Bacterial Opportunistic Pathogens of Fish

Characterization of gill bacterial microbiota in wild Arctic char (Salvelinus alpinus) across lakes, rivers, and bays in the Canadian Arctic ecosystems

Teleost gill mucus has a highly diverse microbiota, which plays an essential role in the host's fitness and is greatly influenced by the environment. Arctic char (Salvelinus alpinus), a salmonid well adapted to northern conditions, faces multiple stressors in the Arctic, including water chemistry modifications, that could negatively impact the gill microbiota dynamics related to the host's health. In the context of increasing environmental disturbances, we aimed to characterize the taxonomic distribution of transcriptionally active taxa within the bacterial gill microbiota of Arctic char in the Canadian Arctic in order to identify active bacterial composition that correlates with environmental factors. For this purpose, a total of 140 adult anadromous individuals were collected from rivers, lakes, and bays belonging to five Inuit communities located in four distinct hydrologic basins in the Canadian Arctic (Nunavut and Nunavik) during spring (May) and autumn (August). Various environmental factors were collected, including latitudes, water and air temperatures, oxygen concentration, pH, dissolved organic carbon (DOC), salinity, and chlorophyll-a concentration. The taxonomic distribution of transcriptionally active taxa within the gill microbiota was quantified by 16S rRNA gene transcripts sequencing. The results showed differential bacterial activity between the different geographical locations, explained by latitude, salinity, and, to a lesser extent, air temperature. Network analysis allowed the detection of a potential dysbiosis signature (i.e., bacterial imbalance) in fish gill microbiota from Duquet Lake in the Hudson Strait and the system Five Mile Inlet connected to the Hudson Bay, both showing the lowest alpha diversity and connectivity between taxa.IMPORTANCEThis paper aims to decipher the complex relationship between Arctic char (Salvelinus alpinus) and its symbiotic microbial consortium in gills. This salmonid is widespread in the Canadian Arctic and is the main protein and polyunsaturated fatty acids source for Inuit people. The influence of environmental parameters on gill microbiota in wild populations remains poorly understood. However, assessing the Arctic char's active gill bacterial community is essential to look for potential pathogens or dysbiosis that could threaten wild populations. Here, we concluded that Arctic char gill microbiota was mainly influenced by latitude and air temperature, the latter being correlated with water temperature. In addition, a dysbiosis signature detected in gill microbiota was potentially associated with poor fish health status recorded in these disturbed environments. With those results, we hypothesized that rapid climate change and increasing anthropic activities in the Arctic might profoundly disturb Arctic char gill microbiota, affecting their survival.

Contrasted Antibiotics and Pesticides Occurrence in Fish Exposed In Situ to Urban Effluents: A 20-Day Caging Experiment

Urban freshwater ecosystems receive a wide array of organic pollutants through wastewater-treatment plant (WWTP) discharges and agricultural runoff. Evaluating the fate and effects of antibiotics and pesticides can be a challenging task, especially the effects on freshwater vertebrates because of their abilities to metabolize and excrete these chemicals and because of their high mobility and escape behavior when exposed to stressful environmental conditions. In the present study, 37 wild gudgeons (Gobio gobio) were caged for a period of up to 20 days, upstream and downstream of a WWTP effluent discharge in the Orge River (a tributary of the Seine River, France). Levels of pesticides and antibiotics in fish muscles were monitored weekly and compared with environmental contamination (water and sediments). Our results highlighted a slight bioaccumulation of pesticides in the gudgeon muscles at the downstream site after 20 days of exposure. Concerning antibiotics, ofloxacin was the most detected compound in fish muscles (85% of occurrence) and ranged from undetectable to 8 ng g-1  dry weight. Antibiotic levels in fish muscle were not higher at the downstream site and did not increase with exposure duration, despite high levels in the water (up to 29 times greater than upstream). Potential ecotoxicological effects were also evaluated: Body condition did not differ between the caging location and exposure time. Three oxidative status markers in the fish livers showed significant shifts after 14 days of caging. Our results suggest a high clearance rate of antibiotics and, to a lesser extent, of pesticides in wild gudgeons, which could be explained by changes in xenobiotic metabolism with pollutant exposure. Environ Toxicol Chem 2024;00:1-11. © 2023 SETAC.

