Effects of dietary co-exposure to fungal and herbal functional feed additives on immune parameters and microbial intestinal diversity in rainbow trout (Oncorhynchus mykiss).

Misuse and overuse of antibiotics in aquaculture has proven to be an unsustainable practice leading to increased bacterial resistance. An alternative strategy involves the inclusion of immunostimulants in fish diets, especially fungal and herbal compounds already authorized for human consumption, hence without environmental or public health concerns. In this study, we used a holistic and cross-disciplinary pipeline to assess the immunostimulatory properties of two fungi: Trametes versicolor and Ganoderma lucidum; one herbal supplement, capsaicin in the form of Espelette pepper (Capsicum annuum), and a combination of these fungal and herbal additives on rainbow trout (Oncorhynchus mykiss). We investigated the impact of diet supplementation for 7 weeks on survival, growth performance, cellular, humoral, and molecular immune parameters, as well as the intestinal microbial composition of the fish. Uptake of herbal and fungal compounds influenced the expression of immune related genes, without generating an inflammatory response. Significant differences were detected in the spleen-tlr2 gene expression. Supplementation with herbal additives correlated with structural changes in the fish intestinal microbiota and enhanced overall intestinal microbial diversity. Results demonstrated that the different treatments had no adverse effect on growth performance and survival, suggesting the safety of the different feed additives at the tested concentrations. While the mechanisms and multifactorial interactions remain unclear, this study provides insights not only in regard to nutrition and safety of these compounds, but also how a combined immune and gut microbiota approach can shed light on efficacy of immunostimulant compounds for potential commercial inclusion as feed supplements.

Structure and biological activities of a hexosamine-rich cell wall polysaccharide isolated from the probiotic Lactobacillus farciminis.

Lactobacillus farciminis CIP 103136 is a bacterial strain with recognized probiotic properties. However, the mechanisms underlying such properties have only been partially elucidated. In this study, we isolated and purified a cell-wall associated polysaccharide (CWPS), and evaluated its biological role in vitro. The structure of CWPS and responses from stimulation of (i) human macrophage-like THP-1 cells, (ii) human embryonal kidney (HEK293) cells stably transfected with Toll-like receptors (TLR2 or TLR4) and (iii) human colonocyte-like T84 intestinal epithelial cells, upon exposure to CWPS were studied. The structure of the purified CWPS from L. farciminis CIP 103136 was analyzed by nuclear magnetic resonance (NMR), MALDI-TOF-TOF MS, and methylation analyses in its native form and following Smith degradation. It was shown to be a novel branched polysaccharide, composed of linear backbone of trisaccharide repeating units of: [→6αGlcpNAc1 → 4ßManpNAc1 → 4ßGlcpNAc1→] highly substituted with single residues of αGlcp, αGalp and αGlcpNAc. Subsequently, the lack of pro- or anti-inflammatory properties of CWPS was established on macrophage-like THP-1 cells. In addition, CWPS failed to modulate cell signaling pathways dependent of TLR2 and TLR4 in transfected HEK-cells. Finally, in T84 cells, CWPS neither influenced intestinal barrier integrity under basal conditions nor prevented TNF-α/IFN-γ cytokine-mediated epithelium impairment.

Vibrio species involved in seafood-borne outbreaks (Vibrio cholerae, V. parahaemolyticus and V. vulnificus): Review of microbiological versus recent molecular detection methods in seafood products.

Seafood products are widely consumed all around the world and play a significant role on the economic market. Bacteria of the Vibrio genus can contaminate seafood and thus pose a risk to human health. Three main Vibrio species, V. cholerae, V. parahaemolyticus and V. vulnificus, are potentially pathogenic to humans. These species are responsible for a dramatic increase of seafood-borne infections worldwide. Hence, early detection of total and pathogenic Vibrio is needed and should rely on quick and effective methods. This review aims to present the standard methods FDA-BAM, ISO/TS 21872-1:2007 and TS 21872-2:2007 and compare them to recent molecular biology methods including endpoint PCR, quantitative real-time PCR (qPCR) and PCR-derived methods with a focus on LAMP (loop-mediated isothermal amplification). The available methods presented here are dedicated to the detection and identification of the Vibrio species of interest in seafood.

