Antagonistic effect of indigenous skin bacteria of brook charr (Salvelinus fontinalis) against Flavobacterium columnare and F. psychrophilum

Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish

Variation in the composition of skin-associated microbiomes has been attributed to host species, geographical location and habitat, but the role of intraspecific phenotypic variation among host individuals remains elusive. We explored if and how host environment and different phenotypic traits were associated with microbiome composition. We conducted repeated sampling of dorsal and ventral skin microbiomes of carp individuals (Cyprinus carpio) before and after translocation from laboratory conditions to a semi-natural environment. Both alpha and beta diversity of skin-associated microbiomes increased substantially within and among individuals following translocation, particularly on dorsal body sites. The variation in microbiome composition among hosts was significantly associated with body site, sun-basking, habitat switch and growth, but not temperature gain while basking, sex, personality nor colour morph. We suggest that the overall increase in the alpha and beta diversity estimates among hosts were induced by individuals expressing greater variation in behaviours and thus exposure to potential colonizers in the pond environment compared with the laboratory. Our results exemplify how biological diversity at one level of organization (phenotypic variation among and within fish host individuals) together with the external environment impacts biological diversity at a higher hierarchical level of organization (richness and composition of fish-associated microbial communities).

Teleost skin microbiome: An intimate interplay between the environment and the host immunity

The mucosal microbiome plays a role in regulating host health. The research conducted in humans and mice has governed and detailed the information on microbiome-host immunity interactions. Teleost fish, different from humans and mice, lives in and relies on the aquatic environment and is subjected to environmental variation. The growth of teleost mucosal microbiome studies, the majority in the gastrointestinal tract, has emphasized the essential role of the teleost microbiome in growth and health. However, research in the teleost external surface microbiome, as the skin microbiome, has just started. In this review, we examine the general findings in the colonization of the skin microbiome, how the skin microbiome is subjected to environmental change and the reciprocal regulation with the host immune system, and the current challenges that potential study models can address. The information collected from teleost skin microbiome-host immunity research would help future teleost culturing from the potential parasitic infestation and bacterial infection as foreseeing growing threats.

Investigating the Ability of Edwardsiella ictaluri and Flavobacterium covae to Persist within Commercial Catfish Pond Sediments under Laboratory Conditions

Two prevalent bacterial diseases in catfish aquaculture are enteric septicemia of catfish and columnaris disease caused by Edwardsiella ictaluri and Flavobacterium covae, respectively. Chronic and recurring outbreaks of these bacterial pathogens result in significant economic losses for producers annually. Determining if these pathogens can persist within sediments of commercial ponds is paramount. Experimental persistence trials (PT) were conducted to evaluate the persistence of E. ictaluri and F. covae in pond sediments. Twelve test chambers containing 120 g of sterilized sediment from four commercial catfish ponds were inoculated with either E. ictaluri (S97-773) or F. covae (ALG-00-530) and filled with 8 L of disinfected water. At 1, 2, 4-, 6-, 8-, and 15-days post-inoculation, 1 g of sediment was removed, and colony-forming units (CFU) were enumerated on selective media using 6 × 6 drop plate methods. E. ictaluri population peaked on Day 3 at 6.4 ± 0.5 log₁₀ CFU g^-1. Correlation analysis revealed no correlation between the sediment physicochemical parameters and E. ictaluri log₁₀ CFU g^-1. However, no viable F. covae colonies were recovered after two PT attempts. Future studies to improve understanding of E. ictaluri pathogenesis and persistence, and potential F. covae persistence in pond bottom sediments are needed.

Isolation and characterization of autochthonous probiotics from skin mucus and their in vivo validation with dietary probiotic bacteria on growth performance and immunity of Labeo calbasu (Hamilton, 1822)

The present study was performed to isolate and identify antimicrobial bacteria from the skin mucus of Labeo calbasu and assess their effects as water additives alone and in synergism, with dietary probiotic bacteria Aneurinibacillus aneurinilyticus LC1 isolated from intestinal tracts of L. calbasu on physiology and survival of same fish. Eight treatments (T1-T8) were conducted in triplicate, containing 10 fishes (2.02 ± 0.01 g) in each treatment: T1, control group (diet without probiotics); T2-T4, a diet with water additive probiotics; Bacillus cereus LC1, B. albus LC7, and B. cereus LC10, respectively, at 1000 CFU ml^-1; T5, a diet with dietary probiotic A. aneurinilyticus at 3000 CFU g^-1, T6-T8, a diet with water additives Bacillus cereus LC1, B. albus LC7, and B. cereus LC10 at 1000 CFU ml^-1 along with dietary probiotic A. aneurinilyticus at 3000 CFU g^-1. Results revealed improved growth, nutritive physiology, immune response, water quality, and survival in fish of group T8 (fingerlings fed on a probiotic diet at 3000 CFU g^-1 and reared in holding water treated with skin mucus bacteria B. cereus LC10 at 1000 CFU g^-1) as compared to other treatments, suggesting autochthonous intestinal and cutaneous mucosal bacteria as robust candidates for their collective application in aquaculture.

The Pathogen Aeromonas salmonicida achromogenes Induces Fast Immune and Microbiota Modifications in Rainbow Trout

Environmental stressors can disrupt the relationship between the microbiota and the host and lead to the loss of its functions. Among them, bacterial infection caused by Aeromonas salmonicida, the causative agent of furunculosis, results in high mortality in salmonid aquaculture. Here, rainbow trout were exposed to A. salmonicida achromogenes and its effects on the taxonomic composition and structure of the microbiota was assessed on different epithelia (gills, skin, and caudal fin) at 6 and 72 h post-infection (hpi) using the V1-V3 region of the 16S rRNA sequencing. Moreover, the infection by the pathogen and immune gene responses were evaluated in the head kidney by qPCR. Our results suggested that α-diversity was highly diverse but predominated by a few taxa while β-diversity was affected very early by infection in the gills after 6 h, subsequently affecting the microbiota of the skin and caudal fin. A dysbiosis of the microbiota and an increase in genera known to be opportunistic pathogens (Aeromonas, Pseudomonas) were also identified. Furthermore, an increase in pro-inflammatory cytokines and virulence protein array (vapa) was observed in trout head kidney as soon as 6 hpi and remained elevated until 72 hpi, while the anti-inflammatory genes seemed repressed. This study suggests that the infection by A. salmonicida achromogenes can alter fish microbiota of gills in the few hours post-infection. This result can be useful to develop a non-invasive technique to prevent disease outbreak in aquaculture.

