Characterization of Deep Sea Fish Gut Bacteria with Antagonistic Potential, from Centroscyllium fabricii (Deep Sea Shark)

The Marine Fish Gut Microbiome as a Source of Novel Bacteriocins

The marine environment is the largest ecological habitat on Earth, albeit one of the least explored, particularly in terms of its microbial inhabitants. The marine fish gut is host to a diverse microbial community from which diverse bioactive molecules can be sourced. Due to the unique environmental pressures these microbial communities experience, the bioactive molecules they produce often evolve unique adaptations that give them diverse structures and activities, differentiating them from terrestrial homologues. Of particular interest, due to their structural and functional diversity, are the ribosomally-synthesized antimicrobial peptides (bacteriocins). With increasing pressure from emerging antibiotic-resistant disease and industrial demand for novel therapeutics, the marine fish gut microbiome represents a relatively untapped resource of novel bacteriocins that could prove beneficial to human health and aquaculture. This review presents an overview of the marine fish gut microbiome and explores its potential as a source of bacteriocins for human health with considerations for applications and future research in this area.

Bioactivity Screening and Genomic Analysis Reveals Deep-Sea Fish Microbiome Isolates as Sources of Novel Antimicrobials

With the increase in antimicrobial resistance and the subsequent demand for novel therapeutics, the deep-sea fish microbiome can be a relatively untapped source of antimicrobials, including bacteriocins. Previously, bacterial isolates were recovered from the gut of deep-sea fish sampled from the Atlantic Ocean.In this study, we used in vitro methods to screen a subset of these isolates for antimicrobial activity, and subsequently mined genomic DNA from isolates of interest for bacteriocin and other antimicrobial metabolite genes. We observed antimicrobial activity against foodborne pathogens, including Staphylococcus aureus, Listeria monocytogenes, Enterococcus faecalis and Micrococcus luteus. In total, 147 candidate biosynthetic gene clusters were identified in the genomic sequences, including 35 bacteriocin/RiPP-like clusters. Other bioactive metabolite genes detected included non-ribosomal peptide synthases (NRPS), polyketide synthases (PKS; Types 1 and 3), beta-lactones and terpenes. Moreover, four unique bacteriocin gene clusters were annotated and shown to encode novel peptides: a class IIc bacteriocin, two class IId bacteriocins and a class I lanthipeptide (LanM subgroup). Our dual in vitro and in silico approach allowed for a more comprehensive understanding of the bacteriocinogenic potential of these deep-sea isolates and an insight into the antimicrobial molecules that they may produce.

Whole genome sequence analysis enabled affirmation of the probiotic potential of marine sporulater Bacillus amyloliquefaciens BTSS3 isolated from Centroscyllium fabricii

Probiotics are microorganisms when administered in adequate amounts, confer health benefits on the host. Many probiotics find application in various industries however, probiotic bacteria linked to marine environments are less explored.Although Bifidobacteria, Lactobacilli, and Streptococcus thermophilus are the most frequently used probiotics, Bacillus spp. have acquired much acceptance in human functional foods due to their increased tolerance and enduring competence in harsh environments like the gastrointestinal (GI) tract. In this study, the 4 Mbp genome sequence of Bacillus amyloliquefaciens strain BTSS3, a marine spore former isolated from deep-sea shark Centroscyllium fabricii, with antimicrobial and probiotic properties was sequenced, assembled, and annotated. Analysis revealed the presence of numerous genes presenting probiotic traits like production of vitamins, secondary metabolites, amino acids, secretory proteins, enzymes and other proteins that allow survival in GI tract as well as adhesion to intestinal mucosa. Adhesion by colonization in the gut was studied in vivo in zebrafish (Danio rerio) using FITC labelled B.amyloliquefaciens BTSS3. Preliminary study revealed the ability of the marine Bacillus to attach to the intestinal mucosa of the fish gut. The genomic data and the in vivo experiment affirms that this marine spore former is a promising probiotic candidate with potential biotechnological applications.

