Functional Characterization of Probiotic Potential of Novel Pigmented Bacterial Strains for Aquaculture Applications

Host Gut-Derived Probiotic, Exiguobacterium acetylicum G1-33, Improves Growth, Immunity, and Resistance to Vibrio harveyi in Hybrid Grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂)

Several exogenous probiotics are applicable in fish culture; however, challenges in isolation and verification have hindered the full utilization of numerous host probiotics. Therefore, this study aimed to apply the host probiotic Exiguobacterium acetylicum G1-33 to hybrid grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) cultures and explore its mechanism of action. In total, 360 hybrid grouper were divided into four groups, which were fed the following for 60 days: three received commercial feed with varying concentrations of E. acetylicum G1-33 (106, 108, and 1010 CFU/g), while a control group received commercial feed. The results showed that supplementation with 106 and 108 CFU/g of E. acetylicum G1-33 enhanced gut morphology, upregulated growth-related genes (ghr1, igf-2, s6k1, tor), and promoted growth, with supplementation with 108 CFU/g resulting in the most notable enhancement. However, supplementation with 1010 CFU/g inhibited growth, possibly because of changes in intestinal morphology. Additionally, supplementation with E. acetylicum G1-33 upregulated the expression of immune-related genes (c3, myd88, Cu/Zn-sod, tlr3, and tnf2) in the liver and head kidney but led to an increase in malondialdehyde content, as well as a decrease in alkaline phosphatase and acid phosphatase activities, in the liver and serum, indicating increased oxidative stress. Moreover, supplementation with 106 and 108 CFU/g E. acetylicum G1-33 enhanced the widespread expression of immune-related genes in the head kidney and liver, respectively, and improved resistance to Vibrio harveyi, whereas supplementation with 1010 CFU/g weakened this resistance. In conclusion, E. acetylicum G1-33, particularly at 108 CFU/g, emerged as an effective probiotic, optimizing growth performance and immunity in hybrid grouper. This research is pioneering in its application of E. acetylicum in mariculture, potentially broadening the range of probiotic strategies in aquaculture.

Eubiotic Effect of a Dietary Bio-Aqua® and Sodium Diformate (NaDF) on Salmo trutta caspius: Innate Immune System, Biochemical Indices, Antioxidant Defense, and Expression of Immunological and Growth-Related Genes

The present study investigated the effects of combined and singular oral administration of Bio-Aqua® with different dosages of sodium diformate (NaDF) on biochemical indices, innate immune responses, antioxidant effects, and expressions of immunological related genes of Caspian brown trout (Salmo trutta caspius). Fingerlings Salmo trutta caspius (n = 1800; initial weight 15 ± 3 g) were randomly allocated into five groups (120 fish group-1 in triplicates). Control diet: without any addition, G1, G2, G3, and G4 received diets containing 0.2 g kg-1 commercial probiotic Bio-Aqua® combined with 0, 0.5, 1.0, and 1.5% NaDF to the basal diet for 60 days according to recommended dosages reported in previous studies. Results indicated that serum bactericidal activity (G3 on day 60 and G1 on day 30) and classic complement in all groups (on day 60) (G1 and G2 on day 30) were significantly elevated (P < 0.05). The serum lysozyme, glucose, globulin, and albumin levels showed no significant differences between all groups compared to the control group (P > 0.05). On days 30 and 60 of the sampling, no significant difference was observed in the amount of superoxide disotase (SOD) and catalase (CAT) between the treatments (P > 0.05) but activity of malondialdehyde (MDA) was lower in G1 than the control (P < 0.05). The expression of the immune-regulating genes IL-10, IL-1β, GTP, FATP, and IGF was significantly improved in all probiotic + acidifier-treated groups (P < 0.05). The current findings showed that mixture of Bio-Aqua® and NaDF (1.5% + pro) is beneficial, as it effectively improves some immune parameters and expression of immunological and growth-related genes in Caspian brown trout.

