In Vitro Selection and Identification of Potential Probiotics Isolated from the Gastrointestinal Tract of Nile Tilapia, Oreochromis niloticus

Infection dynamics of Shewanella spp. in Nile tilapia under varied water temperatures: A hematological, biochemical, antioxidant-immune analysis, and histopathological alterations

In aquaculture, fluctuating water temperatures can act as a potent stressor, influencing the virulence and transmission dynamics of pathogenic bacteria, potentially triggering outbreaks and impacting fish health. The purpose of this work was to examine the impact of Shewanella spp. infection on hematological, biochemical, and antioxidant-immune parameters of Nile tilapia (Oreochromis niloticus) under different water temperatures. For this purpose, 180 fish were divided into 6 groups in triplicate (30 fish per group; 10 fish per replicate). Group 1 (G1), G2, and G3 were reared at varying water temperatures (22 °C, 28 °C, and 31 °C, respectively) without infection. While G4, G5, and G6 were IP-injected with 0.2 mL of Shewanella spp. (0.14 × 105) and reared at 22 °C, 28 °C, and 31 °C, respectively. Shewanella spp. infection induced significant lowering (p < 0.05) in hematological parameters (red and white blood cells, hemoglobin, and packed cell volume%) and immune-antioxidant responses (phagocytic activity%, phagocytic index, lysozyme, nitric oxide), total antioxidant capacity, catalase, and reduced glutathione, especially at 22 °C. Moreover, a significant increase (p < 0.05) in the hepato-renal function indicators (alanine aminotransferase, aspartate aminotransferase, urea, and creatinine), stress biomarkers (glucose and cortisol), malondialdehyde, and pro-inflammatory cytokines (interleukin-1β and tumor necrosis factor-α) were the consequences of the Shewanella spp. infection, especially at 22 °C. The Shewanella spp. infection exhibited marked histopathological changes in the hepatic and renal tissues. Worthily, Shewanella spp. can cause detrimental alterations in Nile tilapia's hematological, biochemical, and antioxidant-immune parameters at various water temperatures, but the major detrimental changes were observed at a water temperature of 22 °C. Consequently, we can conclude that the infection dynamics of Shewanella spp. are exaggerated at 22 °C. These outcomes could help in understanding the nature of such an infection in Nile tilapia.

Unveiling the Probiotic Potential of the Anaerobic Bacterium Cetobacterium sp. nov. C33 for Enhancing Nile Tilapia (Oreochromis niloticus) Cultures

The bacterium strain Cetobacterium sp. C33 was isolated from the intestinal microbial content of Nile tilapia (O. niloticus) under anaerobic conditions. Given that Cetobacterium species are recognized as primary constituents of the intestinal microbiota in cultured Nile tilapia by culture-independent techniques, the adaptability of the C33 strain to the host gastrointestinal conditions, its antibacterial activity against aquaculture bacterial and its antibiotic susceptibility were assessed. The genome of C33 was sequenced, assembled, annotated, and subjected to functional inference, particularly regarding pinpointed probiotic activities. Furthermore, phylogenomic comparative analyses were performed including closely reported strains/species relatives. Comparative genomics with closely related species disclosed that the isolate is not phylogenetically identical to other Cetobacterium species, displaying an approximately 5% sequence divergence from C. somerae and a 13% sequence divergence from Cetobacterium ceti. It can be distinguished from other species through physiological and biochemical criteria. Whole-genome annotation highlighted that Cetobacterium sp. nov. C33 possesses a set of genes that may contribute to antagonism against competing bacteria and has specific symbiotic adaptations in fish. Additional in vivo experiments should be carried out to verify favorable features, reinforcing its potential as a probiotic bacterium.

