QUANTIFYING ALLO-COPROPHAGY IN LABORATORY RATS FROM DEEP SHOTGUN SEQUENCING DATA OF THE GUT

Abstract

Commensal microorganisms can be transferred between humans who come in contact and/or who share a living space. The transmission of these commensal microorganisms could have important health consequences. It is therefore important to understand the processes that facilitate microbiome transfer. Allo-coprophagy in rodents can be used as a model to study the transmission of commensal microorganisms. Allo-coprophagy is difficult to detect via direct observation and/or through video recording. This study aimed to detect and quantify allo coprophagy from deep shotgun data in outbred laboratory rats, which is the first step towards understanding the transfer of microorganisms that occurs through allo-coprophagy. The study relied on the hypothesis that the cells and DNA present in a rat's faeces, which originate from gut epithelial cell shedding, get ingested during allo-coprophagy. As a result, both their own DNA and that of the cage mate can be found in the gut of a rat that ingested the faeces and detected by sequencing. The DNA present in the gut of 32 pair-housed "heterogeneous stock” (HS) rats was sequenced at depth of 69 million paired end reads per sample and the reads mapping to the rat genome were used. Rat DNA sequences from metagenomics data and rat genotypes were compared and a multinomial equation model used to identify origin of each read in order to identify sample mixtures and sample swaps. The experimental factors tissue type and fasting stater affected the proportion of rat reads in the metagenomic dataset. This was accessed across a bigger dataset of 96 rats from which the 32 rats used to study allo-coprophagy were obtained from. The 32 pair-housed rats had reads originating from themselves, their cage mates and other rats in the experiment. One rat, rat 32 was found to have a lot of cage mate DNA in its gut, but across all of the 32 experimental rats, the evidence for allo-coprophagy was not significant. This study highlights the potential of using deep shotgun sequencing of the gut content to quantify a behaviour that is important for microbial transfer between individuals. This provided valuable information in understanding the process of microbial transfer.