Isolation of vB_AsaM_LPM4 reveals the dynamics of Prophage 3 in Aeromonas salmonicida subsp. salmonicida

Aeromonas salmonicida subsp. salmonicida causes furunculosis, a major infection that affects fish farms worldwide. We isolated phage vB_AsaM_LPM4 (LPM4) from a diseased fish. Based on its DNA sequence, LPM4 is identical to the uncharacterized Prophage 3, a prophage present mostly in North American A. salmonicida subsp. salmonicida isolates that bear the genomic island AsaGEI2a. Prophage 3 and AsaGEI2a are inserted side by side in the bacterial chromosome. The LPM4/Prophage 3 sequence is similar to that of other prophages found in various members of the genus Aeromonas. LPM4 specifically infects A. salmonicida subsp. salmonicida strains that do not already bear Prophage 3. The presence of an A-layer on the surface of the bacteria is not necessary for the adsorption of phage LPM4 but seems to facilitate its infection process. We also successfully produced lysogenic strains that bear Prophage 3 using sensitive strains with different genetic backgrounds, suggesting that there is no interdependency between LPM4 and AsaGEIs. PCR analysis of the excision dynamics of Prophage 3 and AsaGEIs revealed that these genetic elements can spontaneously excise themselves from the bacterial chromosome independently of one another. Through the isolation and characterization of LPM4, this study reveals new facets of Prophage 3 and AsaGEIs.

Perturbation by Antimicrobial Bacteria of the Epidermal Bacterial Flora of Rainbow Trout in Flow-Through Aquaculture

The bacterial flora of the epidermal mucus of fish is closely associated with the host’s health and susceptibility to pathogenic infections. In this study, we analyzed the epidermal mucus bacteria of rainbow trout (Oncorhynchus mykiss) reared in flow-through aquaculture under environmental perturbations. Over ~2 years, the bacteria present in the skin mucus and water were analyzed based on the 16S rDNA sequences. The composition of the mucus bacterial community showed significant monthly fluctuations, with frequent changes in the dominant bacterial species. Analysis of the beta- and alpha-diversity of the mucus bacterial flora showed the fluctuations of the composition of the flora were caused by the genera Pseudomonas, Yersinia, and Flavobacterium, and some species of Pseudomonas and Yersinia in the mucus were identified as antimicrobial bacteria. Examination of the antimicrobial bacteria in the lab aquarium showed that the natural presence of antimicrobial bacteria in the mucus and water, or the purposeful addition of them to the rearing water, caused a transition in the mucus bacteria community composition. These results demonstrate that specific antimicrobial bacteria in the water or in epidermal mucus comprise one of the causes of changes in fish epidermal mucus microflora.

Community Structure and Functional Annotations of the Skin Microbiome in Healthy and Diseased Catfish, Heteropneustes fossilis

The skin mucosa of fish serves as a primary barrier against pathogens. In lesion sites in diseased fish, the mucosal barrier is expected to be compromised, with a substantial presence of potential pathogens. An understanding of the skin microbiome and its functional repertoire would provide important insights into host-microbe interactions, which has important implications for prophylactic measures in aquaculture. This study revealed the skin microbiomes and their functional annotations from healthy and diseased stinging catfish (Heteropneustes fossilis) based on 16S rRNA metagenomics. The OTUs consisted of four major phyla, Proteobacteria, Bacteroidota, Actinobacteriota and Firmicutes. Among members of the predominant phyla, Proteobacteria were rich in healthy fishes, but Bacteroidota and Firmicutes were significantly differentiated in healthy and diseased fish. The diversified microbiome was high in the skin of healthy fishes and did not significantly differ from that of the diseased groups. At the genus level, Pseudomonas showed the highest abundance in healthy fish but was nearly absent in diseased fish, whereas Flavobacterium showed the highest abundance in diseased fish. Linear discriminant analysis identified two phyla (Bacteroidota, Firmicutes) and two genera (Flavobacterium, Allorhizobium) that were consistently identified in diseased fishes. Functional prediction analysis specified that the genes related to physiological functions such as metabolism, immune and digestive systems and environmental adaptations could be highly expressed in diseased fishes. The present study indicates that the compositions, richness and functions of the bacterial community could influence the health status of cultured stinging catfish. Aquaculture-associated pathogenic bacteria may be identified, and preventive measures can be taken for the surveillance of fish health.

Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish

The microbial gut communities of fish are receiving increased attention for their relevance, among others, in a growing aquaculture industry. The members of these communities are often split into resident (long-term colonisers specialised to grow in and adhere to the mucus lining of the gut) and transient (short-term colonisers originated from food items and the surrounding water) microorganisms. Separating these two communities in small fish are impeded by the small size and fragility of the gastrointestinal tract. With the aim of testing whether it is possible to recover two distinct communities in small species of fish using a simple sampling technique, we used 16S amplicon sequencing of paired intestinal wall and digesta samples from three small Cyprinodontiformes fish. We examined the diversity and compositional variation of the two recovered communities, and we used joint species distribution modelling to identify microbes that are most likely to be a part of the resident community. For all three species we found that the diversity of intestinal wall samples was significantly lower compared to digesta samples and that the community composition between sample types was significantly different. Across the three species we found seven unique families of bacteria to be significantly enriched in samples from the intestinal wall, encompassing most of the 89 ASVs enriched in intestinal wall samples. We conclude that it is possible to characterise two different microbial communities and identify potentially resident microbes through separately analysing samples from the intestinal wall and digesta from small species of fish. We encourage researchers to be aware that different sampling procedures for gut microbiome characterization will capture different parts of the microbiome and that this should be taken into consideration when reporting results from such studies on small species of fish.

