Changes in the gut microbiome of the Chinese mitten crab (Eriocheir sinensis) in response to White spot syndrome virus (WSSV) infection

Intestinal microorganisms play important roles in maintaining host health, but their functions in aquatic animal hosts have yet to be fully elucidated. The Chinese mitten crab, Eriocheir sinensis, is one such example. We attempted to identify the shift of gut microbiota that occurred in response to infection of white spot syndrome virus (WSSV), an emerging viral pathogen in the crab aquaculture industry. The microbiota may exert some control over aspects of the viral pathogenesis. We investigated the changes in composition and structure of the crab gut microbiome during various WSSV infection stages of 6 h post‐infection (hpi) and 48 hpi, using a 16S rRNA approach on the MiSeq Illumina sequencing platform. Four phyla (Firmicutes, Proteobacteria, Tenericutes and Bacteroidetes) were most dominant in the gut of E. sinensis regardless of the WSSV infection stages. However, further analysis revealed that over 12 bacterial phyla, 44 orders and 68 families were significantly different in abundance at various states of WSSV infection. Several intriguing aspects of E. sinensis gut bacteria that had not been previously reported were also uncovered, such as class Mollicutes was dominant here, but absent in crabs from Yangtze River estuary and Chongming Islands. Overall, this study provided the first evidence that changes in gut microbiome were closely associated with the severity of WSSV infection and that indicator taxa could be used to evaluate the crab health status.     

Response of the intestinal mucosal barrier of carp (Cyprinus carpio) to a bacterial challenge by Aeromonas hydrophila intubation after feeding with β‐1,3/1,6‐glucan

The effect of dietary β‐glucan on the bacterial community in the gut of common carp (Cyprinus carpio) was examined after oral application of Aeromonas hydrophila. Carp received either feed supplemented with 1% MacroGard^®, a β‐1,3/1,6‐glucan, or a β‐glucan‐free diet. Fourteen days after feeding, half of the carp from each group were intubated with 10⁹ colony‐forming units (CFU) of a pathogenic strain of A. hydrophila. Gut samples were taken 12 hr to 7 days after application and analysed using microbiological and molecular biological techniques (NGS, RT‐PCR‐DGGE). The reaction of the mucosa and the microbiota to an A. hydrophila intubation differed in carp fed with β‐glucan compared to carp from the control group. In β‐glucan fed carp, the total bacterial amount was lower but the number of bacterial species was higher. Bacterial composition was different for carp from both treatment groups. The number of mucin filled goblet cells was reduced in carp fed the β‐glucan diet. Mucus was obviously released from the goblet cells and was probably washed out of the gut together with high numbers of bacteria. This might be protective against pathogenic bacteria and, therefore, feeding with β‐glucan may provide protection against infections of the gut in carp.     

Formulated diet alters gut microbiota compositions in marine fish Nibea coibor and Nibea diacanthus

Nibea, an economical marine fish, is generally fed on trash fish (the low‐value fish), which can cause high feed costs and waste pollutions in high‐density aquaculture. To assess the effect of formulated diet on the gut microbiota in Nibea coibor and Nibea diacanthus, denaturing gradient gel electrophoresis, clone libraries analysis and Illumina sequencing of the 16S ribosomal RNA gene were used in this study. Two Nibea fishes were both dominated by Gammaproteobacteria (especially Photobacterium) and shared a set of gut microbiota, including Bacilli, Mollicutes, Alphaproteobacteria and Fusobacteriia. Statistical analyses revealed that formulated diet led to lower feed conversion ratio (p < 0.001), lower abundance of Vibrio (p = 0.040) and infectious diseases pathways (p = 0.001), higher abundance of polysaccharide‐degrading bacterium Cellvibrio (p = 0.006) in two Nibea species, with higher weight gain rate (p = 0.023) and microbial diversity (Shannon, p = 0.049 and Simpson, p = 0.044) and more carbohydrate metabolism (p = 0.020) observed in N. coibor. The distribution and correlation network of 17 potential short‐chain fatty acid producing bacteria were obtained and visualized in all treatment groups. The results reveal that formulated diet has beneficial effects on the gut microbial ecology in two Nibea fishes, which suggests the possibility of replacing trash fish diet with formulated diet in Nibea aquaculture.     