Identification and analysis of pathogenic bacteria causing outbreaks in Indian major carp aquaculture of Tripura

OBJECTIVE

The objective of this study was to investigate bacterial disease outbreaks in Indian major carp from aquaculture systems in Tripura, India, and identify the bacterial species associated with those outbreaks.

METHODS

A 3-year surveillance was conducted in eight districts of Tripura, during which nine bacterial disease outbreaks were recorded. Fourteen bacterial strains isolated from diseased Indian major carp were selected and identified using phenotypic, molecular (16S ribosomal RNA gene), and phylogenetic analyses. In vitro pathogenicity studies were performed to assess the potential pathogenicity of the isolated bacteria.

RESULT

The selected isolated strains were preliminarily identified under the genera Aeromonas (9 isolates), Acinetobacter (1 isolate), Citrobacter (3 isolates), and Pseudomonas (1 isolate). Molecular and phylogenetic analyses confirmed the species of the isolated bacteria, including Aeromonas jandaei (strains COF_AHE09 and COF_AHE61), Aeromonas veronii (strains COF_AHE13, COF_AHE52, COF_AHE55, COF_AHE56, and COF_AHE62), Aeromonas hydrophila (strains COF_AHE51 and COF_AHE58), Acinetobacter pittii (strain COF_AHE14), Citrobacter freundii (strains COF_AHE20, COF_AHE57, and COF_AHE59), and Pseudomonas aeruginosa (strain COF_AHE54). Behavioral and clinical signs observed in the diseased fish, such as lethargy, skin hemorrhaging, ulcers, fin and tail rot, exophthalmia, distended abdomen, scale loss, and skin discoloration, indicated the presence of bacterial septicemia. The in vitro pathogenicity studies highlighted the potential role of these bacteria in disease development, especially under environmental stress.

CONCLUSION

This study provides valuable insights into the diversity of bacterial species associated with bacterial disease outbreaks in Indian major carp from aquaculture systems in Tripura. It serves as the first comprehensive investigation of its kind, contributing to our understanding of bacterial infections in Indian major carp.

Cold temperature stress and damaged skin induced high mortality in barramundi (Lates calcarifer) challenged with Vibrio harveyi

Most diseases in aquaculture are caused by opportunistic pathogens. One of them, Vibrio harveyi, is a widespread Gram-negative bacterium that has become an important pathogen of aquatic species in marine environments. Here, we propose the use of the causal pie model as a framework to conceptualize the causation of vibriosis in juvenile barramundi (Lates calcarifer) and to establish an effective challenge model. In the model, a sufficient cause, or the causal pie, is a constellation of component causes that lead to an outcome (e.g. vibriosis). In the pilot study, a high cumulative mortality (63.3% ± 10.0%, mean ± SE) was observed when V. harveyi was administered by intraperitoneal injection using a high challenge dose [10⁷ colony-forming units (CFU) fish^-1 ], but low or no mortality was observed in fish subject to cold stress or fish with intact skin when challenged by immersion. We, therefore, tested the use of a skin lesion (induced with a 4-mm biopsy punch) combined with cold temperature stress to induce vibriosis following the causal pie model. After challenge, fish were immediately subject to cold stress (22°C) or placed at an optimal temperature of 30°C. All groups were challenged with 10⁸  CFU mL^-1 for 60 min. A considerably higher mortality level (72.7% ± 13.9%) was observed in fish challenged with both a skin lesion and cold stress compared with mortality in fish only having a skin lesion (14.6% ± 2.8%). V. harveyi was re-isolated from all moribund fish and was detected by species-specific real-time PCR in gills, head kidney and liver, regardless of challenge treatment confirming vibriosis as the cause of disease. Parenchymal tissues had histopathological changes consistent with vibriosis. Whole-genome sequence (WGS) is provided for the Vibrio harveyi isolate examined in this study. Overall, the causal pie model was a useful framework to conceptualize the design of the experimental challenge model, in which both cold stress and skin damage were identified as component causes of vibriosis with high mortality. This conceptual framework can be applied to other opportunistic pathogens in aquaculture or to the study of co-infections in fish.

Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems

BACKGROUND

Microbial communities in recirculating aquaculture systems (RAS) play a role in system success, nutrient cycling, and water quality. Considering the increasing socio-economic role of fish farming, e.g., regarding food security, an in-depth understanding of aquaculture microbial communities is also relevant from a management perspective, especially regarding the growth, development, and welfare of the farmed animal. However, the current data on the composition of microbial communities within RAS is patchy, which is partly attributable to diverging method choices that render comparative analyses challenging. Therefore, there is a need for accurate, standardized, and user-friendly methods to study microbial communities in aquaculture systems.

RESULTS

We compared sequencing approach performances (3 types of 16S short amplicon sequencing, PacBio long-read amplicon sequencing, and amplification-free shotgun metagenomics) in the characterization of microbial communities in two commercial RAS fish farms. Results showed that 16S primer choice and amplicon length affect some values (e.g., diversity measures, number of assigned taxa or distinguishing ASVs) but have no impact on spatio-temporal patterns between sample types, farms and time points. This implies that 16S rRNA approaches are adequate for community studies. The long-read amplicons underperformed regarding the quantitative resolution of spatio-temporal patterns but were suited to identify functional services, e.g., nitrification cycling and the detection of pathogens. Finally, shotgun metagenomics extended the picture to fungi, viruses, and bacteriophages, opening avenues for exploring inter-domain interactions. All sequencing datasets agreed on major prokaryotic players, such as Actinobacteriota, Bacteroidota, Nitrospirota, and Proteobacteria.

CONCLUSION

The different sequencing approaches yielded overlapping and highly complementary results, with each contributing unique data not obtainable with the other approaches. We conclude that a tiered approach constitutes a strategy for obtaining the maximum amount of information on aquaculture microbial communities and can inform basic research on community evolution dynamics. For specific and/or applied questions, single-method approaches are more practical and cost-effective and could lead to better farm management practices.

Effect of Different Levels of Chlorogenic Acid on Growth Performance, Immunological Responses, Antioxidant Defense, and Disease Resistance of Rainbow Trout (Oncorhynchus mykiss) Juveniles

The current study is designed to assay the efficacy of chlorogenic acid (ChA) in the diet on growth performance, digestive enzyme activity, serum immunological, biochemical, and antioxidant variables, and mucosal immune response as well as disease resistance of rainbow trout (Oncorhynchus mykiss) juveniles. Rainbow trout juveniles received diets supplemented with different inclusion levels of ChA (0 (ctrl), 200 (CA1), 400 (CA2), 600 (CA3), and 800 (CA4) mg kg^-1 diet) for 60 days. According to the findings, fish from CA3 and CA4 groups demonstrated the best results considering the final weight (FW) and weight gain (WG) (P < 0.05). Also, the group that received 600 mg kg^-1 ChA-supplemented diet showed the lowest feed conversion ratio (FCR) and the highest specific growth rate (SGR) compared to other groups (P < 0.05). Moreover, the minimum survival rate (SR) was only detected in the CA4 treatment (P < 0.05). Regression analysis exhibited that rainbow trout growth indices were polynomially linked to dietary chlorogenic acid concentrations. In this regard, the optimal levels of chlorogenic acid according to growth parameters (FCR and SGR) were 0.71 and 0.62 gr kg^-1 diet, respectively. The results exhibited superior performance of protease and amylase activities in CA2, CA3, and CA4 groups with the maximum amount in the group receiving 600 mg kg^-1 ChA-enriched diet (P < 0.05). Serum lysozyme (LYZ), immunoglobulin (Ig), and components 3 and 4 (C3 and C4) values of CA2, CA3, and CA4 groups were significantly higher than others with the highest amount in the CA3 group (P <0.05). Additionally, serum nitroblue tetrazolium (NBT) value in the CA3 and CA4 groups and myeloperoxidase (MPO) in the CA3 group were notably more than others (P < 0.05). Moreover, the lowest aspartate aminotransferase (AST), alkaline phosphatase (ALP), alanine aminotransferase (ALT), and lactate dehydrogenase (LDH) and the highest total protein (TP) and globulin (GLO) values were observed in CA3 treatment (P < 0.05). CA2 and CA3 groups demonstrated increased serum catalase (CAT) and decreased malondialdehyde (MDA) values compared to the control while the highest CAT and lowest MDA values were observed in CA3 treatment (P < 0.05). Considering mucus immunity, the significantly maximum LYZ and protease values were demonstrated in CA2 and CA3 groups, and the highest ALP, Ig, and esterase values were demonstrated in the CA3 group. In comparison with the control, the mortality rates of the groups that received the ChA diets were remarkably (P < 0.05) lower postchallenge with Y. ruckeri, and the highest survival and relative percentage of survival (RPS) (P < 0.05) belonged to the CA3 group. Results obtained from the current study suggested ChA as a functional dietary additive to raise growth parameters, immune indices, antioxidant capacity, and resistance to disease in rainbow trout.

