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

PeerJ
Zachery T LewisDavid A Mills

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 afte...Continue Reading

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Citations

Feb 6, 2017·Scientific Reports·Zachery T LewisDavid A Mills
Nov 8, 2017·The Journal of Maternal-fetal & Neonatal Medicine : the Official Journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians·Won-Ho HahnNam Mi Kang
Aug 16, 2016·Clinical & Translational Immunology·Robert J Moore, Dragana Stanley
Jun 4, 2020·Genome Biology·Sumeed Syed ManzoorMichael B Burns

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Datasets Mentioned

BETA
ERP012928

Methods Mentioned

BETA
amplicon sequencing
Illumina
PCR
chip

Clinical Trials Mentioned

NCT01817127

Software Mentioned

ANOSIM
QIIME
PyNAST
UCLUST
LefSe
Find
Agilent MassHunter Qualitative Analysis

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