Assessment of Flavobacterium psychrophilum-associated mortality in Atlantic salmon (Salmo salar) and brook trout (Salvelinus fontinalis)

Salmonid diseases caused by infections of Flavobacterium psychrophilum, the causative agent of bacterial coldwater disease, remain difficult to manage as novel, pathogenic strains continue to emerge in aquaculture settings globally. To date, much of the research regarding treatment options and vaccine development has focused on rainbow trout (Oncorhynchus mykiss), but other inland-reared salmonids are also impacted by this Gram-negative bacterium. As such, Atlantic salmon (Salmo salar) and brook trout (Salvelinus fontinalis) were injection-challenged with a variety of previously reported F. psychrophilum strains isolated from disease diagnostic cases in salmonids, as well as a standard and well-studied F. psychrophilum strain (CSF 259-93) known to be virulent in rainbow trout. In three separate virulence assessments (Trials A, B and C), strains US063 (isolated from lake trout; Salvelinus namaycush) and US149 (isolated from Atlantic salmon) caused a significantly higher cumulative per cent mortality (CPM) relative to other strains in Atlantic salmon (p <.001 for all trials), with US149 causing significantly greater mortality than US063 in Trials A (CPM 97% vs. 65%, p =.008) and B (CPM 96% ± 2.3% vs. 81.33% ± 4.8%, p =.014). Trial C used a lower dose (1.86 × 10⁸  CFU/mL) for US149, resulting in a lower mortality (78.67% ± 9.33%) relative to Trials A and B. CSF259-93 did not cause significant mortality in any trials. In brook trout, the strain 03-179 (originally isolated from steelhead trout; Oncorhynchus mykiss) was significantly more virulent than any other (CPM 100% ± 0%, p <.001), followed by US063 (73% ± 3.8%) and US149 (40% ± 6.1%,) respectively. Again, CSF259-93 did not cause significant mortality relative to a mock challenge treatment. Results provide information about the applicability of strain selection in F. psychrophilum virulence testing in Atlantic salmon and brook trout, demonstrating the high virulence of US063 and US149 for these salmonid species. This information is applicable for the development of therapeutics and vaccines against F. psychrophilum infections and demonstrates the reproducibility of the experimental challenge model.

Interactions Between Commensal Microbiota and Mucosal Immunity in Teleost Fish During Viral Infection With SVCV

The mucosa of vertebrates is a particularly complex but dynamic environment in which the host constantly interacts with trillions of commensal microorganisms and pathogens. Although the internal and external mucosal microbiomes with immune defense of mammals have been well investigated, the relationship between mucosal microbes and their host’s immune responses has not been systematically understood in the early vertebrates. In this study, we compared the composition and distribution of mucosal microbiota in common carp (Cyprinus carpio), and found that there were significant differences of microbiota between in the internal (gut) and external mucosal (buccal mucosa, gills and skin) tissues. Next, we successfully constructed an infection model with spring viremia of carp virus (SVCV). Specifically, following viral infection, the immune and antiviral related genes showed different up-regulation in all selected mucosal tissues while significant morphological changes were only found in external tissues including buccal mucosa, gills and skin. Using 16S rRNA gene sequence, we revealed that the abundance of Proteobacteria in mucosal tissues including buccal mucosa, gills and gut showed increased trend after viral infection, whereas the abundance of Fusobacteria significantly decreased in gut. In addition, the loss of dominant commensal microorganisms and increased colonization of opportunistic bacteria were discovered in the mucosal surfaces indicating that a secondary bacterial infection might occur in these mucosal tissues after viral infection. Overall, our results firstly point out the distribution of internal and external mucosal microbiota and analyze the changes of mucosal microbiota in common carp after SVCV infection, which may indicated that the potential role of mucosal microbiota in the antiviral process in early vertebrates.

Skin bacteria of rainbow trout antagonistic to the fish pathogen Flavobacterium psychrophilum

Rainbow trout fry syndrome (RTFS) and bacterial coldwater disease (BCWD) is a globally distributed freshwater fish disease caused by Flavobacterium psychrophilum. In spite of its importance, an effective vaccine is not still available. Manipulation of the microbiome of skin, which is a primary infection gate for pathogens, could be a novel countermeasure. For example, increasing the abundance of specific antagonistic bacteria against pathogens in fish skin might be effective to prevent fish disease. Here, we combined cultivation with 16S rRNA gene amplicon sequencing to obtain insight into the skin microbiome of the rainbow trout (Oncorhynchus mykiss) and searched for skin bacteria antagonistic to F. psychrophilum. By using multiple culture media, we obtained 174 isolates spanning 18 genera. Among them, Bosea sp. OX14 and Flavobacterium sp. GL7 respectively inhibited the growth of F. psychrophilum KU190628-78 and NCIMB 1947^T, and produced antagonistic compounds of < 3 kDa in size. Sequences related to our isolates comprised 4.95% of skin microbial communities, and those related to strains OX14 and GL7 respectively comprised 1.60% and 0.17% of the skin microbiome. Comparisons with previously published microbiome data detected sequences related to strains OX14 and GL7 in skin of other rainbow trout and Atlantic salmon.

Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health

Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two case studies, that of toxic cyanobacteria and microplastics. Most studies to date are focused on host-associated microbiomes of individual organisms, however, few studies take an integrative approach to examine aquatic vertebrate microbiomes by considering both host-associated and free-living microbiota within an ecosystem. We highlight what is known about microbiota in aquatic ecosystems, with a focus on the interface between water, fish, and marine mammals. Though microbiomes in water vary with geography, temperature, depth, and other factors, core microbial functions such as primary production, nitrogen cycling, and nutrient metabolism are often conserved across aquatic environments. We outline knowledge on the composition and function of tissue-specific microbiomes in fish and marine mammals and discuss the environmental factors influencing their structure. The microbiota of aquatic mammals and fish are highly unique to species and a delicate balance between respiratory, skin, and gastrointestinal microbiota exists within the host. In aquatic vertebrates, water conditions and ecological niche are driving factors behind microbial composition and function. We also generate a comprehensive catalog of marine mammal and fish microbial genera, revealing commonalities in composition and function among aquatic species, and discuss the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems. We also discuss the importance of a focus on the functional relevance of microbial communities in relation to organism physiology and their ability to overcome stressors related to global change. Understanding the dynamic relationship between aquatic microbiota and the animals they colonize is critical for monitoring water quality and population health.

