Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units

Study information

EditHistoryDelete

Mark reviewed

Your review change was submittedAdd a new Experiment

• Quality control
  • Retracted paper
  • Contamination issues suspected
  • Batch effect issues suspected
  • Uncontrolled confounding suspected
  • Results are suspect (various reasons)
  • Apply tags

    Tags applied

Needs review

study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

29554907

DOI Digital object identifier for electronic documents.

10.1186/s12941-018-0264-y

URI

Authors

Zou ZH, Liu D, Li HD, Zhu DP, He Y, Hou T, Yu JL

Journal

Annals of clinical microbiology and antimicrobials

Year

2018

Keywords:

Anti-bacterial agents, Gastrointestinal microbiome, High-throughput nucleotide sequencing, Infant, premature, Intensive care unit, neonatal

BACKGROUND: To explore the influences of prenatal antibiotic exposure, the intensity of prenatal and postnatal antibiotic exposure on gut microbiota of preterm infants and whether gut microbiota and drug resistant strains in the neonatal intensive care unit (NICU) over a defined period are related. METHODS: Among 28 preterm infants, there were two groups, the PAT (prenatal antibiotic therapy) group (12 cases), and the PAF (prenatal antibiotic free) group (12 cases). Fecal samples from both groups were collected on days 7 and 14. According to the time of prenatal and postnatal antibiotic exposure, cases were divided into two groups, H (high) group (11 cases) and L (low) group (11 cases), and fecal samples on day 14 were collected. Genomic DNA was extracted from the fecal samples and was subjected to high throughput 16S rRNA amplicon sequencing. Bioinformatics methods were used to analyze the sequencing results. RESULTS: Prenatal and postnatal antibiotic exposure exercised influence on the early establishment of intestinal microflora of preterm infants. Bacteroidetes decreased significantly in the PAT group (p < 0.05). The number of Bifidobacterium significantly decreased in the PAT group and H group (p < 0.05). The early gut microbiota of preterm infants with prenatal and postnatal antibiotic exposure was similar to resistant bacteria in NICU during the same period. CONCLUSION: Prenatal and postnatal antibiotic exposure may affect the composition of early gut microbiota in preterm infants. Antibiotic-resistant bacteria in NICU may play a role in reshaping the early gut microbiota of preterm infants with prenatal and postnatal antibiotic exposure.

Experiment 1

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Subjects

Location of subjects

China

Host species Species from which microbiome was sampled. Contact us to have more species added.

Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,Antimicrobial agent,antimicrobial agent

Group 0 name Corresponds to the control (unexposed) group for case-control studies

prenatal antibiotic free group (PAF group)

Group 1 name Corresponds to the case (exposed) group for case-control studies

infants(14-d old) exposed to prenatal antibiotic therapy (PAT group)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Pre-term infants

Group 0 sample size Number of subjects in the control (unexposed) group

12

Group 1 sample size Number of subjects in the case (exposed) group

12

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

V3-V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

relative abundances

Statistical test

LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool

2

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness

unchanged

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks

Source: Figure 1b, c; Figure 4a,b

Description: LEfSe results on gut microbiomes of preterm infants

Abundance in Group 1: increased abundance in infants(14-d old) exposed to prenatal antibiotic therapy (PAT group)

NCBI	Quality Control	Links
Saccharicrinis
Campylobacterota
Flavobacteriales

Revision editor(s): WikiWorks

Signature 2

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks

Source: Figure 1b, c; Figure 4a,b

Description: LEfSe results on gut microbiomes of preterm infants

Abundance in Group 1: decreased abundance in infants(14-d old) exposed to prenatal antibiotic therapy (PAT group)

NCBI	Quality Control	Links
Eubacteriales
Clostridia
Bifidobacterium

Revision editor(s): WikiWorks

Experiment 2

EditHistoryDelete

Mark reviewed

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

infants exposed to antibiotic <=7day (L group)

Group 1 name Corresponds to the case (exposed) group for case-control studies

infants exposed to antibiotic >7day (H group)

Group 0 sample size Number of subjects in the control (unexposed) group

11

Group 1 sample size Number of subjects in the case (exposed) group

11

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness

unchanged

Signature 1

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks

Source: Figure 8

Description: LEfSe analysis showed significant differences in microbial community structure between the H and L groups.

Abundance in Group 1: increased abundance in infants exposed to antibiotic >7day (H group)

NCBI	Quality Control	Links
Betaproteobacteria

Revision editor(s): WikiWorks

Signature 2

EditHistoryDelete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2021/01/10

Curator: Mst Afroza Parvin

Revision editor(s): WikiWorks

Source: Figure 8

Description: LEfSe analysis showed significant differences in microbial community structure between the H and L groups.

Abundance in Group 1: decreased abundance in infants exposed to antibiotic >7day (H group)

NCBI	Quality Control	Links
Bifidobacterium
Bifidobacteriales
Bifidobacteriaceae

Revision editor(s): WikiWorks