Abstract Investigated are the microbial communities of the stomach, gut, and faeces of pre-adult and adult Pontastacus leptodactylus (Eschscholtz, 1823) naturally infected with the oomycete Aphanomyces astaci, the causative agent of crayfish plague. Using shotgun metagenomics, we characterised bacterial, archaeal, fungal, viral, and eukaryotic assemblages across samples and developmental stages of the crayfish to explore microbiome structure and potential microbial interactions. Bacterial communities were dominated by Proteobacteria, although their abundance decreased in adult gut and stomach samples, accompanied by increases in Firmicutes, Mycoplasmatota (Tenericutes), and viral taxa. Fungal communities exhibited tissue-specific patterns, with Glomeromycetes and Umbelopsidomycetes prevalent in the gut, Saccharomycetes in faeces, and Ustilaginomycetes and Malasseziomycetes enriched in adult stomachs. Despite this variation, gut and stomach samples suggested the presence of a stable core microbiome. Viral communities were dominated by Caudovirales (phages), particularly in the adult stomach, indicating potential roles in shaping microbial composition. Faecal samples showed higher diversity and evenness compared to gut and stomach samples, highlighting their role as microbial reservoirs. Overall, microbiota composition appeared to be more strongly influenced by tissue type than by developmental stage.
Bouchorikou et al. (Wed,) studied this question.