Gnotobiotic rainbow trout (Oncorhynchus mykiss) model reveals endogenous bacteria that protect against Flavobacterium columnare infection

The health and environmental risks associated with antibiotic use in aquaculture have promoted bacterial probiotics as an alternative approach to control fish infections in vulnerable larval and juvenile stages. However, evidence-based identification of probiotics is often hindered by the complexity of bacteria-host interactions and host variability in microbiologically uncontrolled conditions. While these difficulties can be partially resolved using gnotobiotic models harboring no or reduced microbiota, most host-microbe interaction studies are carried out in animal models with little relevance for fish farming. Here we studied host-microbiota-pathogen interactions in a germ-free and gnotobiotic model of rainbow trout (Oncorhynchus mykiss), one of the most widely cultured salmonids. We demonstrated that germ-free larvae raised in sterile conditions displayed no significant difference in growth after 35 days compared to conventionally-raised larvae, but were extremely sensitive to infection by Flavobacterium columnare, a common freshwater fish pathogen causing major economic losses worldwide. Furthermore, re-conventionalization with 11 culturable species from the conventional trout microbiota conferred resistance to F. columnare infection. Using mono-re-conventionalized germ-free trout, we identified that this protection is determined by a commensal Flavobacterium strain displaying antibacterial activity against F. columnare. Finally, we demonstrated that use of gnotobiotic trout is a suitable approach for the identification of both endogenous and exogenous probiotic bacterial strains protecting teleostean hosts against F. columnare. This study therefore establishes an ecologically-relevant gnotobiotic model for the study of host-pathogen interactions and colonization resistance in farmed fish.

Characterization of bacteriophage T7-Ah reveals its lytic activity against a subset of both mesophilic and psychrophilic Aeromonas salmonicida strains

Aeromonas salmonicida strains cause problematic bacterial infections in the aquaculture industry worldwide. The genus Aeromonas includes both mesophilic and psychrophilic species. Bacteriophages that infect Aeromonas spp. strains are usually specific for mesophilic or psychrophilic species; only a few bacteriophages can infect both types of strains. In this study, we characterized the podophage T7-Ah, which was initially found to infect the Aeromonas salmonicida HER1209 strain. The burst size of T7-Ah against its original host is 72 new virions per infected cell, and its burst time is 30 minutes. It has been found that this phage can lyse both mesophilic and psychrophilic A. salmonicida strains, as well as one strain of Escherichia coli. Its genome comprises 40,153 bp of DNA and does not contain any recognizable toxin or antibiotic resistance genes. The adsorption rate of the phage on highly sensitive bacterial strains was variable and could not be related to the presence or absence of a functional A-layer on the surface of the bacterial strains. The lipopolysaccharide migration patterns of both resistant and sensitive bacterial strains were also studied and compared to investigate the nature of the potential receptor of this phage on the bacterial surface. This study sheds light on the surprising diversity of lifestyles of the bacterial strains sensitive to phage T7-Ah and opens the door to the potential use of this phage against A. salmonicida infections in aquaculture.

Innate Immune Responses of Skin Mucosa in Common Carp (Cyprinus Carpio) Fed a Diet Supplemented with Galactooligosaccharides

Galactooligosaccharides (GOS) are well-known immunomodulatory prebiotics. We hypothesize that GOS supplemented in feed modulates innate immune responses in the skin-associated lymphoid tissue (SALT) of common carp. The aim of this study was to determine the impact of GOS on mRNA expression of the immune-related genes in skin mucosa. During the feeding trial, the juvenile fish (bodyweight 180 ± 5 g) were fed two types of diet for 50 days: control and supplemented with 2% GOS. At the end of the trial, a subset of fish was euthanized (n = 8). Skin mucosa was collected, and RNA was extracted. Gene expression analysis was performed with RT-qPCR to determine the mRNA abundance of the genes associated with innate immune responses in SALT, i.e., acute-phase protein (CRP), antimicrobial proteins (His2Av and GGGT5L), cytokines (IL1β, IL4, IL8, IL10, and IFNγ), lectin (CLEC4M), lyzosymes (LyzC and LyzG), mucin (M5ACL), peroxidase (MPO), proteases (CTSB and CTSD), and oxidoreductase (TXNL). The geometric mean of 40s s11 and ACTB was used to normalize the data. Relative quantification of the gene expression was calculated with ∆∆Ct. GOS upregulated INFγ (p ≤ 0.05) and LyzG (p ≤ 0.05), and downregulated CRP (p ≤ 0.01). We conclude that GOS modulates innate immune responses in the skin mucosa of common carp.

Environmental conditions and neutral processes shape the skin microbiome of European catfish (Silurus glanis) populations of Southwestern France

Teleost fishes interact with diverse microbial communities, playing crucial functions for host fitness. While gut microbiome has been extensively studied, skin microbiome has been overlooked. Specifically, there is no assessment of the relative impact of host and environmental factors on microbiome variability as well as neutral processes shaping fish skin microbiome. Here, we assessed the skin microbiome of a Siluriforme, the European catfish (Silurus glanis) sampled in four sites located in Southwestern France. We assessed the relative roles of individual features (body size and genetic background), local environment and neutral processes in shaping skin microbiome. Catfish skin microbiome composition was distinct to that of other freshwater fish species previously studied with high abundances of Gammaproteobacteria and Bacteroidetes. We found no effect of catfish individual genotype and body size on the structure of its associated skin microbiome. Geographical location was the best catfish skin microbiome structure predictor, together with neutral models of microbiome assembly.

Stimulated Growth and Innate Immunity in Brook Charr (Salvelinus fontinalis) Treated with a General Probiotic (Bactocell®) and Two Endogenous Probiotics That Inhibit Aeromonas salmonicida In Vitro

Aeromonas salmonicida subsp. salmonicida is a Gram-negative bacterium causing furunculosis, an opportunistic infection of farmed salmonid fish. Current treatment methods against furunculosis rely heavily on antibiotherapy. However, strains of this opportunistic fish pathogen were found to possess genes that confer resistance to major antibiotics including those used to cure furunculosis. Therefore, dispensing bacterial symbionts as probiotics to susceptible hosts appears to be a promising alternative. Here, we present the genomic characterization and in vivo safety assessment of two brook charr (Salvelinus fontinalis) bacterial symbionts that inhibited A. salmonicida subsp. salmonicida growth in vitro (Pseudomonas fluorescens ML11A and Aeromonas sobria TM18) as well as a commercialized probiotic, Pediococcus acidilactici MA18/5M (Bactocell^®). The genomic sequences of ML11A and TM18 obtained by whole-genome shotgun sequencing lack key virulence factor genes found in related pathogenic strains. Their genomic sequences are also devoid of genes involved in the inactivation (or target modification of) several key antimicrobial compounds used in salmonid aquaculture. Finally, when administered daily to live brook charr fingerlings, ML11A, TM18 and Bactocell^® helped improve several physiological condition metrics such as mean body weight, Fulton's condition factor and blood plasma lysozyme activity (an indicator for innate immune activity).