Sparus aurata and Lates calcarifer skin microbiota under healthy and diseased conditions in UV and non-UV treated water

Background

The welfare of farmed fish is influenced by numerous environmental and management factors. Fish skin is an important site for immunity and a major route by which infections are acquired. The objective of this study was to characterize bacterial composition variability on skin of healthy, diseased, and recovered Gilthead Seabream (Sparus aurata) and Barramundi (Lates calcarifer). S. aurata, which are highly sensitive to gram-negative bacteria, were challenged with Vibrio harveyi. In addition, and to provide a wider range of infections, both fish species (S. aurata and L. calcarifer) were infected with gram-positive Streptococcus iniae, to compare the response of the highly sensitive L. calcarifer to that of the more resistant S. aurata. All experiments also compared microbial communities found on skin of fish reared in UV (a general practice used in aquaculture) and non-UV treated water tanks.

Results

Skin swab samples were taken from different areas of the fish (lateral lines, abdomen and gills) prior to controlled infection, and 24, 48 and 72 h, 5 days, one week and one-month post-infection. Fish skin microbial communities were determined using Illumina iSeq100 16S rDNA for bacterial sequencing. The results showed that naturally present bacterial composition is similar on all sampled fish skin sites prior to infection, but the controlled infections (T₁ 24 h post infection) altered the bacterial communities found on fish skin. Moreover, when the naturally occurring skin microbiota did not quickly recover, fish mortality was common following T₁ (24 h post infection). We further confirmed the differences in bacterial communities found on skin and in the water of fish reared in non-UV and UV treated water under healthy and diseased conditions.

Conclusions

Our experimental findings shed light on the fish skin microbiota in relation to fish survival (in diseased and healthy conditions). The results can be harnessed to provide management tools for commercial fish farmers; predicting and preventing fish diseases can increase fish health, welfare, and enhance commercial fish yields.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00191-y.

Enterococcus faecium are associated with the modification of gut microbiota and shrimp post-larvae survival

BACKGROUND

Probiotics are widely used to promote host health. Compared to mammals and terrestrial invertebrates, little is known the role of probiotics in aquatic invertebrates. In this study, eighteen tanks with eight hundred of shrimp post-larvae individuals each were randomly grouped into three groups, one is shrimps administered with E. faecium as probiotic (Tre) and others are shrimps without probiotic-treatment (CK1: blank control, CK2: medium control). We investigated the correlations between a kind of commercial Enterococcus faecium (E. faecium) powder and microbiota composition with function potentials in shrimp post-larvae gut.

RESULTS

We sequenced the 16S rRNA gene (V4) of gut samples to assess diversity and composition of the shrimp gut microbiome and used differential abundance and Tax4Fun2 analyses to identify the differences of taxonomy and predicted function between different treatment groups. The ingested probiotic bacteria (E. faecium) were tracked in gut microbiota of Tre and the shrimps here showed the best growth performance especially in survival ratio (SR). The distribution of SR across samples was similar to that in PCoA plot based on Bray-Curits and two subgroups generated (SL: SR < 70%, SH: SR ≥ 70%). The gut microbiota structure and predicted function were correlated with both treatment and SR, and SR was a far more important factor driving taxonomic and functional differences than treatment. Both Tre and SH showed a low and uneven community species and shorted phylogenetic distance. We detected a shift in composition profile at phylum and genus level and further identified ten OTUs as relevant taxa that both closely associated with treatment and SR. The partial least squares path model further supported the important role of relevant taxa related to shrimp survival ratio.

