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Methods for exploring the faecal microbiome of premature infants: a review
Jacob A F Westaway1, Roger Huerlimann2, Catherine M Miller3
1James Cook University, 1 McGregor Road, Smithfield, QLD, 4878, Australia. jacob.westaway@my.jcu.edu.au.
Insights
Investigating the premature infant gut microbiome requires careful method selection. While 16S rRNA sequencing is common, potential biases necessitate cautious interpretation and study design for accurate results.
Area of Science:
- Microbiology
- Neonatology
- Genomics
Background:
- The gut microbiome is crucial for premature infant health and development.
- Microbial dysbiosis in preterm infants is a significant concern, driving research.
- Methodological variations in microbiome studies contribute to inconsistent findings.
Purpose of the Study:
- To review common techniques for studying the preterm infant microbiome.
- To detail the limitations of each methodology.
- To guide researchers in selecting appropriate methods and interpreting results.
Main Methods:
- Review of common techniques for preterm infant microbiome research.
- Analysis of benefits and limitations of each method.
- Focus on 16S rRNA short amplicon sequencing as a prevalent technique.
Main Results:
- 16S rRNA short amplicon sequencing is the most frequently used method.
- This technique offers high accuracy, discoverability, and throughput.
- Limitations exist at each protocol stage, introducing potential bias.
Conclusions:
- Methodological choices significantly impact preterm infant microbiome study outcomes.
- Bias in 16S rRNA sequencing can cause inter-study variability.
- Careful consideration of methodology is vital for interpreting existing data and designing future research.
Abstract:
The premature infant gut microbiome plays an important part in infant health and development, and recognition of the implications of microbial dysbiosis in premature infants has prompted significant research into these issues. The approaches to designing investigations into microbial populations are many and varied, each with its own benefits and limitations. The technique used can influence results, contributing to heterogeneity across studies. This review aimed to describe the most common techniques used in researching the preterm infant microbiome, detailing their various limitations. The objective was to provide those entering the field with a broad understanding of available methodologies, so that the likely effects of their use can be factored into literature interpretation and future study design. We found that although many techniques are used for characterising the premature infant microbiome, 16S rRNA short amplicon sequencing is the most common. 16S rRNA short amplicon sequencing has several benefits, including high accuracy, discoverability and high throughput capacity. However, this technique has limitations. Each stage of the protocol offers opportunities for the injection of bias. Bias can contribute to variability between studies using 16S rRNA high throughout sequencing. Thus, we recommend that the interpretation of previous results and future study design be given careful consideration.