Development of an SPME-GC-MS method for the specific quantification of dimethylamine and trimethylamine: use of a new ratio for the freshness monitoring of cod fillets.

BACKGROUND: Fish is a highly perishable food, so it is important to be able to estimate its freshness to ensure optimum quality for consumers. The present study describes the development of an SPME-GC-MS technique capable of quantifying both trimethylamine (TMA) and dimethylamine (DMA), components of what has been defined as partial volatile basic nitrogen (PVB-N). This method was used, together with other reference methods, to monitor the storage of cod fillets (Gadus morhua) conserved under melting ice. RESULTS: Careful optimisation enabled definition of the best parameters for extracting and separating targeted amines and an internal standard. The study of cod spoilage by sensory analysis and TVB-N assay led to the conclusion that the shelf-life of cod fillet was between 6 and 7 days. Throughout the study, TMA and DMA were specifically quantified by SPME-GC-MS; the first was found to be highly correlated with the values returned by steam distillation assays. Neither TMA-N nor DMA-N were able to successfully characterise the decrease in early freshness, unlike dimethylamine/trimethylamine ratio (DTR), whose evolution is closely related to the results of sensory analysis until the stage where fillets need to be rejected. CONCLUSION: DTR was proposed as a reliable indicator for the early decrease of freshness until fish rejection. © 2015 Society of Chemical Industry.

Monitoring the freshness of fish: development of a qPCR method applied to MAP chilled whiting.

BACKGROUND: Monitoring of early stages of freshness decay is a major issue for the fishery industry to guarantee the best quality for this highly perishable food matrix. Numerous techniques have been developed, but most of them have the disadvantage of being reliable only either in the last stages of fish freshness or for the analysis of whole fish. This study describes the development of a qPCR method targeting the torA gene harboured by fish spoilage microorganisms. torA encodes an enzyme that leads to the production of trimethylamine responsible for the characteristic spoiled-fish odour. RESULTS: A degenerate primer pair was designed. It amplified torA gene of both Vibrio and Photobacterium with good efficiencies on 7-log DNA dilutions. The primer pair was used during a shelf-life monitoring study achieved on modified atmosphere packed, chilled, whiting (Merlangius merlangus) fillets. The qPCR approach allows the detection of an increase of torA copies throughout the storage of fillets in correlation with the evolution of both total volatile basic nitrogen (-0.86) and trimethylamine concentrations (-0.81), known as spoilage markers. CONCLUSION: This study described a very promising, sensitive, reliable, time-effective, technique in the field of freshness characterisation of processed fish.

Temporal and Spatial Dynamics of Vibrio harveyi: An Environmental Parameter Correlation Investigation in a 4-Metre-Deep Dicentrarchus labrax Aquaculture Tank.

Nowadays, European seabass (Dicentrarchus labrax) aquaculture is undergoing a significant expansion. Nevertheless, the aquaculture industry is plagued by vibriosis. The spatial and temporal dynamics of Vibrio harveyi were studied on a European seabass farm in northern France during seven months of 2022. Concrete specimens were suspended and water was pumped from different depths (0.3 m, 2.15 m and 4 m deep), providing insights into the biofilm and planktonic V. harveyi dynamics. The abundances of V. harveyi, in the biofilm and free-living forms, were positively correlated. The water parameters revealed seasonal fluctuations in temperature, pH, and salinity, with no significant differences observed across the water column. Quantification of V. harveyi revealed no significant differences between depths, but seasonality, with peak abundances observed in August, correlated with temperature increases. Principal component analysis identified temperature as a primary driver, but also additional parameters, such as salinity and pH. Vibriosis occurred during the sampling period, providing valuable insights into the conditions before, during, and after the outbreaks. This study underscores the importance of understanding V. harveyi behaviour in aquaculture, particularly in the context of global warming, for effective disease management and sustainable practices.

Structural studies of the deacylated glycolipids and lipoteichoic acid of Lactococcus cremoris 3107.