Effect of Arthrospira supplementation on Oreochromis niloticus gut microbiota and flesh quality

Supplementing fish feed with Arthrospira platensis has several beneficial effects, such as improved growth, survival and feed conversion, but little is known about how it affects gut microbiota or flesh quality. In this trial, feed with 3% A. platensis was given to Oreochromis niloticus (SPR, spirulina supplemented) over a period of 50 days and their gut microbiota and flesh quality were compared with controls (CTRs, no supplementation). Average daily growth was higher in SPR fish (p < 0.05). Regarding microbiota, a total of 5,470,272 readings (individuals) were obtained from 16 gut samples (n = 8 CTR, n = 8 SPR), with a gamma diversity of 1,563 species but no significant differences were found between treatments. Among the high inter‐individual variability found, some individual microbiota were dominated by Proteobacteria (36.6%) and Fusobacteria (32.9%) and others more by Actinobacteria (37%). Regarding flesh quality, significant differences were observed in flesh colour post‐mortem (a*, b* and chroma) (p < 0.05), with higher reflectance in the range of 470–500 and 620–670 nm in SPR tilapia, which corresponds with the reflectance range of β‐carotene and phycocyanin. However, rigor mortis was resolved earlier in SPR fish (p < 0.05), which suggests a shorter shelf life. Adding 3% of A. platensis in O. niloticus diet can improve growth and flesh colour and does not appear to modify intestinal microbiota.     

Microbial communities associated with early stages of intensively reared orange‐spotted grouper (Epinephelus coioides)

The gut microbiota plays key roles in the health and general welfare of fish larvae, the present study characterized the bacterial communities associated with grouper Epinephelus coioides larvae during a period of 22 days post hatch (DPH) in an intensive hatchery using both cultivation‐based and cultivation‐independent approaches. Both approaches confirmed that bacteria were present in the gut of larvae before and after the onset of exogenous feeding, and the number of cultiviable bacteria increased gradually from 2 DPH to 22 DPH. A more complex bacterial profile was present in larvae fed fertilizer oyster eggs for 4 days (8 DPH), probably as a result of the onset of exogenous feeding. Interestingly, similar internal microbiota were observed in larvae fed fertilized oyster eggs for 4 days (8 DPH) and rotifers for 2 weeks (22 DPH), although different microbial communities were present in the two feeds. This might suggest that the gut environment of E. coioides larvae selects for a common microbiota, which is more closely related with the rearing water than the two feeds. Therefore, bacterial community of the rearing water may play a critical role in the establishment of gut microbiota of fish larvae and more attention should be paid to its practical modulation by using probiotics. In addition, some potentially beneficial bacteria, such as Lactococcus spp., were the major components of the microbiota associated with fertilized oyster eggs, while these bacteria were not detected in larvae samples.     

Rhodopseudomonas palustris in effluent enhances the disease resistance,TOR and NF‐κB signalling pathway,intestinal microbiota and aquaculture water quality of Pelteobagrus vachelli

