Adaptive shifts of the skin and gut microbiomes during metamorphosis of anuran amphibians
Authors: Li Xiaobing , Wang Hai , Li Yiliang , Chen Rujian , Zhang Ping , Wang Xiao , Zou Zanjian , Shen Xuejuan , Roy Ayan , Luo Wen , Irwin David M. , Wang Chunfeng , Shen Yongyi 
Published: September 2023

The gut and skin microbiota play critical roles in host fitness. Anuran amphibian metamorphosis reshapes and restructures their morphology, physiology, and behavior and usually prepares them for a transformation from an aquatic to a terrestrial or semi-terrestrial lifestyle, with drastic changes in food and habitat. Changes in the microbiota on amphibian skin and their gut microbiota through development and the impact of antimicrobial peptides on skin and gut microbiota at different developmental stages is currently not well understood. Here, we use high-throughput 16S amplicon and metagenomic sequencing to characterize the gut and skin microbiota of three wild anurans, namely, Bufo melanostictus, Kaloula pulchra, and Polypedates megacephalus, and two commercially breed amphibians, namely, Rana catesbeiana and Xenopus laevis during metamorphosis. We found evidence for an adaptive shift in the gut microbiome of these amphibians that is consistent with the transition from a herbivorous to an insectivorous diet during metamorphosis. Multiple members of Actinobacteria, associated with cellulose degradation, were enriched in the early stages of metamorphosis. However, specific Bacteroides from the phylum Bacteroidetes, and associated with proteolysis, were enriched in the later stages of metamorphosis. Additionally, carbohydrate active enzymes (CAZymes) associated with cellulose degradation were enriched in the early stages, whereas insect tissue degrading CAZymes were enriched in later stages. Similarly, the skin bacterial community structure was significantly altered after metamorphosis. Specifically, the abundance anti-Batrachochytrium dendrobatidis (anti-Bd) bacteria increased through developmental and peaked at the adult stage. Antimicrobial peptide bath treatment with PGLa, Magainin I, Magainin II, cecropin, or a cocktail of antimicrobial peptides increased the relative abundance of anti-Bd bacteria including those from the genera Aeromonas, Pseudomonas, and Citrobacter on the skin at different developmental stages in Xenopus laevis. Meanwhile, antimicrobial peptides, especially Magainin II, increased the abundance of beneficial bacteria, namely, Bacteroides, Sphingomonas, and Christensenella, and reduced the abundance of pathogenic bacteria that included Escherichia, Haemophilus, Klebsiella, Serratia, Streptococcus, and Plesiomonas in the gut. In addition, unlike antibiotics that greatly reduce microbial diversity, these AMPs in general had no significant effect on microbial diversity of the intestinal and skin microbiota. Our study not only provides compelling evidence for the adaptation of gut microbiota composition and function to the dietary transition during amphibian metamorphosis, but also reveals variations in the anti-Bd bacteria on amphibian skin during development. Our findings also provide new insights into the beneficial effects of antimicrobial peptides on the skin and gut microbiota during the entire amphibian developmental process and may be useful for amphibian breeding and protection.