Effects of dietary supplementation with prebiotics and Pediococcus acidilactici on gut health, transcriptome, microbiota, and metabolome in Atlantic salmon (Salmo salar L.) after seawater transfer

Cichlid fishes are promising underutilized models to investigate helminth-host-microbiome interactions

The "Old Friends Hypothesis" suggests insufficient exposure to symbionts hinders immune development, contributing to increased immune-related diseases in the Global North. The microbiome is often the focus; helminths, potentially also offering health benefits, lack attention. Infection and effect of helminths are influenced and perhaps determined by micro-organisms. Mechanisms behind parasite-microbiome interactions are poorly understood, despite implications on host health. These interactions are typically studied for single helminth species in laboratory animal models, overlooking helminth diversity. Reviewing research on relationships between helminth and microbial diversity yielded 27 publications; most focused on human or other mammalian hosts, relying on natural exposure rather than experimental helminth inoculation. Only about half investigated host health outcomes. Remaining knowledge gaps warrant considering additional candidate model systems. Given the high helminthiasis burden and species diversity of helminths, we propose seeking models in the Global South, where a considerable proportion of research on diversity aspects of helminth-microbiome interactions took place. Low availability of genomic resources for helminths in the Global South, however, necessitates more integrative helminthological research efforts. Given substantial similarities in immune systems, several fishes are models for human health/disease. More effort could be done to establish this for cichlids, whose representatives in the African Great Lakes provide a well-delineated, closed natural system relevant to human health in view of fish-borne zoonoses and other water-borne parasites. A good baseline exists for these cichlids' genomics, parasitology, and microbiology. We suggest exploring African Great Lake cichlids as model hosts for interactions between microbial diversity, helminth diversity, and host health.

Longitudinal study on the effects of a synbiotic supplement to Atlantic salmon diets on performance, gut microbiota and immune responses during antibiotic treatment and subsequent recovery

BACKGROUND

Antibiotic use has undesirable side-effects on the host, including perturbations of gut microbiota, immunity, and health. Mammalian studies have demonstrated that concomitant/post antibiotic use of pro-, pre-, and synbiotics could re-establish gut microbiota and prevent detrimental host effects. However, studies evaluating similar effects in fish are scanty. This study evaluated the effects of dietary supplementation with a synbiotic mixture on the post-smolt Atlantic salmon gut microbiota, growth performance, and health during antibiotic treatment and subsequent recovery. Fish in five tanks each were fed either a commercial control diet or a synbiotic diet containing Pediococcus acidilactici and fructo-oligosaccharides, for 6 weeks (S1). Then, fish in three tanks per treatment were fed with medicated diets, containing 3500 ppm florfenicol coated onto the control or synbiotic diets, for 2 weeks (S2) and refed with the respective nonmedicated diets for another 3 (S3) and 5 (S4) weeks of recovery period. The fish not subjected to medication were fed the control or synbiotic diets throughout the experimental period. Samples were collected at S1-S4 from both the nonmedicated and medicated fish.

RESULTS

Florfenicol decreased the feed intake in control group. It reduced the growth rate in both control and synbiotic groups with lesser reduction in synbiotic group. Florfenicol did not significantly affect observed taxa and Shannon indexes. Bacterial composition before and after medication clustered distinctly in control and clustered together in synbiotic groups. Lactobacillus dominated in control while Lactobacillus and Pediococcus dominated in synbiotic group during medication and recovery. Florfenicol did not significantly influence the immune or stress response marker gene expressions, though the expression patterns differed between diet groups. Florfenicol did not cause inflammation in the distal intestine or change hepatosomatic index.

CONCLUSIONS

This study highlighted the negative impact of a two-week florfenicol treatment on feed intake and growth performance in Atlantic salmon, with moderate effects on gut microbiota and gene expression. Concomitant use of a synbiotic diet helped to maintain the gut microbial composition and influenced the performance positively and immune gene expressions differently during medication. This study indicates the importance of nutritional interventions through synbiotic supplementation as a possible strategy for managing Atlantic salmon during antibiotic treatment.

Dietary Chlorella vulgaris supplementation modulates health, microbiota and the response to oxidative stress of Atlantic salmon

Microalgae are emerging as functional feed ingredients in aquaculture due to their immune-stimulating and stress-modulating properties. We investigated the potential of the microalgae Chlorella vulgaris as a feed supplement to improve the health and modulate microbiota and stress responses of Atlantic salmon. Triplicate groups of Atlantic salmon (~ 126 g) were reared in a recirculating aquaculture system (RAS) at 15 °C and received diets supplemented with 2% (CV2) or 14% (CV14) spray-dried C. vulgaris daily, 14% once weekly (CV14w), or a control diet (CD) for 8 weeks. Subsequently, all groups were exposed to an acute one-hour peracetic acid (CH3CO3H; PAA) treatment, a commonly used disinfectant in RAS. While CV14 increased feed conversion (FCR) significantly, feeding the diets CV2 and CV14w improved protein retention efficiency. CV14 significantly modulated beta-diversity in the intestinal digesta and mucosa, but this effect was already visible in fish fed CV2. Feeding CV14 and, to a lesser degree, CV2 increased the relative abundances of Paenarthrobacter and Trichococcus in the digesta and mucosa, which are able to metabolize complex carbohydrates. However, the same diets reduced the abundance of the lactic acid bacteria Lactobacillus and Weissella in the digesta and Floricoccus in the mucosa. Peracetic acid exposure induced systemic stress (increase in plasma glucose and cortisol) and a local immune response in the gill, with the most prominent upregulation of several immune- and stress-regulated genes (clra, cebpb, marco, tnfrsf14, ikba, c1ql2, drtp1) 18 h after exposure in fish fed the control diet. Fish receiving CV14 once a week showed a reduced transcriptional response to PAA exposure. Catalase protein abundance in the liver increased following exposure to PAA, while superoxide dismutase abundance in the gill and liver was increased in response to C. vulgaris inclusion before stress. Overall, the results highlight that a high (14%) inclusion rate of C. vulgaris in feed for Atlantic salmon impairs feed conversion and shifts the intestinal microbiota composition in digesta and mucosa. Weekly feeding of C. vulgaris proves a viable approach in improving protein retention and improving transcriptional resilience towards oxidative stress in increasingly intensive production systems. Thereby this study may motivate future studies on optimizing temporal feeding schedules for health-promoting aquafeeds.