Lysinibacillus capsici 38,328 isolated from agricultural soils as a promising probiotic candidate for intestinal health

There is an increasing interest in the use of spore-forming Bacillus spp. as probiotic ingredients on the market. However, probiotics Bacillus species are insufficient, and more safe Bacillus species were required. In the study, traditional fermented foods and soil samples were collected from more than ten provinces in China, and 506 Bacillus were selected from 109 samples. Using the optimized procedure, we screened nine strains, which successfully passed the acid, alkali, bile salt, and trypsin resistance test. Drug sensitivity test results showed that three Bacillus out of the nine isolates exhibited antibiotic sensitivity to more than 29 antibiotics. The three strains sensitive to antibiotics were identified by 16S ribosomal RNA, recA, and gyrB gene analysis, two isolates (38,327 and 38,328) belong to the species Lysinibacillus capsici and one isolate (37,326) belong to Bacillus halotolerans. Moreover, the three strains were confirmed safe through animal experiments. Finally, L. capsici 38,327 and 38,328 showed protections in the Salmonella typhimurium infection mouse model, which slowed down weight loss, reduced bacterial load, and improved antioxidant capacity. Altogether, our data demonstrated that selected L. capsici strains can be used as novel probiotics for intestinal health.

Lactiplantibacillus argentoratensis and Candida tropicalis Isolated from the Gastrointestinal Tract of Fish Exhibited Inhibitory Effects against Pathogenic Bacteria of Nile Tilapia

Nile tilapia is one of the most consumed farmed fish in the world. The outbreak of pathogenic bacterial diseases causes high mortality rates and economic losses in Nile tilapia farming. Antibiotic administrations are commonly utilized to inhibit and prevent bacterial infections. However, antibiotics are expensive and cause serious concerns for antibiotic resistance in fish that can be potentially transferred to humans. As an alternative solution, probiotics can be used to prevent infection of pathogenic bacteria in fish. In this work, both bacteria and yeast were isolated from fish gastrointestinal tracts and their inhibitory activity against Nile tilapia pathogenic bacteria was evaluated, as well as other probiotic properties. In this study, 66 bacteria and 176 acid tolerant yeasts were isolated from fish gastrointestinal tracts. Of all isolated microorganisms, 39 bacterial and 15 yeast isolates with inhibitory effect against pathogens were then examined for their probiotic properties (acidic and bile salt resistance, adhesion potential, and biofilm formation), formation of antibacterial factor survival rate under simulated gastrointestinal fluid, and safety evaluation. AT8/5 bacterial isolate demonstrated probiotic properties and the highest inhibition against all 54 tested pathogens while YON3/2 yeast isolate outperformed the inhibitory effect among all yeast isolates. These two probiotic isolates were further identified by 16S rDNA and the D1/D2 domain of 26S rDNA sequence analysis for bacterial and yeast identification, respectively. AT8/5 and YON3/2 showed the highest similarity to Lactiplantibacillus argentoratensis and Candida tropicalis, respectively. This is the first report on isolated L. argentoratensis and C. tropicalis with antipathogenic bacteria of Nile tilapia properties. Collectively, AT8/5 and YON3/2 could be potentially used as promising alternatives to existing antibiotic methods to prevent pathogenic bacteria infection in Nile tilapia farming.

Effects of dietary Bacillus amyloliquefaciens on the growth, immune responses, intestinal microbiota composition and disease resistance of yellow catfish, Pelteobagrus fulvidraco

