Gut microbes provide essential services to their host and shifts in their composition can impact host fitness. However, despite advances in our understanding of how microbes are assembled in the gut, we understand little about the stability of these communities within individuals, nor what factors influence its composition over the life of an animal. For this reason, we conducted a longitudinal survey of the gut microbial communities of individual free-ranging woodrats (Neotoma spp.) across a hybrid zone in the Mojave Desert, USA, using amplicon sequencing approaches to characterize gut microbial profiles and diet. We found that gut microbial communities were individualized and experienced compositional restructuring as a result of seasonal transitions and changes in diet. Turnover of gut microbiota was highest amongst bacterial subspecies and was much lower at the rank of Family, suggesting there may be selection for conservation of core microbial functions in the woodrat gut. Lastly, we identified an abundant core gut bacterial community that may aid woodrats in metabolizing a diet of plants and their specialized metabolites. These results demonstrate that the gut microbial communities of woodrats are highly dynamic and experience seasonal restructuring which may facilitate adaptive plasticity in response to changes in diet. 

Woodrats were repeatedly live-trapped across 8 sampling events from January 2019 to November 2020 at a site known as “Whitewater” located in the San Gorgonio Pass, Riverside County, CA, USA within creosote bush (Larrea tridentata) shrublands (latitude/longitude: 33° 55’ N; 116° 38’). We extracted DNA from feces using the Qiagen PowerFecal DNA Isolation Kit (#12830) following the manufacturers protocol. We included negative controls for each extraction kit to assess for the potential contamination of reagents. Library preparation and sequencing of DNA extracts were conducted by the University of Chicago at Urbana-Champaign DNA Sequencing Facility. Individual libraries were prepared using a two-stage PCR protocol as described in Naqib et al., 2018. For each DNA sample, we generated both 16S rRNA (V4) libraries using the unmodified 515F/806R primer pair (Caporaso et al., 2011; Parada et al., 2016) and chloroplast trnL (UAA) intron libraries using the unmodified g/h primer pair (Taberlet et al., 2007). Libraries were pooled and sequenced in batches across 3 lanes of an Illumina Miniseq to generate 2x150 bp paired-end reads. To control for any potential batch effects, we included controls consisting of the repeated sequencing of a single 16S rRNA library generated from woodrat feces and a 16S rRNA library generated from an artificial microbial mock community (ZymoBIOMICS Microbial Community Standard D6300). This repository contains the resulting raw sequence data for each library type for the fecal samples as well as the raw sequence data for the 16S rRNA control samples.

This dataset was originally processed using the dada2 workflow v.1.24.0 (Callahan et al., 2016) and followed by downstream analyses using phyloseq v.1.40.0 (McMurdie and Holmes, 2013) running in an R environment (v.4.2.1).