Microbiome turnover during offspring development varies with maternal care, but not moult, in a hemimetabolous insect

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This repositery contains all dataset that allow to reproduce this study (16S rRNA sequences in .fastq format, the R script and the informative file realted with the sequences (env_succession.txt). It also contains Supplementary material to complete the related manuscript.

1) The file "env_succession.txt" 

It contains the informations regarding the samples. The description of the variables follows:

clutch : The name of the family

ID : The identifiant of the sample (host)

stage : the sampled stage where L1 are the 1st instar, L2 the 2nd instar, L3 the 3rd instar, L4 the 4th instar. The following letter Y (for Young moulted nymphs) and O (for Old nymphs) if the sampling was made, respectively, immediately after the moulting event, or before.

nymph_stage: for the stage of the larvae whitout taking into account the moulting event

after_molt: whether sampling was made after or before the moulting event. If yes, it is a young nymphs, if no, it is an old nymph, whatever its developmental stage.

mother_presence:  the mother has been removed just after the hatching period (no) or the mother was removed from the clutch after 14 days (yes) i.e., the natural period of the family life in this species.

sex: M (male) or F (female) only identified at adult stage with the morphology of the forceps.

type: type of sample 'forficula'

2) The file "Earwig_succession_script.R" 

This script allows to perform all the bioinformatical process and analyses that were made for this study. It was made on R version 4.4.

3) The file "Supplemental File.xlsx" 

This table contains 5 sheets.

Info : this sheets contains the general information of the file with details regarding the labels

Stage.Alpha pairwise details: this table contains all pairwise results (contrasts emmeans) for the four alpha diversity indices measured (Observed richness, Shannon, Faith and Allen indices), between all stages and adult sex (Egg, L1-Y, L1-O, L2-Y, L2-O, L3-Y, L3-O, L4-Y, L4-O, Adult-F, Adult-M). Results take the form of the estimate mean (Estimate), the standard error (SE), the degree of freedom (df), the value of the t-ratio or z-ration (for observed richness), the p-value, and the significance of the resuts (Sign). 

Stage. ASVs Beta pairwise: this table contains all pairwise results (pairwise adonis) for the four beta diversity distance measured (Jaccard, Bray-Curtis, Unweighted and Weighted Unifrac) on the ASVs compositions, between all stages and adult sex (Egg, L1-Y, L1-O, L2-Y, L2-O, L3-Y, L3-O, L4-Y, L4-O, Adult-F, Adult-M). Results take the form of the explained variance by the stage (R2), the p-value (P), and the significance of the resuts (sign). 

Stage. KEGG Beta pairwise: this table contains all pairwise results (pairwise adonis) for the four beta diversity distance measured (Jaccard, Bray-Curtis, Unweighted and Weighted Unifrac) on the KEGG orthologs (predicted functions after PICRUSt2 algorithm made on the ASVs) compositions, between all stages and adult sex (Egg, L1-Y, L1-O, L2-Y, L2-O, L3-Y, L3-O, L4-Y, L4-O, Adult-F, Adult-M). Results take the form of the explained variance by the stage (R2), the p-value (P), and the significance of the resuts (sign). 

Stage. Discriminant KEGG pathway: this table contains both the description of the KO (Kegg orthologs) and the results of the DESeq2 discriminant analysis between stage. Specifically, KO (Kegg orthologs), method (deseq2), the first contrast (group1), the second contrast to compare (group2), p_values, the method used for correction (adj_method) where BH is the Benjamin-Hochberg correction, the value of the p-values corrected (p_adjust), the contrast, the name of the pathway level 1 (pathway_name), the pathway_description, the class of the pathway (pathway_class), the pathway level 3 (pathway_map)

4) The file "R1R2_sequences.zip" 

This folder zip contains all sequence at fastaq format. These sequences are from the V3-V4 of the 16S rRNA genes sequenced by Illumina MiSeq 2x250 bp.

5) The file "Supplemental Material.pdf" 

This pdf contains all supplemental tables and figures related with our study. Specifically,

Table S1: Detailed table of the collection.

Table S2: Core microbiome by developmental stages.

Figure S1: Species Abundance Distribution (SAD) pattern.

Figure S2: Rarefaction curves for each sample.

Figure S3: ASVs partition between life stages.

Figure S4: Alpha diversity values comparison between stages, moults and sex.

Figure S5: Beta diversity comparison of the European earwig microbiome throughout life cycles.

Figure S6: Alpha diversity calculated in microbiomes associated with 1st instar nymphs and adults according to the presence or absence of the mother during family life.

Figure S7: Beta diversity of earwigs microbiome.

Figure S8: Jaccard distance comparisons of predicted functions (KOs) associated with microbiome of the European earwig throughout life cycles.