Abstract
Rectal swabs are potentially a valuable method for monitoring the gut microbiome in research and clinical settings, where it is important to adhere to strict timing, or where acute sampling is needed. It is currently unknown whether rectal swabs give comparable results to faecal samples regarding microbiota community composition in neonates and infants. To study how well the two sampling methods correlate in infants, we compared the 16S-rRNA-based sequencing results of 131 paired rectal swabs and faecal samples collected from 116 infants at two timepoints in early life. The paired samples were highly comparable regarding both diversity and overall community composition, and strongly correlated on taxonomical level. We observed no significant nor relevant contribution of sampling method to the variation in overall gut microbiota community composition in a multivariable model. Our study provides evidence supporting the use of rectal swabs as a reliable proxy for faecal samples in infant gut microbiota research.
Highlights
The interest in studying the gut microbiome in relation to health and disease is rapidly growing[1]
A closely paired sample is defined as a matched faecal sample and rectal swab collected within a timeframe of 24 hours from an individual participant
In a total of cases the rectal swab was collected before the faecal sample, in 20 cases the rectal swab was collected after the faecal sample and in 88 cases the rectal swab and faecal sample were collected at almost the same time, where in practice a trained physician collected the rectal swab first and a nurse collected the faeces shortly hereafter, the rectal swab being a stimulatory trigger for defaecation
Summary
The interest in studying the gut microbiome in relation to health and disease is rapidly growing[1]. On the other hand, can be collected and at any time, allowing flexible and consistent sampling between individuals and in relation to interventions. Rectal swabs have been compared to faecal samples with respect to the detection of specific pathogens, such as norovirus[8], but not yet on their performance in analysing the overall microbiota composition. Rectal swabs could be an ideal sampling method for the monitoring of treatment or study interventions on the neonatal ward or paediatric intensive care unit or in (longitudinal) population-based studies. We compared the alpha and beta diversity between rectal swabs and faecal samples collected at the same time from the same individual at two sampling moments, and studied how well the sampling methods correlate on taxonomical level. The objective of our study was to determine whether rectal swabs are a good proxy for faecal samples in infant gut microbiota research
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