Prevalence of opportunistic pathogens and anti-microbial resistance in urban aquaculture ponds.

Bacterial antimicrobial resistance (AMR) has emerged as a significant concern worldwide. The microbial community profile and potential AMR level in aquaculture ponds are often undervalued and attract less attention than other aquatic environments. We used amplicon and metagenomic shotgun sequencing to study microbial communities and AMR in six freshwater polyculture ponds in rural and urban areas of Bangladesh. Amplicon sequencing revealed different community structures between rural and urban ponds, with urban ponds having a higher bacterial diversity and opportunistic pathogens including Streptococcus, Staphylococcus, and Corynebacterium. Despite proteobacterial dominance, Firmicutes was the most interactive in the community network, especially in the urban ponds. Metagenomes showed that drug resistance was the most common type of AMR found, while metal resistance was only observed in urban ponds. AMR and metal resistance genes were found mainly in beta and gamma-proteobacteria in urban ponds, while AMR was found primarily in alpha-proteobacteria in rural ponds. We identified potential pathogens with a high profile of AMR and metal resistance in urban aquaculture ponds. As these ponds provide a significant source of protein for humans, our results raise significant concerns for the environmental sustainability of this food source and the dissemination of AMR into the food chain.

Whole-genome sequence of Proteus faecis CR112, isolated from the gut of a healthy Labeo rohita.

Bacteria of the genus Proteus are gram-negative bacilli. Proteus faecis CR112 was isolated from fish gut based on its antibacterial activity against fish pathogens. The genome sequence of CR112 provided valuable information about its secondary metabolite gene clusters.

Whole-Genome Sequence of Bacillus pacificus CR121, a Fish Probiotic Candidate.

We describe a promising fish probiotic, Bacillus pacificus CR121, which was isolated from the intestine of a healthy Indian major carp species, rohu (Labeo rohita) and shown to possess in vivo disease prevention efficacy in L. rohita and Oreochromis niloticus. The genome sequence information will help us make use of the probiotic potential of this strain.

Friend or Foe: Whole-Genome Sequence of Pseudomonas aeruginosa TG523, Isolated from the Gut of a Healthy Nile Tilapia (Oreochromis niloticus).

Here, we present the genomic features of Pseudomonas aeruginosa TG523, which was isolated from the gut of a healthy Nile tilapia (Oreochromis niloticus). With a genome size of 6,381,902 bp with 5,931 open reading frames, the genome harbored genes predicted to have antibacterial activity and those which are implicated in virulence.

Virulence and antibiotic-resistance genes in Enterococcus faecalis associated with streptococcosis disease in fish.

Enterococcus faecalis is associated with streptococcosis like infection in fish. A whole-genome sequence study was conducted to investigate the virulence factor and antibiotic-resistance genes in three fish pathogenic E. faecalis. Genomic DNA was extracted from three strains of E. faecalis isolated from streptococcosis infected Nile tilapia (strains BF1B1 and BFFF11) and Thai sarpunti (strain BFPS6). The whole genome sequences of these three strains were performed using a MiSeq sequencer (Illumina, Inc.). All three strains conserved 69 virulence factor such as genes associated with protection against oxidative stress, bacterial cell wall synthesis, gelatinase toxin, multiple biofilm-associated genes and capsule producing genes. Moreover, 39 antibiotic-resistance genes against sixteen major groups of antibiotics were identified in the genome sequences of all three strains. The most commonly used antibiotic Tetracycline resistance genes were found only in BFPS6 strain, whereas, Bacteriocin synthesis genes were identified in both BFFF11 and BFPS6 strain. Phylogenetic analysis revealed that strains BF1B1 and BFFF1 form a different cluster than BFPS6. This is one of the first whole-genome sequence study of fish pathogenic E. faecalis, unfold new information on the virulence factor and Antibiotic resistance genes linked to pathogenicity in fish.

Suppression of Streptococcosis and Modulation of the Gut Bacteriome in Nile Tilapia (Oreochromis niloticus) by the Marine Sediment Bacteria Bacillus haynesii and Advenella mimigardefordensis.

