The larval waste, exoskeleton shedding, and leftover feed components of the black soldier fly and its larvae make up the by-product known as frass. In this study, we subjected channel catfish (
) to ...a 10-week feeding trial to assess how different dietary amounts of frass inclusion would affect both systemic and mucosal tissue gene expression, especially in regard to growth and immune-related genes. Fish were divided in quadruplicate aquaria, and five experimental diets comprising 0, 50, 100, 200, and 300 g of frass per kilogram of feed were fed twice daily. At the end of the trial, liver, head kidney, gill, and intestine samples were collected for gene expression analyses. First, liver and intestine samples from fish fed with a no frass inclusion diet (control), low-frass (50 g/kg) inclusion diet, or a high-frass (300 g/kg) inclusion diet were subjected to Illumina RNA sequencing to determine global differential gene expression among diet groups. Differentially expressed genes (DEGs) included the upregulation of growth-related genes such as glucose-6-phosphatase and myostatin, as well as innate immune receptors and effector molecules such as toll-like receptor 5, apolipoprotein A1, C-type lectin, and lysozyme. Based on the initial screenings of low/high frass using RNA sequencing, a more thorough evaluation of immune gene expression of all tissues sampled, and all levels of frass inclusion, was further conducted. Using targeted quantitative PCR panels for both innate and adaptive immune genes from channel catfish, differential expression of genes was identified, which included innate receptors (TLR1, TLR5, TLR9, and TLR20A), proinflammatory cytokines (IL-1β type a, IL-1β type b, IL-17, IFN-γ, and TNFα), chemokines (CFC3 and CFD), and hepcidin in both systemic (liver and head kidney) and mucosal (gill and intestine) tissues. Overall, frass from black soldier fly larvae inclusion in formulated diets was found to alter global gene expression and activate innate and adaptive immunity in channel catfish, which has the potential to support disease resistance in this species in addition to demonstrated growth benefits.
White bass (
) are a popular sportfish throughout the southern United States, and one parent of the commercially-successful hybrid striped bass (
♂
♀). Currently, white bass are cultured using diets ...formulated for other carnivorous fish, such as largemouth bass (
) or hybrid striped bass and contain a significant percentage of marine fish meal. Since there are no studies regarding the utilization of alternative proteins in this species, we evaluated the global gene expression of white bass fed diets in which fish meal was partially or totally replaced by various combinations of soybean meal, poultry by-product meal, canola meal, soy protein concentrate, wheat gluten, or a commercial protein blend (Pro-Cision™). Six isonitrogenous (40% protein), isolipidic (11%), and isocaloric (17.1 kJ/g) diets were formulated to meet the known nutrient and energy requirements of largemouth bass and hybrid striped bass using nutrient availability data for most of the dietary ingredients. One of the test diets consisted exclusively of plant protein sources. Juvenile white bass (40.2 g initial weight) were stocked into a flow-through aquaculture system (three tanks/diet; 10 fish/tank) and fed the test diets twice daily to satiation for 60 days. RNA sequencing and bioinformatic analyses revealed significant differentially expressed genes between all test diets when compared to fish meal control. A total of 1,260 differentially expressed genes were identified, with major ontology relating to cell cycle and metabolic processes as well as immune gene functions. This data will be useful as a resource for future refinements to moronid diet formulation, as marine fish meal becomes limiting and plant ingredients are increasingly added as a reliable protein source.
The exposure of fish to environmental free-living microbes and its effect on early colonization in the gut have been studied in recent years. However, little is known regarding how the host and ...environment interact to shape gut communities during early life. Here, we tested whether the early microbial exposure of tilapia larvae affects the gut microbiota at later life stages. The experimental period was divided into three stages: axenic, probiotic and active suspension. Axenic tilapia larvae were reared either under conventional conditions (active suspension systems) or exposed to a single strain probiotic (Bacillus subtilis) added to the water. Microbial characterization by Illumina HiSeq sequencing of 16S rRNA gene amplicons showed the presence of B. subtilis in the gut during the seven days of probiotic application. Although B. subtilis was no longer detected in the guts of fish exposed to the probiotic after day 7, gut microbiota of the exposed tilapia larvae remained significantly different from that of the control treatment. Compared with the control, fish gut microbiota under probiotic treatment was less affected by spatial differences resulting from tank replication, suggesting that the early probiotic contact contributed to the subsequent observation of low inter-individual variation.