Synthesis and Structural Characterization of Selenium Nanoparticles-Bacillus sp. MKUST-01 Exopolysaccharide (SeNPs-EPS) Conjugate for Biomedical Applications

Exopolysaccharides (EPS) are exogenous microbial metabolites generated predominantly during the development of bacteria. They have several biological potentials, including antibacterial, antioxidant, and anticancer actions. Polysaccharide-coated nanoparticles have high biological activity and are used in treatments and diagnostics. In this research, selenium nanoparticles (SeNPs) are synthesized and conjugated with bacterial (Bacillus sp. MKUST-01) exopolysaccharide (EPS). Initially, the creation of SeNPs conjugates was verified through UV-Vis spectral examination, which exhibited a prominent peak at 264 nm. Additionally, X-ray diffraction (XRD) analysis further substantiated the existence of crystalline Se, as evidenced by a robust reflection at 29.78°. Another reflection observed at 23.76° indicated the presence of carbon originating from the EPS. Fourier transform infrared spectroscopy (FT-IR) analysis of the EPS capped with SeNPs displayed characteristic peaks at 3425 cm-1, 2926 cm-1, 1639 cm-1, and 1411 cm-1, corresponding to the presence of O-H, C-H, C=O, and COO-groups. The SeNPs themselves were found to possess elongated rod-shaped structures with lengths ranging from 250 to 550 nm and a diameter of less than 70 nm, as confirmed using scanning electron microscopy and particle size analysis. In contrast to the SeNPs, the SeNPs-EPS conjugates showed no hemolytic activity. The overall antioxidant activity of SeNPs-EPS conjugates outperformed 20% higher than SeNPs and EPS. Additionally, experimental observations involving gnotobiotic Artemia nauplii experiments were also recorded, such as the supplementation of EPS and SeNPs-EPS conjugates corresponding to enhanced growth and increased survival rates compared to Artemia nauplii fed with SeNPs and a microalgal diet.

Improvement of growth, yield and associated bacteriome of rice by the application of probiotic Paraburkholderia and Delftia

Plant probiotic bacteria enhance growth and yield of crop plants when applied at the appropriate time and dose. Two rice probiotic bacteria, Paraburkholderia fungorum strain BRRh-4 and Delftia sp. strain BTL-M2 promote growth and yield of plants. However, no information is available on application of these two bacteria on growth, yield, and diversity and population of bacteriome in roots and rhizosphere soils of the treated rice plants. This study aimed to assess the effect of BRRh-4 and BTL-M2 application on growth, yield and bacteriome in roots and rhizosphere soil of rice under varying doses of N, P and K fertilizers. Application of BRRh-4 and BTL-M2 strains significantly (p < 0.05) increased seed germination, growth and yield of rice compared to an untreated control. Interestingly, the grain yield of rice by these bacteria with 50% less of the recommended doses of N, P, and K fertilizers were statistically similar to or better than the rice plants treated with 100% doses of these fertilizers. Targeted amplicon (16S rRNA) sequence-based analysis revealed significant differences (PERMANOVA, p = 0.00035) in alpha-diversity between the root (R) and rhizosphere soil (S) samples, showing higher diversity in the microbial ecosystem of root samples. Additionally, the bacteriome diversity in the root of rice plants that received both probiotic bacteria and chemical fertilizers were significantly higher (PERMANOVA, p = 0.0312) compared to the rice plants treated with fertilizers only. Out of 185 bacterial genera detected, Prevotella, an anaerobic and Gram-negative bacterium, was found to be the predominant genus in both rhizosphere soil and root metagenomes. However, the relative abundance of Prevotella remained two-fold higher in the rhizosphere soil metagenome (52.02%) than in the root metagenome (25.04%). The other predominant bacterial genera detected in the rice root metagenome were Bacillus (11.07%), Planctomyces (4.06%), Faecalibacterium (3.91%), Deinococcus (2.97%), Bacteroides (2.61%), and Chryseobacterium (2.30%). On the other hand, rhizosphere soil metagenome had Bacteroides (12.38%), Faecalibacterium (9.50%), Vibrio (5.94%), Roseomonas (3.40%), and Delftia (3.02%). Interestingly, we found the presence and/or abundance of specific genera of bacteria in rice associated with the application of a specific probiotic bacterium. Taken together, our results indicate that improvement of growth and yield of rice by P. fungorum strain BRRh-4 and Delftia sp. strain BTL-M2 is likely linked with modulation of diversity, structures, and signature of bacteriome in roots and rhizosphere soils. This study for the first time demonstrated that application of plant growth promoting bacteria significantly improve growth, yield and increase the diversity of bacterial community in rice.

