The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content

• DOI: 10.7717/peerj.1612
• Publication Date: 2016-01-21T07:36:02Z
• Authors: Zachery T. Lewis; Jasmine C.C. Davis; Jennifer T. Smilo...; J. Bruce German; Carlito B. Lebrilla; David A. Mills
• Keywords: Pediatric; 2. Zero hunger; 0303 health sciences; QH301-705.5; Breastfeeding; Human milk oligosaccharides; R; 500; Biological Sciences; Microbiology; Medical and Health Sciences; Human microbiome; Biochemistry; Lyophilization; 03 medical and health sciences; Freeze-drying; Lactation and Breast Milk; Fecal microbiome; Medicine; Biology (General); Infants; Nutrition; Biotechnology

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 ofBacteriodesand 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.