Pseudomonas fluorescens Filamentous Hemagglutinin, an Iron-Regulated Protein, Is an Important Virulence Factor that Modulates Bacterial Pathogenicity

Comparative Analysis of Physiological Responses and Intestinal Microbiota in Juvenile Soft-Shelled Turtle (Pelodiscus sinensis) Fed Four Types of Dietary Carbohydrates

A 60 day feeding trial was conducted to evaluate the impacts of dietary carbohydrates with different complexities and configurations on the growth, plasma parameters, apparent digestibility, intestinal microbiota, glucose, and lipid metabolism of soft-shelled turtles (Pelodiscus sinensis). Four experimental diets were formulated by adding 170 g/kg glucose, fructose, α-starch, or cellulose, respectively. A total of 280 turtles (initial body weight 5.11 ± 0.21 g) were distributed into 28 tanks and were fed twice daily. The results showed that the best growth performance and apparent digestibility was observed in the α-starch group, followed by the glucose, fructose, and cellulose groups (p < 0.05). Monosaccharides (glucose and fructose) significantly enhanced the postprandial plasma glucose levels and hepatosomatic index compared to polysaccharides, due to the un-inhibited gluconeogenesis (p < 0.05). Starch significantly up-regulated the expression of the genes involved in glycolysis, pentose phosphate pathway, lipid anabolism and catabolism, and the transcriptional regulation factors of glycolipid metabolism (srebp and chrebp) (p < 0.05), resulting in higher plasma triglyceride levels and lipid contents in the liver and the whole body. The fructose group exhibited a lower lipid deposition compared with the glucose group, mainly by inhibiting the expression of srebp and chrebp. Cellulose enhanced the proportion of opportunistic pathogenic bacteria. In conclusion, P. sinensis utilized α-starch better than glucose, fructose, and cellulose.

Haemolysins are essential to the pathogenicity of deep-sea Vibrio fluvialis

Vibrio fluvialis is an emerging foodborne pathogen that produces VFH (Vibrio fluvialis hemolysin) and δVFH (delta-Vibrio fluvialis hemolysin). The function of δVFH is unclear. Currently, no pathogenic V. fluvialis from deep sea has been reported. In this work, a deep-sea V. fluvialis isolate (V13) was examined for pathogenicity. V13 was most closely related to V. fluvialis ATCC 33809, a human isolate, but possessed 262 unique genes. V13 caused lethal infection in fish and induced pyroptosis involving activation of the NLRP3 inflammasome, caspase 1 (Casp1), and gasdermin D (GSDMD). V13 defective in VFH or VFH plus δVFH exhibited significantly weakened cytotoxicity. Recombinant δVFH induced NLRP3-Casp1-GSDMD-mediated pyroptosis in a manner that depended on K+ efflux and intracellular Ca2+ accumulation. δVFH bound several plasma membrane lipids, and these bindings were crucial for δVFH cytotoxicity. Together these results provided new insights into the function of δVFH and the virulence mechanism of V. fluvialis.

Metagenomic insights into the response of soil microbial communities to pathogenic Ralstonia solanacearum

Understanding the response of soil microbial communities to pathogenic Ralstonia solanacearum is crucial for preventing bacterial wilt outbreaks. In this study, we investigated the soil physicochemical and microbial community to assess their impact on the pathogenic R.solanacearum through metagenomics. Our results revealed that certain archaeal taxa were the main contributors influencing the health of plants. Additionally, the presence of the pathogen showed a strong negative correlation with soil phosphorus levels, while soil phosphorus was significantly correlated with bacterial and archaeal communities. We found that the network of microbial interactions in healthy plant rhizosphere soils was more complex compared to diseased soils. The diseased soil network had more linkages, particularly related to the pathogen occurrence. Within the network, the family Comamonadaceae, specifically Ramlibacter_tataouinensis, was enriched in healthy samples and showed a significantly negative correlation with the pathogen. In terms of archaea, Halorubrum, Halorussus_halophilus (family: Halobacteriaceae), and Natronomonas_pharaonis (family: Haloarculaceae) were enriched in healthy plant rhizosphere soils and showed negative correlations with R.solanacearum. These findings suggested that the presence of these archaea may potentially reduce the occurrence of bacterial wilt disease. On the other hand, Halostagnicola_larseniia and Haloterrigena_sp._BND6 (family: Natrialbaceae) had higher relative abundance in diseased plants and exhibited significantly positive correlations with R.solanacearum, indicating their potential contribution to the pathogen's occurrence. Moreover, we explored the possibility of functional gene sharing among the correlating bacterial pairs within the Molecular Ecological Network. Our analysis revealed 468 entries of horizontal gene transfer (HGT) events, emphasizing the significance of HGT in shaping the adaptive traits of plant-associated bacteria, particularly in relation to host colonization and pathogenicity. Overall, this work revealed key factors, patterns and response mechanisms underlying the rhizosphere soil microbial populations. The findings offer valuable guidance for effectively controlling soil-borne bacterial diseases and developing sustainable agriculture practices.

