Sustainable plant-based diets promote rainbow trout gut microbiota richness and do not alter resistance to bacterial infection.
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ABSTRACT: Background
Farmed fish food with reduced fish-derived products are gaining growing interest due to the ecological impact of fish-derived protein utilization and the necessity to increase aquaculture sustainability. Although different terrestrial plant proteins could replace fishmeal proteins, their use is associated with adverse effects. Here, we investigated how diets composed of terrestrial vegetal sources supplemented with proteins originating from insect, yeast or terrestrial animal by-products affect rainbow trout (Onchorynchus mykiss) gut microbiota composition, growth performance and resistance to bacterial infection by the fish pathogen Flavobacterium psychrophilum responsible for frequent outbreaks in aquaculture settings.Results
We showed that the tested regimes significantly increased gut bacterial richness compared to full vegetal or commercial-like diets, and that vegetal diet supplemented with insect and yeast proteins improves growth performance compared to full vegetal diet without altering rainbow trout susceptibility to F. psychrophilum infection.Conclusion
Our results demonstrate that the use of insect and yeast protein complements to vegetal fish feeds maintain microbiota functions, growth performance and fish health, therefore identifying promising alternative diets to improve aquaculture's sustainability.
SUBMITTER: Perez-Pascual D
PROVIDER: S-EPMC8256591 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Background: The decreasing availability of fishmeal as a protein source in aquaculture diets will require aquaculture to develop an econmoical and sustainable protien replacement. Plant proteins are readily available and are being tested as a promising alternative to replace a substantial portion of fishmeal which currently provides most of the protein content in aquaculture diets. The types of plant protein feasible for incorporation into aquaculture diets will likely contain various anti-nutritional compounds, carbohydrates, fiber, and a different amino acid profile than what is found in fishmeal. Substantial genetic variation was previously observed for growth on plant based dits in rainbow trout Hence, it will be beneficial to identify metabolic and physiologic pathways related to enhanced plant protein utilization which will aid in identifying genes that contribute to this genetic variation. Results: Microarray analysis of liver samples from two families of rainbow trout that differed in their growth responses when compared between individuals grown on a fish meal or plant protein based diet. Differential expression relating to dietary utilization between the two families found significant changes in expression of 33 ESTs. Eight of the differntially expressed ESTs had identified mammalian homologs that had been previously researched with identified cellular interactions and functions. Conclusions: Utilizing pathway analysis software to analyze sequences annotated with known mammalian genes were were ablet o map gene pathway and process interactions. From this information we were able to infer that the metabolic changes associated with utilization of plant protein versus fishmeal were associated with differential reaulation of genes related to cell oxidative stress, proliferation, growth, and survival. Furthermore, we inferred from the changes we observed in immune response genes expression that ingestion of this plant based diet upregulated the expression of genes involved in immunoregulatroy processes.
2011-04-01 | GSE28310 | GEO
Project description:Background: The decreasing availability of fishmeal as a protein source in aquaculture diets will require aquaculture to develop an econmoical and sustainable protien replacement. Plant proteins are readily available and are being tested as a promising alternative to replace a substantial portion of fishmeal which currently provides most of the protein content in aquaculture diets. The types of plant protein feasible for incorporation into aquaculture diets will likely contain various anti-nutritional compounds, carbohydrates, fiber, and a different amino acid profile than what is found in fishmeal. Substantial genetic variation was previously observed for growth on plant based dits in rainbow trout Hence, it will be beneficial to identify metabolic and physiologic pathways related to enhanced plant protein utilization which will aid in identifying genes that contribute to this genetic variation. Results: Microarray analysis of liver samples from two families of rainbow trout that differed in their growth responses when compared between individuals grown on a fish meal or plant protein based diet. Differential expression relating to dietary utilization between the two families found significant changes in expression of 33 ESTs. Eight of the differntially expressed ESTs had identified mammalian homologs that had been previously researched with identified cellular interactions and functions. Conclusions: Utilizing pathway analysis software to analyze sequences annotated with known mammalian genes were were ablet o map gene pathway and process interactions. From this information we were able to infer that the metabolic changes associated with utilization of plant protein versus fishmeal were associated with differential reaulation of genes related to cell oxidative stress, proliferation, growth, and survival. Furthermore, we inferred from the changes we observed in immune response genes expression that ingestion of this plant based diet upregulated the expression of genes involved in immunoregulatroy processes. Genotyped samples linked to families that had 4 or more members sampled on each diet were identified and ranked according to average family weight on each diet. Size rankings corresponded to large (>750 g), medium (600-640 g), and small (<500 g). From these identified groups 2 families were chosen for microarray expression analysis that demonstrated individuals with growth differences between the two diets. Data for the two families used for analysis and slide arrangements are listed in table 3. The families compared for growth differences between diets used for this study only differed by one growth range, large fish on fish meal compared to medium fish on plant-based diet and medium sized fish on fishmeal diet compared to small fish on plant-based diet. This strategy to use size separation within family was an attempt to identify gene changes more specific to diet utilization than specific for growth differences.
