Effect of Streptomyces probiotics on the gut microbiota of Litopenaeus vannamei challenged with Vibrio parahaemolyticus

Probiotic potential of a novel endophytic Streptomyces griseorubens CIBA-NS1 isolated from Salicornia sp. against Vibrio campbellii infection in shrimp

A novel endophytic Streptomyces griseorubens CIBA-NS1 was isolated from a salt marsh plant Salicornia sp. The antagonistic effect of S. griseorubens against Vibrio campbellii, was studied both in vitro and in vivo. The strain was validated for its endophytic nature and characterized through scanning electron microscopy, morphological and biochemical studies and 16SrDNA sequencing. The salinity tolerance experiment has shown that highest antibacterial activity was at 40‰ (16 ± 1.4 mm) and lowest was at 10 ‰ salinity (6.94 ± 0.51 mm). In vivo exclusion of Vibrio by S. griseorubens CIBA-NS1 was studied in Penaeus indicus post larvae and evaluated for its ability to improve growth and survival of P. indicus. After 20 days administration of S. griseorubens CIBA-NS1, shrimps were challenged with V. campbellii. The S. griseorubens CIBA-NS1 reduced Vibrio population in test group when compared to control, improved survival (60.5 ± 6.4%) and growth, as indicated by weight gain (1.8 ± 0.05g). In control group survival and growth were 48.4 ± 3.5% and 1.4 ± 0.03 g respectively. On challenge with V. campbellii, the S. griseorubens CIBA-NS1 administered group showed better survival (85.6 ± 10%) than positive control (64.3 ± 10%). The results suggested that S. griseorubens CIBA-NS1 is antagonistic to V. campbellii, reduce Vibrio population in the culture system and improve growth and survival. This is the first report on antagonistic activity of S. griseorubens isolated from salt marsh plant Salicornia sp, as a probiotic candidate to prevent V. campbellii infection in shrimps.

A comprehensive review on the utilization of probiotics in aquaculture towards sustainable shrimp farming

Probiotics in shrimp aquaculture have gained considerable attention as a potential solution to enhance production efficiency, disease management, and overall sustainability. Probiotics, beneficial microorganisms, have shown promising effects when administered to shrimp as dietary supplements or water additives. Their inclusion has been linked to improved gut health, nutrient absorption, and disease resistance in shrimp. Probiotics also play a crucial role in maintaining a balanced microbial community within the shrimp pond environment, enhancing water quality and reducing pathogen prevalence. This article briefly summarizes the many ways that probiotics are used in shrimp farming and the advantages that come with them. Despite the promising results, challenges such as strain selection, dosage optimization, and environmental conditions are carefully addressed for successful probiotic integration in shrimp aquaculture. The potential of probiotics as a sustainable and ecologically friendly method of promoting shrimp development and health while advancing environmentally friendly shrimp farming techniques is highlighted in this analysis. Further research is required to fully exploit probiotics' benefits and develop practical guidelines for their effective implementation in shrimp aquaculture.

Present Status, Limitations, and Prospects of Using Streptomyces Bacteria as a Potential Probiotic Agent in Aquaculture

Streptomyces is a Gram-positive bacterium, belonging to the family Streptomycetaceae and order Streptomycetales. Several strains from different species of Streptomyces can be used to promote the health and growth of artificially cultured fish and shellfish by producing secondary metabolites including antibiotics, anticancer agents, antiparasitic agents, antifungal agents, and enzymes (protease and amylase). Some Streptomyces strains also exhibit antagonistic and antimicrobial activity against aquaculture-based pathogens by producing inhibitory compounds such as bacteriocins, siderophores, hydrogen peroxide, and organic acids to compete for nutrients and attachment sites in the host. The administration of Streptomyces in aquaculture could also induce an immune response, disease resistance, quorum sensing/antibiofilm activity, antiviral activity, competitive exclusion, modification in gastrointestinal microflora, growth enhancement, and water quality amelioration via nitrogen fixation and degradation of organic residues from the culture system. This review provides the current status and prospects of Streptomyces as potential probiotics in aquaculture, their selection criteria, administrative methods, and mechanisms of action. The limitations of Streptomyces as probiotics in aquaculture are highlighted and the solutions to these limitations are also discussed.

