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- Microbiome and transcriptome ontogeny with a focus on the fish immune system: insights into developmental biology and host-bacteria interactionsPublication . Najafpour, Babak; Power, Deborah M.; Pinto, Patricia I.Aquaculture hatcheries face persistent challenges concerning poor larvae quality and high mortality rates. The early developmental stages and the transition from larvae to juveniles are critical periods characterized by heightened vulnerability to environmental stressors. Researchers have turned to next-generation sequencing techniques, which have provided invaluable insights into organism biology and symbiotic bacteria. In the present research, RNA-seq and 16S rRNA gene sequencing have been employed to illuminate the microbiome and transcriptome during fish early development, focusing on two commercially farmed species, gilthead sea bream, and European sea bass. This investigation further delves into the host's vital biological responses to pathogens, such as the complement system, using a comprehensive phylogenetic analysis, and reveals that species-specific gene duplication and functional diversity of complement C3 may enhance the capacity of fish to activate complement through direct interaction of C3 isoforms with pathogenic agents. Designing bacterial genus-specific primers and complementary techniques like quantitative PCR enables targeted tracking of the colonization of larvae by abundant bacteria during their ontogeny. The analyses of the microbiome and transcriptome revealed dynamic profiles of bacteria and host gene expression during larval development, underscoring their potential interaction and stage-specific adaptability to rearing practices. This uncovers new management opportunities as manipulating microbiome profiles may be a potentially effective method to modulate larvae quality during the hatchery phase. Comparing larvae from different sites, stages, and species identified the different changes in the core gene expression or microbiome profiles during metamorphosis at the hatchery phase. This investigation also hints at the intriguing interaction between the microbiota and specific pathways, such as muscle development, immune response, and energy homeostasis. The study demonstrates how rearing water, live feed, season, and age are coupled with host selection of beneficial bacteria and are the main drivers of the microbiome in fish larvae. This comprehensive investigation contributes new knowledge to improve management strategies and fish health in the hatchery phase. The importance of this research extends beyond aquaculture, as transcriptome and microbiome changes associated with age provide crucial insights into the basic biology of the host and the changing holobiont throughout development.