Abstract
In addition to providing nutritional and bioactive factors necessary for infant development, human breast milk contains bacteria that contribute to the establishment of commensal microbiota in the infant. However, the composition of this bacterial community differs considerably between studies. We hypothesised that bacterial DNA extraction methodology from breast milk samples are a substantial contributor to these inter-study differences. We tested this hypothesis by applying five widely employed methodologies to a mock breast milk sample and four individual human breast milk samples. Significant differences in DNA yield and purity were observed between methods (P < 0.05). Microbiota composition, assessed by 16S rRNA gene amplicon sequencing, also differed significantly with extraction methodology (P < 0.05), including in the contribution of contaminant signal. Concerningly, many of the bacterial taxa identified here as contaminants have been reported as components of the breast milk microbiome in other studies. These findings highlight the importance of using stringent, well-validated, DNA extraction methodologies for analysis of the breast milk microbiome, and exercising caution interpreting microbiota data from low-biomass contexts.
Highlights
In addition to providing nutritional and bioactive factors necessary for infant development, human breast milk contains bacteria that contribute to the establishment of commensal microbiota in the infant
As assessed by 260 nm/280 nm absorbance ratios, differed significantly between methods (ANOVA, P = 0.005), with mean ratios achieved with QIAamp DNA stool Mini Kit plus bead beating significantly higher than those achieved using other methods (Tukey’s Honest Significant Difference (HSD), P < 0.05)
Suboptimal extraction of bacterial DNA has the potential to distort the relative abundance of constituent taxa, and to influence the contribution of artefactual bacterial signal that is considered unavoidable in the analysis of low biomass samples[37,42,43,44,45,46,47,48]
Summary
In addition to providing nutritional and bioactive factors necessary for infant development, human breast milk contains bacteria that contribute to the establishment of commensal microbiota in the infant. Microbiota composition, assessed by 16S rRNA gene amplicon sequencing, differed significantly with extraction methodology (P < 0.05), including in the contribution of contaminant signal. Many of the bacterial taxa identified here as contaminants have been reported as components of the breast milk microbiome in other studies These findings highlight the importance of using stringent, well-validated, DNA extraction methodologies for analysis of the breast milk microbiome, and exercising caution interpreting microbiota data from low-biomass contexts. In addition to nutrients and bioactive components, human breast milk contains bacteria[1], commonly referred to as the breast milk microbiome These bacterial populations are thought to contribute to the establishment of commensal bacterial communities in the infant, as well as supporting the maturation of the gut, and development of the immune system[1,2]. No assessment of microbiota variation arising as a result of differences in DNA extraction methodologies has been conducted in relation to breast milk
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
