Individual diet has sex-dependent effects on vertebrate gut microbiota

Vertebrates harbour diverse communities of symbiotic gut microbes. Host diet is known to alter microbiota composition, implying that dietary treatments might alleviate diseases arising from altered microbial composition ('dysbiosis'). However, it remains unclear whether diet effects are general or depend on host genotype. Here we show that gut microbiota composition depends on interactions between host diet and sex within populations of wild and laboratory fish, laboratory mice and humans. Within each of two natural fish populations (threespine stickleback and Eurasian perch), among-individual diet variation is correlated with individual differences in gut microbiota. However, these diet-microbiota associations are sex dependent. We document similar sex-specific diet-microbiota correlations in humans. Experimental diet manipulations in laboratory stickleback and mice confirmed that diet affects microbiota differently in males versus females. The prevalence of such genotype by environment (sex by diet) interactions implies that therapies to treat dysbiosis might have sex-specific effects.

Spontaneously productive C-type retrovirus infection of fish cell lines

The spontaneous production and release of morphologically typical, 85 to 90 nm diameter C-type retrovirus particles from four cell lines derived from three species of warmwater fish have been identified. Virus pellets from cell culture supernatants showed high levels of Mn(2+)-dependent reverse transcriptase activity at 24 degrees C. Peak enzyme activity was associated with a 1 x 16 g/ml sucrose gradient fraction. All four isolates induced a cytolytic infection of a bluegill fry cell line within 6 to 10 days.

Effects of storage temperature and preservative treatment on shelf life of the pond-raised freshwater fish, silver perch (Bidyanus bidyanus)

Sensory and microbiological characteristics of pond-raised freshwater silver perch (Bidyanus bidyanus) fish, during cold storage over a period of 25 days were evaluated. Whole fish (averaging 400 g each) were stored in cold storage rooms at either 0 to 2 degrees C, 5 degrees C, or 5 degrees C + potassium sorbate as a preservative. The organoleptic and hypoxanthine test results show that the treatment of potassium sorbate can slow the process of spoilage by about 5 days. Yet, the most important factor affecting the shelf life of these fish is the storage temperature. Keeping the fish at 0 to 2 degrees C can prolong the storage prior to spoilage by 10 days compared with those kept at 5 degrees C. These results obtained through organoleptic tests are corroborated by both the chemical (hypoxanthine and total volatile basic nitrogen) and to some extent by the physical (cosmos) tests. The initial total bacteriological counts were 5 x 10(2) CFU/cm2 for fish surface and <10(2) CFU/g for fish flesh, and these counts rose continuously, reaching about 106 CFU/g (0 to 2 degrees C) and 10(7) CFU/g (5 degrees C) in flesh and 10(7) to 10(8) CFU/cm2 on the surface by the end of the storage period. The addition of potassium sorbate led to a smaller increase in bacterial numbers, especially during the first 15 days. Bacterial composition fluctuated during storage. The initial load on the fish surface was predominantly mesophilic and gram positive and consisted mostly (80%) of Micrococci, Bacillus, and Corynebacterium. During the next 10 days, these bacteria were practically replaced by gram-negative flora comprised mostly of Pseudomonas fluorescens that rapidly increased with storage time and accounted for 95% after 15 days.

Effects of predation stress and food ration on perch gut microbiota

BACKGROUND

Gut microbiota provide functions of importance to influence hosts' food digestion, metabolism, and protection against pathogens. Factors that affect the composition and functions of gut microbial communities are well studied in humans and other animals; however, we have limited knowledge of how natural food web factors such as stress from predators and food resource rations could affect hosts' gut microbiota and how it interacts with host sex. In this study, we designed a two-factorial experiment exposing perch (Perca fluviatilis) to a predator (pike, Esox lucius), and different food ratios, to examine the compositional and functional changes of perch gut microbiota based on 16S rRNA amplicon sequencing. We also investigated if those changes are host sex dependent.

