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Inulin affects nutrition and metabolism in many animals. Although inulin is widely used in the diet of teleosts, its mechanism of action is unknown. Here, we investigated the effect of inulin (2 %) on the intestinal microbiome and metabolism in rainbow trout (Oncorhynchus mykiss) selected for growth and survival when fed a 100 % plant-based diet (suave) and a control line (temoin). Metabolic responses to the two factors (line and inulin) in liver, intestine, muscle and adipose were tissue-specific, with line and interaction between the two factors influencing overall expression in liver. In the intestine, inulin and line and in muscle, line influenced the expression of metabolic genes. Microbiota between the mucus and digestive contents was significantly different, with genera from Proteobacteria being more abundant in the mucus, whereas genera from the Firmicutes and Planctomycetes being more abundant in contents. Effect of inulin and interaction between factors on the microbiome was evident in contents. The significant taxa of control and inulin-fed groups differed greatly with Streptococcus and Weissella being significantly abundant in the inulin-fed group. There was a general trend showing higher levels of all SCFA in temoin group with propionic acid levels being significantly higher. An operational taxonomic unit (OTU) belonging to the Ruminococcaceae was significantly abundant in suave. The tissue-specific correlations between OTU and gene expression may indicate the link between microbiome and metabolism. Together, these results suggest that line and inulin impact the gene expression in a tissue-specific manner, possibly driven by specific OTUs enriched in inulin-fed groups and suave. [ABSTRACT FROM AUTHOR]

To understand the physiological roles of antimicrobial peptide ( AMP) families in Atlantic cod, fish were subjected to abiotic (crowding/temperature rise) or biotic (commensal or pathogenic bacterium) stimuli, following which the transcriptional profiles of piscidin 1 ( pis1), piscidin 2 ( pis2), beta defensin ( defb), hepcidin ( hep) and cathelicidin 1 ( cath1) in selected mucosal tissues were analysed using qPCR. Unlike the crowding condition, the temperature change affected the transcripts of AMP genes - after the rise in temperature (0 h), cath1 was downregulated mainly in gills, defb was downregulated in gills and skin, while hep was downregulated in gills, skin and rectum. These gene transcripts returned to their basal levels at 72 h, by which time pis1 gene was upregulated in gills and skin. The pis2 gene was apparently not altered by temperature change. Bath exposure to commensal bacterium affected only defb gene in gills (downregulated) and skin (upregulated). Bath challenge with live pathogen upregulated cath1 gene mainly in gills, and hep gene in gills, skin and rectum, while pis1 and pis2 genes remained unaltered. The differential modulation of the AMP genes examined suggests that these peptides maintain distinct functions with respect to mucosal defence mechanisms in Atlantic cod. [ABSTRACT FROM AUTHOR]

Host-associated microbiota undergoes a continuous transition, from the birth to adulthood of the host. These developmental stage-related transitions could lead to specific microbial signatures that could impact the host biological processes. In this study, the succession of early-life and intestinal bacterial communities of Atlantic salmon (starting from embryonic stages to 80-week post hatch; wph) was studied using amplicon sequencing of 16S rRNA. Stage-specific bacterial community compositions and the progressive transitions of the communities were evident in both the early life and the intestine. The embryonic communities showed lower richness and diversity (Shannon and PD whole tree) compared to the hatchlings. A marked transition of the intestinal communities also occurred during the development; Proteobacteria were dominant in the early stages (both embryonic and intestinal), though the abundant genera under this phylum were stage-specific. Firmicutes were the most abundant group in the intestine of late freshwater; Weissella being the dominant genus at 20 wph and Anaerofilum at 62 wph. Proteobacteria regained its dominance after the fish entered seawater. Furthermore, LEfSe analysis identified genera under the above - mentioned phyla that are significant features of specific stages. The environmental (water) bacterial community was significantly different from that of the fish, indicating that the host is a determinant of microbial assemblage. Overall the study demonstrated the community dynamics during the development of Atlantic salmon., (© 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)