The Change of Teleost Skin Commensal Microbiota Is Associated With Skin Mucosal Transcriptomic Responses During Parasitic Infection by Ichthyophthirius multifillis

Teleost skin serves as the first line of defense against invading pathogens, and contain a skin-associated lymphoid tissue (SALT) that elicit gut-like immune responses against antigen stimulation. Moreover, exposed to the water environment and the pathogens therein, teleost skin is also known to be colonized by diverse microbial communities. However, little is known about the interactions between microbiota and the teleost skin mucosal immune system, especially dynamic changes about the interactions under pathogen infection. We hypothesized that dramatic changes of microbial communities and strong mucosal immune response would be present in the skin of aquatic vertebrate under parasite infection. To confirm this hypothesis, we construct an infected model with rainbow trout (Oncorhynchus mykiss), which was experimentally challenged by Ichthyophthirius multifiliis (Ich). H & E staining of trout skin indicates the successful invasion of Ich and shows the morphological changes caused by Ich infection. Critically, increased mRNA expression levels of immune-related genes were detected in trout skin from experimental groups using qRT-PCR, which were further studied by RNA-Seq analysis. Here, through transcriptomics, we detected that complement factors, pro-inflammatory cytokines, and antimicrobial genes were strikingly induced in the skin of infected fish. Moreover, high alpha diversity values of microbiota in trout skin from the experimental groups were discovered. Interestingly, we found that Ich infection led to a decreased abundance of skin commensals and increased colonization of opportunistic bacteria through 16S rRNA pyrosequencing, which were mainly characterized by lose of Proteobacteria and increased intensity of Flavobacteriaceae. To our knowledge, our results suggest for the first time that parasitic infection could inhibit symbionts and offer opportunities for other pathogens' secondary infection in teleost skin.

A Comparative Review on Microbiota Manipulation: Lessons From Fish, Plants, Livestock, and Human Research

During recent years the impact of microbial communities on the health of their host (being plants, fish, and terrestrial animals including humans) has received increasing attention. The microbiota provides the host with nutrients, induces host immune development and metabolism, and protects the host against invading pathogens (1-6). Through millions of years of co-evolution bacteria and hosts have developed intimate relationships. Microbial colonization shapes the host immune system that in turn can shape the microbial composition (7-9). However, with the large scale use of antibiotics in agriculture and human medicine over the last decades an increase of diseases associated with so-called dysbiosis has emerged. Dysbiosis refers to either a disturbed microbial composition (outgrowth of possible pathogenic species) or a disturbed interaction between bacteria and the host (10). Instead of using more antibiotics to treat dysbiosis there is a need to develop alternative strategies to combat disturbed microbial control. To this end, we can learn from nature itself. For example, the plant root (or "rhizosphere") microbiome of sugar beet contains several bacterial species that suppress the fungal root pathogen Rhizoctonia solani, an economically important fungal pathogen of this crop (11). Likewise, commensal bacteria present on healthy human skin produce antimicrobial molecules that selectively kill skin pathogen Staphylococcus aureus. Interestingly, patients with atopic dermatitis (inflammation of the skin) lacked antimicrobial peptide secreting commensal skin bacteria (12). In this review, we will give an overview of microbial manipulation in fish, plants, and terrestrial animals including humans to uncover conserved mechanisms and learn how we might restore microbial balance increasing the resilience of the host species.

Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet

BACKGROUND

The surface of marine animals is covered by abundant and diversified microbial communities, which have major roles for the health of their host. While such microbiomes have been deeply examined in marine invertebrates such as corals and sponges, the microbiomes living on marine vertebrates have received less attention. Specifically, the diversity of these microbiomes, their variability among species, and their drivers are still mostly unknown, especially among the fish species living on coral reefs that contribute to key ecosystem services while they are increasingly affected by human activities. Here, we investigated these knowledge gaps analyzing the skin microbiome of 138 fish individuals belonging to 44 coral reef fish species living in the same area.

RESULTS

Prokaryotic communities living on the skin of coral reef fishes are highly diverse, with on average more than 600 OTUs per fish, and differ from planktonic microbes. Skin microbiomes varied between fish individual and species, and interspecific differences were slightly coupled to the phylogenetic affiliation of the host and its ecological traits.

CONCLUSIONS

These results highlight that coral reef biodiversity is greater than previously appreciated, since the high diversity of macro-organisms supports a highly diversified microbial community. This suggest that beyond the loss of coral reefs-associated macroscopic species, anthropic activities on coral reefs could also lead to a loss of still unexplored host-associated microbial diversity, which urgently needs to be assessed.

Antimicrobial susceptibility of Flavobacterium psychrophilum isolates from the United Kingdom

Routine application of antimicrobials is the current treatment of choice for rainbow trout fry syndrome (RTFS) or bacterial coldwater disease (BCWD) caused by Flavobacterium psychrophilum. In this study, the antimicrobial susceptibilities of 133 F. psychrophilum isolates, 118 of which were from the UK, were evaluated by broth microdilution and disc diffusion methods following VET04-A2 and VET03-A guidelines of Clinical and Laboratory Standards Institute (CLSI), respectively. Isolates were categorized as wild type (fully susceptible, WT) or non-wild type (NWT) using normalized resistance interpretation (NRI)-determined cut-off values (CO_WT ). Broth microdilution testing showed that only 12% of UK isolates were WT to oxolinic acid (MIC CO_WT  ≤ 0.25 mg/L) and 42% were WT for oxytetracycline (MIC CO_WT  ≤ 0.25 mg/L). In contrast, all the isolates tested were WT (MIC CO_WT  ≤ 2 mg/L) for florfenicol, the main antimicrobial for RTFS control in the UK. Disc diffusion-based CO_WT values were ≥51 mm for 10 μg amoxicillin, ≥44 mm for 30 μg florfenicol, ≥30 mm for 2 μg oxolinic acid and ≥51 mm for 30 μg oxytetracycline. There was a high categorical agreement between the classifications of the isolates by two testing methods for florfenicol (100%), oxytetracycline (93%) and oxolinic acid (99%).