The use of filamentous hemagglutinin adhesin to detect immune responses to Campylobacter hepaticus infections in layer hens

Campylobacter hepaticus is the aetiological agent of Spotty Liver Disease (SLD). SLD can cause significant production loss and mortalities among layer hens at and around peak of lay. We previously developed an enzyme linked immunosorbent assay (ELISA), SLD-ELISA1, to detect C. hepaticus specific antibodies from bird sera using C. hepaticus total proteins and sera pre-absorbed with Campylobacter jejuni proteins. The high specificity achieved with SLD-ELISA1 indicated the presence of C. hepaticus specific antibodies in sera of infected birds. However, some of the reagents used in SLD-ELISA1 are time consuming to prepare and difficult to quality control. This understanding led to the search for C. hepaticus specific immunogenic proteins that could be used in recombinant forms as antibody capture antigens in immunoassay design. In this study, an immunoproteomic approach that combined bioinformatics analysis, western blotting, and LC MS/MS protein profiling was used, and a fragment of filamentous hemagglutinin adhesin (FHA), FHA_1,628-1,899 with C. hepaticus specific antigenicity was identified. Recombinant FHA_1,628-1,899 was used as antigen coating on ELISA plates to capture FHA_1,628-1,899 specific antibodies in sera of infected birds. SLD-ELISA2, based on the purified recombinant FHA fragment, is more user-friendly and standardizable than SLD-ELISA1 for screening antibody responses to C. hepaticus exposure in hens. This study is the first report of the use of FHA from a Campylobacter species in immunoassays, and it also opens future research directions to investigate the role of FHA in C. hepaticus pathogenesis and its effectiveness as a vaccine candidate.

Effect of UV Light and Sodium Hypochlorite on Formation and Destruction of Pseudomonas fluorescens Biofilm In Vitro

Pseudomonas fluorescens is one of the first colonizers of bacterial biofilm in water systems and a member of opportunistic premise plumbing pathogens (OPPPs). The aim of this study was to examine the effect of UV light and sodium hypochlorite on the formation and destruction of mature P. fluorescens biofilm on ceramic tiles. Planktonic bacteria or bacteria in mature biofilm were exposed to UV light (254 nm) for 5, 20 s. and to 0.4 mg/L sodium hypochlorite for 1 min. Mature biofilm was also exposed to increased concentration of sodium hypochlorite of 2 mg/L for 0.5, 1 and 2 h and combined with UV. Prolonged action of sodium hypochlorite and an increase in its concentration in combination with UV gave the best results in the inhibition of biofilm formation after the pre-treatment and destruction of mature biofilm. The effect of hyperchlorination in combination with UV radiation shows better results after a long exposure time, although even after 120 min there was no completely destroyed biofilm. Furthermore, the mechanism of the effect of combined methods should be explored as well as the importance of mechanical cleaning that is crucial in combating bacterial biofilm in swimming pools.

Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics

Bacterial soft rot is a devastating disease for a wide range of crops, vegetables, and ornamental plants including konjac (Amorphophallus konjac). However, the pangenome and genomic plasticity of the konjac soft rot pathogens is little explored. In this study, we reported the complete genome sequences of 11 bacterial isolates that can cause typical soft rot symptoms in konjac by in vitro and in vivo pathogenicity tests. Based on in silico DNA–DNA hybridization, average nucleotide identity and phylogenomic analysis, all 11 isolates were determined to be Pectobacterium aroidearum. In addition, synteny analysis of these genomes revealed considerable chromosomal inversions, one of which is triggered by homologous recombination of ribose operon. Pangenome analysis and COG enrichment analysis showed that the pangenome of P. aroidearum is open and that accessory genes are enriched in replication, recombination, and repair. Variations in type IV secretion system and type VI secretion system were found, while plant cell wall degrading enzymes were conserved. Furthermore, sequence analyses also provided evidence for the presence of a type V secretion system in Pectobacterium. These findings advance our understanding of the pathogenicity determinants, genomic plasticity, and evolution of P. aroidearum.

Condensins are essential for Pseudomonas aeruginosa corneal virulence through their control of lifestyle and virulence programs

Pseudomonas aeruginosa is a significant opportunistic pathogen responsible for numerous human infections. Its high pathogenicity resides in a diverse array of virulence factors and an ability to adapt to hostile environments. We report that these factors are tied to the activity of condensins, SMC and MksBEF, which primarily function in structural chromosome maintenance. This study revealed that both proteins are required for P. aeruginosa virulence during corneal infection. The reduction in virulence was traced to broad changes in gene expression. Transcriptional signatures of smc and mksB mutants were largely dissimilar and non-additive, with the double mutant displaying a distinct gene expression profile. Affected regulons included those responsible for lifestyle control, primary metabolism, surface adhesion and biofilm growth, iron and sulfur assimilation, and numerous virulence factors, including type 3 and type 6 secretion systems. The in vitro phenotypes of condensin mutants mirrored their transcriptional profiles and included impaired production and secretion of multiple virulence factors, growth deficiencies under nutrient limiting conditions, and altered c-di-GMP signaling. Notably, c-di-GMP mediated some but not all transcriptional responses of the mutants. Thus, condensins are integrated into the control of multiple genetic programs related to epigenetic and virulent behavior of P. aeruginosa.

Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper

MOTIVATION

Identifying variant forms of gene clusters of interest in phylogenetically proximate and distant taxa can help to infer their evolutionary histories and functions. Conserved gene clusters may differ by only a few genes, but these small differences can in turn induce substantial phenotypes, such as by the formation of pseudogenes or insertions interrupting regulation. Particularly as microbial genomes and metagenomic assemblies become increasingly abundant, unsupervised grouping of similar, but not necessarily identical, gene clusters into consistent bins can provide a population-level understanding of their gene content variation and functional homology.

RESULTS

We developed GeneGrouper, a command-line tool that uses a density-based clustering method to group gene clusters into bins. GeneGrouper demonstrated high recall and precision in benchmarks for the detection of the 23-gene Salmonella enterica LT2 Pdu gene cluster and four-gene Pseudomonas aeruginosa PAO1 Mex gene cluster among 435 genomes spanning mixed taxa. In a subsequent application investigating the diversity and impact of gene-complete and -incomplete LT2 Pdu gene clusters in 1130 S.enterica genomes, GeneGrouper identified a novel, frequently occurring pduN pseudogene. When investigated in vivo, introduction of the pduN pseudogene negatively impacted microcompartment formation. We next demonstrated the versatility of GeneGrouper by clustering distant homologous gene clusters and variable gene clusters found in integrative and conjugative elements.

AVAILABILITY AND IMPLEMENTATION

GeneGrouper software and code are publicly available at https://pypi.org/project/GeneGrouper/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Comparative roles of three adhesin genes (adh1-3) in insect-pathogenic lifecycle of Beauveria bassiana

Adherence of conidia to insect integument is crucial for initiation of fungal infection through cuticular penetration and was previously reported to rely upon the Metarhizium-type adhesin Mad1 rather than Mad2, another adhesin crucial for conidial adherence of Metarhizium anisopliae to plant root surface. Mad1 and Mad2 have since been considered to function in fungal insect pathogenesis and plant root colonization respectively. Here, three adhesins were characterized in Beauveria bassiana, including Adh1/Mad1, Adh2/Mad2, and Adh3 known as filamentous hemagglutinin/adhesin and virulence factor in animal-pathogenic bacteria. Among those, only Adh2 was found to play a substantial role in sustaining the fungal virulence and some phenotypes associated with biological control potential. Disruption of adh2 resulted in decreased conidial adherence to insect wing cuticle, attenuated virulence via normal cuticle infection or cuticle-bypassing infection (injection), reduced blastospore production in an insect hemolymph-mimicking broth, largely reduced conidiation capacity, impaired conidial quality indicative of lowered viability, hydrophobicity, and UV resistance, but no growth defects on rich and scant media under normal or stressful culture conditions. The main phenotypic changes correlated well with repressed expression of developmental activator genes required for aerial conidiation and submerged blastospore production and of key hydrophobin genes essential for hydrophobin synthesis and assembly into rodlet bundles of conidial coat crucial for conidial adherence. In contrast, either adh1 or adh3 disruption caused insignificant changes in all phenotypes examined. These findings offer novel insight into a significance of Adh2, but a dispensability of Adh1 or Adh3, for insect-pathogenic lifecycle of B. bassiana. KEY POINTS: • Three adhesins (Adh1-3) of Beauvera bassiana are functionally characterized. • Adh2 plays a role in sustaining virulence and lifecycle-related cellular events. • Either Adh1 or Adh3 is dispensable for insect-pathogenic lifecycle of B. bassiana.

Draft genome sequence of the strain 16-537536, isolated from a patient with bronchiectasis and its relationship to the Pseudomonas koreensis group of the Pseudomonas fluorescens complex

Objective

The Pseudomonas koreensis group bacteria are usually found in soil and are associated with plants. Currently they are poorly described. Here we report on the whole genome sequence of a bacterial isolate from a patient with bronchiectasis that was first identified as P. koreensis, and on its position in the P. koreensis group.

Results

Strain 16-537536 was isolated from a patient with bronchiectasis from Spain and initially identified by MALDI-TOF as P. koreensis, a member of the Pseudomonas fluorescens complex. However, the average nucleotide identity analysis (ANIb) and whole genome alignments of the draft genome sequence of this strain showed it to be a member of the P. koreensis group of the P. fluorescens complex, but belonging to an undescribed species. In addition, based on ANIb analysis, the P. koreensis group contains several other unnamed species. Several genes for putative virulence factors were identified. The only antibiotic resistance gene present in strain 16-537536 was a class C β-lactamase. The correct identification of bacterial species from patients is of utmost importance in order to understand their pathogenesis and to track the potential spread of pathogens between patients. Whole genome sequence data should be included for the description of new species.

