Fish microbiota and its role in fish physiology and diseases regulation

Transcriptome analysis of grass carp provides insights into disease-related genes and novel regulation pattern of bile acid feedback in response to lithocholic acid

High-throughput sequencing was applied to compare the intestinal microbiota in largemouth bronze gudgeon either healthy or affected by furunculosis. Proteobacteria, Actinobacteria, Tenericutes, Firmicutes and Bacteroidetes were detected as the predominant bacterial phyla in the gut of both diseased and healthy fish. The abundance of Proteobacteria differed significantly between the two groups of fish, mainly due to the overwhelming prevalence of Aeromonas in the diseased fish (81% ± 17%), while the genus was unevenly spread among the apparently healthy fish (33% ± 33%). The bacterial diversity in the intestine of diseased fish was markedly lower than in healthy fish. Analysis revealed the significant dissimilarity between the gut microbiota of diseased and healthy fish. The bacterial profiles in the gut were further characterized with the 28 phylotypes that were shared by the two groups. In diseased fish, two shared OTUs (OTU0001 and OTU0013) were closely related to Aeromonas salmonicida, their total proportion exceeding 70% of the sequences in diseased fish, while averaging 5.2% ± 4.6% in the healthy fish. This result suggested the presence of healthy carriers of pathogenic A. salmonicida among the farmed fish, and the gut appeared as a probable infection source for furunculosis in largemouth bronze gudgeon.

Fish gut microbiota play important roles in fish immunity, nutrition, and the adaptation to environmental changes. To date, few studies have focused on the interactions among environmental factors, fish diseases, and gut microbiota compositions. We compared the gut bacterial communities of healthy crucian carps (Carassius auratus) with those of individuals affected by "red-operculum" disease and corresponding water and sediment microbiota in four fish farm ponds. Distinct gut bacterial communities were observed in healthy and diseased fish. The bacterial communities of diseased fish were less diverse and stable than those of healthy individuals. The differences in bacterial community compositions between diseased and healthy fish were explained by the changes in the relative abundances of some specific bacterial OTUs, which belonged to the genera such as Vibrio, Aeromonas, and Shewanella, and they were prevalent in diseased fish, but rare or even absent in environmental samples. Water temperature and ammonia concentration were the two most important environmental factors that impacted gut microbiota in diseased fish. These results highlighted the surge of some potential pathogens as bacterial signatures that were associated with "red-operculum" disease in crucian carps.

Comparison of intestinal bacterial communities in asymptomatic and diseased Asian seabass (Lates calcarifer) with chronic enteritis and mixed bacterial infections

Comprehensive study on the effect of dietary leucine supplementation on intestinal physiology, TOR signaling and microbiota in juvenile turbot (Scophthalmus maximus L.)

Assessment of patho-physiological responses, gill histopathology and SEM analysis in common carp (Cyprinus carpio) exposed to varied doses of chloramine-T: A potent chemotherapeutic agent

Seasonal variation of water characteristics, predominantly temperature, is considered to strongly affect fish physiology and immunology. In nature, this variation directly influences the life cycle especially in fish parasites, but the infection of parasites is also altered by the host immune response. This study is aimed to analyze the seasonal changes in selected physiological and immunological parameters, the latter a potential measure of fish immunocompetence. Moreover, the seasonal changes in metazoan parasite infection were investigated, and the potential associations between fish physiology, immunocompetence, and parasitism were estimated. No differences in gender were recognized for immunological parameters. The significant differences in the spleen-somatic index were found among fish samples of different seasons indicating higher investment in spleen size in April (after winterizing) and August (post-breeding with low gonado-somatic index [GSI]). The significant seasonal differences in erythrocyte and leukocyte cell counts, as well as in phagocyte count affecting respiratory burst, were recorded. The general trend of leukocyte composition was similar in all seasons investigated; however, the changes in proportion of different neutrophilic cells were reported. The parasite diversity and the infection parameters in parasite communities were highest in spring and early summer. When comparing parasite abundance in infracommunities among seasons, the statistically highest values were observed in April and June for Monogenea, in April and November for Acanthocephala, and in April for Cestoda. The positive correlations between GSI and the parasite abundance of groups with higher infection parameters were found in males. Moreover, the positive association between Monogenea as the dominant parasite group and respiratory burst was observed. The higher investment in condition and the seasonal variation in GSI were associated with a decrease immune function measured by spleen size or leukocyte cell count especially for males suggesting the seasonal energy allocation between immune function and somatic or reproductive investment.