Lactococcus cremoris and Lactococcus lactis are among the most extensively exploited species of lactic acid bacteria in dairy fermentations. The cell wall of lactococci, like other Gram-positive bacteria, possesses a thick peptidoglycan layer, which may incorporate cell wall polysaccharides (CWPS), wall teichoic acids (WTA), and/or lipoteichoic acids (LTA). In this study, we report the isolation, purification and structural analysis of the carbohydrate moieties of glycolipids (GL) and LTA of the L. cremoris model strain 3107. Chemical structures of these compounds were studied by chemical methods, NMR spectroscopy and positive and negative mode ESI MS. We found that the LTA of strain 3107 is composed of short chains of 1,3-polyglycerol phosphate (PGP), attached to O-6 of the non-reducing glucose of the kojibiose-Gro backbone of the glycolipid anchor. Extraction of cells with cold TCA afforded the detection of 1,3-glycerol phosphate chains randomly substituted at O-2 of glycerol by D-Ala. Unlike the LTA of L. lactis strains studied to date, the PGP backbone of the LTA of L. cremoris 3107 did not carry any glycosyl substitution. The deacylated glycolipid fraction contained the free kojibiose-Gro oligosaccharide, identical to the backbone of the GL anchor of LTA, and its shorter fragment α-Glc-1-Gro. These OS may have originated from the GL precursors of LTA biosynthesis.

Measurement of fish freshness: Flow cytometry analysis of isolated muscle mitochondria.

Mitochondria are real sensors of the physiological status of tissues. After the death of an animal, they maintain physiological activity for several days. This activity is highly dependent on the availability of nutrients in the tissue. In this study, flow cytometry was used to measure the membrane potential of mitochondria isolated from European seabass (Dicentrarchus labrax) red muscle stored in ice for seven days in order to characterize fish freshness. Two probes, TMRM and Rhodamine 123, were used to measure mitochondrial potential. During the first few days (D0 to D3), isolated mitochondria maintained high potential, and then lost their potential (from D3 to D5), but were always re-polarizable after addition of substrates (glutamate, malate and succinate). From D7, the mitochondria were more strongly depolarized and were difficult to repolarize by the substrates. Using flow cytometry, we demonstrated that mitochondria were an excellent marker to confirm seabass freshness.

Rapid Identification of Vibrio Species of the Harveyi Clade Using MALDI-TOF MS Profiling With Main Spectral Profile Database Implemented With an In-House Database: Luvibase.

Vibrio bacteria, and particularly members of the Harveyi clade, are the causative agents of vibriosis. This disease is responsible for mass mortality events and important economic losses on aquaculture farms. Improvements in surveillance and diagnosis are needed to successfully manage vibriosis outbreaks. 16S rRNA gene sequencing is generally considered to be the gold standard for bacterial identification but the cost and long processing time make it difficult to apply for routine identification. In contrast, MALDI-TOF MS offers rapid diagnosis and is commonly used in veterinary laboratories today. The major limiting factor for using this technique is the low environmental bacterial diversity in the commonly available databases. Here, we demonstrate that the sole use of the commercially available Bruker BioTyper database is not fully adequate for identifying Vibrio bacteria isolated from aquaculture farms. We therefore developed a new in-house database named Luvibase, composed of 23 reference MALDI-TOF mass spectra profiles obtained from Vibrio collection strains, mostly belonging to the Harveyi clade. The comparison of the accuracy of MALDI-TOF MS profiling and 16S rRNA gene sequencing revealed a lack of resolution for 16S rRNA gene sequencing. In contrast, MALDI-TOF MS profiling proved to be a more reliable tool for resolving species-level variations within the Harveyi clade. Finally, combining the Luvibase with the Bruker ver.9.0.0.0 database, led to successful identification of 47 Vibrio isolates obtained from moribund abalone, seabass and oysters. Thus, the use of Luvibase allow for increased confidence in identifying Vibrio species belonging to the Harveyi clade.

Genome Sequencing and Analysis of Bacillus pumilus ICVB403 Isolated from Acartia tonsa Copepod Eggs Revealed Surfactin and Bacteriocin Production: Insights on Anti-Staphylococcus Activity.