An analog to digital converter controls bistable transfer competence development of a widespread bacterial integrative and conjugative element

Conjugative transfer of the integrative and conjugative element ICEclc in Pseudomonas requires development of a transfer competence state in stationary phase, which arises only in 3–5% of individual cells. The mechanisms controlling this bistable switch between non-active and transfer competent cells have long remained enigmatic. Using a variety of genetic tools and epistasis experiments in P. putida, we uncovered an ‘upstream’ cascade of three consecutive transcription factor-nodes, which controls transfer competence initiation. One of the uncovered transcription factors (named BisR) is representative for a new regulator family. Initiation activates a feedback loop, controlled by a second hitherto unrecognized heteromeric transcription factor named BisDC. Stochastic modelling and experimental data demonstrated the feedback loop to act as a scalable converter of unimodal (population-wide or ‘analog’) input to bistable (subpopulation-specific or ‘digital’) output. The feedback loop further enables prolonged production of BisDC, which ensures expression of the ‘downstream’ functions mediating ICE transfer competence in activated cells. Phylogenetic analyses showed that the ICEclc regulatory constellation with BisR and BisDC is widespread among Gamma- and Beta-proteobacteria, including various pathogenic strains, highlighting its evolutionary conservation and prime importance to control the behaviour of this wide family of conjugative elements.

Mobile DNA elements are pieces of genetic material that can jump from one bacterium to another, and even across species. They are often useful to their host, for example carrying genes that allow bacteria to resist antibiotics.

One example of bacterial mobile DNA is the ICEclc element. Usually, ICEclc sits passively within the bacterium’s own DNA, but in a small number of cells, it takes over, hijacking its host to multiply and to get transferred to other bacteria. Cells that can pass on the elements cannot divide, and so this ability is ultimately harmful to individual bacteria. Carrying ICEclc can therefore be positive for a bacterium but passing it on is not in the cell’s best interest. On the other hand, mobile DNAs like ICEclc have evolved to be disseminated as efficiently as possible. To shed more light on this tense relationship, Carraro et al. set out to identify the molecular mechanisms ICEclc deploys to control its host.

Experiments using mutant bacteria revealed that for ICEclc to successfully take over the cell, a number of proteins needed to be produced in the correct order. In particular, a protein called BisDC triggers a mechanism to make more of itself, creating a self-reinforcing ‘feedback loop’.

Mathematical simulations of the feedback loop showed that it could result in two potential outcomes for the cell. In most of the ‘virtual cells’, ICEclc ultimately remained passive; however, in a few, ICEclc managed to take over its hosts. In this case, the feedback loop ensured that there was always enough BisDC to maintain ICEclc’s control over the cell. Further analyses suggested that this feedback mechanism is also common in many other mobile DNA elements, including some that help bacteria to resist drugs.

These results are an important contribution to understand how mobile DNAs manipulate their bacterial host in order to propagate and disperse. In the future, this knowledge could help develop new strategies to combat the spread of antibiotic resistance.

Biofilm and Pathogenesis-Related Proteins in the Foodborne P. fluorescens ITEM 17298 With Distinctive Phenotypes During Cold Storage

In food chain, Pseudomonas spp. cause spoilage by reducing shelf life of fresh products, especially during cold storage, with a high economic burden for industries. However, recent studies have shed new light on health risks occurring when they colonize immunocompromised patient tissues. Likewise to P. aeruginosa, they exhibit antibiotic resistance and biofilm formation, responsible for their spread and persistence in the environment. Biofilm formation might be induced by environmental stresses, such as temperature fluctuations causing physiological and metabolic changes exacerbating food spoilage (by protease and pigment synthesis), and the production of adhesion molecules, chemotactic or underestimated virulence factors. In order to provide a new insight into phenotypic biodiversity of Pseudomonas spoilers isolated from cold stored cheese, in this work 19 Pseudomonas spp. were investigated for biofilm, pigments, exopolysaccharide production and motility at low temperature. Only nine strains showed these phenotypic traits and the blue pigmenting cheese strain P. fluorescens ITEM 17298 was the most distinctive. In addition, this strain decreased the survival probability of infected Galleria mellonella larvae, showing, for the first time, a pathogenic potential. Genomic and proteomic analyses performed on the ITEM 17298 planktonic cells treated or not with lactoferrin derived antibiofilm peptides allowed to reveal specific biofilm related-pathways as well as proteins involved in pathogenesis. Indeed, several genes were found related to signaling system by cGMP-dependent protein kinases, cellulose, rhamnolipid and alginate synthesis, antibiotic resistance, adhesion and virulence factors. The proteome of the untreated ITEM 17298, growing at low temperature, showed that most of the proteins associated with biofilm regulation, pigmentation motility, antibiotic resistance and pathogenecity were repressed, or decreased their levels in comparison to that of the untreated cultures. Thus, the results of this work shed light on the complex pathways network allowing psychrotrophic pseudomonads to adapt themselves to food-refrigerated conditions and enhance their spoilage. In addition, the discovery of virulence factors and antibiotic resistance determinants raises some questions about the need to deeper investigate these underestimated bacteria in order to increase awareness and provide input to update legislation on their detection limits in foods.

