Longitudinal 16S rRNA data derived from limb regenerative tissue samples of axolotl Ambystoma mexicanum

Abstract

The Mexican axolotl (Ambystoma mexicanum) is a critically endangered species and a fruitful amphibian model for regenerative biology. Despite growing body of research on the cellular and molecular biology of axolotl limb regeneration, microbiological aspects of this process remain poorly understood. Here, we describe bacterial 16S rRNA amplicon dataset derived from axolotl limb tissue samples in the course of limb regeneration. The raw data was obtained by sequencing V3-V4 region of 16S rRNA gene and comprised 14,569,756 paired-end raw reads generated from 21 samples. Initial data analysis using DADA2 pipeline resulted in amplicon sequence variant (ASV) table containing a total of ca. 5.9 million chimera-removed, high-quality reads and a median of 296,971 reads per sample. The data constitute a useful resource for the research on the microbiological aspects of axolotl limb regeneration and will also broadly facilitate comparative studies in the developmental and conservation biology of this critically endangered species.

Fig. 1

Experimental design. (a) The datasets generated in these experiments were derived from 21 samples in total (18 limb tissue samples and 3 aquarium water samples). Post amputation limb tissue samples were collected at these experimental timepoints: 0 dpa, 1 dpa, 4 dpa, 7 dpa, 30 dpa and 60 dpa; “dpa” denoting day post amputation. At each experimental time point groups included 3 biological replicates (R1, R2 and R3) and each replicate was formed by pooling limb tissue samples from 3 animals to minimize interindividual variation. The aquarium water samples were collected at 3 time points (day 0, day 30 and day 60) in 3 replicates (R1, R2, and R3). (b) The workflow of data analysis, the employed tools and changes in the number of processed reads at each step are shown.

Fig. 2

Structure and diversity of bacterial communities associated with regenerating axolotl limb tissues. (a) Stacked bar chart of shows shifts in relative bacterial abundance on phylum level in the course axolotl limb regeneration. The microbial profile demonstrates temporal dynamics with the underlying differential phyla abundances in this biological process and depicts separation of aquarium control groups. (b) Hierarchical clustering of samples based on Beta-diversity analysis of ASV abundances. This chart was generated using Bray-Curtis distance metric and Ward’s method (as linkage method). (c) Principal Coordinate Analysis (PCoA) of all studies samples based on Beta-diversity analysis of ASV abundances. This chart was generated using Bray-Curtis distance metric and PCoA ordination method. The Fig. 2b,c shows clustering of treatment samples into three main groups (corresponding to the three main stages of axolotl limb regeneration, namely wound healing, dedifferentiation and re-development) and their separation from the control group.