The use of traditional bait and medicament in freshwater aquaculture exacerbates environmental pollution and leads to frequent occurrence of diseases. Effluent collected after Rhodopseudomonas palustris‐mediated wastewater treatment could be reutilized as microbial feeds, medicament and aquaculture water to culture Pelteobagrus vachelli. Therefore, a novel integrated system of wastewater treatment using effluent containing R. palustris that improves yield, increases disease resistance and enhances the quality of aquaculture water for P. vachelli culture was proposed and investigated. P. vachelli can grow well in effluent containing R. palustris (ER). The survival rate, yield and whole‐body composition of the ER group were all increased compared to those of the control group (CK). The biochemical (B vitamin) and other substances in the effluent of R. palustris enhanced the activity of proteases, amylases, lipases, alkaline phosphatase (AKP), acid phosphatase (ACP), phagocytic, superoxide dismutase (SOD) and catalase (CAT) by up‐regulating the expression of AKP, ACP, SOD and CAT genes. Theoretical analysis showed that biochemical substances regulated the expression of these genes and enzyme activities as stimulus signal, component and active centre. Moreover, R. palustris and biochemical substances improved the target of rapamycin (TOR) and nuclear factor kappa B (NF‐κB) signalling pathways and intestinal microbiota. Furthermore, R. palustris inhibited Aeromonas hydrophila, which increased resistance to fish diseases and promoted the growth of intestinal probiotics. Meanwhile, R. palustris in effluent also purified the quality of aquaculture water. Use of this technology simultaneously helped improve aquaculture water quality, reduce water pollution and wastewater discharge and increased the output and disease resistance of P. vachelli.     

Influence of different dietary carbohydrate sources on the growth and intestinal microbiota of Litopenaeus vannamei at low salinity

Because of the increasing market potential of Pacific white shrimp (Litopenaeus vannamei) and limited availability of coastal areas for production, culture of L. vannamei at low salinity is a growing trend throughout the world. Dietary manipulation could improve the growth performance of L. vannamei at low salinity. This study reared L. vannamei with glucose, sucrose and corn starch as dietary carbohydrate sources, respectively, at a low salinity. The results indicated that the sucrose and glucose feeding groups showed better growth performance. An Illumina‐based sequencing method was used to examine the intestinal bacterial composition and the results indicated that Proteobacteria were the most prevalent members, but abundance of Actinobacteria decreased while Firmicutes increased in the corn starch‐fed group. Furthermore, bacteria related to complex carbohydrate degradation were in lower abundance, whereas the abundance of opportunistic pathogenic bacteria increased in corn starch‐fed group than the other two groups, suggesting that the diet imposes selective pressure on the intestinal microbiota. Complex carbohydrates were not the ideal energy sources for L. vannamei at low salinity because the host has higher energy demand in the stressful conditions while the complex carbohydrate degradation efficiency of the gut microbiota in L. vannamei is limited.     

A metabolomic investigation into the temperature‐dependent virulence of Pseudomonas plecoglossicida from large yellow croaker (Pseudosciaena crocea)

Pseudomonas plecoglossicida is associated with multiple fish diseases, and temperature is one of the most important environmental factors related to its outbreak. To elucidate the influence of temperature variation on the pathogen, the global metabolomics of P. plecoglossicida (NZBD9) were analysed at the virulent (18°C) and avirulent (12°C and 28°C) temperatures. The result showed that the levels of Phosphoric acid, Tyrosine, Spermidine and Sucrose were significantly reduced,while Itaconic acid, Glucaric acid and Isomaltose were increased in P. plecoglossicida at 18°C. These metabolic adjustments assist P. plecoglossicida to survive in adverse environments, proliferate in the host, colonize and resist host immune clearance during the initial steps of infection. The results suggested that L321_03626 and L321_18122 genes played a key role in the regulation of these metabolic adaptions and thus regulated P. plecoglossicida virulence at virulent temperature, which was proved by further gene silencing and artificial infection. The present study, for the first time, determines the P. plecoglossicida metabolomic responses to temperature variation, which is helpful to explore its pathogenic mechanism and provides reference for disease control.     

