DOI: 10.5061/dryad.02v6wwq3m
title: Drivers of change and stability in the gut microbiota of an omnivorous avian migrant exposed to artificial food supplementation

description: Human activities shape resources available to wild animals, impacting diet
 and likely altering their microbiota and overall health. We examined
 drivers shaping microbiota profiles of common cranes (Grus grus) in
 agricultural habitats by comparing gut microbiota and crane movement
 patterns (GPS-tracking) over three periods of their migratory cycle, and
 by analyzing the effect of artificially-supplemented food provided as part
 of a crane-agriculture management program. We sampled fecal droppings in
 Russia (non-supplemented, pre-migration) and in Israel in late fall
 (non-supplemented, post-migration) and winter (supplemented and
 non-supplemented, wintering). As supplemented food is typically
 homogenous, we predicted lower microbiota diversity and different
 composition in birds relying on supplementary feeding. We did not observe
 changes in microbial diversity with food supplementation, as diversity
 differed only in samples from non-supplemented wintering sites. However,
 both food supplementation and season affected bacterial community
 composition and led to increased abundance of specific genera (mostly
 Firmicutes). Cranes from the non-supplemented groups spent most of their
 time in agricultural fields, likely feeding on residual grain when
 available, while food-supplemented cranes spent most of their time at the
 feeding station. Thus, non-supplemented and food-supplemented diets likely
 diverge only in winter, when crop rotation and depletion of anthropogenic
 resources may lead to a more variable diet in non-supplemented sites. Our
 results support the role of diet in structuring bacterial communities and
 show that they undergo both seasonal and human-induced shifts. Movement
 analyses provide important clues regarding host diet and behavior towards
 understanding how human-induced changes shape the gut microbiota in wild
 animals.
description: Fecal samples were
 collected for microbiome analysis. PCR-amplification, library preparation
 and sequencing of the 16s V4 region for each sample was conducted at the
 Argonne Sequencing Center at Argonne National Laboratory (Lemont, IL).
 QIIME 2 was used to demultiplex the raw sequence data and DADA2 was used
 to infer amplicon sequence variants. Movement data was collected
 using GPS-GSM transmitters on free ranging cranes that visited sampled
 fields up to three days prior to fecal sample collection for
 host-associated bacterial analysis. Habitat annotation was done using
 satellite imagery from Sentinel-2 in Russia and GIS information provided
 by the Ministry of Agriculture and Rural Development in Israel.
description: The database includes: 
 <strong>R scripts used for microbiome statistical
 analysis,</strong> including the phyloseq object input in the base
 of the pipeline. Input:
             phyloseq object:
 <em>Israel_microbiome_run2_crane_phyloseq_data_Updated</em> Scripts: Sample&OTU_filtering: initial filtering of the data Sample_rarefaction: refaction Working_database_creation: addition of relevant metadata Prevelence&Abundance: creation of prevelanve and abundance table Alpha_Diversity: alpha diversity metrics calculation and plotting Beta_Diversity: beta diversity metrics calculation and plotting ANCOM: Analysis of Composition of Microbiomes and plotting <strong>R script used for movement statistical analysis</strong> of individual of individual GPS-tagged cranes and the input file used for the script. Input: <em>Daily_locations_MoveMicrobiome</em> (CSV) input file includes GPS data for tagged cranes visiting microbiome sampling locations with annotations to habitat type visited in each location. Script: Movement4MicrobiomeSamples: proportion of time spent in different habitats. <strong>    </strong>3<strong>. Metadata for amplicon sequence data archived in the Sequence Read Archive </strong>(https://www.ncbi.nlm.nih.gov/sra/PRJNA578383) Links_to_the_sample_sequence_dattxt: links to the sequences Accession_numbers_for_the_sample_sequence_data.txt: sample access numbers