RESULTS

We showed that overall gut microbiota composition among individual perch significantly responded to food ration and predator presence. We found that species richness decreased with predator presence, and we identified 23 taxa from a diverse set of phyla that were over-represented when a predator was present. For example, Fusobacteria increased both at the lowest food ration and at predation stress conditions, suggesting that Fusobacteria are favored by stressful situations for the host. In concordance, both food ration and predation stress seemed to influence the metabolic repertoire of the gut microbiota, such as biosynthesis of other secondary metabolites, metabolism of cofactors, and vitamins. In addition, the identified interaction between food ration and sex emphasizes sex-specific responses to diet quantity in gut microbiota.

CONCLUSIONS

Collectively, our findings emphasize an alternative state in gut microbiota with responses to changes in natural food webs depending on host sex. The obtained knowledge from this study provided us with an important perspective on gut microbiota in a food web context.

Mycobacteriosis in yellow perch (Perca flavescens) from two lakes in Alberta

Granulomatous skin lesions were identified in a population of yellow perch (Perca flavescens) from Sandy Lake (Alberta, Canada) in 1985. Severe granulomatous peritonitis and hepatitis was identified subsequently in a separate population of yellow perch from Wolf Lake (Alberta, Canada). Mycobacterium chelonae was isolated from affected fish in both epizootics. The source and route of infection were not determined in either case. The nature of the inflammatory reaction in both cases suggested a depressed immunity.

Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations

BACKGROUND

The eco-evolutionary processes ruling post-disturbance microbial assembly remain poorly studied, particularly in host-microbiome systems. The community recovery depends not only on the type, duration, intensity, and gradient of disturbance, but also on the initial community structure, phylogenetic composition, legacy, and habitat (soil, water, host). In this study, yellow perch (Perca flavescens) juveniles were exposed over 90 days to constant and gradual sublethal doses of cadmium chloride. Afterward, the exposure of aquaria tank system to cadmium was ceased for 60 days. The skin, gut and water tank microbiomes in control and treatment groups, were characterized before, during and after the cadmium exposure using 16s rDNA libraries and high throughput sequencing technology (Illumina, Miseq).

RESULTS

Our data exhibited long-term bioaccumulation of cadmium salts in the liver even after two months since ceasing the exposure. The gradient of cadmium disturbance had differential effects on the perch microbiota recovery, including increases in evenness, taxonomic composition shifts, as well as functional and phylogenetic divergence. The perch microbiome reached an alternative stable state in the skin and nearly complete recovery trajectories in the gut communities. The recovery of skin communities showed a significant proliferation of opportunistic fish pathogens (i.e., Flavobacterium). Our findings provide evidence that neutral processes were a much more significant contributor to microbial community turnover in control treatments than in those treated with cadmium, suggesting the role of selective processes in driving community recovery.

CONCLUSIONS

The short-term metallic disturbance of fish development has important long-term implications for host health. The recovery of microbial communities after metallic exposure depends on the magnitude of exposure (constant, gradual), and the nature of the ecological niche (water, skin, and gut). The skin and gut microbiota of fish exposed to constant concentrations of cadmium (CC) were closer to the control negative than those exposed to the gradual concentrations (CV). Overall, our results show that the microbial assembly during the community recovery were both orchestrated by neutral and deterministic processes. Video Abtract.

Epizootic haematopoietic necrosis virus (EHNV): improved ELISA for detection in fish tissues and cell cultures and an efficient method for release of antigen from tissues