The influence of dietary probiotic Bacillus amyloliquefaciens on the growth performance, digestive enzyme activity, immune parameters and disease resistance of yellow catfish (Pelteobagrus fulvidraco) was evaluated. Commercial diet (C) or diet containing 106 cfu/g B. amyloliquefaciens (T) was fed for 4 weeks, and final weight (FW), specific growth rate (SGR) and feed conversion ratio (FCR) were improved (p<0.05) in the T group. Dietary B. amyloliquefaciens increased protease and amylase activities in the digestive tract after 2 and 4 weeks, respectively. Respiratory burst (RB), plasma lysozyme (LZM) activity, total antioxidant capacity (T-AOC) and superoxide dismutase (SOD) activity were also elevated (p<0.05). Immune-related genes signal transducer and activator of transcription 1 (STATA-1), immunoglobulin M (IgM) and C-type lectin (CTL) were upregulated (p<0.05), but interleukin-1 β (IL-1β) was not (p >0.05). Intestinal microbiota analysis showed that the community structure was significantly different between the two groups; the relative abundance of Cetobacterium was increased but Plesiomonas was decreased in T. Moreover, challenge tests showed that the resistance of fish fed B. amyloliquefaciens against Aeromonas veronii and Edwardsiella ictaluri was significantly enhanced (p<0.05). In conclusion, dietary supplementation of B. amyloliquefaciens can effectively improve the growth performance, digestive enzyme activity, immune responses, intestinal microbiota composition and disease resistance of yellow catfish.

Efficacy of Single and Multi-Strain Probiotics on In Vitro Strain Compatibility, Pathogen Inhibition, Biofilm Formation Capability, and Stress Tolerance

Compatibility of each strain in a multi-strain probiotic (MSP), along with its properties, becomes a strong base for its formulation. In this study, single-strain probiotics (SSPs) and multi-strain probiotics (MSPs) were evaluated in vitro for strain compatibility, microbial antagonism, biofilm formation capacity, and stress tolerance. Bacillus amyloliquefaciens L11, Enterococcus hirae LAB3, and Lysinibacillus fusiformis SPS11 were chosen as MSP1 candidates because they showed much stronger antagonism to Aeromonas hydrophila and Streptococcus agalactiae than a single probiotic. MSP 2 candidates were Lysinibacillus fusiformis strains SPS11, A1, and Lysinibacillus sphaericus strain NAS32 because the inhibition zone produced by MSP 2 against Vibrio harveyi and Vibrio parahaemolyticus was much higher than that produced by its constituent SSPs. MSP1 in the co-culture assay reduced (p < 0.05) A. hydrophila count from 9.89 ± 0.1 CFU mL−1 to 2.14 ± 0.2 CFU mL−1. The biofilm formation of both MSPs were significantly higher (p < 0.05) than its constituent SSPs and the pathogens. The SSPs in both MSPs generally showed resistance to high temperatures (80, 90, and 100 °C) and a wide range of pH (2 to 9). This in vitro assessment study demonstrates that MSP1 and 2 have the potential to be further explored as multi-strain probiotics on selected aquatic species.

Substrate preferences, phylogenetic and biochemical properties of proteolytic bacteria present in the digestive tract of Nile tilapia (Oreochromis niloticus)

Vertebrate intestine appears to be an excellent source of proteolytic bacteria for industrial and probiotic use. We therefore aimed at obtaining the gut-associated proteolytic species of Nile tilapia (Oreochromis niloticus). We have isolated twenty six bacterial strains from its intestinal tract, seven of which showed exoprotease activity with the formation of clear halos on skim milk. Their depolymerization ability was further assessed on three distinct proteins including casein, gelatin, and albumin. All the isolates could successfully hydrolyze the three substrates indicating relatively broad specificity of their secreted proteases. Molecular taxonomy and phylogeny of the proteolytic isolates were determined based on their 16S rRNA gene barcoding, which suggested that the seven strains belong to three phyla viz. Firmicutes, Proteobacteria, and Actinobacteria, distributed across the genera Priestia, Citrobacter, Pseudomonas, Stenotrophomonas, Burkholderia, Providencia, and Micrococcus. The isolates were further characterized by a comprehensive study of their morphological, cultural, cellular and biochemical properties which were consistent with the phylogenetic annotations. To reveal their proteolytic capacity alongside substrate preferences, enzyme-production was determined by the diffusion assay. The Pseudomonas, Stenotrophomonas and Micrococcus isolates appeared to be most promising with maximum protease production on casein, gelatin, and albumin media respectively. Our findings present valuable insights into the phylogenetic and biochemical properties of gut-associated proteolytic strains of Nile tilapia.