Here we show that Bacillus pumilus ICVB403 recently isolated from copepod eggs is able to produce, after 48-72 h of growth in Landy medium, extracellular inhibitory compounds, which are active against Staphylococcus aureus ATCC 25923, methicillin-resistant S. aureus (MRSA) ATCC 43300, MRSA-S1, Staphylococcus epidermidis 11EMB, Staphylococcus warneri 27EMB, and Staphylococcus hominis 13EMB. Moreover, these extracellular inhibitory compound(s) were able to potentiate erythromycin against the aforementioned staphylococci. The minimum inhibitory concentration (MIC) of erythromycin was reduced from 32 µg/mL to 8 µg/mL for MRSA ATCC 43300 and MRSA SA-1 strains, and from 32-64 µg/mL to 4 µg/mL for S. epidermidis 11EMB and S. hominis 13EMB strains.The genome sequencing and analysis of B. pumilus ICVB403 unveiled 3.666.195 nucleotides contained in 22 contigs with a G + C ratio of 42.0%, 3.826 coding sequences, and 73 RNAs. In silico analysis guided identification of two putative genes coding for synthesis of surfactin A, a lipopeptide with 7 amino acids, and for a circular bacteriocin belonging to the circularin A/uberolysin family, respectively.

Occurrence and identification of microplastics in beach sediments from the Hauts-de-France region.

The present work was carried out to quantify microplastics (MP) from three sandy beaches along the Côte d'Opale coastline located in the Hauts-de-France region of northern France. Three different study sites located along the English Channel were investigated due to different levels of anthropopression and hydrodynamic conditions. Sediments were collected at three different tide lines: high tide line (HTL), middle of the intertidal zone (IZ), and low tide line (LTL), to investigate the effects of tide line on microplastic contamination. Particles and fibers were counted and colors were recorded; polymer identification was then performed using pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS). Particle and fiber abundances ranged from 23.4 ± 18.9 to 69.3 ± 30.6 items kg-1 dry weight sediment, with a trend towards fiber predominance, were observed. No difference in particle and fiber abundance was found between the different beaches and tide lines, except for Boulogne-sur-Mer, where the particle number was significantly different between tide lines. Major polymers identified were polyethylene (36.6%) and polypropylene (10.7%). This citizen science project provided preliminary data about the abundance and polymeric nature of MP along the Côte d'Opale coastline.

Mitochondrial activity as an indicator of fish freshness.

The current methods used to routinely assess freshness in the fishing industry reflect more a state of spoilage than a state of freshness. Mitochondria, the seat of cellular respiration, undergo profound changes in post mortem tissues. The objective of this study was to demonstrate that mitochondrial activity constitutes a putative early fish freshness marker. The structure of gilthead sea bream (Sparus aurata) muscle tissue was evaluated over time by transmission electron microscopy. Respiration was assessed in mitochondria isolated from sea bream fillets using oxygraphy. Membrane potential (ΔΨm) was determined by fluorescence (Rhodamine 123). Mitochondrial activity of fillets stored at +4 °C was studied for 6 days. Changes in mitochondrial cristae structure appeared from Day 3 highlighting the presence of dense granules. ΔΨm and mitochondrial activity were significantly disrupted in sea bream fillets after 96 h of storage at +4 °C. Mitochondrial activity constituted a reliable and early indicator of fish freshness.

Population response of the estuarine copepod Eurytemora affinis to its bioaccumulation of trace metals.

We evaluated the acute toxicities of metals cadmium (Cd), copper (Cu) and nickel (Ni) to a widely-distributed copepod Eurytemora affinis isolated from the Seine estuary. Both sexes of adult E. affinis were exposed separately to the three metals at concentration gradients to determine its 50% lethal concentration (LC50). After 4 days of exposure, both males and females showed a higher sensitivity to Cu (male LC50: 25.0 µg.L-1 and female LC50: 38.0 µg.L-1) than to Ni (male LC50: 90.0 µg.L-1 and female 161.0 µg.L-1) and Cd (male LC50: 127.8 µg.L-1 and female LC50: 90.0 µg.L-1). To assess for the first time, the extend of metal bioaccumulation and its effect at population scale, late stages (>200 µm) were collected and exposed to each metal at the concentration of 1/3 LC50, and to their mixture during 144 h without feeding. The Cd concentration consistently increased with time until the end of the experiment, whereas the Ni and Cu concentrations reached a plateau after 24 h and 72 h exposure, respectively. The results revealed that the copepods could accumulate Cu faster than Ni and Cd either in the treatment alone (0.58 L g-1.d-1) or in the three-metal mixture (0.72 L g-1.d-1) after 50% of exposure time (72 h). The number of individuals decreased in copepod populations except for the Cd treatment, where the number of nauplii increased. In addition, all treatments of metal exposure negatively affected bacterial densities in the copepod cultures, where the Cu treatment showed a negative remarkable effect compared with Cd and Ni treatment did.