Bacterial Carotenoids: Extraction, Characterization, and Applications

Natural carotenoids are secondary metabolites that exhibit antioxidant, anti-inflammatory, and anti-cancer properties. These types of compounds are highly demanded by pharmaceutical, cosmetic, nutraceutical, and food industries, leading to the search for new natural sources of carotenoids. In recent years, the production of carotenoids from bacteria has become of great interest for industrial applications. In addition to carotenoids with C40-skeletons, some bacteria have the ability to synthesize characteristic carotenoids with C30-skeletons. In this regard, a great variety of methodologies for the extraction and identification of bacterial carotenoids has been reported and this is the first review that condenses most of this information. To understand the diversity of carotenoids from bacteria, we present their biosynthetic origin in order to focus on the methodologies employed in their extraction and characterization. Special emphasis has been made on high-performance liquid chromatography-mass spectrometry (HPLC-MS) for the analysis and identification of bacterial carotenoids. We end up this review showing their potential commercial use. This review is proposed as a guide for the identification of these metabolites, which are frequently reported in new bacteria strains.

Isolation of Lactic Acid Bacteria from Intestine of Freshwater Fishes and Elucidation of Probiotic Potential for Aquaculture Application

Probiotics play significant roles in enhancing systemic immunity, improving intestinal balance and feed value, enhancing enzymatic digestion, and inhibiting pathogenic microorganisms of freshwater fish. Probiotics from an identical organism's gastrointestinal system promote effective colonization and provide greater benefits than other sources. This study aimed to evaluate the usefulness of probiotic bacteria isolated from the intestines of freshwater fishes for a dietary supplement of freshwater aquaculture. A total of 120 isolates were collected from freshwater fishes of Channa striata, Puntius filamentosus, Oreochromis mossambicus, Cirrhinus mrigala, and Rasbora daniconius. Seven of these isolates exhibited antagonistic activity against fish pathogens: Aeromonas hydrophila, Staphylococcus epidermidis, Staphylococcus aureus, Bacillus cereus, Escherichia coli, and Pseudomonas aeruginosa. Using 16S rRNA gene sequencing analysis, the isolates were identified as Enterococcus sp., Lactococcus lactis, Weissella cibaria, and Limosilactobacillus fermentum. Of these tolerates, L. fermentum URLP18 isolated from C. mrigala exhibited high tolerance to low acidic (pH 2.0) and high bile salt (2%) concentrations, exhibiting a significant hydrophobicity and extracellular enzyme secretions like amylase, protease, and lipase. In vitro evaluations on intestinal mucus indicate that L. fermentum URLP18 have strong adherence capacity, and its survival rate increased after being administered to Artemia nauplii. The results suggest that L. fermentum URLP18 has high probiotic potential and is an effective dietary supplement for freshwater aquaculture.

Characterisation of a potential probiotic strain Paracoccus marcusii KGP and its application in whey bioremediation

Whey, the main by-product obtained from the manufacture of cheese, which contains a very high organic load (mainly due to the lactose content), is not easily degradable and creates concern over environmental issues. Hydrolysis of lactose present in whey and conversion of whey lactose into valuable products such as bioethanol, sweet syrup, and animal feed offers the possibility of whey bioremediation. The increasing need for bioremediation in the dairy industry has compelled researchers to search for a novel source of β-galactosidase with diverse properties. In the present study, the bacterium Paracoccus marcusii KGP producing β-galactosidase was subjected to morphological, biochemical, and probiotic characterisation. The bacterial isolate was found to be non-pathogenic and resistant to low pH (3 and 4), bile salts (0.2%), salt (10%), pepsin (at pH 3), and pancreatin (at pH 8). Further characterisation revealed that the bacteria have a good auto-aggregation ability (40% at 24 h), higher hydrophobicity (chloroform-60%, xylene-50%, and ethyl acetate-40%) and a broad spectrum of antibiotic susceptibility. The highest growth of P. marcusii KGP was achieved at pH 7 and 28 °C, and the yeast extract, galactose, and MgSO₄ were the best for the growth of the bacterial cells. The bacterium KGP was able to utilise whey as a substrate for its growth with good β-galactosidase production potential. Furthermore, the β-galactosidase extracted from the isolate KGP could hydrolyse 47% whey lactose efficiently at 50 °C. The study thus reveals the potential application of β-galactosidase from P. marcusii KGP in whey bioremediation.

