Abstract
Experimental animals including the ferret, marmoset, woodchuck, mini pig, and tree shrew have been used in biomedical research. However, their gut microbiota have not been fully investigated. In this study, the gut microbiota of these five experimental animals were analyzed with 16S rRNA sequencing. The phyla Firmicutes, Bacteroidetes, and Fusobacteria were present in the gut microbiota of all the species. Specific phyla were present in different animals: Proteobacteria in the ferret, Tenericutes in the marmoset, and Spirochaetes in the mini pig. Fusobacterium and unidentified Clostridiales were the dominant genera in the ferret, whereas Libanicoccus, Lactobacillus, Porphyromonas, and Peptoclostridium were specific to marmoset, mini pig, woodchuck, and tree shrew, respectively. A clustering analysis showed that the overall distribution of microbial species in the guts of these species mirrored their mammalian phylogeny, and the microbiota of the marmoset and tree shrew showed the closest bray_curtis distances to that of humans. PICRUSt functional prediction separated the woodchuck from the other species, which may reflect its herbivorous diet. In conclusion, both the evolutionary phylogeny and daily diet affect the gut microbiota of these experimental animals, which should not be neglected for their usage in biomedical research.
Highlights
Experimental animals including the ferret, marmoset, woodchuck, mini pig, and tree shrew have been used in biomedical research
The age and sex information were listed in supplementary Table S1. These sequence data were annotated to Operational taxonomic units (OTUs) in a comparison with the Silva Database and the quantities of reads for each sample were provided in supplementary table about reads per sample
The genus Collinsella occurred in the gut microbiota of human, marmoset and tree shrew, whereas it was limited in the gut microbiota of the ferret, mini pig, and woodchuck
Summary
Experimental animals including the ferret, marmoset, woodchuck, mini pig, and tree shrew have been used in biomedical research. Their gut microbiota have not been fully investigated. PICRUSt functional prediction separated the woodchuck from the other species, which may reflect its herbivorous diet Both the evolutionary phylogeny and daily diet affect the gut microbiota of these experimental animals, which should not be neglected for their usage in biomedical research. The gut microbiota datasets for these experimental animals were generated from fecal samples, which may serve as references to support their roles in comparative medicine
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