Diversity of autochthonous bacterial communities in the intestinal mucosa of grass carp (Ctenopharyngodon idellus) (Valenciennes) determined by culture‐dependent and culture‐independent techniques

Traditional culture‐based technique and 16S rDNA sequencing method were used to investigate the mucosa‐associated autochthonous microbiota of grass carp (Ctenopharyngodon idellus). Twenty‐one phylotypes were detected from culturable microbiota, with Aeromonas, Shewanella, Lactococcus, Serratia, Brevibacillus, Delftia, Pseudomonas, Pantoea, Enterobacter, Buttiauxella and Yersinia as their closest relatives. Genomic DNA was directly extracted from the gut mucosa of C. idellus originating from six different geographical regions, and used to generate 609 random bacterial clones from six clone libraries and 99 archaeal clones from one library, which were grouped into 67 bacterial and four archaeal phylotypes. Sequence analysis revealed that the intestinal mucosa harboured a diversified bacterial microbiota, where Proteobacteria, Firmicutes and Bacteroidetes were dominant, followed by Actinobacteria, Verrucomicrobia and Deinococcus‐Thermus. The autochthonous bacterial communities in the gut mucosa of fish from different aquatic environments were not similar (C_s < 0.80), but γ‐Proteobacteria was a common bacterial class. In comparison to bacterial communities, the archaeal community obtained from one library consisted of Crenarchaeota and Euryarchaeota. These results demonstrate that molecular methods facilitate culture‐independent studies, and that fish gut mucosa harbours a larger bacterial diversity than previously recognized. The grass carp intestinal habitat selects for specific bacterial taxa despite pronounced differences in host environments.     

Mucus piRNAs profiles of Vibrio harveyi-infected Cynoglossus semilaevis: A hint for fish disease monitoring

The half-smooth tongue sole, Cynoglossus semilaevis, is an important cultured flatfish species. Vibrio harveyi is a common pathogen to this fish, which may result in great economic loss to C. semilaevis culture industry. piRNAs, a non-coding RNAs with 26–32 nt, have been regarded as promising biomarkers for cancer diagnosis and fish diseases. Here, we extracted the RNA from mucus of C. semilaevis and constructed the differential expression profiles of piRNAs between the sick fish (MS) and healthy fish (MC). We identified 45,696 differentially expressed piRNAs including 22,735 up-regulated piRNAs and 22,961 down-regulated piRNAs in MS group compared with MC group. The GO enrichment and KEGG pathway enrichment analyses of the differential piRNAs were carried out. The result showed immunity-related target genes mainly involved in immune system process, response to stimulus, cell killing, immune system, infectious diseases and cell growth and death. The 10 most differentially expressed piRNAs were chosen to perform the qRT-PCR, while only seven piRNAs were consistent with the sequence result. Compared with MC group, the expression levels of piR-mmu-72173>piR-rno-62831>piR-xtr-704880, piR-dme-15546979, piR-mmu-49941660, piR-mmu-29283297 and piR-mmu-1758399 were significantly lower, and piR-gga-10574 and piR-gga-134812 were significantly higher in MS group. These piRNAs may be potential biomarkers during the V. harveyi infection of C. semilaevis. This study could provide a new method to identify the infection status of C. semilaevis and understand better about the innate and adaptive immune system in C. semilaevis during bacterial infection.     

Effects of clioquinol on the scuticociliatosis‐causing protozoan Miamiensis avidus in olive flounder Paralichthys olivaceus

Scuticociliatosis is a devastating and intractable protozoal disease in olive flounder, leading to a significant loss throughout the year. This study aimed to investigate a systemically effective antiscuticociliatosis agent for olive flounder for better absorption into the infected internal organs. The in vitro and in vivo antiscuticociliatosis effects of clioquinol (CQ) were examined after screening 30 biocidal agents against the highly pathogenic scuticociliate Miamiensis avidus. CQ was the most potent in vitro drug of those tested against cultured M. avidus. CQ was the least toxic in healthy olive flounder among the drugs that exhibit high potencies. In olive flounder, a single intramuscular injection of 40 mg/kg CQ significantly reduced mortality caused by artificial infection with M. avidus, and 10–20 mg/kg CQ increased fish survival times. CQ was also effective in naturally infected scuticociliatosis. Ciliate cell numbers were lower when CQ was injected in most organs, including the brain. CQ was well absorbed by the internal organs after intramuscular injection. This study suggests that CQ can be considered as a potential antiscuticociliatosis agent for systemic administration in olive flounder.     