Elasmobranch-associated microbiota: a scientometric literature review

Elasmobranchs provide greatly relevant ecosystem services for the balance of the environments in which they are inserted. In recent decades, sharp population declines have been reported for many species in different regions worldwide, making this taxonomic group currently one of the most threatened with extinction. This scenario is almost entirely due to excessive fishing pressure, but any contributing factor that may cause additional mortality to populations must be mapped and monitored. In a fast-changing world, emerging marine pollution associated with climate change display the potential to increase the spread of infectious agents. These can, in turn, lead to mortality events, both directly and indirectly, by reducing immune responses and the physical and nutritional condition of affected individuals. In this context, the present study aimed to analyze data concerning elasmobranch-associated microbiota, identifying study trends and knowledge gaps in order to direct future studies on this topic of growing relevance for the health of wild populations, as well as individuals maintained in captivity, considering the zoonotic potential of these microorganisms.

Indian oil sardine (Sardinella longiceps) gut derived Bacillus safensis SDG14 with enhanced probiotic competence for food and feed applications

Probiotics are considered as functional food as they provide health benefits along with traditional nutrition. Spore forming probiotic Bacillus are of commercial interest than Lactic Acid Bacillus due to their relatively lower cost of production and higher survivability. In the present study we identified the bacterial strain SDG14 isolated from Indian oil Sardine by Average Nucleotide Identity of whole genome sequence. The whole genome of SDG14 was also explored for pathogenicity, the presence of genes responsible for probiotic traits such as spore formation, resistance to host gastrointestinal tract conditions, adhesion to intestinal mucosa, interference in pathogen survival, expression of bacteriocins, oxidative and other stress responses, absorption of nutrition, production of essential amino acids and vitamins. Wet lab experiments for probiotic characterization were also conducted. The organism was confirmed to be Bacillus safensis SDG14. The possible pathogenicity of the organism was also ruled out by in silico analysis. Bacillus safensis SDG14 was able to survive at pH 3 and bile salt concentration of 0.5% (w/v). The adhesion index of Bacillus safensis SDG14 on HEp-2 was 36.82 ± 5.93 and 45.54 ± 9.55 respectively after 60 and 90 min of incubation and self aggregation percentage was 18.4 ± 0.48% after 3 h. Bacillus safensis SDG14 produced bacteriocin and co-aggregated with E. coli, Salmonella Typhimurium and Pseudomonas aeruginosa. The genomic data supported the findings of wet lab study and vice versa. Bacillus safensis SDG14 was proved to be a non-pathogenic, spore forming, pH and bile salt resistant, bacteriocin, amino acid and vitamin producing probiotic with proposed food and feed applications.

A magainin-2 like bacteriocin BpSl14 with anticancer action from fish gut Bacillus safensis SDG14

Bacteriocins are gaining utmost importance in antimicrobial and chemotherapy due to their diverse structure and activity. This study centres on magainin-2 like bacteriocin with anticancer action, produced by Bacillus safensis strain SDG14 isolated from gut of marine fish Sardinella longiceps. The purified bacteriocin designated as BpSl14 was thermostable and pH tolerant. The molecular weight of BpS114 was estimated to be 6061.2 Da using MALDI-ToF MS. The partial primary sequence was elucidated by peptide mass fingerprinting using MALDI MS/MS. The tertiary structure of the partial sequence was similar to that of two magainin-2 α-helices joined together by extended indolicidin. The BpSl14 protein inhibited the cells of lung carcinoma, one of the deadliest cancers. Docking studies conducted with DR5 and TGF-β, two of the most prominent apoptotic receptors in adenocarcinoma, also proved the anti-apoptotic action of BpSl14.