Streptococcosis is one of the major threats to Nile tilapia (Oreochromis niloticus) in most regions of the world. Recently, Enterococcus faecalis has been widely reported to be involved in streptococcosis in O. niloticus in Asia and Africa. This study aimed to isolate beneficial marine bacteria to evaluate their effects on growth, hematological parameters, nonspecific immunity, the gut bacteriome, and streptococcosis prevention efficacy in O. niloticus. A total of 36 marine soil bacteria were isolated, and in vitro screening was conducted to determine their antibacterial activities against fish pathogens. Two antagonistic bacteria were identified based on 16S rRNA gene sequencing, Bacillus haynesii CD223 and Advenella mimigardefordensis SM421. These bacteria were incorporated into fish feed and fed to O. niloticus for 90 days. The application of these strains via incorporation into fish feed significantly promoted growth, improved hematological parameters and immunoglobulin M (IgM) levels, modulated the gut bacteriome by reducing the load of pathogenic Enterococcus spp., and developed disease prevention efficacy in O. niloticus. Furthermore, in vivo assays revealed that the inclusion of extracellular products (ECPs) (at 250 µg mL-1) of CD223 and SM421 with feed significantly enhanced the rate of survival (100%) of O. niloticus from streptococcosis compared to the controls (only 30%). The ECPs of these bacteria also prevented 90 to 100% of fish from developing streptococcosis. These strains could be promising for safe use in O. niloticus farming to prevent and control the emergence of streptococcosis caused by E. faecalis. IMPORTANCE Nile tilapia (Oreochromis niloticus) is one of the most economically important cultured fish species throughout the world. Streptococcosis is a significant threat to global Nile tilapia farming. Enterococcus faecalis has recently emerged as an important pathogen of streptococcosis in Asia and Africa. The application of antibiotics and probiotics and vaccination are the major ways to combat streptococcosis. However, the extensive use of antibiotics leads to the development of antibiotic resistance in pathogenic as well as environmental bacteria, which is a great threat to public health. There is no study on preventing streptococcosis caused by E. faecalis using beneficial bacteria. For the first time, the present study demonstrated that two marine bacteria, Bacillus haynesii strain CD223 and Advenella mimigardefordensis strain SM421, have great potential for controlling streptococcosis in Nile tilapia. These bacteria also enhanced the growth, improved hematological parameters and IgM levels, and positively modulated the gut bacteriome of Nile tilapia.

Whole-Genome Sequence of Aneurinibacillus migulanus TP115, a Potential Fish Probiotic Isolated from Oreochromis niloticus Gut.

We report the whole-genome sequence of a promising fish probiotic, Aneurinibacillus migulanus TP115, which was isolated from the gut of Nile tilapia (Oreochromis niloticus). The de novo assembly resulted in an estimated chromosome size of 5,556,554 bp, with 5,576 open reading frames.

Draft Genome Sequence of Bacillus subtilis YBS29, a Potential Fish Probiotic That Prevents Motile Aeromonas Septicemia in Labeo rohita.

We report the draft genome sequence of the promising fish probiotic Bacillus subtilis YBS29. This strain exhibits in vitro antimicrobial activity against Aeromonas veronii and enhances growth and disease resistance in the Indian major carp species Labeo rohita against motile Aeromonas septicemia (MAS). Its genome contains a gene cluster encoding multiple bacteriocins and lacks genes for virulence factors. These genomic features signify potential for safe use as a probiotic in aquaculture.

Microbiome data reveal significant differences in the bacterial diversity in freshwater rohu (Labeo rohita) across the supply chain in Dhaka, Bangladesh.

The present study aimed to characterize and compare the skin and gut microbial communities of rohu at various post-harvest stages of consumption using quantitative real-time polymerase chain reaction and 16S rRNA-based amplicon sequencing. Real-time PCR amplification detected higher copy numbers for coliform bacteria-Escherichia coli, Salmonella enterica and Shigella spp. in the marketed fish-compared to fresh and frozen samples. The 16S rRNA data revealed higher alpha diversity measurements in the skin of fish from different retail markets of Dhaka city. Beta ordination revealed distinct clustering of bacterial OTUs for the skin and gut samples from three different groups. At the phylum level, Proteobacteria was most abundant in all groups except the Fusobacteria in the control fish gut. Although Aeromonas was found ubiquitous in all types of samples, diverse bacterial genera were identified in the marketed fish samples. Nonetheless, low species richness was observed for the frozen fish. Most of the differentially abundant bacteria in the skin samples of marketed fish are opportunistic human pathogens enriched at different stages of postharvest handling and processing. Therefore, considering the microbial contamination in the aquatic environment in Bangladesh, post-harvest handling should be performed with proper methods and care to minimize bacterial transmission into fish.

Effect of different wavelengths of LED light on the growth, chlorophyll, ß-carotene content and proximate composition of Chlorella ellipsoidea.