Use of Ratiometric Probes with a Spectrofluorometer for Bacterial Viability Measurement.

Assessment of microorganism viability is useful in many industrial fields. A large number of methods associated with the use of fluorescent probes have been developed, including fluorimetry, fluorescence microscopy, and cytometry. In this study, a microvolume spectrofluorometer was used to measure the membrane potential variations of Escherichia coli. In order to estimate the sensitivity of the device, the membrane potential of E. coli was artificially disrupted using an ionophore agent: carbonyl cyanide 3-chlorophenylhydrazone. The membrane potential was evaluated using two ratiometric methods: a Rhodamine 123/4',6-diamidino-2-phenylindole combination and a JC-10 ratiometric probe. These methods were used to study the impact of freezing on E. coli, and were compared with the conventional enumeration method. The results showed that it was beneficial to use this compact, easy-to-use, and inexpensive spectrofluorometer to assess the viability of bacterial cells via their membrane potential.

Determination of the cell wall polysaccharide and teichoic acid structures from Lactococcus lactis IL1403.

In the lactic acid bacterium Lactococcus lactis, a cell wall polysaccharide (CWPS) is the bacterial receptor of the majority of infecting bacteriophages. The diversity of CWPS structures between strains explains, at least partially, the narrow host range of lactococcal phages. In the present work, we studied the polysaccharide components of the cell wall of the prototype L. lactis subsp. lactis strain IL1403. We identified a rhamnose-rich complex polysaccharide, carrying a glycerophosphate substitution, as the major component. Its structure was analyzed by 2D NMR spectroscopy, methylation analysis and MALDI-TOF MS and shown to be distinctly different from currently known lactococcal CWPS structures. It contains a linear backbone of repeated α-l-Rha disaccharide subunits, which is irregularly substituted with a trisaccharide occasionally bearing a glycerophosphate group. A poly (glycerol phosphate) teichoic acid, another important carbohydrate component of the IL1403 cell wall, was also isolated and structurally characterized.

Structural studies of the cell wall polysaccharide from Lactococcus lactis UC509.9.

Lactococcus lactis is the most widely utilised starter bacterial species in dairy fermentations. The L. lactis cell envelope contains polysaccharides, which, among other known functions, serve as bacteriophage receptors. Our previous studies have highlighted the structural diversity of these so-called cell wall polysaccharides (CWPSs) among L. lactis strains that could account for the narrow host range of most lactococcal bacteriophages. In the present work, we studied the CWPS of L. lactis strain UC509.9, an Irish dairy starter strain that is host to the temperate and well-characterized P335-type phage Tuc2009. The UC509.9 CWPS structure was analyzed by methylation, deacetylation/deamination, Smith degradation and 2D NMR spectroscopy. The CWPS consists of a linear backbone composed of a tetrasaccharide repeat unit, partially substituted with a branched phosphorylated oligosaccharide having a common trisaccharide and three non-stoichiometric substitutions.

Isolation and Characterization of Bacteria Colonizing Acartia tonsa Copepod Eggs and Displaying Antagonist Effects against Vibrio anguillarum, Vibrio alginolyticus and Other Pathogenic Strains.

Copepods represent a major source of food for many aquatic species of commercial interest for aquaculture such as mysis shrimp and early stages of fishes. For the purpose of this study, the culturable mesophilic bacterial flora colonizing Acartia tonsa copepod eggs was isolated and identified. A total of 175 isolates were characterized based on their morphological and biochemical traits. The majority of these isolates (70%) were Gram-negative bacteria. Matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) was used for rapid identification of bacterial isolates. Here, 58% of isolates were successfully identified at the genus level and among them, 54% were identified at the species level. These isolates belong to 12 different genera and 29 species. Five strains, identified as Bacillus pumilus, named 18 COPS, 35A COPS, 35R COPS, 38 COPS, and 40A COPS, showed strong antagonisms against several potential fish pathogens including Vibrio alginolyticus, V. anguillarum, Listeria monocytogenes, and Staphylococcus aureus. Furthermore, using a differential approach, we show that the antimicrobial activity of the 35R COPS strain is linked primarily to the production of antimicrobial compounds of the amicoumacin family, as demonstrated by the specific UV-absorbance and the MS/MS fragmentation patterns of these compounds.