16S rRNA Gene Amplicon Sequencing of Gut Microbiota in Three Species of Deep-Sea Fish in Suruga Bay, Japan

We report here 16S rRNA gene amplicon sequence analysis of the gut microbiota in three species of deep-sea fish collected from Suruga Bay, Japan. Of the three species, two were dominated by the phylum Proteobacteria (genus Photobacterium), while one was dominated by the phyla Spirochaetes (genus Brevinema) and Tenericutes (unclassified Mycoplasmataceae).

We report here 16S rRNA gene amplicon sequence analysis of the gut microbiota in three species of deep-sea fish collected from Suruga Bay, Japan. Of the three species, two were dominated by the phylum Proteobacteria (genus Photobacterium), while one was dominated by the phyla Spirochaetes (genus Brevinema) and Tenericutes (unclassified Mycoplasmataceae).

Gut microbiota metagenomics in aquaculture: factors influencing gut microbiome and its physiological role in fish

Fish gut microbiome confers various effects to the host fish; this includes overall size, metabolism, feeding behaviour and immune response in the fish. The emergence of antimicrobial‐resistant (AMR) bacteria and hard to cure fish diseases warrant the possible utilization of gut microbes that exhibits a positive effect on the fish and thus lead to the usage of these microbes as probiotics. The widespread and systematic use of antibiotics has led to severe biological and ecological problems, especially the development of antibiotic resistance that affects the gut microbiota of aquatic organisms. Probiotics are proposed as an effective and environmentally friendly alternative to antibiotics, known as beneficial microbes. At the same time, prebiotics are considered beneficial to the host's health and growth by decreasing the prevalence of intestinal pathogens and/or changing the development of bacterial metabolites related to health. Uprise of sequencing technology and the development of intricate bioinformatics tools has provided a way to study these gut microbes through metagenomic analysis. From various metagenomic studies, ample of information was obtained; such information includes the effect of the gut microbiome on the physiology of fish, gut microbe composition of different fish, factors affecting the gut microbial composition of the fish and the immunological effect of gut microbes in fish; such this information related to the fish gut microbiome, their function and their importance in aquaculture is discussed in this review.

Evaluation of the Antibacterial Material Production in the Fermentation of Bacillus amyloliquefaciens-9 from Whitespotted Bamboo Shark (Chiloscyllium plagiosum)

Bacillus amyloliquefaciens-9 (GBacillus-9), which is isolated from the intestinal tract of the white-spotted bamboo shark (Chiloscyllium plagiosum), can secrete potential antibacterial materials, such as β-1,3-1,4-glucanase and some antimicrobial peptides. However, the low fermentation production has hindered the development of GBacillus-9 as biological additives. In this study, the Plackett–Burman design and response surface methodology were used to optimize the fermentation conditions in a shake flask to obtain a higher yield and antibacterial activity of GBacillus-9. On the basis of the data from medium screening, M9 medium was selected as the basic medium for fermentation. The data from the single-factor experiment showed that sucrose had the highest antibacterial activity among the 10 carbon sources. The Plackett–Burman design identified sucrose, NH₄Cl, and MgSO₄ as the major variables altering antibacterial activity. The optimal concentrations of these compounds to enhance antibacterial activity were assessed using the central composite design. Data showed that sucrose, NH₄Cl, and MgSO₄ had the highest antibacterial activities at concentrations of 64.8, 1.84, and 0.08 g L⁻¹, respectively. The data also showed that the optimal fermentation conditions for the antibacterial material production of GBacillus-9 were as follows: Inoculum volume of 5%, initial pH of 7.0, temperature of 36 °C, rotating speed of 180 rpm, and fermentation time of 10 h. The optimal fermentation medium and conditions achieved to improve the yield of antibacterial materials for GBacillus-9 can enhance the process of developing biological additives derived from GBacillus-9.

