DOI: 10.5061/dryad.zpc866tg1
title: Warming effects on lizard gut microbiome depend on habitat connectivity

description: Climate warming and landscape fragmentation are both factors well known to
 threaten biodiversity and to generate species responses and adaptation.
 However, the impact of warming and fragmentation interplay on organismal
 responses remains largely under-explored, especially when it comes to gut
 symbionts, which may play a key role in essential host functions and
 traits by extending its functional and genetic repertoire. Here, we
 experimentally examined the combined effects of climate warming and
 habitat connectivity on the gut bacterial communities of the common lizard
 (Zootoca vivipara) over three years. While the strength of effects varied
 over the years, we found that a 2°C warmer climate decreases lizard gut
 microbiome diversity in isolated habitats. However, enabling connectivity
 among habitats with warmer and cooler climates offset or even reversed
 warming effects. The warming effects and the association between host
 dispersal behaviour and microbiome diversity appear to be a potential
 driver of this interplay. This study suggests that preserving habitat
 connectivity will play key role in mitigating climate change impacts,
 including the diversity of the gut microbiome and calls for more studies
 combining multiple anthropogenic stressors when predicting the persistence
 of species and communities to global changes.
description: # File : MS1\_rawdata.tar.gz Contains raw sequencing data (R1 and R2 fastq
 files). Number of raw sequencing reads in R1 and R2 files: 5899356 reads
 each. # File : MS1\_ngsfilter\_16S\_Lez\_2015\_2018.tsv Tab-sep text file
 containing the information to retrieve the sample origin of each
 sequencing reads. Provided in a format compatible with the use of
 OBITools. # File : MS1\_obitab.tsv Contains an MOTU (Molecular Operational
 Taxonomic Unit) by sample table after basic bioinformatic analysis with
 the OBITools package.\ Basic bioinformatics procedure includes reads
 pairing (default parameters), demultiplexing (2 errors on primers, 0 on
 tags), exclusion of sequences with counts = 1 (i.e. singletons), too short
 (&gt;100 bp) or containing ambiguous bases, and clustering into OTUs at
 97% sequence similarity Number of sequencing reads : 11183625 Number of
 OTUs 97% : 8070 Description of the variables : * GC_content: %GC of the
 MOTU sequence * ID: Identification name of the sample in which the MOTU is
 present\ NA for multiple samples. * ali_length: length of the reads
 pairing alignment (an integer value)\ NA due to merge of info after the
 clustering * class: identification name of the cluster (MOTU) center used
 to aggregate the reads count * cluster: identification name of the cluster
 * cluster_center: true if the sequence is the center of the cluster. *
 cluster_score: similarity score of the sequence with the cluster center *
 cluster_weight: abundance of the MOTU before data cleaning * count: total
 abundance of the MOTU (an integer value) * direction: sense of the read,
 either ‘forward’ or ‘reverse’\ NA due to merge of info after clustering *
 distance: distance between the optimal value and the value computed for
 the sequence record * experiment: name of the experiment * forward_match:
 sequence of the forward priming site * forward_primer: sequence of the
 forward primer * forward_score: score of the priming site match with the
 primer * forward_tag: sequence of the forward tag.\ NA for multiple
 samples, as each sample has a different tag * mode: mode of the read
 pairing alignment. * primers: name of the primer pair. * reverse_match:
 sequence of the reverse priming site * reverse_primer: sequence of the
 reverse primer * reverse_score: score of the reverse priming site match
 with the primer * reverse_tag: sequence of the reverse tag\ NA for
 multiple samples, as each sample has a different tag. * sampling_date:
 sampling year\ NA for multiple samples after sequence aggregation *
 seq_a_deletion:  number of deletions on the forward read compared to the
 consensus sequence (an integer value) * seq_a_insertion: number of
 insertions on the forward read compared to the consensus sequence (an
 integer value) * seq_a_mismatch: number of mismatches on the forward read
 compared to the consensus sequence (an integer value) * seq_a_single:
 number of nucleotides on the forward read that belong to the consensus
 sequence and not aligned with the reverse read (an integer value) *
 seq_ab_match: number of matches in the paired end alignment (an integer
 value) * seq_b_deletion: number of deletions on the reverse read compared
 to the consensus sequence (an integer value) * seq_b_insertion: number of
 insertions on the reverse read compared to the consensus sequence (an
 integer value) * seq_b_mismatch: number of mismatches on the reverse read
 compared to the consensus sequence (an integer value) * seq_b_single:
 number of nucleotides on the reverse read that belong to the consensus
 sequence and not aligned with the forward read (an integer value) *
 seq_length: length of the sequence of the MOTU * seq_length_ori: length of
 the sequence of the MOTU before tag and primer trimming * status: ‘full’
 if the amplicon has been sequenced entirely or “partial” if not. *
 sequence: sequence of the MOTU (most abundant sequence) * The following
 columns count the number of motus in each sample. # File:
 MS1\_metabaR\_diagnostic.html A diagnostic file reporting on the
 Fromm_MS1_obitab characteristics and additional filtering (contaminents,
 tagsjumps) made using the metabaR R package. Chloroplastic and
 Mitochondrial sequences were removed after this step.