Browsing by Author "Najafpour, Babak"
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- Comparative ontogeny of the digestive tract of Oncorhynchus mykiss female x Salmo trutta caspius male triploid hybrids to their parental speciesPublication . Najafpour, Babak; Dorafshan, Salar; Paykan Heyrati, Fatemeh; Canario, Adelino; Power, Deborahthe ontogeny of the gastrointestinal tract of the hybrid between female rainbow trout, RT (Oncorhynchus mykiss) and male Caspian brown trout, CBT (Salmo trutta caspius) was compared to the parental species. Larvae were collected for histology and enzymatic assays (amylase, lipase and trypsin) at 3, 6, 9, 12, 15, 18, 21, 26, 31, 35, 40 and 45 days post-hatch (dph). the development of the gastrointestinal tract (GI-tract) and the onset of digestive enzyme production was variable between groups. the GI-tract post-hatch was a relatively simple tubular structure, and a rudimentary oesophagus was differentiated from other regions at 3 dph in all studied groups. the pyloric caeca and the U-shaped stomach were clearly visible at 26, 35 and 40 dph in RT, triploid hybrid and CBT, respectively. An abrupt increase in trypsin activity at 31, 35 and 45 dph was identified in CBT, RT and the triploid hybrid, respectively. the increasing activity of trypsin and decreasing activity of lipase during larval development suggests that the CBT, RT and triploid hybrid rely more on dietary proteins than lipids with increasing age. the hybrid grew better and had a faster GI-tract development than CBT, while RT performed best overall.
- Core microbiome profiles and their modification by environmental, biological, and rearing factors in aquaculture hatcheriesPublication . Najafpour, Babak; Pinto, Patricia IS; Sanz, Eric Climent; Martinez-Blanch, Juan F.; Canario, Adelino; Moutou, Katerina A.; Power, Deborah16S rRNA gene sequencing and bacteria-and genus-specific quantitative PCR was used to profile microbial communities and their associated functions in water, live feed (microalgae, Artemia, and rotifer), and European sea bass and gilthead sea bream larvae from hatcheries in Greece and Italy. The transfer to larvae of genus containing potential pathogens of fish was more likely with Artemia and rotifer than with microalgae or water, irrespective of geographic location. The presence of potentially pathogenic bacteria (Vibrio and Pseudoalter-omonas) in the core microbiota of water, live feed, and fish larvae, the enrichment of different bacterial resistance pathways and biofilm formation, and the overall low beneficial bacteria load during larval ontogeny emphasizes the risk for disease outbreaks. The present data characterizing microbiota in commercial aquaculture hatcheries provides a baseline for the design of strategies to manage disease and to model or remediate potential adverse environmental impacts.
- Embryonic development of the endangered Caspian brown trout, Salmo trutta caspius (Kessler, 1877)Publication . Najafpour, Babak; Dorafshan, Salar; Heyrati, Fatemeh Paykan; Power, DeborahThe Caspian brown trout, Salmo trutta caspius is an endangered species of economic value and better knowledge of its biology will contribute to conservation measures. In the present study we characterized its early development to identify critical embryonic stages, by observing embryos and larvae from a broodstock maintained in captivity incubated at 9 +/- 1 degrees C. Morphological analysis of landmark stages of embryonic development revealed that first cleavage occurred at 189 degree-h, a many-celled blastoderm formed at 62 degree-days (dd), a germ ring at 72 dd, the neural keel stage at 88 dd, the blastopore closed at 137 dd, the eye became pigmented at 188 dd and the larvae hatched at 373 dd. The detailed timing of these landmark features will help development of strategies aiming at increased aquaculture production of this species.