Development of a qPCR Method for the Identification and Quantification of Two Closely Related Tuna Species, Bigeye Tuna (Thunnus obesus) and Yellowfin Tuna (Thunnus albacares), in Canned Tuna.

Bigeye tuna (Thunnus obesus) and yellowfin tuna (Thunnus albacares) are among the most widely used tuna species for canning purposes. Not only substitution but also mixing of tuna species is prohibited by the European regulation for canned tuna products. However, as juveniles of bigeye and yellowfin tunas are very difficult to distinguish, unintentional substitutions may occur during the canning process. In this study, two mitochondrial markers from NADH dehydrogenase subunit 2 and cytochrome c oxidase subunit II genes were used to identify bigeye tuna and yellowfin tuna, respectively, utilizing TaqMan qPCR methodology. Two different qPCR-based methods were developed to quantify the percentage of flesh of each species used for can processing. The first one was based on absolute quantification using standard curves realized with these two markers; the second one was founded on relative quantification with the universal 12S rRNA gene as the endogenous gene. On the basis of our results, we conclude that our methodology could be applied to authenticate these two closely related tuna species when used in a binary mix in tuna cans.

Structural studies of the rhamnose-rich cell wall polysaccharide of Lactobacillus casei BL23.

Lactobacillus casei is a Gram positive lactic acid bacterium used in dairy fermentations and present in the normal human gut microbiota. Certain strains are recognized as probiotics with beneficial effects on human and animal health. L. casei BL23 is a potential probiotic strain endowed with anti-inflammatory properties and a model strain widely used in genetic, physiological and biochemical studies. A number of bacterial cell surface polysaccharides have been shown to play a role in the immune modulation activities observed for probiotic lactic acid bacteria. In the present work, we purified the most abundant carbohydrate polymer of L. casei BL23 cell wall, a neutral wall polysaccharide (WPS) and established its chemical structure by periodate oxidation, methylation analysis and 2D NMR spectroscopy. The WPS of L. casei BL23 was shown to contain α-Rha, α-Glc, ß-GlcNAc and ß-GalNAc forming a branched heptasaccharide repeating unit (variant 1) with an additional partial substitution with α-Glc (variant 2). A modified non-reducing end octasaccharide, corresponding to a terminal unit of the WPS (variant 3), was also identified and allowed to define the biological repeating unit of the WPS. To our knowledge, this is the first report of the identification of a biological repeating unit based on a chemical evidence, in a cell wall polysaccharide of a Gram positive bacterial species.

Assessment of freshness and freeze-thawing of sea bream fillets (Sparus aurata) by a cytosolic enzyme: Lactate dehydrogenase.

The evaluation of freshness and freeze-thawing of fish fillets was carried out by assessment of autolysis of cells using a cytosolic enzyme lactate dehydrogenase. Autolysis plays an important role in spoilage of fish and postmortem changes in fish tissue are due to the breakdown of the cellular structures and release of cytoplasmic contents. The outflow of a cytosolic enzyme, lactate dehydrogenase, was studied in sea bream fillets and the Sparus aurata fibroblasts (SAF-1) cell-line during an 8day storage period at +4°C. A significant increase of lactate dehydrogenase release was observed, especially after 5days of storage. The ratio between the free and the total lactate dehydrogenase activity is a promising predictive marker to measure the quality of fresh fish fillets. The effect of freeze-thawing on cytosolic lactate dehydrogenase and lysosomal α-d-glucosidase activities was also tested. Despite the protecting effect of the tissue compared to the cell-line, a loss of lactate dehydrogenase activity, but not of α-d-glucosidase, was observed. In conclusion, lactate dehydrogenase may be used as a marker to both assess freshness of fish and distinguish between fresh and frozen-thawed fish fillets.