Effect of Enterococcus faecium as a Water and/or Feed Additive on the Gut Microbiota, Hematologic and Immunological Parameters, and Resistance Against Francisellosis and Streptococcosis in Nile Tilapia (Oreochromis niloticus)

In the present study, we evaluated the effects of administering Enterococcus faecium in food and/or water on the hematological and immunological parameters, intestinal microbiota, resistance to bacterial diseases (streptococcosis and francisellosis) and growth of Nile tilapia. Before the in vivo experiment, probiotic bacteria isolated from Nile tilapia were selected via inhibition tests. Sequencing, annotation, and assembly of the complete genome of the selected bacteria as well as other tests were performed using bioinformatics tools. Three treatments were implemented: G1 (probiotic feeding), G2 (probiotic in water), and G3 (probiotic in food and water); and a negative control (NC) was also employed. Treatment lasted 38 days, and each group consisted of fish and two repetitions. The fish were divided and infected with Streptococcus agalactiae S13 (serotype Ib) and Francisella orientalis. The G1 group had a higher average final weight gain than the G2, G3, and NC groups. Further, a significant increase in the number of thrombocytes was observed in the groups administered probiotics in the diet (G1 and G3). A statistical difference was observed in the mortality of fish infected with S. agalactiae in the NC compared to the treated groups. Cetobacterium was the 43 most abundant genus in the intestinal microbiota of all groups, including the NC group. E. faecium increased the immunity of fish administered the treatment and decreased the mortality caused by S. agalactiae. As an autochtone probiotic, E. faecium does not interfere with the local ecosystem and thus has a great probiotic potential for Nile tilapia in Brazil.

Influence of Symbiotic Probiont Strains on the Growth of Amphora and Chlorella and Its Potential Protections Against Vibrio spp. in Artemia

The emerging aquaculture industry is in need of non-antibiotic-based disease control approaches to minimize the risk of antibiotic-resistant bacteria. Bacterial infections mainly caused by Vibrio spp. have caused mass mortalities of fish especially during the larval stages. The objectives of this study were to verify the potential of symbiotic probiont strains, isolated from microalgae (Amphora, Chlorella, and Spirulina) for suppressing the growth of Vibrio spp. and at the same time ascertain their abilities to enhance microalgal biomass by mutualistic interactions through microalgae-bacteria symbiosis. In addition, in vivo studies on Artemia bioencapsulated with probiont strains (single strain and mix strains) and microalgae were evaluated. The selected potential probionts were identified as Lysinibacillus fusiformis strain A-1 (LFA-1), Bacillus sp. strain A-2 (BA-2), Lysinibacillus fusiformis strain Cl-3 (LFCl-3), and Bacillus pocheonensis strain S-2 (BPS-2) using 16s rRNA. The cell densities of Amphora culture supplemented with BA-2 and Chlorella culture supplemented with LFCl-3 were higher than those of the controls. Artemia bioencapsulated with mix strains (LFA-1 + BA-2 + LFCl-3 + BPS-2) and Amphora demonstrated the highest survival rate compared to the controls, after being challenged with V. harveyi (60 ± 4%) and V. parahaemolyticus (78 ± 2%). Our study postulated that BA-2 and LFCl-3 were found to be good promoting bacteria for microalgal growth and microalgae serve as a vector to transport probiotic into Artemia. Moreover, mixture of potential probionts is beneficial for Artemia supplementation in conferring protection to Artemia nauplii against pathogenic Vibrios.

