DOI: 10.5061/dryad.ghx3ffbss
title: Data from: Seasonal restructuring facilitates compositional convergence of gut microbiota in free-ranging rodents

description: 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. 
description: 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
 (<em>Larrea tridentata</em>) 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 <em>et
 al</em>., 2018. For each DNA sample, we generated both 16S rRNA (V4)
 libraries using the unmodified 515F/806R primer pair (Caporaso
 <em>et al</em>., 2011; Parada <em>et al</em>.,
 2016) and chloroplast trnL (UAA) intron libraries using the unmodified
 <em>g</em>/<em>h</em> primer pair (Taberlet
 <em>et al</em>., 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.
description: 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).