Characterization of Antimicrobial Effects of Plasma-Treated Water (PTW) Produced by Microwave-Induced Plasma (MidiPLexc) on Pseudomonas fluorescens Biofilms

For the decontamination of surfaces in the food production industry, plasma-generated compounds such as plasma-treated water or plasma-processed air offer many promising possibilities for future applications. Therefore, the antimicrobial effect of water treated with microwave-induced plasma (MidiPLexc) on Pseudomonas fluorescens biofilms was investigated. A total of 10 mL deionized water was treated with the MidiPLexc plasma source for 100, 300 and 900 s (pretreatment time) and the bacterial biofilms were exposed to the plasma-treated water for 1, 3 and 5 min (post-treatment time). To investigate the influence of plasma-treated water on P. fluorescens biofilms, microbiological assays (colony-forming units, fluorescence and XTT assay) and imaging techniques (fluorescence microscopy, confocal laser scanning microscopy, and atomic force microscopy) were used. The colony-forming units showed a maximum reduction of 6 log10 by using 300 s pretreated plasma water for 5 min. Additionally, a maximum reduction of 81% for the viability of the cells and a 92% reduction in the metabolic activity of the cells were achieved by using 900 s pretreated plasma water for 5 min. The microscopic images showed evident microbial inactivation within the biofilm even at the shortest pretreatment (100 s) and post-treatment (1 min) times. Moreover, reduction of the biofilm thickness and increased cluster formation within the biofilm was detected. Morphologically, the fusion of cell walls into a uniform dense cell mass was detectable. The findings correlated with a decrease in the pH value of the plasma-treated water, which forms the basis for the chemically active components of plasma-treated water and its antimicrobial effects. These results provide valuable insights into the mechanisms of inactivation of biofilms by plasma-generated compounds such as plasma-treated water and thus allow for further parameter adjustment for applications in food industry.

Thymol Inhibits Biofilm Formation, Eliminates Pre-Existing Biofilms, and Enhances Clearance of Methicillin-Resistant Staphylococcus aureus (MRSA) in a Mouse Peritoneal Implant Infection Model

Methicillin-resistant Staphylococcus aureus (MRSA) is a common human pathogen that causes several difficult-to-treat infections, including biofilm-associated infections. The biofilm-forming ability of S. aureus plays a pivotal role in its resistance to most currently available antibiotics, including vancomycin, which is the first-choice drug for treating MRSA infections. In this study, the ability of thymol (a monoterpenoid phenol isolated from plants) to inhibit biofilm formation and to eliminate mature biofilms, was assessed. We found that thymol could inhibit biofilm formation and remove mature biofilms by inhibiting the production of polysaccharide intracellular adhesin (PIA) and the release of extracellular DNA (eDNA). However, cotreatment with thymol and vancomycin was more effective at eliminating MRSA biofilms, in a mouse infection model, than monotherapy with vancomycin. Comparative histopathological analyses revealed that thymol reduced the pathological changes and inflammatory responses in the wounds. Assessments of white blood cell counts and serum TNF-α and IL-6 levels showed reduced inflammation and an increased immune response following treatment with thymol and vancomycin. These results indicate that combinatorial treatment with thymol and vancomycin has the potential to serve as a more effective therapy for MRSA biofilm-associated infections than vancomycin monotherapy.

Game animals as a reservoir of rarely recorded opportunistic bacteria

In Poland, the population of game animals, including wild boars, roe and deer, is constantly increasing. The tonsils of wild game animals are a place of large variety of microorganisms. The pathogenic bacteria present in them, such as E. coli, Y. enterocolitica and Salmonella sp. are the most common source of meat infection. The opportunistic bacteria R. aquatilis, P. fluorescens, S. liquefaciens, S. fonticola and S. plymuthica also play an important role in public health. S. liquefaciens may be an opportunistic pathogen and in people causes sepsis and inflammation of the cornea. The protease, nuclease, phospholipase A, flagella, elastase and toxins haemolysin and proteolysin are responsible for its ability to cause disease symptoms. S. plymuthica, a rod commonly found in the environment, produces a red dye. It is most often isolated from soil, water and food. In humans, it causes infections of burn wounds, soft leg tissue as well as post-operative wounds and bacteraemia. Typically, the environmental rod S. fonticola differs from other Serratia sp. by the lack of extracellular enzymes. It causes wound infections and bacteraemia resulting from urinary tract infections. Bacteria from the genus Serratia sp. show a natural resistance to glycopeptides, rifampicin and erythromycin. The aquatic rod R. aquatilis in humans causes opportunistic infections of the urinary tract, wounds, bacteraemia and endocarditis. It exhibits natural resistance to antibiotics from the group of cephalosporins, penicillins and macrolides and quinolones. It is conditioned by the presence of class 1 integrons and class A β-lactamases. The virulence factors of R. aquatilis are also LPS and adhesin. P. fluorescens in humans is responsible for bacteraemia. It also exhibits resistance to human serum thanks to outer membrane proteins and has T3SS, which effectively infects the host.