An improved antigen capture ELISA for the detection of epizootic haematopoietic necrosis virus (EHNV) is described. Affinity purified rabbit anti-EHNV immunoglobulin was used as capture antibody, enabling the detection of EHNV at a concentration of 10(3.5) TCID50/ml cell culture supernatant. The sensitivity and specificity of the ELISA, determined by examination of clarified tissue homogenates from 55 infected fish and 348 uninfected fish in relation to virus isolation, were 81.2% and 98.9%, respectively. Specificity for redfin perch (Perca fluviatilis) tissue samples was 100%, however, high background optical density (OD) in samples from uninfected rainbow trout (Oncorhynchus [corrected] mykiss) resulted in lower specificity (98.5%). Specificity for rainbow trout tissues was increased to 100% by testing clarified tissue homogenates that had been diluted 1:10. Sensitivity and specificity estimates for cell culture supernatants were 96.2% and 99.9% based on the results obtained for 158 infected and 355 uninfected samples. Incubation steps in the ELISA can be shortened to enable its completion in less than 4 h if a rapid qualitative diagnosis is required. Of eight methods of releasing EHNV from infected tissue that were evaluated, manual grinding of tissue with a fitted pestle in a 1.5-ml plastic disposable tube, followed by vortexing in the same tube with 3 mm diameter glass beads and clarification in a microcentrifuge was the most efficient. Samples from 150-200 individual fish could be prepared for ELISA and cell culture by a single operator in a day. Antigen capture ELISA can replace virus isolation as the method of choice for diagnosis of EHNV.

Dietary bile acids reduce liver lipid deposition via activating farnesoid X receptor, and improve gut health by regulating gut microbiota in Chinese perch (Siniperca chuatsi)

The aim of this study is to explore the effects of dietary bile acids (BAs) supplementation on lipid metabolism and gut health of Chinese perch (Siniperca chuatsi), and its possible mechanisms. Two isonitrogenous and isolipidic diets were formulated to supplement different levels of BAs (0 and 900 mg BAs kg^-1 diet, respectively). All fish (Initial mean body weight: 171.29 ± 0.77g) were randomly divided into 2 groups (triplicate, 54 fish/group) and were fed with different experimental diets for 56 days, respectively. Dietary exogenous BAs supplementation at the concentration of 900 mg kg^-1 significantly increased weight gain and survival rate, and decreased feed conversion ratio. BAs could inhibit lipid synthesis and promote lipid oxidation to reduce lipid deposition by activating farnesoid X receptor (FXR). Dietary BAs supplementation increased the abundance of Lactobacilli in Firmicutes, and the increase of Lactobacillus caused the increase of lactic acid level and the decrease of pH, which might be the reason for the gut villus length and gut wall high in this study. Dietary BAs supplementation increased the levels of catalase and superoxide dismutase and decreased the level of malondialdehyde in the gut and plasma, which might be contributed to the regulating the antioxidant stress phenotype of gut microbiota by the increased abundance of Firmicutes. Then it caused the increase of the globulin level in the plasma, meaning the enhancement of immune state. The increased immunity might also be thought to be responsible for increased survival rate. These results suggest dietary BAs reduce liver lipid deposition via activating FXR, and improve gut health by regulating gut microbiota in Chinese perch.

Opportunistic disease in yellow perch in response to decadal changes in the chemistry of oil sands-affected waters

Oil sands-affected water from mining must eventually be incorporated into the reclaimed landscape or treated and released. However, this material contains petrogenic organic compounds, such as naphthenic acids and traces of polycyclic aromatic hydrocarbons. This has raised concerns for impacts of oil sands process-affected waters on the heath of wildlife and humans downstream of receiving environments. The objective of this study was to evaluate the temporal association of disease states in fish with water chemistry of oil sands-affected waters over more than a decade and determine the pathogens associated with disease pathologies. Yellow perch (Perca flavescens) captured from nearby lakes were stocked into two experimental ponds during 1995-1997 and 2008-2010. South Bison Pond is a drainage basin that has received unextracted oil sands-contaminated material. Demonstration Pond is a constructed pond containing mature fine tailings capped with fresh water. Two disease pathologies, fin erosion for which a suspected bacterial pathogen (Acinetobacter Iwoffi) is identified, and lymphocystis (confirmed using a real-time PCR) were associated with oil sands-affected water exposure. From 1995 to 1997 pathologies were most prevalent in the South Bison Pond; however, from 2008 to 2009, disease was more frequently observed in the Demonstration Pond. CYP1A activity was 3-16 fold higher in fish from experimental ponds as compared to reference populations and this pattern was consistent across all sampling years. Bile fluorescence displayed a gradient of exposure with experimental ponds being elevated over local perch populations. Naphthenic acids decreased in the Bison Pond from approximately 12 mg/L to <4 mg/L while naphthenic acids increased in the Demonstration Pond from 6 mg/L to 12 mg/L due to tailings densification. Temporal changes in naphthenic acid levels, CYP1A activity and bile fluorescent metabolites correlate positively with incidence of disease pathologies whereas all inorganic water quality changes (major ions, pH, metals) were not associated with disease responses.

