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Updated: Aug 18, 2026
Quantitative Polymerase Chain Reaction-based Analyses of Murine Intestinal Microbiota After Oral Antibiotic Treatment
Published on: November 17, 2018
Quantitative real-time PCR assays to identify and quantify fecal Bifidobacterium species in infants receiving a
1Microbiology Section, Biomedical Research Department, Numico Research BV., P.O. Box 7005, 6700 CA Wageningen, The Netherlands.
Insights
Prebiotic infant formula supplementation significantly increased beneficial Bifidobacterium levels in infants, promoting a gut microbiota composition similar to breast-fed infants. This supports the development of a healthy infant immune system through targeted nutrition.
Area of Science:
- Microbiology
- Immunology
- Pediatrics
Background:
- A healthy intestinal microbiota is crucial for infant immune system development.
- Breast-fed infants typically exhibit a Bifidobacterium-dominated gut microbiota.
- Allergic infants may have altered Bifidobacterium species levels compared to healthy infants.
Purpose of the Study:
- To develop and validate accurate methods for quantifying specific Bifidobacterium species in infant fecal samples.
- To investigate the impact of a prebiotic (galacto- and fructo-oligosaccharides) infant formula on the infant gut microbiota composition.
- To compare the microbiota of formula-fed infants with and without prebiotics to breast-fed infants.
Main Methods:
- Developed and validated duplex 5' nuclease assays for accurate quantification of eight Bifidobacterium species.
- Compared 5' nuclease assays with conventional PCR and fluorescent in situ hybridization.
- Analyzed Bifidobacterium species distribution in fecal samples from three infant groups: standard formula, prebiotic formula, and breast-fed.
Main Results:
- The prebiotic infant formula significantly increased total fecal bifidobacteria from 54.8% to 73.4%.
- Infants receiving the prebiotic formula showed a Bifidobacterium diversity similar to breast-fed infants.
- Standard formula-fed infants had an adult-like bifidobacteria distribution with higher B. catenulatum and B. adolescentis levels.
Conclusions:
- The specific prebiotic infant formula effectively modulates the gut microbiota in infants.
- The induced microbiota composition closely resembles that of breast-fed infants, including specific Bifidobacterium species.
- Prebiotic supplementation offers a promising strategy for promoting a healthy infant gut microbiome and immune priming.
Abstract:
A healthy intestinal microbiota is considered to be important for priming of the infants' mucosal and systemic immunity. Breast-fed infants typically have an intestinal microbiota dominated by different Bifidobacterium species. It has been described that allergic infants have different levels of specific Bifidobacterium species than healthy infants. For the accurate quantification of Bifidobacterium adolescentis, Bifidobacterium angulatum, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium catenulatum, Bifidobacterium dentium, Bifidobacterium infantis, and Bifidobacterium longum in fecal samples, duplex 5' nuclease assays were developed. The assays, targeting rRNA gene intergenic spacer regions, were validated and compared with conventional PCR and fluorescent in situ hybridization methods. The 5' nuclease assays were subsequently used to determine the relative amounts of different Bifidobacterium species in fecal samples from infants receiving a standard formula or a standard formula supplemented with galacto- and fructo-oligosaccharides (OSF). A breast-fed group was studied in parallel as a reference. The results showed a significant increase in the total amount of fecal bifidobacteria (54.8% +/- 9.8% to 73.4% +/- 4.0%) in infants receiving the prebiotic formula (OSF), with a diversity of Bifidobacterium species similar to breast-fed infants. The intestinal microbiota of infants who received a standard formula seems to resemble a more adult-like distribution of bifidobacteria and contains relatively more B. catenulatum and B. adolescentis (2.71% +/- 1.92% and 8.11% +/- 4.12%, respectively, versus 0.15% +/- 0.11% and 1.38% +/- 0.98% for the OSF group). In conclusion, the specific prebiotic infant formula used induces a fecal microbiota that closely resembles the microbiota of breast-fed infants also at the level of the different Bifidobacterium species.