Effects of host-associated low-temperature probiotics in olive flounder (Paralichthys olivaceus) aquaculture

This study investigated the effects of supplementation of low-temperature probiotics isolated from the intestines of olive flounder on the growth performance, digestibility, and regulation of intestinal microbiota and the expression of genes related to growth, immunity, and apoptosis in olive flounder. Bacteria showing high growth at approximately 15-20 °C, which is the temperature of olive flounder culture, were isolated and confirmed to be Pseudomonas species through 16S rRNA gene sequence analysis. Whole-genome sequencing revealed that the strain has a 6,195,122 bp single circular chromosome and a guanine-cytosine content of 59.9%. In the feeding trial, supplementation with 1 × 108 CFU/g of the isolate strain positively modulated growth performances, digestive enzyme activity, and gut microbiota composition of olive flounder. RT-qPCR for the comparison of growth, immunity, and apoptosis-related gene expression levels showed no significant differences between the groups. Therefore, the isolated host-associated low-temperature probiotics improved the growth performance of olive flounder by causing positive changes in digestive activity and intestinal microbial composition without affecting host gene expression.

Deciphering the gut microbiome of grass carp through multi-omics approach

BACKGROUND

Aquaculture plays an important role in global protein supplies and food security. The ban on antibiotics as feed additive proposes urgent need to develop alternatives. Gut microbiota plays important roles in the metabolism and immunity of fish and has the potential to give rise to novel solutions for challenges confronted by fish culture. However, our understanding of fish gut microbiome is still lacking.

RESULTS

We identified 575,856 non-redundant genes by metagenomic sequencing of the intestinal content samples of grass carp. Taxonomic and functional annotation of the gene catalogue revealed specificity of the gut microbiome of grass carp compared with mammals. Co-occurrence analysis indicated exclusive relations between the genera belonging to Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes, suggesting two independent ecological groups of the microbiota. The association pattern of Proteobacteria with the gene expression modules of fish gut and the liver was consistently opposite to that of Fusobacteria, Firmicutes, and Bacteroidetes, implying differential functionality of Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes. Therefore, the two ecological groups were considered as two functional groups, i.e., Functional Group 1: Proteobacteria and Functional Group 2: Fusobacteria/Firmicutes/Bacteroidetes. Further analysis revealed that the two functional groups differ in genetic capacity for carbohydrate utilization, virulence factors, and antibiotic resistance. Finally, we proposed that the ratio of "Functional Group 2/Functional Group 1" can be used as a biomarker that efficiently reflects the structural and functional characteristics of the microbiota of grass carp.

CONCLUSIONS

The gene catalogue is an important resource for investigating the gut microbiome of grass carp. Multi-omics analysis provides insights into functional implications of the main phyla that comprise the fish microbiota and shed lights on targets for microbiota regulation. Video Abstract.

Microbiome analysis reveals potential for modulation of gut microbiota through polysaccharide-based prebiotic feeding in Oreochromis niloticus (Linnaeus, 1758)

Characterization and functional profiling of the gut microbiota are essential for guiding nutritional interventions in fish and achieving favorable host-microbe interactions. Thus, we conducted a 30 days study to explore and document the gut microbial community of O. niloticus, as well as to evaluate the effects of a polysaccharide-based prebiotics with 0.5% and 0.75% Aloe vera extract on the gut microbiome through genomic analysis. The V3-V4 region of 16S rRNA was amplified and sequenced using Illumina HiSeq 2500, resulting in 1,000,199 reads for operational taxonomic unit (OTU) identification. Out of 8,894 OTUs, 1,181 were selected for further analysis. Our results revealed that Planctomycetes, Firmicutes, Proteobacteria, Verrucomicrobia, Actinobacteria, and Fusobacteria were the dominant phyla in both control and treatment samples. Higher doses of prebiotics were found to improve Planctomycetes and Firmicutes while decreasing Proteobacteria and Verrucomicrobia. We observed increasing trends in the abundance of Bacilli, Bacillaceae, and Bacillus bacteria at the class, family, and genus levels, respectively, in a dose-dependent manner. These findings were consistent with the conventional colony count data, which showed a higher prevalence of Bacillus in prebiotic-supplemented groups. Moreover, predicted functional analysis using PICRUSt indicated a dose-dependent upregulation in glycolysis V, superpathway of glycol metabolism and degradation, glucose and xylose degradation, glycolysis II, and sulfoglycolysis pathways. Most of the energy, protein, and amino acid synthesis pathways were upregulated only at lower doses of prebiotic treatment. Our findings suggest that the gut microbiome of O. niloticus can be optimized through nutritional interventions with plant-based polysaccharides for improved growth performance in commercial fish.