Strong Genomic and Phenotypic Heterogeneity in the Aeromonas sobria Species Complex

Aeromonas sobria is a mesophilic motile aeromonad currently depicted as an opportunistic pathogen, despite increasing evidence of mutualistic interactions in salmonid fish. However, the determinants of its host-microbe associations, either mutualistic or pathogenic, remain less understood than for other aeromonad species. On one side, there is an over-representation of pathogenic interactions in the A. sobria literature, of which only three articles to date report mutualistic interactions; on the other side, genomic characterization of this species is still fairly incomplete as only two draft genomes were published prior to the present work. Consequently, no study specifically investigated the biodiversity of A. sobria. In fact, the investigation of A. sobria as a species complex may have been clouded by: (i) confusion with A. veronii biovar sobria because of their similar biochemical profiles, and (ii) the intrinsic low resolution of previous studies based on 16S rRNA gene sequences and multilocus sequence typing. So far, the only high-resolution, phylogenomic studies of the genus Aeromonas included one A. sobria strain (CECT 4245 / Popoff 208), making it impossible to robustly conclude on the phylogenetic intra-species diversity and the positioning among other Aeromonas species. To further understand the biodiversity and the spectrum of host-microbe interactions in A. sobria as well as its potential genomic diversity, we assessed the genomic and phenotypic heterogeneity among five A. sobria strains: two clinical isolates recovered from infected fish (JF2635 and CECT 4245), one from an infected amphibian (08005) and two recently isolated brook charr probionts (TM12 and TM18) which inhibit in vitro growth of A. salmonicida subsp. salmonicida (a salmonid fish pathogen). A phylogenomic assessment including 2,154 softcore genes corresponding to 946,687 variable sites from 33 Aeromonas genomes confirms the status of A. sobria as a distinct species divided in two subclades, with 100% bootstrap support. The phylogenomic split of A. sobria in two subclades is corroborated by a deep dichotomy between all five A. sobria strains in terms of inhibitory effect against A. salmonicida subsp. salmonicida, gene contents and codon usage. Finally, the antagonistic effect of A. sobria strains TM12 and TM18 suggests novel control methods against A. salmonicida subsp. salmonicida.

Walleye Autochthonous Bacteria as Promising Probiotic Candidates against Flavobacterium columnare

Walleye (Sander vitreus) is the second most fished freshwater species in Canada. While much sought by anglers, walleye also supports substantial commercial fisheries. To cope with the recent decline of wild walleye populations, fish farmers produce juveniles for lake stocking. However, walleye breeding is particularly tedious, mostly due to high disease susceptibility at larval and juvenile developmental stages. The main threat is the columnaris disease, which is caused by Flavobacterium columnare, an opportunistic bacteria. As F. columnare strains exhibit increasing antibiotic resistance, there is a strong need to develop efficient and sustainable alternative strategies to control columnaris disease. Bacterial probiotics have been shown to mitigate infections either by enhancing host immune response or by inhibiting pathogen growth. Being successfully assessed in many fish/pathogen combinations, we developed a tailored probiotic strategy for walleye to prevent and treat columnaris disease. Thirty-seven endogenous bacterial strains were isolated from healthy walleye’s skin and gut, were tested in vitro against F. columnare. Significant antagonistic effect against F. columnare was measured for 2 out of 37 endogenous strains. These two probiotic strains were identified as Pseudomonas fluorescens. The antagonistic effect of these two successful probiotics was further validated in vivo during a 2-month stress trial: groups receiving probiotic treatments showed on average 53.74% survival improvement.

Salmonid alphavirus infection causes skin dysbiosis in Atlantic salmon (Salmo salar L.) post-smolts

Interactions among host, microbiota and viral pathogens are complex and poorly understood. The goal of the present study is to assess the changes in the skin microbial community of Atlantic salmon (Salmo salar L.) in response to experimental infection with salmonid alphavirus (SAV). The salmon skin microbial community was determined using 16S rDNA pyrosequencing in five different experimental groups: control, 7 days after infection with low-dose SAV, 14 days after infection with low-dose SAV, 7 days after infection with high-dose SAV, and 14 days after infection with high-dose SAV. Both infection treatment and time after infection were strong predictors of the skin microbial community composition. Skin samples from SAV3 infected fish showed an unbalanced microbiota characterized by a decreased abundance of Proteobacteria such as Oleispira sp. and increased abundances of opportunistic taxa including Flavobacteriaceae, Streptococcaceae and Tenacibaculum sp. These results demonstrate that viral infections can result in skin dysbiosis likely rendering the host more susceptible to secondary bacterial infections.

Draft Genome Sequence of Pseudomonas fluorescens ML11A, an Endogenous Strain from Brook Charr with Antagonistic Properties against Aeromonas salmonicida subsp. salmonicida

Pseudomonas fluorescens ML11A, isolated from brook charr, showed a strong in vitro inhibitory effect against Aeromonas salmonicida subsp. salmonicida, a bacterial fish pathogen. Its genome harbors gene clusters for siderophore and bacteriocin biosynthesis and shares 99% whole-genome identity with P. fluorescens A506, a biological control strain used in agriculture.

Temporal Stability and the Effect of Transgenerational Transfer on Fecal Microbiota Structure in a Long Distance Migratory Bird

Animal bodies are inhabited by a taxonomically and functionally diverse community of symbiotic and commensal microorganisms. From an ecological and evolutionary perspective, inter-individual variation in host-associated microbiota contributes to physiological and immune system variation. As such, host-associated microbiota may be considered an integral part of the host’s phenotype, serving as a substrate for natural selection. This assumes that host-associated microbiota exhibits high temporal stability, however, and that its composition is shaped by trans-generational transfer or heritable host-associated microbiota modulators encoded by the host genome. Although this concept is widely accepted, its crucial assumptions have rarely been tested in wild vertebrate populations. We performed 16S rRNA metabarcoding on an extensive set of fecal microbiota (FM) samples from an insectivorous, long-distance migratory bird, the barn swallow (Hirundo rustica). Our data revealed clear differences in FM among juveniles and adults as regards taxonomic and functional composition, diversity and co-occurrence network complexity. Multiple FM samples from the same juvenile or adult collected within single breeding seasons exhibited higher similarity than expected by chance, as did adult FM samples over two consecutive years. Despite low effect sizes for FM stability over time at the community level, we identified an adult FM subset with relative abundances exhibiting significant temporal consistency, possibly inducing long-term effects on the host phenotype. Our data also indicate a slight maternal (but not paternal) effect on FM composition in social offspring, though this is unlikely to persist into adulthood. We discuss our findings in the context of both evolution and ecology of microbiota vs. host interactions and barn swallow biology.