Seasonal patterns in the community of gill monogeneans on wild versus cultured orange‐spotted grouper,Epinephelus coioides Hamilton, 1822 in Daya Bay,South China Sea

Epinephelus is among the most important fish genera in the Southeast Asian Pacific coastal systems. In Chinese coast, the orange‐spotted grouper Epinephelus coioides is one of the most significant species based on culture volume, and it is consumed all over the world. Very little information exists on this species’ parasitofauna. Composition and temporal variation in the community structure of the gill monogeneans on wild versus cultured E. coioides from Daya Bay (23°25′N, 117°2′E), South China Sea were determined using seasonal samples taken between April 2008 and January 2009. Eight species of monogeneans of three families and four genera on the gills of E. coioides were found: Neobenedenia melleni, Haliotrema cromileptis, Diplectanum grouperi, Pseudorhabdosynochus justinei, P. lantauensis, P. coioidesis, P. serrani and P. shenzhenensis. Eight of the monogenean species exhibited seasonal variation in their infection dynamics associated with environmental changes during seasons. The variations in the infection dynamics generated changes in the community structure during the sampling periods. Moreover, in the three different host living environments (wild, monocultured and polycultured), the monogenean communities exhibited the different seasonal patterns.     

The high prevalence of pathogenic Vibrio harveyi with multiple antibiotic resistance in scale drop and muscle necrosis disease of the hybrid grouper,Epinephelus fuscoguttatus (♀) × E. lanceolatus (♂), in China

Scale drop and muscle necrosis disease with high mortality widely occurred recently in the hybrid grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂), a crucial cultured marine fish species in China. In this study, 30 Harveyi clade isolates of 27 Vibrio harveyi strains were isolated from diseased hybrid groupers in the south‐east and north‐east coastal areas of China. A total of 22 V. harveyi strains were determined to be pathogenic, and most challenged fish died within 2 days of infection; surviving individuals exhibited scale drop and deep dermal lesions as naturally diseased fish. Although five typical virulence genes, including luxR, toxR_Vh, chiA, serine protease and vhh widely existed in V. harveyi, no obvious correlation was established between virulent strains and virulence genes harboured in them. Furthermore, multiple antibiotic resistance was widely exhibited in Harveyi clade strains, particularly for penicillins, polypeptides, lincomycins, acetylspiramycin, streptomycin, metronidazole and bacitracin. And the multiple antibiotic resistance indices were gradually decreased from southern to northern areas of China. This study demonstrated that the pathogenic V. harveyi with multiple antibiotic resistance is highly prevalent in hybrid grouper in China, which requires particular attention.     

Effects of dietary 60 g kg−1 dried distiller's grains in least‐cost practical diets on production and gut allochthonous bacterial composition of cage‐cultured fish: comparison among fish species with different natural food habits

Dried distiller's grain (DDG) is considered as an alternative ingredient of dietary feed due to its high contents of protein, fibre and fat. In this study, 60 g kg^‐1 of DDG was used to feed grass carp (Ctenopharyngodon idella), bluntnose black bream (Megalobrama amblycephala), gibel carp (Carassius gibelio) and black carp (Mylopharyngodon piceus) for 8 weeks, and its effect on fish production and gut allochthonous microbiota was investigated for the development of a suitable fish feed high in nutrients and low in cost for polyculture freshwater fish. DDG supplementation resulted in the less weight gain and higher feed conversion ratio of black carp (P < 0.05), but had no significant effects on other fish or parameters. PCR–denaturing gradient gel electrophoresis (DGGE) analysis indicated that all four fish species had some common and unique bacteria in their digestive tracts, and the gut microbiota of bluntnose black and gibel carp fed the control diet and DDG diets were very similar (Cs > 91%); of them, the total counts of intestinal bacteria studied by qPCR increased in grass carp (P < 0.05) and depressed in black carp (P < 0.05) when fed dietary DDG. Thus, we assumed that dietary DDG modulated production and gut microbiota of fish in a host‐specific way.     

