| Summary: | <p>Abstract</p> <p>Background</p> <p>Guinea pig (<it>Cavia porcellus</it>) is an important model for human intestinal research. We have characterized the faecal microbiota of 60 guinea pigs using Illumina shotgun metagenomics, and used this data to compile a gene catalogue of its prevalent microbiota. Subsequently, we compared the guinea pig microbiome to existing human gut metagenome data from the MetaHIT project.</p> <p>Results</p> <p>We found that the bacterial richness obtained for human samples was lower than for guinea pig samples. The intestinal microbiotas of both species were dominated by the two phyla <it>Bacteroidetes</it> and <it>Firmicutes</it>, but at genus level, the majority of identified genera (320 of 376) were differently abundant in the two hosts. For example, the guinea pig contained considerably more of the mucin-degrading <it>Akkermansia</it>, as well as of the methanogenic archaea <it>Methanobrevibacter</it> than found in humans. Most microbiome functional categories were less abundant in guinea pigs than in humans. Exceptions included functional categories possibly reflecting dehydration/rehydration stress in the guinea pig intestine. Finally, we showed that microbiological databases have serious anthropocentric biases, which impacts model organism research.</p> <p>Conclusions</p> <p>The results lay the foundation for future gastrointestinal research applying guinea pigs as models for humans.</p>
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