Marine actinomycete Streptomyces variabilis S26 as a biocontrol agent for vibriosis in shrimp larval rearing systems

Indiscriminate use of antibiotics has led to the emergence of antibiotic-resistant microbes and the loss of natural flora in aquaculture systems necessitating the ban of many of these chemotherapeutants in aquaculture. Actinobacteria play a profound role in the biogeochemical cycling in the marine environment and represent the principal source of secondary metabolites with antimicrobial property. In the present study, 98 marine-derived actinomycete isolates were screened for antimicrobial activity against the common aquatic pathogens. A potent actinomycete isolate S26, identified as Streptomyces variabilis based on 16 S ribosomal RNA (rRNA) gene sequencing was then checked for the production of antibiotic in five different fermentation media and the one which showed maximum production was chosen for further study. Optimization of the fermentation medium for secondary metabolite production was carried out by response surface methodology (RSM) using DESIGN EXPERT. The analysis of variance (ANOVA) of the quadratic regression model demonstrated that the model was highly significant for the response concerned that is, antimicrobial activity as evident from the Fisher's F- test with a very low probability value [(P model>F) = 0.0001]. Of the 10 different solutions suggested by the software, the most suitable composition was found to be starch, 1.38%; soy powder, 0.88%; ammonium sulfate, 0.16% and salinity, 27.76‰. S. variabilis S26 cultured in the optimized production medium was applied in the Penaeus monodon larval rearing system and the total Vibrio count and survival rate were estimated. S. variabilis S26 treatment showed a significant reduction in vibrios and conferred better protection to P. monodon in culture system compared with control.

Dietary Astragalus polysaccharides improve the growth and innate immune response of giant freshwater prawn Macrobrachium rosenbergii: Insights from the brain-gut axis

Supplementation with Astragalus polysaccharides (APS) has beneficial effects on aquatic animals. Herein, we aimed to investigate the effects of different doses of APS on the growth, innate immune response, and brain-gut axis of Macrobrachium rosenbergii. The molecular weight and the monosaccharide composition of APS were analyzed. APS were added at concentration of 0 (control), 0.05, 0.10, 0.15, and 0.20 % in practical diets. Growth performance increased significantly under 0.05 to 0.20 % APS, with enhanced lipase and protease activities in intestinal tissues. Prawns receiving APS supplementation had significantly lower amounts of pathogenic intestinal bacteria (Vibrio and Aeromonas) and a markedly different microbial community structure compared with those of the control group. The fecal short chain fatty acid (SCFA) and neurotransmitters γ-aminobutyric acid contents increased in the brains of prawns receiving APS, which was potentially associated with increased Lactobacillus and Bacillus levels. Prawns receiving APS supplementation displayed a significantly enhanced immune function (such as total hemocyte count, total protein concentration, phenoloxidase activity, serum agglutination titer, and lysozyme activity) and improved disease resistance to Vibrio anguillarum compared those in the control group. Thus, dietary APS positively affected the gut-brain axis by altering the microbiota composition, increasing the fecal SCFA content, and enhancing prawn immunity.

Host-microbiome interaction in fish and shellfish: An overview

The importance of the gut microbiome in the management of various physiological activities including healthy growth and performance of fish and shellfish is now widely considered and being studied in detail for potential applications in aquaculture farming and the future growth of the fish industry. The gut microbiome in all animals including fish is associated with a number of beneficial functions for the host, such as stimulating optimal gastrointestinal development, producing and supplying vitamins to the host, and improving the host's nutrient uptake by providing additional enzymatic activities. Besides nutrient uptake, the gut microbiome is involved in strengthening the immune system and maintaining mucosal tolerance, enhancing the host's resilience against infectious diseases, and the production of anticarcinogenic and anti-inflammatory compounds. Because of its significant role, the gut microbiome is very often considered an "extra organ," as it plays a key role in intestinal development and regulation of other physiological functions. Recent studies suggest that the gut microbiome is involved in energy homeostasis by regulating feeding, digestive and metabolic processes, as well as the immune response. Consequently, deciphering gut microbiome dynamics in cultured fish and shellfish species will play an indispensable role in promoting animal health and aquaculture productivity. It is mentioned that the microbiome community available in the gut tract, particularly in the intestine acts as an innovative source of natural product discovery. The microbial communities that are associated with several marine organisms are the source of natural products with a diverse array of biological activities and as of today, more than 1000 new compounds have been reported from such microbial species. Exploration of such new ingredients from microbial species would create more opportunities for the development of the bio-pharma/aquaculture industries. Considering the important role of the microbiome in the whole life span of fish and shellfish, it is necessary to understand the interaction process between the host and microbial community. However, information pertaining to host-microbiome interaction, particularly at the cellular level, gene expression, metabolic pathways, and immunomodulation mechanisms, the available literature is scanty. It has been reported that there are three ways of interaction involving the host-microbe-environment operates to maintain homeostasis in the fish and shellfish gut i.e. host intrinsic factors, the environment that shapes the gut microbiome composition, and the core microbial community present in the gut system itself has equal influence on the host biology. In the present review, efforts have been made to collect comprehensive information on various aspects of host-microbiome interaction, particularly on the immune system and health maintenance, management of diseases, nutrient uptake, digestion and absorption, gene expression, and metabolism in fish and shellfish.