Ocular bacterial signatures of exophthalmic disease in farmed turbot (Scophthalmus maximus)

As is the case at other sites in the body (e.g. the gut, skin and mouth), the ocular microbiota plays a crucial role in their host, as disturbances of the composition and function of the ocular microbiota are known to be associated with ocular disorders. Exophthalmic disease (ED) is a significant cause of high mortality in fish species, including farmed turbot (Scophthalmus maximus). However, the relationship between alterations in the ocular microbiota and ED in turbot is unclear. In this work, we collected turbot samples from farmed ponds with ED and healthy samples to understand changes in the ocular microbiota of turbot suffering from ED. We compared the structural and metabolic differences of ocular bacterial communities from farmed turbot with exophthalmic disease and those of healthy controls. Besides less microbial diversity found in turbot with ED regarding the control group, we also found that Aeromonas was the dominant bacteria both in controls and ED samples, but the abundance of Aeromonas was significantly greater in ED individuals. Moreover, the results of correlation test further suggest that Aeromonas overgrowth was correlated with the progress of the disease and shifts in ocular microbiota functional pathways in turbot. These findings emphasize that an increased abundance of Aeromonas serves as an ocular bacterial signature associated with ED in turbot, which provide basic information useful for diagnoses, prevention and treatment of ocular diseases occurring in cultured fish.     

Weaning methods using formulated feeds for snakehead (Channa striata and Channa micropeltes) larvae

The culture of snakehead fish (Channa striata and Channa micropeltes) in Vietnam is limited, and snakehead culture has been banned in Cambodia, because traditional practices include capture of fingerlings from the wild as seed, as well as capture of small‐size (also known as trash fish or low‐value) fish. As hatchery breeding technology has improved, we investigated the optimal weaning practices for these two species. Both laboratory experiments and farm trials were conducted. For C. striata, the optimal weaning procedure is to begin at 17 days after hatch (dah) and wean the fish at 10% replacement of live feed with formulated feed per day. However, for C. micropeltes, the optimal procedure is to wait until 40 dah to begin weaning and then to wean the fish with a 10% replacement of live feed with formulated feed every 3 days. These results should enable farmers to domesticate snakehead culture in Vietnam and Cambodia and eliminate reliance on fish captured from the wild as both seed and feed.     

Comparison between the intestinal microbiome of healthy fish and fish experimentally infected with Streptococcus agalactiae

Nile tilapia (Oreochromis niloticus) farming is an economic activity that is soaring in the whole world. Septicemia due to Streptococcus agalactiae is the main disease impacting fish farming. The aim of this study was to compare the gut microbiome of healthy animals and animals experimentally infected with S. agalactiae strain 21171A. The microbiome was established with 16S ribosomal DNA next‐generation sequencing (NGS). One hundred Nile tilapias, with an average weight of 35 g, were distributed into two groups. Fifty fish from the challenged group were orally inoculated with 100 μl of a bacterial solution containing 1.98 × 10³ CFU/ml of S. agalactiae strain 21171A, while 50 controls were orally inoculated with sterile saline. After the experiment, 24 fish from the challenged group and 27 fish from the control group were analysed. For both groups, bacteria attached to the mucosa (M) and present in faeces (F) were analysed. The mean of the number of taxa identified in the infected group (M + F) (45.87 ± 30.13) was lower than in the control (M + F) (67.70 ± 21.10) (p < .01). Nineteen bacterial taxa were more abundant in faecal samples from the infected group when compared with the control group (p < .01). Thirty‐nine taxa were associated with mucosa samples from the challenged group when compared to the control samples (p < .01). No OTU was associated with healthy samples. The results demonstrate that the infection with S. agalactiae reduces the variability of the gut microbiota. Moreover, some bacteria proliferate during the infection.     

PCR survey for Paramoeba perurans in fauna,environmental samples and fish associated with marine farming sites for Atlantic salmon (Salmo salar L.)