Proteomics for understanding pathogenesis, immune modulation and host pathogen interactions in aquaculture

Proteomic analyses techniques are considered strong tools for identifying and quantifying the protein contents in different organisms, organs and secretions. In fish biotechnology, the proteomic analyses have been used for wide range of applications such as identification of immune related proteins during infections and stresses. The proteomic approach has a significant role in understanding pathogen surviving strategies, host defence responses and subsequently, the fish pathogen interactions. Proteomic analyses were employed to highlight the virulence related proteins secreted by the pathogens to invade the fish host's defence barriers and to monitor the kinetics of protein contents of different fish organs in response to infections. The immune related proteins of fish and the virulence related proteins of pathogens are up or down regulated according to their functions in defence or pathogenesis. Therefore, the proteomic analyses are useful in understanding the virulence mechanisms of microorganisms and the fish pathogen interactions thereby supporting the development of new effective therapies. In this review, we focus and summarise the recent proteomic profiling studies exploring pathogen virulence activities and fish immune responses to stressors and infections.

Virtual screening for quorum-sensing inhibitors of Pseudomonas fluorescens P07 from a food-derived compound database

AIMS

Pseudomonas fluorescens are important psychrotrophic food spoilage bacteria that are frequently detected in dairy, meat and aquatic products. Quorum sensing (QS) is an intercellular communication and gene regulation mechanism that enables bacteria to monitor their cell densities and regulate a variety of physiological processes. Hence, targeting the bacterial QS system might be a feasible approach to improve food quality and safety by regulating the spoilage caused by P. fluorescens.

METHODS AND RESULTS

In this study, we screened a food-derived three-dimensional (3D) compound database to search for potential QS inhibitors (QSIs) with higher security. The 3D structures of LuxI- and LuxR-type proteins of P. fluorescens P07 were used as targets to screen for QSIs. A total of 25 compounds with high docking scores were tested for their anti-QS activities by indicator strains. The results show that 19 compounds possessed anti-QS activities. Among them, (+)-catechin had the strongest anti-QS activity. The results show that (+)-catechin significantly inhibited the production of extracellular enzymes, swimming motility, biofilm formation, acyl-homoserine lactones and extracellular polymeric substances (EPSs) of P. fluorescens P07. The inhibitory mechanism of (+)-catechin on the QS system of P. fluorescens P07 was discussed in the context of molecular docking analysis and real-time quantitative PCR (RT-qPCR).

CONCLUSIONS

Virtual screening was useful in finding novel QSIs with high security of P. fluorescens P07 from a food-derived 3D compound database. The high hit rate suggested that foods are rich sources of QSIs, and have great potential for exploration.

SIGNIFICANCE AND IMPACT OF THE STUDY

The modelled LuxI- and LuxR-type proteins could be used as targets to discover P. fluorescens P07 QSIs. (+)-catechin, (-)-epicatechin, propyl gallate, hesperidin and lycopene which were identified as potent QSIs, and may be applied in food preservation and biofilm elimination.

A First Study of the Virulence Potential of a Bacillus subtilis Isolate From Deep-Sea Hydrothermal Vent

Bacillus subtilis is the best studied Gram-positive bacterium, primarily as a model of cell differentiation and industrial exploitation. To date, little is known about the virulence of B. subtilis. In this study, we examined the virulence potential of a B. subtilis strain (G7) isolated from the Iheya North hydrothermal field of Okinawa Trough. G7 is aerobic, motile, endospore-forming, and requires NaCl for growth. The genome of G7 is composed of one circular chromosome of 4,216,133 base pairs with an average GC content of 43.72%. G7 contains 4,416 coding genes, 27.5% of which could not be annotated, and the remaining 72.5% were annotated with known or predicted functions in 25 different COG categories. Ten sets of 23S, 5S, and 16S ribosomal RNA operons, 86 tRNA and 14 sRNA genes, 50 tandem repeats, 41 mini-satellites, one microsatellite, and 42 transposons were identified in G7. Comparing to the genome of the B. subtilis wild type strain NCIB 3610^T, G7 genome contains many genomic translocations, inversions, and insertions, and twice the amount of genomic Islands (GIs), with 42.5% of GI genes encoding hypothetical proteins. G7 possesses abundant putative virulence genes associated with adhesion, invasion, dissemination, anti-phagocytosis, and intracellular survival. Experimental studies showed that G7 was able to cause mortality in fish and mice following intramuscular/intraperitoneal injection, resist the killing effect of serum complement, and replicate in mouse macrophages and fish peripheral blood leukocytes. Taken together, our study indicates that G7 is a B. subtilis isolate with unique genetic features and can be lethal to vertebrate animals once being introduced into the animals by artificial means. These results provide the first insight into the potential harmfulness of deep-sea B. subtilis.

