Abstract
Infant fecal samples are commonly studied to investigate the impacts of breastfeeding on the development of the microbiota and subsequent health effects. Comparisons of infants living in different geographic regions and environmental contexts are needed to aid our understanding of evolutionarily-selected milk adaptations. However, the preservation of fecal samples from individuals in remote locales until they can be processed can be a challenge. Freeze-drying (lyophilization) offers a cost-effective way to preserve some biological samples for transport and analysis at a later date. Currently, it is unknown what, if any, biases are introduced into various analyses by the freeze-drying process. Here, we investigated how freeze-drying affected analysis of two relevant and intertwined aspects of infant fecal samples, marker gene amplicon sequencing of the bacterial community and the fecal oligosaccharide profile (undigested human milk oligosaccharides). No differences were discovered between the fecal oligosaccharide profiles of wet and freeze-dried samples. The marker gene sequencing data showed an increase in proportional representation of Bacteriodes and a decrease in detection of bifidobacteria and members of class Bacilli after freeze-drying. This sample treatment bias may possibly be related to the cell morphology of these different taxa (Gram status). However, these effects did not overwhelm the natural variation among individuals, as the community data still strongly grouped by subject and not by freeze-drying status. We also found that compensating for sample concentration during freeze-drying, while not necessary, was also not detrimental. Freeze-drying may therefore be an acceptable method of sample preservation and mass reduction for some studies of microbial ecology and milk glycan analysis.
Highlights
Infants go from the womb to abruptly encountering the full microbial diversity of their new ex-utero environment
Infant fecal samples are commonly studied to investigate the impacts of factors such as breastfeeding on the development of the gut microbiota and subsequent health effects
Infant fecal samples were collected at 340–400 days of life from twenty-four breast-fed term infants born to women in the study
Summary
Infants go from the womb to abruptly encountering the full microbial diversity of their new ex-utero environment. How to cite this article Lewis et al (2016), The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content. Infant fecal samples are commonly studied to investigate the impacts of factors such as breastfeeding on the development of the gut microbiota and subsequent health effects. As some of the effects of breastfeeding on the microbiota are mediated by selective microbial consumption of the oligosaccharides found in mother’s milk, the milk-derived fecal oligosaccharide profile is of scientific and practical interest (Lewis et al, 2015). Human milk oligosaccharides have been shown to have antiadhesive properties, to modulate immune cell responses, and are of increasing interest as therapeutic agents in the diet (Bode, 2012; Smilowitz et al, 2014)
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