Dietary Administration of Probiotic Aeromonas veronii V03 on the Modulation of Innate Immunity, Expression of Immune-Related Genes and Disease Resistance Against Aeromonas hydrophila Infection in Common Carp (Cyprinus carpio)

This study investigates the effects of dietary Aeromonas veronii V03 supplementation on growth performances, innate immunity, and expression of immune-related genes in lymphoid organs of Cyprinus carpio and resistance to Aeromonas hydrophila infection. Fish were fed for 4 weeks with basal diet (BD; without probiotic), and experiment diet containing different doses of A. veronii V03 at 3.2 × 10⁷ (DI) and 3.5 × 10⁹ (DII) CFU g^-1 of diet. At the end of the probiotic feeding trial, fish were challenged with A. hydrophila, and the percentage of survival rates was recorded over 7 days. Results revealed that fish fed with A. veronii V03 demonstrated a significant improvement in growth and enhancement of innate immunity, including respiratory burst, myeloperoxidase, and lysozyme activities, and total immunoglobulin level compared with BD fed to fish. Relatively, expression of cytokines (MyD88, IL-1β1, IL-8, and IL-10) and c- and g-type lysozymes were significantly up- and downregulated in lymphoid organs of fish. Moreover, dietary supplementation of A. veronii V03 exhibited significantly (p < 0.001) higher survival rates of DI (90%) and DII (96.66%) compared with BD (53.33%) fed fish against A. hydrophila infection. These findings help to understand the effects of probiotic A. veronii V03 administrated feed influences on growth and ailment resistance to A. hydrophila infection by regulating innate and systemic immunity in common carp fish.

Bacterial Diversity and Antibiotic Susceptibility of Sparus aurata from Aquaculture

In a world where the population continues to increase and the volume of fishing catches stagnates or even falls, the aquaculture sector has great growth potential. This study aimed to contribute to the depth of knowledge of the diversity of bacterial species found in Sparus aurata collected from a fish farm and to understand which profiles of diminished susceptibility to antibiotics would be found in these bacteria that might be disseminated in the environment. One hundred thirty-six bacterial strains were recovered from the S. aurata samples. These strains belonged to Bacillaceae, Bacillales Family XII. Incertae Sedis, Comamonadaceae, Enterobacteriaceae, Enterococcaceae, Erwiniaceae, Micrococcaceae, Pseudomonadaceae and Staphylococcaceae families. Enterobacter sp. was more frequently found in gills, intestine and skin groups than in muscle groups (p ≤ 0.01). Antibiotic susceptibility tests found that non-susceptibility to phenicols was significantly higher in gills, intestine and skin samples (45%) than in muscle samples (24%) (p ≤ 0.01) and was the most frequently found non-susceptibility in both groups of samples. The group of Enterobacteriaceae from muscles presented less decreased susceptibility to florfenicol (44%) than in the group of gills, intestine and skin samples (76%). We found decreased susceptibilities to β-lactams and glycopeptides in the Bacillaceae family, to quinolones and mupirocin in the Staphylococcaceae family, and mostly to β-lactams, phenicols and quinolones in the Enterobacteriaceae and Pseudomonadaceae families. Seven Enterobacter spp. and five Pseudomonas spp. strains showed non-susceptibility to ertapenem and meropenem, respectively, which is of concern because they are antibiotics used as a last resort in serious clinical infections. To our knowledge, this is the first description of species Exiguobacterium acetylicum, Klebsiella michiganensis, Lelliottia sp. and Pantoea vagans associated with S. aurata (excluding cases where these bacteria are used as probiotics) and of plasmid-mediated quinolone resistance qnrB19-producing Leclercia adecarboxylata strain. The non-synonymous G385T and C402A mutations at parC gene (within quinolone resistance-determining regions) were also identified in a Klebsiella pneumoniae, revealing decreased susceptibility to ciprofloxacin. In this study, we found not only bacteria from the natural microbiota of fish but also pathogenic bacteria associated with fish and humans. Several antibiotics for which decreased susceptibility was found here are integrated into the World Health Organization list of "critically important antimicrobials" and "highly important antimicrobials" for human medicine.