- Factors driving bacterial microbiota of eggs from commercial hatcheries of European Seabass and Gilthead SeabreamPublication . Najafpour, Babak; Pinto, Patricia IS; Moutou, Katerina A.; Canario, A.V.M.; Power, Deborah MaryA comprehensive understanding of how bacterial community abundance changes in fishes during their lifecycle and the role of the microbiota on health and production is still lacking. From this perspective, the egg bacterial communities of two commercially farmed species, the European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata), from different aquaculture sites were compared, and the potential effect of broodstock water microbiota and disinfectants on the egg microbiota was evaluated. Moreover, 16S ribosomal RNA gene sequencing was used to profile the bacterial communities of the eggs and broodstock water from three commercial hatcheries. Proteobacteria were the most common and dominant phyla across the samples (49.7% on average). Vibrio sp. was the most highly represented genus (7.1%), followed by Glaciecola (4.8%), Pseudoalteromonas (4.4%), and Colwellia (4.2%), in eggs and water across the sites. Routinely used iodine-based disinfectants slightly reduced the eggs’ bacterial load but did not significantly change their composition. Site, species, and type of sample (eggs or water) drove the microbial community structure and influenced microbiome functional profiles. The egg and seawater microbiome composition differed in abundance but shared similar functional profiles. The strong impact of site and species on egg bacterial communities indicates that disease management needs to be site-specific and highlights the need for species- and site-specific optimization of disinfection protocols.
- 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.
- Quantifying dominant bacterial genera detected in metagenomic data from fish eggs and larvae using genus‐specific primersPublication . Najafpour, Babak; Canario, Adelino; Power, Deborah; Pinto, Patricia ISThe goal of this study was to design genus-specific primers for rapid evaluation of the most abundant bacterial genera identified using amplicon-based sequencing of the 16S rRNA gene in fish-related samples and surrounding water. Efficient genus-specific primers were designed for 11 bacterial genera including Alkalimarinus, Colwellia, Enterovibrio, Marinomonas, Massilia, Oleispira, Phaeobacter, Photobacterium, Polarbacerium, Pseudomonas, and Psychrobium. The specificity of the primers was confirmed by the phylogeny of the sequenced polymerase chain reaction (PCR) amplicons that indicated primers were genus-specific except in the case of Colwellia and Phaeobacter. Copy number of the 16S rRNA gene obtained by quantitative PCR using genus-specific primers and the relative abundance obtained by 16S rRNA gene sequencing using universal primers were well correlated for the five analyzed abundant bacterial genera. Low correlations between quantitative PCR and 16S rRNA gene sequencing for Pseudomonas were explained by the higher coverage of known Pseudomonas species by the designed genus-specific primers than the universal primers used in 16S rRNA gene sequencing. The designed genus-specific primers are proposed as rapid and cost-effective tools to evaluate the most abundant bacterial genera in fish-related or potentially other metagenomics samples.
- Specific evolution and gene family expansion of complement 3 and regulatory factor H in fishPublication . Najafpour, Babak; Cardoso, João CR; Canario, Adelino; Power, DeborahThe complement system comprises a large family of plasma proteins that play a central role in innate and adaptive immunity. To better understand the evolution of the complement system in vertebrates and the contribution of complement to fish immunity comprehensive in silico and expression analysis of the gene repertoire was made. Particular attention was given to C3 and the evolutionary related proteins C4 and C5 and to one of the main regulatory factors of C3b, factor H (Cfh). Phylogenetic and gene linkage analysis confirmed the standing hypothesis that the ancestral c3/c4/c5 gene duplicated early. The duplication of C3 (C3.1 and C3.2) and C4 (C4.1 and C4.2) was likely a consequence of the (1R and 2R) genome tetraploidization events at the origin of the vertebrates. In fish, gene number was not conserved and multiple c3 and cfh sequence related genes were encountered, and phylogenetic analysis of each gene generated two main clusters. Duplication of c3 and cfh genes occurred across the teleosts in a species-specific manner. In common, with other immune gene families the c3 gene expansion in fish emerged through a process of tandem gene duplication. Gilthead sea bream (Sparus aurata), had nine c3 gene transcripts highly expressed in liver although as reported in other fish, extra-hepatic expression also occurs. Differences in the sequence and protein domains of the nine deduced C3 proteins in the gilthead sea bream and the presence of specific cysteine and N-glycosylation residues within each isoform was indicative of functional diversity associated with structure. The diversity of C3 and other complement proteins as well as Cfh in teleosts suggests they may have an enhanced capacity to activate complement through direct interaction of C3 isoforms with pathogenic agents.