The impact of postnatal antibiotics on the preterm intestinal microbiome

Study information

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study design

time series / longitudinal observational

Citation

PMID PubMed identifier for scientific articles.

24819377

DOI Digital object identifier for electronic documents.

10.1038/pr.2014.69

URI

Authors

Dardas M, Gill SR, Grier A, Pryhuber GS, Gill AL, Lee YH, Guillet R

Journal

Pediatric research

Year

2014

BACKGROUND: Development of the intestinal microbiome in preterm infants has significant impact on infant health. Our objective was to determine if duration of antibiotics within the first 10 and 30 d after birth affects the intestinal microbiome. METHODS: Subjects were 24 0/7-31 6/7 wk of gestational age who received ≥ 50% breast milk and a total of ≥ 100 ml/kg of feeds by 10 d. Rectal (fecal) swabs were collected at 10 and 30 d and analyzed by 16S rRNA pyrosequencing. At both time points, we examined the rectal microbiome from infants who received only 2 d of antibiotics and those who received at least 7 d of antibiotics. RESULTS: In the 29 infants enrolled in our study, we found a decrease in diversity index from 10 d samples in those who received more antibiotics. Such difference in diversity and richness was not as pronounced in 30 d samples. Firmicutes and Bacteroidetes were most abundant in the 10 d samples. While these two phyla remained dominant in 30 d samples, there was an increase in Proteobacteria and Actinobacteria. CONCLUSION: Despite antibiotic therapy, neonates continued to acquire bacteria in the gastrointestinal tract. The process of bacterial acquisition is perturbed with the use of antibiotics.

Experiment 1

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Curated date: 2021/01/10

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Subjects

Location of subjects: United States of America

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: 10 d old 2 day treatment infants

Group 1 name Corresponds to the case (exposed) group for case-control studies: 10 d old 7-10 day treatment infants

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Infants who received antibiotics for 7-10 days

Group 0 sample size Number of subjects in the control (unexposed) group: 15

Group 1 sample size Number of subjects in the case (exposed) group: 12

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): None.

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V3

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

Statistical Analysis

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

Statistical test: Kruskall-Wallis

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)?: Yes

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: delivery procedure

Alpha Diversity

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

Richness Number of species: unchanged

Signature 1

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Source: Results within text- Page 4, 3rd paragraph, under subheading "Discussion"

Description: Genus level differential abundance of breast milk–fed infants at age 10 d with 7days of antibiotic treatment

Abundance in Group 1: decreased abundance in 10 d old 7-10 day treatment infants

NCBI	Quality Control	Links
Bacteroides
Lactococcus

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Experiment 2

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Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: 30 d old minimal antibiotics exposure (2 day treatment infants)

Group 1 name Corresponds to the case (exposed) group for case-control studies: 30 d old prolonged antibiotics exposure (>=7 day treatment infants)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: prolonged antibiotics exposure (greater than or equal to 7 day treatment infants)