Hydrolytic Exoenzymes Produced by Bacteria Isolated and Identified From the Gastrointestinal Tract of Bombay Duck

Bacteria producing hydrolytic exoenzymes are of great importance considering their contribution to the host metabolism as well as for their various applications in industrial bioprocesses. In this work hydrolytic capacity of bacteria isolated from the gastrointestinal tract of Bombay duck (Harpadon nehereus) was analyzed and the enzyme-producing bacteria were genetically characterized. A total of twenty gut-associated bacteria, classified into seventeen different species, were isolated and screened for the production of protease, lipase, pectinase, cellulase and amylase enzymes. It was found that thirteen of the isolates could produce at least one of these hydrolytic enzymes among which protease was the most common enzyme detected in ten isolates; lipase in nine, pectinase in four, and cellulase and amylase in one isolate each. This enzymatic array strongly correlated to the previously reported eating behavior of Bombay duck. 16S rRNA gene sequence-based taxonomic classification of the enzyme-producing isolates revealed that the thirteen isolates were grouped into three different classes of bacteria consisting of eight different genera. Staphylococcus, representing ∼46% of the isolates, was the most dominant genus. Measurement of enzyme-production via agar diffusion technique revealed that one of the isolates which belonged to the genus Exiguobacterium, secreted the highest amount of lipolytic and pectinolytic enzymes, whereas a Staphylococcus species produced highest proteolytic activity. The Exiguobacterium sp. expressing a maximum of four hydrolases, appeared to be the most promising isolate of all.

Diapolycopenedioic-acid-diglucosyl ester and keto-myxocoxanthin glucoside ester: Novel carotenoids derived from Exiguobacterium acetylicum S01 and evaluation of their anticancer and anti-inflammatory activities

Inflammation is pivotal for the development of gastrointestinal cancer and linked to poor survival and limited therapeutic options. In this study, six structurally different carotenoids were isolated and identified from the methanolic extract of Exiguobacterium acetylicum S01 namely lycopene (Car-I), diapolycopenedioic-acid-diglucosyl-ester (Car-II), β-carotene (Car-III), zeaxanthin (Car-IV), astaxanthin (Car-V), and keto-myxocoxanthin glucoside-ester (Car-VI). Further, their anti-cancer, anti-inflammatory, and antioxidant potentials were evaluated. The MTT assay was used to determine the effect of carotenoids on viability of colorectal cancer (HT-29) as well as peripheral blood mononuclear cells (PBMCs). Results revealed that all the six carotenoids were demonstrated a significant inhibition of HT-29 cells viability in a dose-dependent manner whereas there was no cytotoxic effect in PBMCs. The study also recorded that six carotenoids considerably inhibited lipopolysaccharide (LPS)-induced nitric oxide (NO) production, tumor necrosis factor-alpha (TNF-α), and lipid peroxidation in PBMCs. Moreover, antioxidant potentials of Car-II and Car-VI were significantly (p = 0.001) higher than ascorbic acid as determined by a 2,2-diphenyl-1-picrylhydrazyl radical scavenging assay. Therefore, our results ascertained the role of carotenoids derived from E. acetylicum S01 in developing potential therapeutic agents for inflammation-associated cancer.

Induction of mitochondria-mediated apoptosis and suppression of tumor growth in zebrafish xenograft model by cyclic dipeptides identified from Exiguobacterium acetylicum