Standardizing the microbiota of fish used in research

Little attention has been paid to the effects of fish microbiotas on the reproducibility and comparability of fish studies so far. Extrinsic and intrinsic factors, such as water quality, environmental microbial populations, diet, host genetic profile, gender, age and stress status, affect fish microbiotas and create significant inter- and intra-species variations. Fish microbiotas play critical roles in many key aspects of host physiology, such as protection against pathogens, digestion and development of the digestive tract and the local immune system. Thus, greater effort should be invested in standardizing the microbiological profiles of research fish. In this context, issues requiring consideration include the establishment of isogenic and isobiotic fish lines, the standardization of rearing conditions and the development of appropriate tests to adequately describe microbial populations. There are many challenges involved in each of these issues, and the research community must decide which aspects should be standardized for each species and each type of research. For all studies in which microbiota is expected to exert an influence, thorough reporting is of paramount importance. Every step towards standardization increases study quality and simultaneously contributes to reducing the number of fish used in research, which is a legal and ethical obligation.

Effects of host genetics and environment on egg-associated microbiotas in brown trout (Salmo trutta)

Recent studies found fish egg-specific bacterial communities that changed over the course of embryogenesis, suggesting an interaction between the developing host and its microbiota. Indeed, single-strain infections demonstrated that the virulence of opportunistic bacteria is influenced by environmental factors and host immune genes. However, the interplay between a fish embryo host and its microbiota has not been studied yet at the community level. To test whether host genetics affects the assemblage of egg-associated bacteria, adult brown trout (Salmo trutta) were sampled from a natural population. Their gametes were used for full-factorial in vitro fertilizations to separate sire from dam effects. In total, 2520 embryos were singly raised under experimental conditions that differently support microbial growth. High-throughput 16S rRNA amplicon sequencing was applied to characterize bacterial communities on milt and fertilized eggs across treatments. Dam and sire identity influenced embryo mortality, time until hatching and composition of egg-associated microbiotas, but no link between bacterial communities on milt and on fertilized eggs could be found. Elevated resources increased embryo mortality and modified bacterial communities with a shift in their putative functional potential. Resource availability did not significantly affect any parental effects on embryo performance. Sire identity affected bacterial diversity that turned out to be a significant predictor of hatching time: embryos associated with high bacterial diversity hatched later. We conclude that both host genetics and the availability of resources define diversity and composition of egg-associated bacterial communities that then affect the life history of their hosts.

Potassium permanganate elicits a shift of the external fish microbiome and increases host susceptibility to columnaris disease

The external microbiome of fish is thought to benefit the host by hindering the invasion of opportunistic pathogens and/or stimulating the immune system. Disruption of those microbial communities could increase susceptibility to diseases. Traditional aquaculture practices include the use of potent surface-acting disinfectants such as potassium permanganate (PP, KMnO₄) to treat external infections. This study evaluated the effect of PP on the external microbiome of channel catfish and investigated if dysbiosis leads to an increase in disease susceptibility. Columnaris disease, caused by Flavobacterium columnare, was used as disease model. Four treatments were compared in the study: (I) negative control (not treated with PP nor challenged with F. columnare), (II) treated but not challenged, (III) not treated but challenged, and (IV) treated and challenged. Ribosomal intergenic spacer analysis (RISA) and pyrosequencing were used to analyze changes in the external microbiome during the experiment. Exposure to PP significantly disturbed the external microbiomes and increased catfish mortality following the experimental challenge. Analysis of similarities of RISA profiles showed statistically significant changes in the skin and gill microbiomes based on treatment and sampling time. Characterization of the microbiomes using 16S rRNA gene pyrosequencing confirmed the disruption of the skin microbiome by PP at different phylogenetic levels. Loss of diversity occurred during the study, even in the control group, but was more noticeable in fish subjected to PP than in those challenged with F. columnare. Fish treated with PP and challenged with the pathogen exhibited the least diverse microbiome at the end of the study.

Variable Number of Tandem Repeats (VNTR) analysis of Flavobacterium psychrophilum from salmonids in Chile and Norway

Background

Flavobacterium psychrophilum causes serious fish diseases such RTFS and BCWD, affecting the aquaculture industry worldwide. Commercial vaccines are not available and control of the disease depends on the use of antibiotics. Reliable methods for detection and identification of different isolates of this bacterium could play an important role in the development of good management strategies. The aim of this study was to identify genetic markers for discrimination between isolates. A selection of eight VNTRs from 53 F. psychrophilum isolates from Norway, Chile, Denmark and Scotland were analyzed. The results were compared with previous work on the same pathogen using MLST for genetic differentiation.

Results

The VNTR analysis gave a separation between the F. psychrophilum isolates supporting the results of previous MLST work. A higher diversity was found among the Chilean isolates compared to those from Norway, which suggests a more homogenous reservoir in Norway. Transgenerational transmission of F. psychrophilum from other countries, exporting salmon embryos to Chile, may explain the differences in diversity. The same transmission mechanisms could also explain the wide geographical distribution of identical isolates in Norway. But, this could also be a result of movement of smolts and embryos. The selected VNTRs are stable genetic markers and no variation was observed after several passages on agar plates at different temperatures.

Conclusions

These VNTRs are important additions for genotyping of F. psychrophilum isolates. Future studies on VNTRs of F. psychrophilum should include isolates from more host species from a wider geographical area. To get a more robust genotyping the VNTRs should be used in concert with MLST. Future studies of isolates with high and low virulence should focus on identifying virulence markers using VTNRs and MLST.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-015-0469-7) contains supplementary material, which is available to authorized users.