CONCLUSIONS

Overall, we found gut microbiota correlated to both shrimp survival and ingested probiotic bacteria (E. faecium). These correlations should not be dismissed without merit and will uncover a promising strategy for developing novel probiotics through certain consortium of gut microbiota.

Profiling Branchial Bacteria of Atlantic Salmon (Salmo salar L.) Following Exposure to Antimicrobial Agents

Microbial gill diseases caused by either opportunistic or specific pathogens are an emerging area of concern for aquaculture producers in part due to their sometimes complex and/or cryptic nature. Many antimicrobial treatments used in aquacultural settings are broad spectrum in nature. The effect of such therapeutics upon reduction and recolonization of commensal or pathogenic microbiota post-treatment has received little attention to date. Commensal bacteria are an integral component of the barrier function of mucosal surfaces in animals. This study evaluated the effect of several commercially relevant antimicrobial treatments upon the diversity and composition of branchial bacteria of Atlantic salmon. Here we exposed Atlantic salmon smolt to a number of commercially relevant antimicrobial treatments including chemotherapeutants (chloramine-t and hydrogen peroxide) and antibiotics (oxytetracycline and florfenicol) in vivo. Subsequently we examined the change in bacterial load, 16S rRNA gene expression, and taxonomic diversity post-treatment upon the gills. Results revealed a decrease in cultivable bacterial colonies after antimicrobial treatment, and a downstream decrease in bacterial richness and abundance post-treatment, with colonization of several prominent pathogenic taxa including Vibrio and Tenacibaculum. Temporal tracing over a 14-day period demonstrated that the bacteriome of gill mucus is sensitive to change, and altered by antimicrobial treatment and handling. This study identified candidate antimicrobial treatments which could be implemented in future studies to illustrate the effect of dysbiosis on microbial gill diseases.

Whole-genome association study searching for QTL for Aeromonas salmonicida resistance in rainbow trout

Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis, has extensive negative effects on wild and farmed salmonids worldwide. Vaccination induces some protection under certain conditions but disease outbreaks occur even in vaccinated fish. Therefore, alternative disease control approaches are required to ensure the sustainable expansion of rainbow trout aquaculture. Selective breeding can be applied to enhance host resistance to pathogens. The present work used genome-wide association study (GWAS) to identify quantitative trait loci (QTL) associated with A. salmonicida resistance in rainbow trout. A total 798 rainbow trout exposed to A. salmonicida by bath challenge revealed 614 susceptible and 138 resistant fish. Genotyping was conducted using the 57 K single nucleotide polymorphism (SNP) array and the GWAS was performed for survival and time to death phenotypes. We identified a QTL on chromosome 16 and located positional candidate genes in the proximity of the most significant SNPs. In addition, samples from exposed fish were examined for expression of 24 immune-relevant genes indicating a systematic immune response to the infection. The present work demonstrated that resistance to A. salmonicida is moderately heritable with oligogenic architecture. These result will be useful for the future breeding programs for improving the natural resistance of rainbow trout against furunculosis.

Urbanization Constrains Skin Bacterial Phylogenetic Diversity in Wild Fish Populations and Correlates with the Proliferation of Aeromonads

Changes in the state of rivers resulting from the activity and expansion of urban areas are likely to affect aquatic populations by increasing stress and disease, with the microbiota playing a potentially important intermediary role. Unraveling the dynamics of microbial flora is therefore essential to better apprehend the impact of anthropogenic disturbances on the health of host populations and the ecological integrity of hydrosystems. In this context, the present study simultaneously examined changes in the microbial communities associated with mucosal skin and gut tissues of eight fish species along an urbanization gradient in the Orge River (France). 16S rRNA gene metabarcoding revealed that the structure and composition of the skin microbiota varied substantially along the disturbance gradient and to a lesser extent according to fish taxonomy. Sequences affiliated with the Gammaproteobacteria, in particular the genus Aeromonas, prevailed on fish caught in the most urbanized areas, whereas they were nearly absent upstream. This rise of opportunistic taxa was concomitant with a decline in phylogenetic diversity, suggesting more constraining environmental pressures. In comparison, fish gut microbiota varied much more moderately with the degree of urbanization, possibly because this niche might be less directly exposed to environmental stressors. Co-occurrence networks further identified pairs of associated bacterial taxa, co-existing more or less often than expected at random. Few correlations could be identified between skin and gut bacterial taxa, supporting the assumption that these two microbial niches are disconnected and do not suffer from the same vulnerability to anthropic pressures.