Colorectal cancer is the most common type of gastrointestinal cancers with poor survival and limited therapeutic options. In this study, four structurally different cyclic dipeptides (or diketopiperazine) were isolated and identified as cyclo (l-Pro-l-Leu), cyclo (l-Pro-l-Val), cyclo (l-Pro-l-Phe) and cyclo (l-Pro-l-Tyr) from the ethyl acetate extract in the cell-free filtrate of Exiguobacterium acetylicum S01. The anticancer potential of identified DKPs on colorectal cancer HT-29 cells in vitro and in vivo zebrafish xenograft model was evaluated. The MTT (3-(4, 5-dimethylthiazol-2yl)-2, 5-diphenyltetrazolium bromide)) assay showed that four DKPs exhibited significant inhibition of HT-29 cells viability in a dose-dependent manner whereas there were no cytotoxic effects on normal mouse fibroblast 3T3 cells. Also, we observed that all DKPs induce early and late apoptotic cell death in HT-29 cells. Moreover, the expression levels of apoptotic (cytochrome-c, caspase-3 and Bid) and anti-apoptotic (Bcl-2) markers were up- and down-regulated in HT-29 cells in response to DKPs treatments. Furthermore, these four DKPs remarkably inhibited the tumor progression in a zebrafish xenograft model within a nonlethal dose range. Overall, our findings suggest that cyclic dipeptides derived from E. acetylicum S01 could be promising chemopreventive/ therapeutic candidates against cancer.

Long-term effects of three probiotics, singular or combined, on serum innate immune parameters and expressions of cytokine genes in rainbow trout during grow-out

The long-term effects of three dietary probiotics on rainbow trout during grow-out (mean body weight = 250 ± 50 g) were investigated by feeding for 130 days on eight diet treatments supplemented with Lactobacillus buchneri, L. fermentum and Saccharomyces cerevisiae at 10⁷ CFU/g, singularly or in combination. Fish samples were taken for biochemical and immunological analysis in addition to growth performance indices at days 30 and 130 of the experiment. The expression levels of TNF-α and IL-1β genes were also measured at day 130. A positive effect on food conversion was observed in rainbow trout with dietary inclusion of S. cerevisiae (P < 0.05) over 130 days. Also, the total number of white blood cells and their differential count (blood neutrophils, lymphocytes and monocytes), as well as respiratory burst activity were all significantly affected by different treatments at 130 days (P < 0.05). Moreover, at 130 days there was a significant increase in the expression of TNF-α and IL-1β in yeast present treatment compared to the control group (P < 0.05), but no significant difference in the combined probiotic treatments from control group. Yeast and L. buchneri showed a contrary effect on the immune gene expression regulation. Serum cholesterol was significantly lower in all treatments receiving yeast as a dietary probiotic, either alone or in combination with other probiotics. However, none of the probiotic treatments had a significant effect on trout growth performance, or total protein, albumin, globulin, triglyceride and the red blood cell count after 30 or 130 days. Overall, the results suggest that inclusion of a single dietary probiotic, especially S. cerevisiae, in rainbow trout during grow-out has a greater positive effect than combinations of probiotics on the immune system.

Optimization of submerged fermentation process for improved production of β-carotene by Exiguobacterium acetylicum S01

Carotenoids are natural pigments with substantial applications in nutraceutical, pharmaceutical, and food industries. In this study, optimization of the fermentation process for enhancement of β-carotene and biomass production by Exiguobacterium acetylicum S01 was achieved by employing statistical designs including the Placket-Burman design (PBD) and response surface methodology (RSM). Among the seven variables investigated by two levels in PBD, glucose, peptone, pH and temperature were indicated as crucial variables (p < 0.0001) for β-carotene and biomass productivity. Response surface methodology was further applied to evaluate the optimal concentrations of these four variables for maximum β-carotene and biomass productivity. The optimized medium contained glucose 1.4 g/L, peptone 26.5 g/L, pH 8.5, and temperature 30 °C, respectively. A significant increase in β-carotene (40.32 ± 2.55 mg/L) and biomass (2.19 ± 0.10 g/L) productivities in E. acetylicum S01 were achieved by using RSM, which was 3.47-fold and 2.36-fold higher in the optimized medium compared to the un-optimized medium. Further, the optimum fermentation condition in the 5-L bioreactor was achieved a maximal β-carotene yield of 107.22 ± 5.78 mg/L within 96 h. Moreover, the expression levels of carotenoid biosynthetic genes (phytoene desaturase (CrtI) and phytoene synthase (CrtB)) were up-regulated (2.89-fold and 3.71-fold) in E. acetylicum under the optimized medium conditions. Overall, these results suggest that E. acetylicum S01 can be used as a promising microorganism for the commercial production of β-carotene.