Comparative bioinformatic and proteomic approaches to evaluate the outer membrane proteome of the fish pathogen Yersinia ruckeri

Yersinia ruckeri is the aetiological agent of enteric redmouth (ERM) disease and is responsible for significant economic losses in farmed salmonids. Enteric redmouth disease is associated primarily with rainbow trout (Oncorhynchus mykiss, Walbaum) but its incidence in Atlantic salmon (Salmo salar) is increasing. Outer membrane proteins (OMPs) of Gram-negative bacteria are located at the host-pathogen interface and play important roles in virulence. The outer membrane of Y. ruckeri is poorly characterised and little is known about its composition and the roles of individual OMPs in virulence. Here, we employed a bioinformatic pipeline to first predict the OMP composition of Y. ruckeri. Comparative proteomic approaches were subsequently used to identify those proteins expressed in vitro in eight representative isolates recovered from Atlantic salmon and rainbow trout. One hundred and forty-one OMPs were predicted from four Y. ruckeri genomes and 77 of these were identified in three or more genomes and were considered as "core" proteins. Gel-free and gel-based proteomic approaches together identified 65 OMPs in a single reference isolate and subsequent gel-free analysis identified 64 OMPs in the eight Atlantic salmon and rainbow trout isolates. Together, our gel-free and gel-based proteomic analyses identified 84 unique OMPs in Y. ruckeri. SIGNIFICANCE: Yersinia ruckeri is an important pathogen of Atlantic salmon and rainbow trout and is of major economic significance to the aquaculture industry worldwide. Disease outbreaks are becoming more problematic in Atlantic salmon and there is an urgent need to investigate in further detail the cell-surface (outer membrane) composition of strains infecting each of these host species. Currently, the outer membrane of Y. ruckeri is poorly characterised and very little is known about the OMP composition of strains infecting each of these salmonid species. This study represents the most comprehensive comparative outer membrane proteomic analysis of Y. ruckeri to date, encompassing isolates of different biotypes, serotypes, OMP-types and hosts of origin and provides insights into the potential roles of these diverse proteins in host-pathogen interactions. The study has identified key OMPs likely to be involved in disease pathogenesis and makes a significant contribution to furthering our understanding of the cell-surface composition of this important fish pathogen that will be relevant to the development of improved vaccines and therapeutics.

Molecular regulation of adhesion and biofilm formation in high and low biofilm producers of Bacillus licheniformis using RNA-Seq

RNA sequencing was used to reveal transcriptional changes during the motile-to-sessile switch in high and low biofilm-forming dairy strains of B. licheniformis isolated from Chinese milk powders. A significant part of the whole gene content was affected during this transition in both strains. In terms of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, seven metabolic pathways were significantly downregulated in the planktonic state compared to the biofilm state in both strains. Lipid and sugar metabolism seemed to play an important role in matrix production. Several genes involved in adhesion, matrix production and the matrix coating were either absent or less expressed in the biofilm state of the low biofilm producer compared to the high biofilm producer. Genes related to sporulation and the production of extracellular polymeric substances were concomitantly expressed in the biofilm state of both strains. These comprehensive insights will be helpful for future research into mechanisms and targets.

Contact-dependent growth inhibition systems in Acinetobacter

In bacterial contact-dependent growth inhibition (CDI) systems, CdiA proteins are exported to the outer membrane by cognate CdiB proteins. CdiA binds to receptors on susceptible bacteria and subsequently delivers its C-terminal toxin domain (CdiA-CT) into neighbouring target cells. Whereas self bacteria produce CdiI antitoxins, non-self bacteria lack antitoxins and are therefore inhibited in their growth by CdiA. In silico surveys of pathogenic Acinetobacter genomes have enabled us to identify >40 different CDI systems, which we sorted into two distinct groups. Type-II CdiAs are giant proteins (3711 to 5733 residues) with long arrays of 20-mer repeats. Type-I CdiAs are smaller (1900-2400 residues), lack repeats and feature central heterogeneity (HET) regions, that vary in size and sequence and can be exchanged between CdiA proteins. HET regions in most type-I proteins confer the ability to adopt a coiled-coil conformation. CdiA-CT and pretoxin modules differ significantly between type-I and type-II CdiAs. Moreover, type-II genes only have remnants of genes in their 3' end regions that have been displaced by the insertion of novel cdi sequences. Type-I and type-II CDI systems are equally abundant in A. baumannii, whereas A. pittii and A. nosocomialis predominantly feature type-I and type-II systems, respectively.

Complete genome sequences of Aeromonas and Pseudomonas phages as a supportive tool for development of antibacterial treatment in aquaculture

Background

Aquaculture is the fastest growing sector of food production worldwide. However, one of the major reasons limiting its effectiveness are infectious diseases among aquatic organisms resulting in vast economic losses. Fighting such infections with chemotherapy is normally used as a rapid and effective treatment. The rise of antibiotic resistance, however, is limiting the efficacy of antibiotics and creates environmental and human safety concerns due to their massive application in the aquatic environment. Bacteriophages are an alternative solution that could be considered in order to protect fish against pathogens while minimizing the side-effects for the environment and humans. Bacteriophages kill bacteria via different mechanisms than antibiotics, and so fit nicely into the ‘novel mode of action’ concept desired for all new antibacterial agents.

Methods

The bacteriophages were isolated from sewage water and characterized by RFLP, spectrum of specificity, transmission electron microscopy (TEM) and sequencing (WGS). Bioinformatics analysis of genomic data enables an in-depth characterization of phages and the choice of phages. This allows an optimised choice of phage for therapy, excluding those with toxin genes, virulence factor genes, and genes responsible for lysogeny.