Isolation and characterization of two virulent Aeromonads associated with haemorrhagic septicaemia and tail-rot disease in farmed climbing perch Anabas testudineus

Diseased Anabas testudineus exhibiting signs of tail-rot and ulcerations on body were collected from a fish farm in Assam, India during the winter season (November 2018 to January 2019). Swabs from the infected body parts were streaked on sterilized nutrient agar. Two dominant bacterial colonies were obtained, which were then isolated and labelled as AM-31 and AM-05. Standard biochemical characterisation and 16S rRNA and rpoB gene sequencing identified AM-31 isolate as Aeromonas hydrophila and AM-05 as Aeromonas jandaei. Symptoms similar to that of natural infection were observed on re-infecting both bacteria to disease-free A. testudineus, which confirmed their virulence. LC50 was determined at 1.3 × 104 (A. hydrophila) and 2.5 × 104 (A. jandaei) CFU per fish in intraperitoneal injection. Further, PCR amplification of specific genes responsible for virulence (aerolysin and enterotoxin) confirmed pathogenicity of both bacteria. Histopathology of kidney and liver in the experimentally-infected fishes revealed haemorrhage, tubular degeneration and vacuolation. Antibiotic profiles were also assessed for both bacteria. To the best of our knowledge, the present work is a first report on the mortality of farmed climbing perch naturally-infected by A. hydrophila as well as A. jandaei, with no records of pathogenicity of the latter in this fish.

Impact of toxic cyanobacterial blooms on Eurasian perch (Perca fluviatilis): experimental study and in situ observations in a peri-alpine lake

Due to the importance of young-of-the-year (YOY) perch in the peri-alpine regions where they are consumed, the microcystin (MC) contamination of YOY perch was analysed both in field (Lake Bourget, France) and experimentally using force-feeding protocols with pure MCs. In-situ, schools of YOY perch present in the epilimnion of the lake were never found in direct contact with the P. rubescens blooms that were present in the metalimnion. However, MCs were detected in the muscles and liver of the fish and were thus assumed to reach YOY perch through dietary routes, particularly via the consumption of MC-containing Daphnia. Force-feeding experiment demonstrates the existence of MC detoxification/excretion processes and suggests that in situ, YOY perch could partly detoxify and excrete ingested MCs, thereby limiting the potential negative effects on perch populations under bloom conditions. However, because of chronic exposure these processes could not allow for the complete elimination of MCs. In both experimental and in situ studies, no histological change was observed in YOY perch, indicating that MC concentrations that occurred in Lake Bourget in 2009 were too low to cause histological damage prone to induce mortality. However, Deoxyribonucleic acid (DNA) damages were observed for both the high and low experimental MC doses, suggesting that similar effects could occur in situ and potentially result in perch population disturbance during cyanobacterial blooms. Our results indicate the presence of MCs in wild perch, the consumption of this species coming from Lake Bourget is not contested but more analyses are needed to quantify the risk.

Identification of bacteria from the normal flora of perch, Perca fluviatilis L., and evaluation of their inhibitory potential towards Aeromonas species

Pathogenic Aeromonas sobria has been identified as a causative agent of ulcerative disease in farmed European perch, Perca fluviatilis L. To study the effect of the normal intestinal bacterial flora of perch against A. sobria, we sampled 193 bacterial isolates from the perch digestive tract. The isolates were identified by sequence analysis of the 16S rRNA gene and their inhibitory potential against A. sobria was evaluated in vitro. Nineteen of the strains isolated showed inhibition and were also tested against other aeromonad and non-aeromonad fish pathogens including Yersinia ruckeri and Vibrio anguillarum. Isolates showing inhibition were primarily Pseudomonas spp.; however, inhibitory Shewanella spp., and Delftia sp. were also identified. A Pseudomonas chlororaphis isolate showed inhibition against all fish pathogens tested.