Evaluation of probiotic properties of Lysinibacillus macroides under in vitro conditions and culture of Cyprinus carpio on growth parameters

Cyprinus carpio is an important freshwater fish in aquaculture. It was used for the isolation of potential probiotic strain for aquaculture applications. The most dominant strain was isolated on MRS agar from the gastrointestinal (GI) of C. carpio and identified as Lysinibacillus macroides using molecular marker 16S rRNA gene. Various probiotic properties such as acid and bile tolerance and antibiotic susceptibility were analysed under in vitro conditions. Further, formulate pelletized feed using probiotic (L. macroides) in different concentrations (2, 4, 6 and 8%). Rearing of C. carpio was carried out 45 days and fed with formulated feed. The highest length (5.14 ± 0.07 cm) and weight (3.56 ± 0.07 g) of C. carpio fingerlings was recorded in the 8% LM probiotic pelletized feed, while in fingerlings fed with control showed lower in the length (3.02 ± 0.13 cm) and the weight (0.92 ± 0.04 g) on the 45th day of the experiment. Both percentage of weight gain (PWG) and specific growth rate (SGR) were significantly increased (P < 0.05) of C. carpio fingerlings fed with probiotic feed compared to control feed. Hence, the use of probiotic bacteria could be an encouraging alternative feed for future endeavours in the field of aquaculture. In conclusion, L. macroides can serve as probiotic for sustainable, competitive and promising beneficial bacteria to aquaculture industry.

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.

Isolation, Identification, and Screening of Lactic Acid Bacteria with Probiotic Potential in Silage of Different Species of Forage Plants, Cocoa Beans, and Artisanal Salami

The objective of this study was to isolate and characterize lactic acid bacteria with probiotic potential in silages of different species of forage plants, cocoa beans, and artisanal salami. The obtained isolates were submitted to the following evaluations: (i) screening for tolerance to pH 2 and bile salts, (ii) genotypic identification of isolates, (iii) survival in simulated gastric and pancreatic conditions, (iv) antimicrobial activity, (v) antibiotic susceptibility and safety, and (vi) properties associated with adhesion capacity. A total of 82 isolates were obtained and were screened for pH 2.0 tolerance and capacity to growth in the presence of bile salts (1.0 and 2.0%). Only 19 strains simultaneously presented tolerance to pH 2.0 and bile salts. These 19 strains were evaluated for genetic profile by Box-PCR. Subsequently, the selected strains were subjected to partial sequencing of the 16S rRNA gene. The species Lactobacillus plantarum was prevalent. The identified strains were evaluated for survival under simulated gastric and pancreatic conditions. Some strains have shown tolerance in both conditions. Different strains showed variations in antimicrobial activity, susceptibility to antibiotics, and properties associated with adhesion (hydrophobicity, autoaggregation, coaggregation, and adhesion to CaCo2 cells). All strains were negative for hemolysis, DNase, gelatinase, and biogenic amine synthesis activity. The L. plantarum SBR64.7 strain can be considered the most promising for it presented the lowest viability reduction when exposed to gastric and pancreatic juices.

Differential study of the Parabramis pekinensis intestinal microbiota according to different habitats and different parts of the intestine

Purpose

To identify the differences in gut bacterial community of Parabramis pekinensis under different growth conditions, and the effect of the diet in a controlled habitat on the community structure, aiming to provide a comprehensive survey of how the gut microbiota in P. pekinensis varies depending on habitat.

Methods

A total of 73 P. pekinensis from Yangtze River (W), rivers in the outskirts of Jingjiang (Jiangsu province, China, R), and farms (C) were collected to analyze the intestinal microbiota using high-throughput sequencing of the V3-V4 16S ribosomal RNA gene. We also subdivided the gut into the foregut (F), midgut (M), and hindgut (B) to analyze the differences between them.

Results

The dominant bacterial phyla in P. pekinensis were Fusobacteria, Firmicutes, Proteobacteria, and Actinobacteria; meanwhile, Cyanobacteria, Bacteroidetes, Chloroflexi, and Verrucomicrobia were also highly abundant. It is worth noting that the abundance of Fusobacteria Cetobacterium was also very high. The abundance and diversity of the intestinal microbiota structure of fish taken from breeding farm were significantly lower than those taken from Yangtze river and Suburban river, and the abundance of Aeromonas in the gut of fish taken from Yangtze river was much higher than that of fish taken from Suburban river. Compared to midgut, foregut and hindgut have similar microbiota structures, but did not differ significantly in them.