The NLRs (nucleotide-binding domain and leucine-rich repeat containing family receptors) are a recently identified family of pattern recognition receptors in vertebrates. Several subfamilies of NLRs ...have been characterized in human, mouse, and zebrafish, but studies of NLRs in other species, especially teleost species, have been lacking. Here we report characterization of five NLRs from channel catfish: NOD1, NOD2, NLRC3, NLRC5, and NLRX1. Structural analysis indicated that the genes were organized in a similar fashion as in the mammals and in zebrafish. Phylogenetic analysis suggested that they were orthologous to the NOD-like subfamily of NLRs. All five NOD-like genes exist as a single copy gene in the catfish genome. Hybridization of gene-specific probes allowed mapping of three NLR genes to the catfish physical map, laying a foundation for genome characterization and for establishing orthologies with NLR genes from other species. These genes are widely expressed in various tissues and leukocyte cell lines. While the majority of the NLR genes appeared to be constitutively expressed, NOD1 was induced after infection with a bacterial pathogen, Edwardsiella ictaluri, the causative agent of enteric septicemia of catfish (ESC), suggesting its involvement in immunity against the intracellular pathogen.
Finding suitable alternative protein sources for diets of carnivorous fish species remains a major concern for sustainable aquaculture. Through genetic selection, we created a strain of rainbow trout ...that outperforms parental lines in utilizing an all-plant protein diet and does not develop enteritis in the distal intestine, as is typical with salmonids on long-term plant protein-based feeds. By incorporating this strain into functional analyses, we set out to determine which genes are critical to plant protein utilization in the absence of gut inflammation. After a 12-week feeding trial with our selected strain and a control trout strain fed either a fishmeal-based diet or an all-plant protein diet, high-throughput RNA sequencing was completed on both liver and muscle tissues. Differential gene expression analyses, weighted correlation network analyses and further functional characterization were performed. A strain-by-diet design revealed differential expression ranging from a few dozen to over one thousand genes among the various comparisons and tissues. Major gene ontology groups identified between comparisons included those encompassing central, intermediary and foreign molecule metabolism, associated biosynthetic pathways as well as immunity. A systems approach indicated that genes involved in purine metabolism were highly perturbed. Systems analysis among the tissues tested further suggests the interplay between selection for growth, dietary utilization and protein tolerance may also have implications for nonspecific immunity. By combining data from differential gene expression and co-expression networks using selected trout, along with ontology and pathway analyses, a set of 63 candidate genes for plant diet tolerance was found. Risk loci in human inflammatory bowel diseases were also found in our datasets, indicating rainbow trout selected for plant-diet tolerance may have added utility as a potential biomedical model.
causes substantial losses among cultured finfish species. The Gram-negative bacterium is an opportunistic pathogen that manifests as biofilms on the host's mucosal surfaces as the disease progresses. ...We previously demonstrated that the dominant mucosal IgM antibody response to
is to the chaperone protein DnaK that is found in the extracellular fraction. To establish the efficacy of using recombinant protein technology to develop a new vaccine against columnaris disease, we are reporting on two consecutive years of vaccine trials using a recombinant
DnaK protein (rDnaK). In year one, three groups of channel catfish (
= 300) were immunized by bath immersion with a live attenuated
isolate, rDnaK or sham immunized. After 6 weeks, an
laboratory challenge showed a significant increase in survival (>30%) in both the live attenuated and rDnaK vaccines when compared to the non-immunized control. A rDnaK-specific ELISA revealed significant levels of mucosal IgM antibodies in the skin of catfish immunized with rDnaK at 4- and 6-weeks post immunization. In the second year, three groups of channel catfish (
= 300) were bath immunized with rDnaK alone or with rDnaK after a brief osmotic shock or sham immunized. After 6 weeks a laboratory challenge with
was conducted and showed a significant increase in survival in the rDnaK (> 25%) and in rDnaK with osmotic shock (>35%) groups when compared to the non-immunized control. The rDnaK-specific ELISA demonstrated significant levels of mucosal IgM antibodies in the skin of catfish groups immunized with rDnaK at 4- and 6-weeks post immunization. To further understand the processes which have conferred immune protection in the rDnaK group, we conducted RNA sequencing of skin samples from the non-immunized (
= 6) and rDnaK treated channel catfish at 1-week (
= 6) and 6 weeks (
= 6) post immunization. Significantly altered gene expression was identified and results will be discussed. Work to further enhance the catfish immune response to
rDnaK is underway as this protein remains a promising candidate for additional optimization and experimental trials in a production setting.