Beneficial bacteria for aquaculture: nutrition, bacteriostasis and immunoregulation

Despite being the fastest growing sector, the modern aquaculture industry faces serious challenges such as the lack of protein source in feed, the susceptibility to pathogens, and deterioration in quality during culture and storage. Bacterial biomass is considered as a proper protein source for feed, and the beneficial bacterial species protect aquatic animals from infection or reduce spoilage of products. In this review, we summarized the application of beneficial bacteria to aquatic products, focusing mainly on the nutritional, anti-pathogenic, anti-spoilage and immunoregulatory functions of these bacteria. We then discussed the relationship between beneficial bacteria, intestinal microbiota and host immunity, and the recent progress and drawbacks of the technology.

BaCf3: highly thermostable bacteriocin from Bacillus amyloliquefaciens BTSS3 antagonistic on food-borne pathogens

In the present study, we characterized bacteriocin BaCf3, isolated and purified from Bacillus amyloliquefaciens BTSS3, and demonstrated its inhibitory potential on growth and biofilm formation of certain food spoilage bacteria and pathogens. Purification was by gel filtration chromatography and its molecular weight was 3028.422 Da after MALDI-TOF MS. The bacteriocin was highly thermostable withstanding even autoclaving conditions and pH tolerant (2.0-13.0). The bacteriocin was sensitive to oxidizing agent (DMSO) and reducing agent (DTT). The de novo sequence of the bacteriocin BaCf3 was identified and was found to be novel. The sequence analysis shows the presence of a disulphide linkage between C6 and C13. The microtitre plate assay proved that BaCf3 could reduce up to 80% biofilm produced by strong biofilm producers from food samples. In addition, BaCf3 did not show cytotoxicity on 3-TL3 cell line.

Lactic Acid Bacteria in Finfish-An Update

A complex and dynamic community of microorganisms, play important roles within the fish gastrointestinal (GI) tract. Of the bacteria colonizing the GI tract, are lactic acid bacteria (LAB) generally considered as favorable microorganism due to their abilities to stimulating host GI development, digestive function, mucosal tolerance, stimulating immune response, and improved disease resistance. In early finfish studies, were culture-dependent methods used to enumerate bacterial population levels within the GI tract. However, due to limitations by using culture methods, culture-independent techniques have been used during the last decade. These investigations have revealed the presence of Lactobacillus, Lactococcus, Leuconostoc, Enterococcus, Streptococcus, Carnobacterium, Weissella, and Pediococcus as indigenous species. Numerous strains of LAB isolated from finfish are able to produce antibacterial substances toward different potential fish pathogenic bacteria as well as human pathogens. LAB are revealed be the most promising bacterial genera as probiotic in aquaculture. During the decade numerous investigations are performed on evaluation of probiotic properties of different genus and species of LAB. Except limited contradictory reports, most of administered strains displayed beneficial effects on both, growth-and reproductive performance, immune responses and disease resistance of finfish. This eventually led to industrial scale up and introduction LAB-based commercial probiotics. Pathogenic LAB belonging to the genera Streptococcus, Enterococcus, Lactobacillus, Carnobacterium, and Lactococcus have been detected from ascites, kidney, liver, heart, and spleen of several finfish species. These pathogenic bacteria will be addressed in present review which includes their impacts on finfish aquaculture, possible routes for treatment. Finfish share many common structures and functions of the immune system with warm-blooded animals, although apparent differences exist. This similarity in the immune system may result in many shared LAB effects between finfish and land animals. LAB-fed fish show an increase in innate immune activities leading to disease resistances: neutrophil activity, lysozyme secretion, phagocytosis, and production of pro-inflammatory cytokines (IL-1β, IL-6, IL-8, and TNF-α). However, some LAB strains preferentially induces IL-10 instead, a potent anti-inflammatory cytokine. These results indicate that LAB may vary in their immunological effects depending on the species and hosts. So far, the immunological studies using LAB have been focused on their effects on innate immunity. However, these studies need to be further extended by investigating their involvement in the modulation of adaptive immunity. The present review paper focuses on recent findings in the field of isolation and detection of LAB, their administration as probiotic in aquaculture and their interaction with fish immune responses. Furthermore, the mode of action of probiotics on finfish are discussed.