Conclusions

The core intestinal microbiota of P. pekinensis is the same to other herbivorous and partially omnivorous fish. There were significant differences in the intestinal microbiota structure of P. pekinensis from different habitats, but no significant differences in the microbiota abundance and diversity between the different parts of the intestine.

Quorum Quenching Properties and Probiotic Potentials of Intestinal Associated Bacteria in Asian Sea Bass Lates calcarifer

Quorum quenching (QQ), the enzymatic degradation of N-acyl homoserine lactones (AHLs), has been suggested as a promising strategy to control bacterial diseases. In this study, 10 AHL-degrading bacteria isolated from the intestine of barramundi were identified by 16S rDNA sequencing. They were able to degrade both short and long-chain AHLs associated with several pathogenic Vibrio species (spp.) in fish, including N-[(RS)-3-Hydroxybutyryl]-l-homoserine lactone (3-oh-C₄-HSL), N-Hexanoyl-l-homoserine lactone (C₆-HSL), N-(β-Ketocaproyl)-l-homoserine lactone (3-oxo-C₆-HSL), N-(3-Oxodecanoyl)-l-homoserine lactone (3-oxo-C₁₀-HSL), N-(3-Oxotetradecanoyl)-l-homoserine lactone (3-oxo-C₁₄-HSL). Five QQ isolates (QQIs) belonging to the Bacillus and Shewanella genera, showed high capacity to degrade both synthetic AHLs as well as natural AHLs produced by Vibrio harveyi and Vibrio alginolyticus using the well-diffusion method and thin-layer chromatography (TLC). The genes responsible for QQ activity, including aiiA, ytnP, and aaC were also detected. Analysis of the amino acid sequences from the predicted lactonases revealed the presence of the conserved motif HxHxDH. The selected isolates were further characterized in terms of their probiotic potentials in vitro. Based on our scoring system, Bacillus thuringiensis QQ1 and Bacillus cereus QQ2 exhibited suitable probiotic characteristics, including the production of spore and exoenzymes, resistance to bile salts and pH, high potential to adhere on mucus, appropriate growth abilities, safety to barramundi, and sensitivity to antibiotics. These isolates, therefore, constitute new QQ probiotics that could be used to control vibriosis in Lates calcalifer.

Establishment and characterization of a competitive exclusion bacterial culture derived from Nile tilapia (Oreochromis niloticus) gut microbiomes showing antibacterial activity against pathogenic Streptococcus agalactiae

This study reports the characterization of the microbial community composition, and the establishment and dynamics of a continuous-flow competitive exclusion culture (CFCEC) derived from gut microbiomes of Nile tilapia (Oreochromis niloticus) specimens reared on aquaculture farms in Colombia. 16S rRNA gene amplicon Illumina sequencing was used to identify taxonomical changes in the CFCEC microbial community over time. The CFCEC was developed from adult tilapia from two farms in Colombia, and CFCEC samples were collected over two months. The pH varied from 6.25 to 6.35 throughout culturing, while anaerobic and aerobic cell counts stabilized at day 9, at 10⁹ CFU mL^-1 and were maintained to day 68. A variation in the CFCEC bacterial composition was observed over time. Cetobacterium was the most abundant in the first two days and coincided with a higher CFCEC supernatant antimicrobial effect against the fish pathogen Streptococcus agalactiae. Antimicrobial activity against S. agalactiae disappeared by day 3. Changes in bacterial composition continued to day 33 with Lactococcus spp. becoming the most abundant member of the community. In conclusion, the study of the CFCEC from intestinal tract of Nile tilapia (Oreochromis niloticus) by 16S rRNA gene sequencing allowed identification of predominant bacterial genera in the continuous-flow competitive exclusion culture exhibiting antibacterial activity against the fish pathogen Streptococcus agalactiae.