Development of a rapid colorimetric strip method for determination of volatile bases in mahi-mahi and tuna

Tuna (Thunnus albacares) and mahi-mahi (Coryphaena hippurus) are two major fish species responsible for scombroid poisoning in the United States. The purpose of this research was to develop a low-cost and easily operated colorimetric strip method for the rapid determination of spoilage degree via amine response in mahi-mahi and tuna. The color strip method was developed by investigating different types of dyes, filter papers, sample volume, water bath temperature, and other parameters. Ultimately rose bengal and bromophenol blue (BPB) dyes were chosen. These two dyes produced standard curves with good linearity (0-50 mg/L for the total biogenic amines) and uniformity of color change. The r² values for the standard curves of the rose Bengal and BPB were 0.9535 and 0.8883, respectively. Significant positive Pearson correlations coefficients (r) between the volatile biogenic amine levels detected by these two colorimetric strip methods with increasing spoilage grade of mahi-mahi (rose bengal: r = 0.8907, p < 0.0001; BPB: r = 0.8711, p < 0.0001) and tuna (rose bengal: r = 0.8351, p < 0.0001; BPB: r = 0.7362, p = 0.0001) were observed. For mahi-mahi, the volatile amines detected by the colorimetric strips correlated positively with increasing levels of eight biogenic amines, free alanine, four aldehydes, isoamyl alcohol, two ketones, and dimethyl disulfide. For tuna, the results determined by colorimetric strips positively correlated with three biogenic amines, three free amino acids, four aldehydes, and ethanol. The two validated colorimetric strips could rapidly monitor the spoilage degree of mahi-mahi and tuna at low-cost. PRACTICAL APPLICATION: Rose bengal strips and BPB strips were developed as a rapid, objective, analytical method that can serve as an alternative to sensory grading methods. These two nonspecific colorimetric strip methods provided good linear response and uniformity of color change. Volatile amine levels in fish determined by these colorimetric strip methods were statistically significant and positively correlated with the spoilage grade of fish.

Application of Quantitative-PCR to Monitor Netpen Sites in British Columbia (Canada) for Tenacibaculum Species

Tenacibaculum are frequently detected from fish with tenacibaculosis at aquaculture sites; however, information on the ecology of these bacteria is sparse. Quantitative-PCR assays were used to detect T. maritimum and T. dicentrarchi at commercial Atlantic salmon (Salmo salar) netpen sites throughout several tenacibaculosis outbreaks. T. dicentrarchi and T. maritimum were identified in live fish, dead fish, other organisms associated with netpens, water samples and on inanimate substrates, which indicates a ubiquitous distribution around stocked netpen sites. Before an outbreak, T. dicentrarchi was found throughout the environment and from fish, and T. maritimum was infrequently identified. During an outbreak, increases in the bacterial load in were recorded and no differences were recorded after an outbreak supporting the observed recrudescence of mouthrot. More bacteria were recorded in the summer months, with more mortality events and antibiotic treatments, indicating that seasonality may influence tenacibaculosis; however, outbreaks occurred in both seasons. Relationships were identified between fish mortalities and antimicrobial use to water quality parameters (temperature, salinity, dissolved oxygen) (p < 0.05), but with low R² values (<0.25), other variables are also involved. Furthermore, Tenacibaculum species appear to have a ubiquitous spatial and temporal distribution around stocked netpen sites, and with the potential to induce disease in Atlantic salmon, continued research is needed.

