Natural diets promote retention of the native gut microbiota in captive rodents

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Wild animals entering captivity experience radical lifestyle changes resulting in microbiome alterations. However, little is known about the factors that drive microbial community shifts in captivity, and what actions could mitigate microbial changes. Using white-throated woodrats (Neotoma albigula), we tested whether offering natural diets in captivity facilitates retention of native microbial communities of captive animals. Wild-caught woodrats were brought to laboratory conditions. Woodrats received either a natural diet of Opuntia cactus or an artificial diet of commercial chow over three weeks. Microbial inventories from woodrat feces at the time of capture and in captivity were generated using Illumina 16S rRNA sequencing. We found that providing woodrats with wild-natural diets significantly mitigated alterations in their microbiota, promoting a 90% retention of native microbial communities across the experiment. In contrast, the artificial diet significantly impacted microbial structure to the extent that 38% of the natural microflora was lost. Core bacteria including Bifidobacterium and Allobaculum were lost, and abundances of microbes related to oxalate degradation decreased in individuals fed artificial but not natural diets. These results highlight the importance of supplementing captive diets with natural foods to maintain native microbiomes of animals kept in artificial conditions for scientific or conservation purposes.

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We thank Michele Skopec, Kika Kitanovic, Tess Stapleton, KayLene Yamada, Sara Weinstein, and Shin Enomoto for their help and comments during the project development. This project was funded by NSF DEB-1342615 to MDD. We also thank the Bonderman Field Station at Rio Mesa, UT for housing during the field work. RMM thanks CONACYT-Mexico for a postdoctoral fellowship.

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Correspondence to M. Denise Dearing.

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Supplementary information

Figure S1. Nitrogen and carbon isotopic signatures of diets and hair of 12 white-throated woodrats (Neotoma albigula)

Figure S2. Mean ± SE measurements of microbial alpha diversity from feces of woodrats fed natural (dark grey) and artificial (light grey) diets

Figure S3. Predicted functions of microbial metagenomes assigned to the KEGG Level 2 Metabolism category from woodrats fed wild, natural, and artificial diets

Table S1. Cleaned up OTU table

Table S2. Results of the GLMM likelihood ratio test comparing a full against a null model for each alpha-diversity metric

Table S3. SIMPER analysis showing the contribution of microbial families to the dissimilarity between wild samples and samples from individuals fed the artificial diet at 3-days in captivity

Table S4. SIMPER analysis showing the contribution of microbial families to the dissimilarity between wild samples and samples from individuals fed the artificial diet at 21-days in captivity

Table S5. Relative abundances (%) of microbial families from feces of woodrats fed the natural diet and from the surface of cactus pads

Table S6. Relative abundances (%) of microbial families from feces of woodrats fed the artificial diet and from rabbit chow pellets

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