · Creagh C · Reynolds AJ · Vatanen T · O'Sullivan JM · Cutfield WS last · Korpela K first · de Vos WM last

Downloads

PRJNA701480.csv.gz (5.4 KB) · parquet (77.6 KB) — all 116 samples, every field with route and confidence · PRJNA701480_determinations.csv.gz (12.0 KB) — 1,555 evidence rows

Samples (116 · every field this project has values for · hover a cell for its source)
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