Results

In this study, we isolated eleven new bacteriophages: seven infecting Aeromonas and four infecting Pseudomonas, which significantly increases the genomic information of Aeromonas and Pseudomonas phages. Bioinformatics analysis of genomic data, assessing the likelihood of these phages to enter the lysogenic cycle with experimental data on their specificity towards large number of bacterial field isolates representing different locations.

Conclusions

From 11 newly isolated bacteriophages only 6 (25AhydR2PP, 50AhydR13PP, 60AhydR15PP, 22PfluR64PP, 67PfluR64PP, 71PfluR64PP) have a potential to be used in phage therapy due to confirmed lytic lifestyle and absence of virulence or resistance genes.

Electronic supplementary material

The online version of this article (10.1186/s12985-018-1113-5) contains supplementary material, which is available to authorized users.

Taxonomic and functional heterogeneity of the gill microbiome in a symbiotic coastal mangrove lucinid species

Lucinidae clams harbor gammaproteobacterial thioautotrophic gill endosymbionts that are environmentally acquired. Thioautotrophic lucinid symbionts are related to metabolically similar symbionts associated with diverse marine host taxa and fall into three distinct phylogenetic clades. Most studies on the lucinid–bacteria chemosymbiosis have been done with seagrass-dwelling hosts, whose symbionts belong to the largest phylogenetic clade. In this study, we examined the taxonomy and functional repertoire of bacterial endosymbionts at an unprecedented resolution from Phacoides pectinatus retrieved from mangrove-lined coastal sediments, which are underrepresented in chemosymbiosis studies. The P. pectinatus thioautotrophic endosymbiont expressed metabolic gene variants for thioautotrophy, respiration, and nitrogen assimilation distinct from previously characterized lucinid thioautotrophic symbionts and other marine symbionts. At least two other bacterial species with different metabolisms were also consistently identified in the P. pectinatus gill microbiome, including a Kistimonas-like species and a Spirochaeta-like species. Bacterial transcripts involved in adhesion, growth, and virulence and mixotrophy were highly expressed, as were host-related hemoglobin and lysozyme transcripts indicative of sulfide/oxygen/CO₂ transport and bactericidal activity. This study suggests the potential roles of P. pectinatus and its gill microbiome species in mangrove sediment biogeochemistry and offers insights into host and microbe metabolisms in the habitat.

Polyvalent protective immunogens identified from outer membrane proteins of Vibrio parahaemolyticus and their induced innate immune response

Vaccines are the most economic, efficient and environment-friendly agents in protecting host against bacterial infection. In aquaculture, polyvalent vaccines targeting more than one bacterial specie are highly demanded due to the presence of various types of bacterial pathogens in farming environment. Here eighteen genes encoding outer membrane proteins of Vibrio parahaemolyticus were cloned and expressed. The expressed recombinant proteins were used for antiserum preparation. Passive and active immune protection of the antiserum and recombinant proteins was investigated in the zebrafish model. Two recombinant proteins, VP1667 and VP2369, showed effective immune protection against at least two genera of bacteria, Vibrio (V. parahaemolyticus and V. alginolyticus), Pseudomonas (P. fluorescens) or/and Aeromonas (A. hydrophila), and thereby are potential polyvalent vaccine candidates to defend against bacterial infection in fish farming. Furthermore, the mechanisms for the two polyvalent vaccines in triggering immune response were explored. Antiserum to VP1667 or VP2369 was not cross-reacted with P. fluorescens and A. hydrophila, whereas both recombinant proteins induced significant innate immune response. Comparatively, VP1667 stimulates stronger lymphokine and monokine, and VP2369 induces stronger humoral immune response, while both produce similar NF-κB, COX-2, TLR-1 and TLR-3 expression. Our results identify two polyvalent vaccines and demonstrate characteristics features of their cross-protection at the content of the innate immune response.

A teleost complement factor Ba possesses antimicrobial activity and inhibits bacterial infection in fish

Complement factor B (Bf) is a component of the complement system. Following activation of the alternative pathway of the complement system, factor B is cleaved into Ba and Bb fragments. In fish, the Bf of rainbow trout is known to act as a C3 convertase, but the function of the Ba fragment is essentially unknown. In this study, we examined the expression patterns of tongue sole Cynoglossus semilaevis Bf (named CsBf) and the biological activity of the Ba fragment of CsBf (named CsBa). CsBf possesses the conserved domains of Bf and shares 39.9%-56.4% sequence identities with other fish Bf. CsBf expression was high in liver, muscle, and heart, and low in intestine, blood, and kidney. Bacterial infection significantly induced CsBf expression in kidney, spleen, and liver in a time-dependent manner. Recombinant CsBa (rCsBa) exhibited apparent binding capacities to bacteria and tongue sole peripheral blood leukocytes, and binding of rCsBa to bacteria inhibited bacterial growth. When overexpressed in tongue sole, CsBa significantly reduced bacterial dissemination in fish tissues. Together these results indicate for the first time that a fish Ba possesses antibacterial effect as well as immune cell-binding capacity, and thus probably plays a role in host immune defense against bacterial infection.