Molecular interactions in an holobiont-pathogen model: Integromics in gilthead seabream infected with Sparicotyle chrysophrii

The gill ectoparasite Sparicotyle chrysophrii is the major parasitic pathogen in gilthead seabream (Sparus aurata) aquaculture with limited management and treatment strategies. In this work, we assessed the modulation of gilthead seabream gill microbiota during sparicotylosis by sequencing the complete 16S rRNA gene, and the host's molecular pathways occurring at local and systemic levels performing RNA sequencing of gill, spleen and liver. The results obtained and other available data from the same animals were integrated to unveil routes and interactions in this host-microbiota-parasite system. Sparicotylosis significantly modulated gill microbiota decreasing diversity in fish with high infection intensity (H). LEfSe analysis revealed nine microbial biomarkers, highlighting 2013Ark19i (Candidatus Ichthyocystis sparus), already present in control fish, but dramatically increasing in H fish. This bacterium, proposed as the causing agent of epitheliocystis, correlated with the bac-terial cysts observed in histopathology, revealing a secondary bacterial infection in these animals. In the RNA sequencing study, 759, 337, and 603 differentially expressed transcripts (DET) were found in gills, spleen and liver, respectively, with 16 commonly regulated transcripts, including genes related to the parasite pathogenesis, such as haemoglobin subunits or hypoxia-inducible factors. Relevant regulated pathways in infected fish were immune system; response to stress, starvation and hypoxia; apoptosis; and haemostasis. Several DET and enriched pathways were shared with a previous plasma proteomics study, particularly in liver. The integrative analysis separated genes and pathways specifically affected by the primary (parasite) and secondary (bacterium) infections. These results show how sparicotylosis changes the gill microbiota, facilitating the growth of patho-genic bacteria and development of secondary infections aggravating the disease outcome. They also evidence host molecular pathways involved in sparicotylosis pathogenesis. Key genes and interactions identified using this integrative approach contribute to the understanding of the disease and can constitute targets for further research pointing to solutions for this infection.