Amoebic gill disease (AGD) caused by the amoeba Paramoeba perurans is an increasing problem in Atlantic salmon aquaculture. In the present PCR survey, the focus was to identify reservoir species or environmental samples where P. perurans could be present throughout the year, regardless of the infection status in farmed Atlantic salmon. A total of 1200 samples were collected at or in the proximity to farming sites with AGD, or with history of AGD, and analysed for the presence of P. perurans. No results supported biofouling organisms, salmon lice, biofilm or sediment to maintain P. perurans. However, during clinical AGD in Atlantic salmon, the amoeba were detected in several samples, including water, biofilm, plankton, several filter feeders and wild fish. It is likely that some of these samples were positive as a result of the continuous exposure through water. Positive wild fish may contribute to the spread of P. perurans. Cleaner fish tested positive for P. perurans when salmon tested negative, indicating that they may withhold the amoeba longer than salmon. The results demonstrate the high infection pressure produced from an AGD‐afflicted Atlantic salmon population and thus the importance of early intervention to reduce infection pressure and horizontal spread of P. perurans within farms.     

Outbreaks of Streptococcosis associated with Streptococcus iniae in Siberian sturgeon (Acipenser baerii) in China

Streptococcus iniae has emerged as an important fish pathogen over the past few decades causing high losses in aquaculture farms all over the world. At least 27 species of fish have been documented to be infected by S. iniae, including cultured and wild populations. In August and October 2013, a serious infectious disease characterized by body ulcer, internal organs haemorrhages and nodules showing on epicardium occurred on the Acipenser baerii farms in Ya'an country, China. Histological examination revealed a multisystemic, necrotising inflammatory response that was particularly marked in liver, kidney, heart and brain. Mass mortality (>40%) was observed in infected fish and two Gram‐positive cocci (Ab130920 and Ab131025) were obtained from kidneys and livers of diseased fish. Experimental infections with these two isolates resulted in marked symptoms in the sturgeons similar to those observed in natural outbreaks, and the LD₅₀ values of the two isolates were 5.1 × 10⁵ and 6.4 × 10⁵ cfu per fish respectively. The two microorganisms were identified as S. iniae through physiological and biochemical tests, 16S rRNA and lctO gene sequence analysis. Both two isolates showed a similar antibiotic susceptibility, which were sensitive to ampicillin, amoxicillin, cefazolin, amikacin, deoxycycline, florfenicol, azithromycin, ciprofloxacin, vancomycin and resistant to streptomycin, gentamicin, kanamycin, norfloxacin and sinomin (SMZ/TMP). Multiplex PCR assay for virulence genes showed both isolates possessed six main virulence genes: simA, scpI, pdi, pgm, cpsD and sagA genes. These results indicated that S. iniae could act as a pathogen of farmed A. baerii. This is the first report of S. iniae infection associated with mass mortality in A. baerii.     

In vitro selection and characterization of putative probiotics isolated from the gut of Acipenser baerii (Brandt, 1869)

To select and characterize potential probiotic bacteria from the gut microbiota of Siberian sturgeon (Acipenser baerii), 129 strains isolated from the hindgut were screened for antagonistic activity against five fish pathogens. Ten isolates showed antagonism towards three or more pathogens. Nine of these isolates were Gram‐positive, belonging to Lactococcus (seven) and Bacillus (two), and a single strain belonging to the Gram‐negative Citrobacter. These inhibitory isolates were identified using genetic, phentotypic and biochemical traits, and further characterized by in vitro tests assessing the adhesion and growth in mucus and resistance to gastric and intestinal fluids. The candidate probiotics were determined to be non‐pathogenic through an in vivo study. Based on these assays, Lactococcus lactis ssp. lactis STG45 and STG81 showed the broadest inhibitory potential, a high viability in simulated gastrointestinal juice and the highest adhesion capacity to mucus. They were therefore selected as the most promising candidate probiotics. This is the first study screening probiotics among the gut microflora of Siberian sturgeon.