Warming effects on lizard gut microbiome depend on habitat connectivity
Data files
Mar 20, 2024 version files 2.49 GB
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MS1_metabaR_diagnostic.html
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MS1_ngsfilter_16S_Lez_2015_2018.tab
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MS1_obitab.tsv
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MSI_rawdata.tar.gz
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README.md
Abstract
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.
README: 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 (>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.