2011-04-01 | E-GEOD-28310 | biostudies-arrayexpress
Project description:Aquaculture's sustainability deeply relies on the identification and inclusion of alternative raw materials. Although meals from insects and/or byproducts from different industries are being recently tested, the meal from terrestrial vegetable species is still the main substitution candidate for fish meal. Here the effects of 0% (Control), 10% (A10) and 30% (A30) inclusion of Narbonne vetch (Vicia narbonensis; ZV-156 strain) meal in rainbow trout (Oncorhynchus mykiss) diets was assessed in a 63-day feeding trial by means of growth performance, histopathological, nutritional value of the fish fillet and blood biochemistry analyses. A dose-response trial was conducted in triplicate with 25 rainbow trout juveniles (20 g average body weight) per 500 L tank. Narbonne vetch meal decreased total intestine protease activity in vitro (from 26.81% to 48% inhibition), although high temperature partially inhibited the action of antinutritional factors (ANFs). No differences in fish growth performance and no severe histopathological alterations on the proximal intestine were observed between 10% Narbonne vetch inclusion and Control groups. In contrast, high inclusion (30%) of Narbonne vetch led to poor growth performance (30% reduction on final growth) and severe histopathological alterations (e.g., loss of brush border integrity, high number of villi fusion, reduced goblet cells density as well as reduced width of submucosa, muscular and serosa layers). Furthermore, while the A30 diet decreased docosahexaenoic fatty acid (FA) content in fish fillets, the A10 diet improved monounsaturated FA content when compared to that of the Control group. No altered levels of cholesterol, glucose or triglycerides in blood plasma and/or histopathological effects on the liver were observed among fish fed the different experimental diets. Although further research efforts (e.g., identifying potential enzymatic treatments to decrease the action of ANFs from Narbonne vetch meal) might be required, present results show that a low inclusion (10%) of Narbonne vetch in rainbow trout diets is possible. The inclusion of locally produced legumes such a Narbonne vetch might be an interesting approach to reduce carbon footprint in European aquaculture and the dependency on other alternative raw materials such as soybean (Glycine max) imported from third countries.
| S-EPMC7700202 | biostudies-literature
Project description:Gut microbiota composition of rainbow trout Raw sequence reads
| PRJNA783153 | ENA
Project description:Effects of dietary inclusion of Tenebrio molitor meal on rainbow trout gut and skin microbiota
| PRJEB38845 | ENA
Project description:Culturable bacteria from rainbow trout larvae
| PRJEB37666 | ENA
Project description:Wild animals entering captivity experience radical lifestyle changes resulting in microbiome alterations. However, little is known about the factors that drive microbial community shifts in captivity, and what actions could mitigate microbial changes. Using white-throated woodrats (Neotoma albigula), we tested whether offering natural diets in captivity facilitates retention of native microbial communities of captive animals. Wild-caught woodrats were brought to laboratory conditions. Woodrats received either a natural diet of Opuntia cactus or an artificial diet of commercial chow over three weeks. Microbial inventories from woodrat feces at the time of capture and in captivity were generated using Illumina 16S rRNA sequencing. We found that providing woodrats with wild-natural diets significantly mitigated alterations in their microbiota, promoting a 90% retention of native microbial communities across the experiment. In contrast, the artificial diet significantly impacted microbial structure to the extent that 38% of the natural microflora was lost. Core bacteria including Bifidobacterium and Allobaculum were lost, and abundances of microbes related to oxalate degradation decreased in individuals fed artificial but not natural diets. These results highlight the importance of supplementing captive diets with natural foods to maintain native microbiomes of animals kept in artificial conditions for scientific or conservation purposes.