High diversity of skin-associated bacterial communities of marine fishes is promoted by their high variability among body parts, individuals and species

Animal-associated microbiotas form complex communities, which are suspected to play crucial functions for their host fitness. However, the biodiversity of these communities, including their differences between host species and individuals, has been scarcely studied, especially in case of skin-associated communities. In addition, the intraindividual variability (i.e. between body parts) has never been assessed to date. The objective of this study was to characterize skin bacterial communities of two teleostean fish species, namely the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata), using a high-throughput DNA sequencing method. In order to focus on intrinsic factors of host-associated bacterial community variability, individuals of the two species were raised in controlled conditions. Bacterial diversity was assessed using a set of four complementary indices, describing the taxonomic and phylogenetic facets of biodiversity and their respective composition (based on presence/absence data) and structure (based on species relative abundances) components. Variability of bacterial diversity was quantified at the interspecific, interindividual and intraindividual scales. We demonstrated that fish surfaces host highly diverse bacterial communities, whose composition was very different from that of surrounding bacterioplankton. This high total biodiversity of skin-associated communities was supported by the important variability, between host species, individuals and the different body parts (dorsal, anal, pectoral and caudal fins).

Inter individual variations of the fish skin microbiota: host genetics basis of mutualism?

The commensal microbiota of fish skin is suspected to provide a protection against opportunist infections. The skin of fish harbors a complex and diverse microbiota that closely interacts with the surrounding water microbial communities. Up to now there is no clear evidence as to whether the host regulates the recruitment of environmental bacteria to build a specific skin microbiota. To address this question, we detected Quantitative Trait Loci (QTL) associated with the abundance of specific skin microbiota bacterial strains in brook charr (Salvelinus fontinalis), combining 16S RNA tagged-amplicon 454 pyrosequencing with genetic linkage analysis. Skin microbiota analysis revealed high inter-individual variation among 86 F2 fish progeny based upon the relative abundance of bacterial operational taxonomic units (OTUs). Out of those OTUs, the pathogenic strain Flavobacterium psychrophilum and the non-pathogenic strain Methylobacterium rhodesianum explained the majority of inter-individual distances. Furthermore, a strong negative correlation was found between Flavobacterium and Methylobacterium, suggesting a mutually competitive relationship. Finally, after considering a total of 266 markers, genetic linkage analysis highlighted three major QTL associated with the abundance of Lysobacter, Rheinheimera and Methylobacterium. All these three genera are known for their beneficial antibacterial activity. Overall, our results provide evidence that host genotype may regulate the abundance of specific genera among their surface microbiota. They also indicate that Lysobacter, Rheinheimera and Methylobacterium are potentially important genera in providing protection against pathogens.

Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries

Indigenous microbiota play a critical role in the lives of their vertebrate hosts. In human and mouse models it is increasingly clear that innate and adaptive immunity develop in close concert with the commensal microbiome. Furthermore, several aspects of digestion and nutrient metabolism are governed by intestinal microbiota. Research on teleosts has responded relatively slowly to the introduction of massively parallel sequencing procedures in microbiomics. Nonetheless, progress has been made in biotic and gnotobiotic zebrafish models, defining a core microbiome and describing its role in development. However, microbiome research in other teleost species, especially those important from an aquaculture perspective, has been relatively slow. In this review, we examine progress in teleost microbiome research to date. We discuss teleost microbiomes in health and disease, microbiome ontogeny, prospects for successful microbiome manipulation (especially in an aquaculture setting) and attempt to identify important future research themes. We predict an explosion in research in this sector in line with the increasing global demand for fish protein, and the need to find sustainable approaches to improve aquaculture yield. The reduced cost and increasing ease of next generation sequencing technologies provides the technological backing, and the next 10 years will be an exciting time for teleost microbiome research.

Network analysis highlights complex interactions between pathogen, host and commensal microbiota

Interactions between bacteria and their host represent a full continuum from pathogenicity to mutualism. From an evolutionary perspective, host-bacteria relationships are no longer considered a two-component system but rather a complex network. In this study, we focused on the relationship between brook charr (Salvelinus fontinalis) and bacterial communities developing on skin mucus. We hypothesized that stressful conditions such as those occurring in aquaculture production induce shifts in the bacterial community of healthy fish, thus allowing pathogens to cause infections. The results showed that fish skin mucus microbiota taxonomical structure is highly specific, its diversity being partly influenced by the surrounding water bacterial community. Two types of taxonomic co-variation patterns emerged across 121 contrasted communities’ samples: one encompassing four genera well known for their probiotic properties, the other harboring five genera mostly associated with pathogen species. The homeostasis of fish bacterial community was extensively disturbed by induction of physiological stress in that both: 1) the abundance of probiotic-like bacteria decreased after stress exposure; and 2) pathogenic bacteria increased following stress exposure. This study provides further insights regarding the role of mutualistic bacteria as a primary host protection barrier.

Probiotic treatment by indigenous bacteria decreases mortality without disturbing the natural microbiota of Salvelinus fontinalis

Next-generation sequencing is revealing the complex interactive networks of host-bacteria interactions, as it is now possible to screen in detail the microbiota harbored by a host. This study investigated the influence of a probiotic treatment on the survival and microbiota of brook charr (Salvelinus fontinalis), focusing on its disturbance of the natural microbiota (dysbiosis). The results indicated that an indigenous probiotic strain (identified as Rhodococcus sp.) colonized neither the fish skin mucus nor the water following the probiotic treatment. Instead, the probiotic strain was detected only in the biofilm of the test tank. Nevertheless, a substantial beneficial effect of the probiotic treatment was observed: the population of the pathogen Flavobacterium psychrophilum decreased in the treated tank water. This study clearly shows that the indigenous strain chosen for the probiotic treatment did not disturb the natural fish skin mucus microbiota but acted directly through the production system to control the growth of the pathogen and, as a consequence, to enhance fish survival.

Columnaris disease in fish: a review with emphasis on bacterium-host interactions

Flavobacterium columnare (F. columnare) is the causative agent of columnaris disease. This bacterium affects both cultured and wild freshwater fish including many susceptible commercially important fish species. F. columnare infections may result in skin lesions, fin erosion and gill necrosis, with a high degree of mortality, leading to severe economic losses. Especially in the last decade, various research groups have performed studies aimed at elucidating the pathogenesis of columnaris disease, leading to significant progress in defining the complex interactions between the organism and its host. Despite these efforts, the pathogenesis of columnaris disease hitherto largely remains unclear, compromising the further development of efficient curative and preventive measures to combat this disease. Besides elaborating on the agent and the disease it causes, this review aims to summarize these pathogenesis data emphasizing the areas meriting further investigation.