Effects of the husky oil spill on gut microbiota of native fishes in the North Saskatchewan River, Canada

In July 2016, a Husky Energy pipeline spilled 225,000 L of diluted heavy crude oil, with a portion of the oil entering the North Saskatchewan River near Maidstone, SK, Canada. This event provided a unique opportunity to assess potential effects of a crude oil constituent (namely polycyclic aromatic hydrocarbons, PAHs) on a possible sensitive indicator of freshwater ecosystem health, the gut microbiota of native fishes. In summer 2017, goldeye (Hiodon alosoides), walleye (Sander vitreus), northern pike (Esox lucius), and shorthead redhorse (Moxostoma macrolepidotum) were collected at six locations upstream and downstream of the spill. Muscle and bile were collected from individual fish for quantification of PAHs and intestinal contents were collected for characterization of the microbial community of the gut. Results suggested that host species is a significant determinant of gut microbiota, with significant differences among the species across sites. Concentrations of PAHs in dorsal muscle were significantly correlated with gut community compositions of walleye, but not of the other fishes. Concentrations of PAHs in muscle were also correlated with abundances of several families of bacteria among fishes. This study represents one of the first to investigate the response of the gut microbiome of wild fishes to chemical stressors.

Composition of the microbial communities in the gastrointestinal tract of perch (Perca fluviatilis L. 1758) and cestodes parasitizing the perch digestive tract

Using the approach of sequencing the V3-V4 region of the 16S rRNA gene, we have analysed the bacterial diversity associated with the distinct compartments of the gastrointestinal tract of perch (Perca fluviatilis) and cestodes (Proteocephalus sp.) parasitizing their digestive tract. The dominant microbiota associated with cestodes (Proteocephalus sp.) was represented by bacteria from the genera Serratia, Pseudomonas and Mycoplasma. By comparing the associated microbiota of perch and cestodes, a clear difference in bacterial composition and diversity was revealed between the community from the stomach content and other parts of the gastrointestinal tract of fish. Microbiota associated with cestodes was not significantly different in comparison with microbiota of different subcompartments of perch (mucosa and content of intestine and pyloric caeca) (ADONIS, p > .05) excluding microbiota of stomach content (ADONIS, p ≤ .05). PICRUSt-based functional assessments of the microbial communities of perch and cestodes indicated that they mainly linked in terms of metabolism and environmental information processing and could play an important role in the nutrition and health of host.

Characterization of the gut microbiota in early life stages of pikeperch Sander lucioperca

This study characterized the gastrointestinal microbiome of nine juvenile farmed pikeperch Sander lucioperca using a metagenomics approach based on bacterial 16S rRNA gene sequencing. Potential changes in the gut microbiota during 2 months of S. lucioperca juvenile life were investigated. Results revealed that gut microbiota was dominated by Proteobacteria (95-92%), while other phyla Firmicutes (1-1·5%) and Actinobacteria (0·9-1·5%) were less abundant. At the family level, fish-gut microbiota were dominated by Enterobacteriaceae, which constituted c. 83% of all DNA sequence reads. Such a situation was present in all of the examined fish except one, which showed a different proportion of particular microbial taxa than the other fish. In this fish, a higher relative abundance (%) of Fusobacteria (21·0%), Bacteroidetes (9·5%) and Firmicutes (7·5%) was observed. There were no significant differences in the gut microbiome structure at different stages of development in the examined fish. This may indicate that Proteobacteria inhabiting the gut microbiota at an early stage of life are a necessary component of the pikeperch microbiome that may support proper nutrition of the fish. The information obtained on the gut microbiome could be useful in determining juvenile S. lucioperca health and improving rearing conditions by welfare monitoring in aquaculture.