Chlorella ellipsoidea is a freshwater green microalga that has great prospect for the sustainable development of aquaculture industry. Microalgae require optimal lighting conditions for efficient photosynthesis. The key to cost-effective algal biomass production is to optimize algae growth conditions. This study aimed to investigate the effects of various wavelengths viz. white (380-750 nm), green (510 nm), blue (475 nm), and red (650 nm) light-emitting diodes (LEDs) on the growth, pigment content (chlorophyll-a, chlorophyll-b, and ß-carotene), and proximate composition of C. ellipsoidea with a photoperiod of 12 h:12 h light: dark cycle under indoor environmental conditions. C. ellipsoidea was cultured in Bold's Basal Medium for 18 days. The cell density (125.36×105 cells ml-1), cell dry weight (58.9 ± 4.57 mg L-1), optical density (1.66 ± 0.08 g L-1), chlorophyll-a (7.31 ± 0.04 µg ml-1), chlorophyll-b (2.73 ± 0.13 µg ml-1), and ß-carotene (0.39 ± 0.04 µg ml-1) content of C. ellipsoidea were significantly (P < 0.05) higher at 15th-day when cultured under blue LED light exposure. Significantly lower growth and nutritional values were obtained under red LED light exposure compared to the control and other LEDs spectra. In Pearson correlation analysis, the cell density and cell dry weight values showed a strong positive correlation with the values of pigment contents of C. ellipsoidea in all the treatments. The LEDs light spectra showed significant effects on proximate composition of C. ellipsoidea. Protein and lipid contents of C. ellipsoidea were significantly higher in blue LED growth conditions compared to white, green, and red LEDs. C. ellipsoidea cells were 3-7.04 µm in size and the maximum area of the cell was 38.94 µm2 in blue LED treatment. Results of this study demonstrated that blue LED light spectra was the most suitable condition to induce nutritionally rich biomass production of C. ellipsoidea, which can be used as a potential source of fish feed towards sustainable aquaculture.

Dietary chitosan promotes the growth, biochemical composition, gut microbiota, hematological parameters and internal organ morphology of juvenile Barbonymus gonionotus.

In this study, we determined the effects of dietary chitosan on the growth, biochemical composition, gut microbiota, and hematological and histological parameters of juvenile Barbonymus gonionotus. Three test diets containing three different concentrations (1, 2, and 3 g kg-1 feed) of dietary chitosan were formulated. A basal diet without dietary chitosan was considered a control, and the fish were reared for 60 days. Comparing the effects of the dietary chitosan-containing diets with those of the control diet, we found that dietary chitosan significantly improved the muscle growth, nutrient and mineral contents, hematological parameters, lactic acid bacterium abundance, and digestive enzyme activities of B. gonionotus. Moreover, dietary chitosan significantly inhibited the growth of pathogenic bacteria in fish. Interestingly, an increase in the dietary chitosan level significantly enhanced the protein contents of the muscles and inversely significantly decreased the lipid contents compared to those with the basal diet. Quantitative study revealed that dietary chitosan significantly enhanced the length of intestinal villi, and qualitative study showed that dietary chitosan considerably reduced the fat content in the liver and improved the morphology of the kidney compared to those with the basal diet. Taken together, our results suggest that the application of dietary chitosan at a dose of 1 g kg-1 feed produced the highest benefit to treated B. gonionotus, indicating its potential for safe use in aquaculture.

Gut probiotic bacteria of Barbonymus gonionotus improve growth, hematological parameters and reproductive performances of the host.

This study aimed to isolate and identify probiotic bacteria from the gut of Barbonymus gonionotus and evaluate their effects on growth, hematological parameters, and breeding performances of the host. Five probiotic bacteria viz. Enterococcus xiangfangensis (GFB-1), Pseudomonas stutzeri (GFB-2), Bacillus subtilis (GFB-3), Citrobacter freundii (GFB-4), and P. aeruginosa (GFB-5) were isolated and identified using 16S rRNA gene sequencing. Application of a consortium of probiotic strains (1-3 × 1.35 × 109 CFU kg-1) or individual strain such as GFB-1 (1.62 × 109 CFU kg-1), GFB-2 (1.43 × 109 CFU kg-1), GFB-3 (1.06 × 109 CFU kg-1), GFB-4 (1.5 × 109 CFU kg-1) or GFB-5 (1.43 × 109 CFU kg-1feed) through feed significantly improved growth, histological and hematological parameters and reproductive performances of B. gonionotus compared to untreated control. Moreover, the application of these probiotics significantly increased gut lactic acid bacteria and activities of digestive enzymes but did not show any antibiotic resistance nor any cytotoxicity in vitro. The highest beneficial effects on treated fishes were recorded by the application of GFB-1, GFB-2, GFB-3, and a consortium of these bacteria (T2). This is the first report of the improvement of growth and health of B. gonionotus fishes by its gut bacteria.

Whole-Genome Sequence of Bacillus subtilis WS1A, a Promising Fish Probiotic Strain Isolated from Marine Sponge of the Bay of Bengal.

This study reports the draft genome sequence of a promising fish probiotic, Bacillus subtilis strain WS1A, that possesses antimicrobial activity against Aeromonas veronii and suppressed motile Aeromonas septicemia in Labeo rohita The de novo assembly resulted in an estimated chromosome size of 4,148,460 bp, with 4,288 open reading frames.