•Growth and survival of trout are poorer in 5th use raceway water compared to 1st & 3rd use.•Increasing dissolved oxygen in 5th use water by aeration or oxygenation to 3rd use levels restores growth ...of trout.•Survival in oxygenated or aerated 5th use water is improved but not restored to 3rd use levels.•Other water quality parameters may play a role in reduced trout survival of 5th use water.
Serial-pass raceway systems are characterized by reduced water quality as water passes from upper to lower raceways. We previously showed that rainbow trout reared in 1st use (source spring) and 3rd use (after 2 raceway passes) water exhibited significantly better growth and survival compared to those in 5th use water (after 4 raceway passes) and directly related to dissolved oxygen (DO) concentration. Our objective was to determine if increasing the DO in 5th use water by aeration or oxygenation to levels in 3rd use water could restore growth and survival of rainbow trout. We stocked rainbow trout (126 ± 9.3 g mean weight) into tanks receiving either 1st use, 3rd use, or 5th use water with and without supplemental air or oxygen (five treatments at four tanks each). Average DO concentration was highest in 1st use (92.0% saturation) followed by 3rd use (79.4%) and 5th use (52.1%) water. In 5th use water, use of aeration (68.4%) or oxygenation (71.7%) raised the DO levels similar to 3rd use water. Growth performance (SGR and FCR) and survival were significantly lower for trout in 5th use compared to 1st and 3rd use water. Aeration and oxygenation of 5th use water restored growth to that observed for trout in 3rd use water. Improvements were limited for survival with 3rd use water (88.8%) showing higher values than 5th use with oxygenation (74.2%) or aeration (53.1%). These treatments were still significantly better than survival observed for trout in untreated 5th use water (35.0%). Dissolved oxygen appears to be the primary water quality parameter limiting performance in this system. However, due to dissimilar survival in 3rd and 5th use water with aeration or oxygenation, other water parameters (e.g. total dissolved solids or turbidity), which increased in 5th use water, may also contribute to the reduced growth and survival.
The genomes of seven Aeromonas veronii strains isolated from tissues of healthy or diseased channel catfish obtained from Alabama, USA, fish farms were sequenced and annotated. These genome sequences ...will enable comparative analyses to determine the roles these bacteria play in catfish aquaculture and the development of new preventative or management strategies.
Columnaris disease generates substantial losses of many freshwater fish species; one is the hybrid striped bass. The ubiquitous aquatic bacterium Flavobacterium columnare can be highly effective in ...biofilm formation on fish skin and gills. Previous research showed a difference between columnaris disease susceptibility of hybrid striped bass (Morone saxatilis × M. chrysops) and white bass (M. chrysops). To understand these differential susceptibilities and possible mucosal relationship, we assessed total bacterial growth and biofilm formation with mucus derived from each moronid parental species: white bass and striped bass (M. saxatilis). Differential susceptibility was confirmed of the other parent species, the striped bass (M. saxatilis). In addition to intraspecies investigations, individual hybrid striped bass mucosal affects were also studied for deferential responses to bacterial growth and biofilm formation. Species‐ and concentration‐dependent differences were detected in the total growth of the bacteria to host mucus. Our data suggest that bass mucus can significantly affect biofilm formation with the F. columnare isolate tested. There appears to be a correlation between the bacteria's response of growth and biofilms and bass species susceptibility. This study provides insight into our understanding of the host–pathogen interaction between F. columnare and moronids.
A genetic linkage map of the channel catfish genome (N=29) was constructed using EST-based microsatellite and single nucleotide polymorphism (SNP) markers in an interspecific reference family. A ...total of 413 microsatellites and 125 SNP markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 allowed mapping of 331 markers (259 microsatellites and 72 SNPs) to 29 linkage groups. Each linkage group contained 3-18 markers. The largest linkage group contained 18 markers and spanned 131.2 cM, while the smallest linkage group contained 14 markers and spanned only 7.9 cM. The linkage map covered a genetic distance of 1811 cM with an average marker interval of 6.0 cM. Sex-specific maps were also constructed; the recombination rate for females was 1.6 times higher than that for males. Putative conserved syntenies between catfish and zebrafish, medaka, and Tetraodon were established, but the overall levels of genome rearrangements were high among the teleost genomes. This study represents a first-generation linkage map constructed by using EST-derived microsatellites and SNPs, laying a framework for large-scale comparative genome analysis in catfish. The conserved syntenies identified here between the catfish and the three model fish species should facilitate structural genome analysis and evolutionary studies, but more importantly should facilitate functional inference of catfish genes. Given that determination of gene functions is difficult in nonmodel species such as catfish, functional genome analysis will have to rely heavily on the establishment of orthologies from model species.
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