Comparative study of immune responses and intestinal microbiota in the gut-liver axis between wild and farmed pike perch (Sander Lucioperca)

Introduction

Pike perch (Sander Lucioperca) is a predatory freshwater fish, which is highly popular amongst consumers, owing to its white flesh with a delicate structure and mild flavor. Compared to wild pike perch, the diet of farmed ones has shifted from natural food to artificial feeds. These changes would affect the gut flora of the pike perch. Endogenous metabolites of the intestinal flora are transferred through the gut-liver axis, which affects the physiological functions of the host. By studying wild and farmed individuals of the pike perch, novel insights into the stability of the intestinal flora can be provided.

Methods and results

In this study, we measured various immune parameters in the blood, liver and intestine of wild and farmed pike perch using enzyme activity assays and real-time fluorescence quantitative PCR. Gut microbes were also collected for 16S rRNA gene sequencing. Our results showed that the serum low-density lipoprotein cholesterol (LDL-C) levels were twice as high in the wild group as in the farmed group. Furthermore, the activities of glutamate pyruvate transaminase (GPT) and glutamate oxaloacetate transaminase (GOT) in the intestinal tissues of the wild group were 733.91 U/g and 375.35 U/g, which were significantly higher than those of the farmed group. Expression of IL10 in the liver of farmed pike perch was also 4-fold higher than that of wild pike perch. The expression of genes related to the p53-BAX/Bcl2 signaling pathway was higher in both intestinal and liver tissues of wild pike perch compared with farmed. 16S rRNA gene analysis of the gut microflora showed a high relative abundance of Cetobacterium in the gut of farmed pike perch.

Conclusion

As a result, our study indicates that dietary differences affect the diversity, composition and relative abundance of the gut flora of the pike perch. Meanwhile, it affects the glycolipid metabolism and immunomodulation of pike perch.

[Intracellular symbiosis and energetic role of bacteria in gill epithelium of freshwater mollusks and fishes]

Penetration of bacteria by endocytosis into gill epithelial cells has been revealed in animals of different evolutionary levels (freshwater mollusks and fishes). These data confirm the leading role of endosymbiosis in the origin of eukaryotes from prokaryotes and in the evolution of animal life.

Network-based integration of omics, physiological and environmental data in real-world Elbe estuarine Zander

Coastal and estuarine environments are under endogenic and exogenic pressures jeopardizing survival and diversity of inhabiting biota. Information of possible synergistic effects of multiple (a)biotic stressors and holobiont interaction are largely missing in estuaries like the Elbe but are of importance to estimate unforeseen effects on animals' physiology. Here, we seek to leverage host-transcriptional RNA-seq and gill mucus microbial 16S rRNA metabarcoding data coupled with physiological and abiotic measurements in a network analysis approach to decipher the impact of multiple stressors on the health of juvenile Sander lucioperca along one of the largest European estuaries. We find mesohaline areas characterized by gill tissue specific transcriptional responses matching osmosensing and tissue remodeling. Liver transcriptomes instead emphasized that zander from highly turbid areas were undergoing starvation which was supported by compromised body condition. Potential pathogenic bacteria, including Shewanella, Acinetobacter, Aeromonas and Chryseobacterium, dominated the gill microbiome along the freshwater transition and oxygen minimum zone. Their occurrence coincided with a strong adaptive and innate transcriptional immune response in host gill and enhanced energy demand in liver tissue supporting their potential pathogenicity. Taken together, we show physiological responses of a fish species and its microbiome to abiotic factors whose impact is expected to increase with consequences of climate change. We further present a method for the close-meshed detection of the main stressors and bacterial species with disease potential in a highly productive ecosystem.

[Sanitary and microbiological evaluation of the hydrosystem in the Volga river estuary upon anthropogenic pollution]

The paper gives many years' data on the size of the opportunistic and sanitary-significant microflora of pike perches (Stizostedion) and water in the producer's food fish areas of the Volga river estuary, as well as the results of ecological and microbiological studies of the water from the above areas, which include the determination of the total amount of the bacterial plankton on membrane filters, the number of heterotrophic bacteria, which has provided an assessment of the habitat quality of hydrocoles in accordance with the complex ecological classification of the quality of the land's surface water. The paper analyzes the seasonal abundance and spatial distribution of the most common opportunistic microorganisms, as well as the markers of their pathogenicity.