| S-EPMC6908644 | biostudies-literature
Project description:Rainbow trout (Oncorhynchus mykiss) and other salmonids are piscivorous fish. In aquaculture, fish-based feed ingredients are rapidly becoming unsustainable due to increased demand and diminishing supply. Total replacement of fishmeal with plant proteins causes severe intestinal enteritis, leading to reduced growth and lower feed efficiency. Through selective breeding, we have developed a strain of rainbow trout that does not develop distal intestine enteritis when reared on a high soy plant protein-based feed and also shows increased growth compared to other strains. Since central metabolism plays a major role in dietary alterations, liver RNA was examined for differential expression of long non-coding RNAs (lncRNAs) between commercial and selected trout strains when fed an alternative diet. These types of non-coding RNA have been previously shown to have a potential role in regulation of gene expression; however, most identified lncRNAs have not been functionally characterized and/or lack definition in many non-model organisms. Their roles in gene regulation and their responsiveness to dietary changes in trout are to be explored. After three months of rearing on a plant protein-based (PM) diet, liver tissues from a domestic non-selected strain (House Creek; develops enteritis) and the plant-diet tolerant selected strain (ARS-KO; no enteritis) were extracted and prepped for Illumina RNA-seq. Raw reads were screened for quality then assembled into transcripts using Trinity. Assembled transcripts were then submitted to the Annocript pipeline to determine their potential as lncRNAs. RNA-seq reads were mapped to putative lncRNAs. Read-counts were used to assess differential expression between strains.
2018-04-10 | GSE85104 | GEO
Project description:A healthy gastrointestinal microbiota is essential for host fitness, and strongly modulated by host diet. In aquaculture, a current challenge is to feed carnivorous fish with plant-feedstuffs in substitution of fish meal, an unsustainable commodity. Plants have a limited nutritive value due to the presence of non-starch polysaccharides (NSP) which are not metabolized by fish. In this work we assessed the effects of NSP-enriched diets on European seabass gut microbiota and evaluate the selective pressure of plant feedstuffs towards gut microbes with NSP-hydrolytic potential, i.e. capable to convert indigestible dietary constituents in fish metabolites. Triplicate groups of European seabass juveniles were fed a fish meal-based diet (control) or three plant-based diets (SBM, soybean meal; RSM, rapeseed meal; SFM, sunflower meal) for 6 weeks, before recovering intestinal samples for microbiota analysis, using the Illumina's MiSeq platform. Plant-based diets impacted differently digesta and mucosal microbiota. A decrease (p = 0.020) on species richness, accompanied by a decline on the relative abundance of specific phyla such as Acidobacteria (p = 0.030), was observed in digesta samples of SBM and RSM experimental fish, but no effects were seen in mucosa-associated microbiota. Plant-based diets favored the Firmicutes (p = 0.01), in particular the Bacillaceae (p = 0.017) and Clostridiaceae (p = 0.007), two bacterial families known to harbor carbohydrate active enzymes and thus putatively more prone to grow in high NSP environments. Overall, bacterial gut communities of European seabass respond to plant-feedstuffs with adjustments in the presence of transient microorganisms (allochthonous) with carbohydrolytic potential, while maintaining a balanced core (autochthonous) microbiota.
| S-EPMC7801451 | biostudies-literature
Project description:The crocodile lizard is a critically endangered reptile, and serious diseases have been found in this species in recent years, especially in captive lizards. Whether these diseases are caused by changes in the gut microbiota and the effect of captivity on disease remains to be determined. Here, we examined the relationship between the gut microbiota and diet and disease by comparing the fecal microbiota of wild lizards with those of sick and healthy lizards in captivity. The gut microbiota in wild crocodile lizards was consistently dominated by Proteobacteria (∼56.4%) and Bacteroidetes (∼19.1%). However, the abundance of Firmicutes (∼2.6%) in the intestine of the wild crocodile lizards was distinctly lower than that in other vertebrates. In addition, the wild samples from Guangdong Luokeng Shinisaurus crocodilurus National Nature Reserve also had a high abundance of Deinococcus-Thermus while the wild samples from Guangxi Daguishan Crocodile Lizard National Nature Reserve had a high abundance of Tenericutes. The gut microbial community in loach-fed crocodile lizards was significantly different from the gut microbial community in the earthworm-fed and wild lizards. In addition, significant differences in specific bacteria were detected among groups. Notably, in the gut microbiota, the captive lizards fed earthworms resulted in enrichment of Fusobacterium, and the captive lizards fed loaches had higher abundances of Elizabethkingia, Halomonas, Morganella, and Salmonella, all of which are pathogens or opportunistic pathogens in human or other animals. However, there is no sufficient evidence that the gut microbiota contributes to either disease A or disease B. These results provide a reference for the conservation of endangered crocodile lizards and the first insight into the relationship between disease and the gut microbiota in lizards.
| S-EPMC5660983 | biostudies-literature