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Updated: Jun 9, 2025
Quantitative Polymerase Chain Reaction-based Analyses of Murine Intestinal Microbiota After Oral Antibiotic Treatment
Published on: November 17, 2018
Investigation of the Impact of Antibiotic Administration on the Preterm Infants' Gut Microbiome Using Next-Generation
Ahmet Aktaş1, Berkay Yekta Ekren2, Beril Yaşa3
1Medical Microbiology Department, Istanbul Faculty of Medicine, Istanbul University, 34093 Istanbul, Türkiye.
Insights
Antibiotic use disrupts infant gut microbiota, leading to dysbiosis and colonization by pathogenic bacteria. This study highlights the critical link between antibiotics and adverse changes in the infant gut microbiome composition.
Area of Science:
- Microbiology
- Genomics
- Pediatrics
Background:
- The human gut microbiota composition varies significantly between health and illness.
- Antibiotic treatment can cause dysbiosis, increasing susceptibility to pathogenic bacteria like VRE and CRKP.
- Infant gut microbiota undergoes dynamic changes, influenced by various factors including antibiotic exposure.
Purpose of the Study:
- To investigate the impact of antibiotic administration on the gut microbiota composition in infants.
- To analyze changes in microbial diversity and abundance following antibiotic treatment.
- To identify specific bacterial phyla affected by antibiotic exposure and their association with pathogenic bacteria colonization.
Main Methods:
- Analysis of first-pass meconiums and rectal swabs from 20 infants using 16S rRNA gene sequencing (Oxford Nanopore).
- Sequencing of the V1-V9 hypervariable regions of the 16S rRNA gene.
- Comparison of microbial diversity (alpha and beta diversity) and relative abundance of bacterial phyla between meconium and post-antibiotic rectal swab samples.
Main Results:
- Antibiotic treatment led to the disappearance of 12 out of 25 detected phyla.
- Significant decrease in the relative abundance of Bacillota, Bacteroidota, and Actinomycetota post-antibiotics (p < 0.05).
- Reduced alpha-diversity and increased beta-diversity variance in rectal swabs compared to meconiums (p < 0.05).
- Pseudomonadota showed increased relative abundance in rectal swabs, while Bacillota was higher in meconiums.
Conclusions:
- Antibiotic administration is strongly linked to gut dysbiosis and pathogenic bacteria colonization in infants.
- Significant alterations in gut microbiota composition and diversity occur after antibiotic exposure.
- Further research is needed to understand the natural development of the infant gut microbiota and its resilience to antibiotics.
Abstract:
Background: The human gut microbiota is an extensive population of microorganisms, and it shows significant variations between periods of optimal health and periods of illness. Vancomycin-resistant Enterococcus (VRE) and carbapenem-resistant Klebsiella pneumoniae (CRKP) are both pathogenic agents (BPAs) that can colonize in the gut after dysbiosis of microbiotal composition following antibiotic treatment. Methods: This study aimed to investigate the impact of antibiotics on the microbiotal composition of the gut. For this purpose, the first pass meconiums of 20 patients and the first rectal swabs containing BPAs of the same patients after antibiotic treatment were studied using next-generation sequencing-based 16S rRNA gene analysis. The V1-V9 region of 16S rRNA was sequenced with Oxford Nanopore. Results: Twenty-five phyla were detected in the meconiums, and 12 of them were absent after antibiotic treatment. The four most prevalent phyla in meconiums were Bacillota, Pseudomonadota, Bacteroidota, and Actinomycetota. Only the relative abundance of Pseudomonadota was increased, while a significant decrease was observed in the other three phyla (p < 0.05). A significant decrease was observed in alpha-diversity in rectal swabs containing BPAs versus meconiums (p = 0.00408), whereas an increased variance was observed in beta-diversity in all samples (p < 0.05). As a result of a LEfSe analysis, Pseudomonadota was found to have a higher relative abundance in rectal swabs, and Bacillota was significantly higher in the meconiums of the twins. Conclusions: Our study strongly verified the relationship between the administration of antibiotics, dysbiosis, and colonization of BPAs in the infants' gut microbiota. Further research would be beneficial and needed, comprising the natural development process of the infants' gut microbiota.