Global climate change has posed significant challenges to the aquaculture industry, leading to the emergence of novel diseases. A recently emerging disease, termed the overwintering syndrome, has been reported in freshwater fish aquaculture systems in China during the winter-spring transition. This syndrome is characterized by weight loss, decreased activity levels, and mass mortality. Currently, little is known about cause of the emerging disease. In this study, the gut microbiota of healthy and diseased channel catfish (Ictalurus punctatus) were analyzed using metagenomic sequencing. Diseased fish exhibited a notable reduction in bacterial diversity compared to healthy controls, while the viral richness was significantly higher. Additionally, random forest models based on gut microbiota composition revealed high accuracy in distinguishing between diseased and healthy fish. Several gut microbiota biomarkers with potential diagnostic value were identified, primarily consisting of rare taxa (relative abundance < 5%), except for Alphaproteobacteira, Siphoviridae and Podoviridae. Furthermore, an increase in the prevalence and abundance of pathogens was observed in the intestines of diseased fish compared to healthy counterparts. Notably, Vibrio cholerae and Dickeya dadantii were enriched in the intestines of fish exhibiting the overwintering syndrome. Concurrently, genes involved in the synthesis of innate immune factors was markedly diminished in the gut microbiota of diseased fish, along with a reduction in the microbial hosts of these genes. Collectively, these findings elucidate the enrichment of pathogens and the attenuation of innate immunity in fish with the overwintering syndrome, correlating with alterations in the gut microbiota.

The mucosal surfaces of fish represent an important barrier that supports and regulates a diverse array of microbial assemblages and contributes to the overall health and fitness of the host. For farmed species, knowledge of how these host–microbial systems adapt and respond to various stressors is pivotal for managing health, nutrition and optimizing productivity in aquaculture. While our understanding of these communities and the factors that shape them now suggest that a diverse balanced microbiota is critical for healthy functioning in fish, the mechanisms behind these interactions are still poorly understood. Much of the existing research has focused on characterizing the taxonomic diversity of these assemblages in different fish species, across body surfaces (e.g. skin, gills and gastrointestinal tract), and in response to changing nutrition, health and environmental conditions. However, the specific functional contributions of these communities (or specific members) remain elusive, especially in farmed or diseased fish. Here, we review our current understanding of the microbiota in fish, their interplay and the likely functional involvement with the host. We also seek to address and identify gaps in knowledge and explore the future prospects for improving our understanding of these communities in aquaculture.

Chlorella vulgaris is one of the most commonly used microalgae in aquaculture feeds. It contains high concentrations of various kinds of nutritional elements that are involved in the physiological regulation of aquaculture animals. However, few studies have been conducted to illustrate their influence on the gut microbiota in fish. In this work, the gut microbiota of Nile tilapia (Oreochromis niloticus) (average weight is 6.64 g) was analyzed by high-throughput sequencing of the 16S rRNA gene after feeding with 0.5% and 2% C. vulgaris additives in diets for 15 and 30 days (average water temperature was 26 °C). We found that the impact of C. vulgaris on the gut microbiota of Nile tilapia was feeding-time dependent. Only by feeding for 30 days (not 15 days) did the addition of 2% C. vulgaris to diets significantly elevate the alpha diversity (Chao1, Faith pd, Shannon, Simpson, and the number of observed species) of the gut microbiota. Similarly, C. vulgaris exerted a significant effect on the beta diversity (Bray–Curtis similarity) of the gut microbiota after feeding for 30 days (not 15 days). During the 15-day feeding trial, LEfSe analysis showed that Paracoccus, Thiobacillus, Dechloromonas, and Desulfococcus were enriched under 2% C. vulgaris treatment. During the 30-day feeding trial, Afipia, Ochrobactrum, Polymorphum, Albidovulum, Pseudacidovorax, and Thiolamprovum were more abundant in 2% C. vulgaris-treated fish. C. vulgaris promoted the interaction of gut microbiota in juvenile Nile tilapia by increasing the abundance of Reyranella. Moreover, during the feeding time of 15 days, the gut microbes interacted more closely than those during the feeding time of 30 days. This work will be valuable for understanding how C. vulgaris in diets impacts the gut microbiota in fish.

Additive effects of enhanced ambient ultraviolet B radiation and increased temperature on immune function, growth and physiological condition of juvenile (parr) Atlantic Salmon, Salmo salar

Symbiotic bacteria within the gut microbiome of various organisms, including fish, provide the host with several functions that improve the immune system. Although the spleen plays an important role in the modulation of immune responses, the role of spleen microbiota in shaping the immune system is unclear. Our study aimed at understanding the relationship between fish health and microbiota composition in the intestine and spleen. Our model organism was the hybrid tilapia (Oreochromis aureus × Oreochromis niloticus). We sampled intestine and spleen from healthy and diseased adult tilapia and determined their microbiota composition by sequencing the 16S rRNA gene. Significant differences were found between the intestine and the spleen microbiota composition of healthy compared to diseased fish as well as between intestines and spleens of fish with the same health condition. The microbiota diversity of healthy fish compared to diseased fish was significantly different as well. In the intestine of healthy fish, Cetobacterium was the most abundant genus while Mycoplasma was the most abundant genus in the spleen. Vibrio was the most abundant genus in the intestine and spleen of diseased fish. Moreover, it seems that there is a co-infection interaction between Vibrio and Aeromonas, which was reflected in the spleen of diseased fish. While Vibrio, Aeromonas and Streptococcus were the probable pathogens in the diseased fish, the role of Mycoplasma as a pathogen of cultured hybrid tilapia remains uncertain. We conclude that the intestine and spleen microbiota composition is strongly related to the health condition of the fish.