The effect of sulfamonomethoxine treatment on the gut microbiota of Nile tilapia (Oreochromis niloticus)

To investigate the possible effects of sulfamonomethoxine (SMM) on Nile tilapia (Oreochromis niloticus), we quantitatively evaluated the microbial shifts in the intestines of Nile tilapia in response to different doses of SMM (200 and 300 mg/kg) using 16S rRNA gene sequencing. At the phylum level, the control group (0 mg kg^-1  SMM) was dominated by Actinobacteria, Proteobacteria, and Firmicutes. In the treatment groups, Firmicutes, Proteobacteria, and Chloroflexi were the dominant phyla. Cluster analysis indicated that the two groups treated with SMM clustered together. Similarly, the bacterial families that dominated the control group differed from those dominating the treatment groups. The changes in intestinal microbial composition over time were similar between the two SMM treatment groups. In both groups, the abundances of some families, including the Bacillaceae, Streptococcaceae, and Pseudomonadaceae, increased first and then decreased. Overall, the addition of SMM to the feed changed the structure of the intestinal microbiota in Nile tilapia. This study improves our understanding of the impact of SMM on the intestinal microenvironment of Nile tilapia. Our results provide guidelines for the feasibility of SMM use in aquaculture production.

Host Species and Body Site Explain the Variation in the Microbiota Associated to Wild Sympatric Mediterranean Teleost Fishes

Microorganisms are an important component in shaping the evolution of hosts and as such, the study of bacterial communities with molecular techniques is shedding light on the complexity of symbioses between bacteria and vertebrates. Teleost fish are a heterogeneous group that live in a wide variety of habitats, and thus a good model group to investigate symbiotic interactions and their influence on host biology and ecology. Here we describe the microbiota of thirteen teleostean species sharing the same environment in the Mediterranean Sea and compare bacterial communities among different species and body sites (external mucus, skin, gills, and intestine). Our results show that Proteobacteria is the dominant phylum present in fish and water. However, the prevalence of other bacterial taxa differs between fish and the surrounding water. Significant differences in bacterial diversity are observed among fish species and body sites, with higher diversity found in the external mucus. No effect of sampling time nor species individual was found. The identification of indicator bacterial taxa further supports that each body site harbors its own characteristic bacterial community. These results improve current knowledge and understanding of symbiotic relationships among bacteria and their fish hosts in the wild since the majority of previous studies focused on captive individuals.

Replacing fishmeal with plant protein in Atlantic salmon (Salmo salar) diets by supplementation with fish protein hydrolysate

The effects of feeding an 80% plant protein diet, with and without fish protein hydrolysate (FPH) supplementation, on the growth and gut health of Atlantic salmon were investigated. Fish were fed either (A) a control diet containing 35% fishmeal, (B) an 80% plant protein diet with 15% fishmeal, (C) an 80% plant protein diet with 5% fishmeal and 10% partly hydrolysed protein, or (D) an 80% plant protein diet with 5% fishmeal and 10% soluble protein hydrolysate. Fish on the 80% plant- 15% fishmeal diet were significantly smaller than fish in the other dietary groups. However, partly-hydrolysed protein supplementation allowed fish to grow as well as fish fed the control 35% fishmeal diet. Fish fed the FPH diets (diets C and D) had significantly higher levels of amino acids in their blood, including 48% and 27% more branched chain amino acids compared to fish on the 35% fishmeal diet, respectively. Plant protein significantly altered gut microbial composition, significantly decreasing α-diversity. Spirochaetes and the families Moritellaceae, Psychromonadaceae, Helicobacteraceae and Bacteroidaceae were all found at significantly lower abundances in the groups fed 80% plant protein diets compared to the control fishmeal diet.

The Pathobiome in Animal and Plant Diseases

A growing awareness of the diversity and ubiquity of microbes (eukaryotes, prokaryotes, and viruses) associated with larger 'host' organisms has led to the realisation that many diseases thought to be caused by one primary agent are the result of interactions between multiple taxa and the host. Even where a primary agent can be identified, its effect is often moderated by other symbionts. Therefore, the one pathogen-one disease paradigm is shifting towards the pathobiome concept, integrating the interaction of multiple symbionts, host, and environment in a new understanding of disease aetiology. Taxonomically, pathobiomes are variable across host species, ecology, tissue type, and time. Therefore, a more functionally driven understanding of pathobiotic systems is necessary, based on gene expression, metabolic interactions, and ecological processes.

