Comparative Analysis of Gut Microbiomes in Laboratory Chinchillas, Ferrets, and Marmots: Implications for Pathogen Infection Research

Abstract

Gut microbes play a vital role in the health and disease of animals, especially in relation to pathogen infections. Chinchillas, ferrets, and marmots are commonly used as important laboratory animals for infectious disease research. Here, we studied the bacterial and fungal microbiota and discovered that chinchillas had higher alpha diversity and a higher abundance of bacteria compared to marmots and ferrets by using the metabarcoding of 16S rRNA genes and ITS2, coupled with co-occurrence network analysis. The dominant microbes varied significantly among the three animal species, particularly in the gut mycobiota. In the ferrets, the feces were dominated by yeast such as Rhodotorula and Kurtzmaniella, while in the chinchillas, we found Teunomyces and Penicillium dominating, and Acaulium, Piromyces, and Kernia in the marmots. Nevertheless, the dominant bacterial genera shared some similarities, such as Clostridium and Pseudomonas across the three animal species. However, there were significant differences observed, such as Vagococcus and Ignatzschineria in the ferrets, Acinetobacter and Bacteroides in the chinchillas, and Bacteroides and Cellvibrio in the marmots. Additionally, our differential analysis revealed significant differences in classification levels among the three different animal species, as well as variations in feeding habitats that resulted in distinct contributions from the host microbiome. Therefore, our data are valuable for monitoring and evaluating the impacts of the microbiome, as well as considering potential applications.

Keywords: chinchillas; diversity; feeding habitat; ferrets; gut mycobiome; high-throughput sequencing; interaction networks; marmots.

Figure 1

Graphical digestive tract structure representation of chinchilla, marmot, and ferret. Reference website https://www.cnsweb.org/digestive_system_of_vertebrates/ (accessed on 15 September 2023) drawing the figure plate.

Figure 2

Comparison of the three animal species of bacteria. (a) The common and unique OTUs among different groups. (b) Comparison of alpha diversity indices. (c) The genus composition shared by three animal species. (d,e) The bacterial compositions at the phylum and genus level. (f) Sankey analysis of bacteria.

Figure 3

Comparison of the three animal species of fungi. (a) The common and unique OTUs among different groups. (b) Comparison of alpha diversity indices. (c) The genus composition shared by three animals. (d,e) The fungal compositions at the phylum and genus level. (f) Sankey analysis of fungi.

Figure 4

Composition differences of bacteria (top) and fungi (bottom) for three animal species. (a,d) Heatmap showing significantly different animal species. The smaller dissimilarity coefficient means the smaller the difference between animal species; in the same grid, the upper and lower values represent the weighted unifrac and unweighted unifrac distances, respectively. (b,e) Unweighted pair-group method with arithmetic mean (UPGMA) analysis. Microbiota profile clustering based on Bray–Curtis dissimilarities was set to form an OTU hierarchical clustering tree of the overall grouped distribution of microbial species in the gut of each host species. The legend boxes list the 10 most abundant taxa at the phylum level. (c,f) The ternary plot at the genus level.

Figure 5

Linear discriminant analysis (LDA) effect size (LEfSe) analysis. Comparison of differential microbiota in three animal species of bacteria (a) and fungi (b). Comparison of differential microbiota in different feeding habits for bacteria (c) and fungi (d).

Figure 6

The network analysis within bacteria (a) and fungi (b). Different node color denotes varied phyla taxa. The weighted node size was based on the connections with other nodes. The weighted edges indicate the correlation coefficient and the thickness of the edge represents the size of the coefficient. Solid lines indicate positive correlation, dashed lines indicate negative correlation.

Figure 7

The network analysis between bacteria and fungi in the marmot (a), chinchilla (b), and ferret (c). Ellipse indicates bacteria and diamond indicates fungi. Different node color denotes varied phyla taxa. The weighted node size was based on the connections with other nodes. The weighted edges indicate the correlation coefficient and the thickness of the edge represents the size of the coefficient. Solid lines indicate positive correlation, dashed lines indicate negative correlation.

Figure 8

Function annotation and the phylogeny for bacteria (top) and fungi (bottom). The overview of bacterial function (a) and the distribution of fungal functions of three animal species (c). The phylogeny is the same as shown in (b,d). From left to right, the data mapped onto the tree are host- and phylum-level classification.