The present study aimed to evaluate the bacterial load of water, Nile Tilapia and common Carp intestines from earthen ponds, isolate lactic acid bacteria (LAB) and assess their antimicrobial activity against fish spoilage and pathogenic bacteria. Following enumeration and isolation of microorganisms the antimicrobial activity of the LAB isolates was evaluated. Taxonomic identification of selected antagonistic LAB strains was assessed, followed by partial characterisation of their antimicrobial metabolites. Results showed that high counts (>4 log c.f.u ml-1 or 8 log c.f.u g-1) of total aerobic bacteria were recorded in pond waters and fish intestines. The microbiota were also found to be dominated by Salmonella spp., Vibrio spp., Staphylococcus spp. and Escherichia coli. LAB isolates (5.60%) exhibited potent direct and extracellular antimicrobial activity against the host-derived and non host-derived spoilage and pathogenic bacteria. These antagonistic isolates were identified and Lactococcus lactis subsp. lactis was found as the predominant (42.85%) specie. The strains displayed the ability to produce lactic, acetic, butyric, propionic and valeric acids. Bacteriocin-like inhibitory substances with activity against Gram-positive and Gram-negative (Vibrio spp. and Pseudomonas aeruginosa) bacteria were produced by three L. lactis subsp. lactis strains. In this study, the LAB from the microbiota of fish and pond water showed potent antimicrobial activity against fish spoilage or pathogenic bacteria from the same host or ecological niche. The studied Cameroonian aquatic niche is an ideal source of antagonistic LAB that could be appropriate as new fish biopreservatives or disease control agents in aquaculture under tropical conditions in particular or worldwide in general.

Maintaining stabilization of the intestinal microbiota is important in preventing bacterial diseases in cultured fish. At present, there have been no reports on the composition and functional analysis of intestinal microbiota in Yunlong Grouper (Epinephelus moara♀ × Epinephelus lanceolatus♂). In this study we analyzed and compared the intestinal microbiota composition of healthy and diseased pond-reared fish to discern the functional profile of a healthy status. The richness and diversity of the intestinal microbiota did not differ significantly between diseased and healthy fish, yet the abundance of predominant phyla like the Proteobacteria were upregulated in the diseased Yunlong Grouper. At the genus level, a significant reduction of Cetobacterium was observed in the intestinal tracts of diseased fish, as Pseudomonas became the most dominant bacterium. To compare the intestinal microorganism abundances between the two health groups of fish, we first screened the gut bacteria and discerned 4 phyla and 12 genera to designate a healthy status in Yunlong Grouper. The environmental bacterial community influenced composition of the intestinal microbiota in Yunlong Grouper, and the intestinal microbiota of diseased fish was more susceptible to the influence of the culture water. In addition, the prediction of functional genes by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) indicated that the intestinal microbiota of Yunlong Grouper is related mainly to the terms “metabolism, environmental information processing, genetic information processing, human diseases, and cellular processing; moreover, the functions of the intestinal microbiota differed between the different health states of this fish. The overall results indicate that the occurrence of disease can affect the composition and function of the intestinal microbiota in a cultured fish.

Aeromonas hydrophila is a major pathogenic species that causes mass mortality in various freshwater fish species including hybrid tilapia, the main fish species in Israeli aquaculture. Our hypothesis was that A. hydrophila infection may cause changes in the microbiota composition of fish internal organs, and therefore we aimed to study the effect of A. hydrophila infection by injection or by net handling on the microbiota compositions of fish intestine, spleen, and liver. Significant differences in the microbiota composition were found between the internal organs of the diseased and the healthy fish in both experimental setups. Fusobacteriota was the most dominant phylum in the microbiota of healthy fish (∼70%, liver). Cetobacterium was the most abundant genus and relatively more abundant in healthy, compared to diseased fish. When A. hydrophila was inoculated by injection, it was the only pathogenic genus in the spleen and liver of the diseased fish. However, in the handling experiment, Vibrio was also detected in the diseased fish, demonstrating coinfection interactions. Based on these experiments, we conclude that indeed, A. hydrophila infection in tilapia causes changes in the microbiota composition of fish internal organs, and that fish net handling may trigger bacterial infection in freshwater aquaculture.