Fish pathogen bacteria: Adhesion, parameters influencing virulence and interaction with host cells

Wild fisheries are declining due to over-fishing, climate change, pollution and marine habitat destructions among other factors, and, concomitantly, aquaculture is increasing significantly around the world. Fish infections caused by pathogenic bacteria are quite common in aquaculture, although their seriousness depends on the season. Drug-supplemented feeds are often used to keep farmed fish free from the diseases caused by such bacteria. However, given that bacteria can survive well in aquatic environments independently of their hosts, bacterial diseases have become major impediments to aquaculture development. On the other hand, the indiscriminate uses of antimicrobial agents has led to resistant strains and the need to switch to other antibiotics, although it seems that an integrated approach that considers not only the pathogen but also the host and the environment will be the most effective method in the long-term to improve aquatic animal health. This review covers the mechanisms of bacterial pathogenicity and details the foundations underlying the interactions occurring between pathogenic bacteria and the fish host in the aquatic environment, as well as the factors that influence virulence. Understanding and linking the different phenomena that occur from adhesion to colonization of the host will offer novel and useful means to help design suitable therapeutic strategies for disease prevention and treatment.

Parasitism perturbs the mucosal microbiome of Atlantic Salmon

Interactions between parasite, host and host-associated microbiota are increasingly understood as important determinants of disease progression and morbidity. Salmon lice, including the parasitic copepod Lepeophtheirus salmonis and related species, are perhaps the most important problem facing Atlantic Salmon aquaculture after feed sustainability. Salmon lice parasitize the surface of the fish, feeding off mucus, scales and underlying tissue. Secondary bacterial infections are a major source of associated morbidity. In this study we tracked the diversity and composition of Salmo salar skin surface microbiota throughout a complete L. salmonis infection cycle among 800 post-smolts as compared to healthy controls. Among infected fish we observed a significant reduction in microbial richness (Chao1, P = 0.0136), raised diversity (Shannon, P < 7.86e-06) as well as highly significant destabilisation of microbial community composition (Pairwise Unifrac, beta-diversity, P < 1.86e-05; P = 0.0132) by comparison to controls. While undetectable on an individual level, network analysis of microbial taxa on infected fish revealed the association of multiple pathogenic genera (Vibrio, Flavobacterium, Tenacibaculum, Pseudomonas) with high louse burdens. We discuss our findings in the context of ecological theory and colonisation resistance, in addition to the role microbiota in driving primary and secondary pathology in the host.

The mosaic architecture of Aeromonas salmonicida subsp. salmonicida pAsa4 plasmid and its consequences on antibiotic resistance

Aeromonas salmonicida subsp. salmonicida, the causative agent of furunculosis in salmonids, is an issue especially because many isolates of this bacterium display antibiotic resistances, which limit treatments against the disease. Recent results suggested the possible existence of alternative forms of pAsa4, a large plasmid found in A. salmonicida subsp. salmonicida and bearing multiple antibiotic resistance genes. The present study reveals the existence of two newly detected pAsa4 variants, pAsa4b and pAsa4c. We present the extensive characterization of the genomic architecture, the mobile genetic elements and the antimicrobial resistance genes of these plasmids in addition to the reference pAsa4 from the strain A449. The analysis showed differences between the three architectures with consequences on the content of resistance genes. The genomic plasticity of the three pAsa4 variants could be partially explained by the action of mobile genetic elements like insertion sequences. Eight additional isolates from Canada and Europe that bore similar antibiotic resistance patterns as pAsa4-bearing strains were genotyped and specific pAsa4 variants could be attributed to phenotypic profiles. pAsa4 and pAsa4c were found in Europe, while pAsa4b was found in Canada. In accordance with their content in conjugative transfer genes, only pAsa4b and pAsa4c can be transferred by conjugation in Escherichia coli. The plasticity of pAsa4 variants related to the acquisition of antibiotic resistance indicates that these plasmids may pose a threat in terms of the dissemination of antimicrobial-resistant A. salmonicida subsp. salmonicida bacteria.