Applications of Actinobacteria in aquaculture: prospects and challenges

Disease outbreaks due to improper culture management, poor water quality, and climate change are major concerns in aquaculture. Most of the aquatic pathogens are opportunistic and any imbalance in the host-pathogen-environment triad will result in a disease outbreak. The indiscriminate use of chemotherapeutics such as antibiotics to prevent diseases in aquaculture will lead to antimicrobial resistance in aquaculture. Hence, the demand for natural microbial strains which can be used as beneficial probiotics and bioaugmentors in fish farming systems has increased to ensure one health in aquaculture. Studies have proved the probiotic and bioremediation potential of several Actinobacterial species that can be applied in aquaculture. Actinobacteria, especially Streptomyces, can be applied in aquaculture for disease prevention, treatment, and bioremediation of organic and inorganic waste in the culture systems. The growth, immunity, and resistance towards aquatic pathogens in cultured organisms also get enhanced through their capability to release potent antimicrobial compounds, bioactive molecules, and novel enzymes. Their broad-spectrum antimicrobial and quorum quenching activity can be well exploited against quorum sensing biofilm forming aquatic pathogens. Even though they impart specific adverse effects like the production of off-flavour compounds, this could be controlled through proper management strategies. This review discusses the applications, challenges, and prospects of Actinobacteria in aquaculture. Research gaps are also highlighted, which may shed light on the existing complexities and should pave the way for their better understanding and utilisation in aquaculture.

Dietary supplementation with Pediococcus pentosaceus enhances the innate immune response in and promotes growth of Litopenaeus vannamei shrimp

To reach the sustainable development goals on health management in Litopenaeus vannamei shrimp culture, Pediococcus pentosaceus AB01 was supplemented in shrimp diet. In this study, the control diet and three experimental diets containing P. pentosaceus AB01 (10⁸ , 10⁹ , 10¹⁰  CFU/g) were separately introduced to L. vannamei for a 28 days feeding trial. After the feeding trial, percent weight gain, feeding efficiency, and feed conversion ratio (FCR) were significantly elevated in L. vannamei administered with P. pentosaceus AB01 at 10⁹ and 10¹⁰ colony-forming unit (CFU)/g. Protease, amylase, and trypsin were found at higher levels in the probiotic-supplied groups. The feeding of shrimps with P. pentosaceus AB01 significantly increased innate immune response and levels of related biochemical parameters in the haemolymph. After the white spot syndrome virus (WSSV) challenge, supplementation of P. pentosaceus AB01 had significant positive effects (p < .05) on survival rate, compared to that of the control diet. The higher resistance of L. vannamei to WSSV might have been due to alterations in the gut microbiome composition and upregulation of the Toll-Like Receptor (TLR) signalling pathway. Hence, P. pentosaceus AB01 may be a promising alternative feed to promote growth rate, modulate microbiota composition, and enhance immunity in L. vannamei shrimp.

Enterococcus faecium are associated with the modification of gut microbiota and shrimp post-larvae survival

BACKGROUND

Probiotics are widely used to promote host health. Compared to mammals and terrestrial invertebrates, little is known the role of probiotics in aquatic invertebrates. In this study, eighteen tanks with eight hundred of shrimp post-larvae individuals each were randomly grouped into three groups, one is shrimps administered with E. faecium as probiotic (Tre) and others are shrimps without probiotic-treatment (CK1: blank control, CK2: medium control). We investigated the correlations between a kind of commercial Enterococcus faecium (E. faecium) powder and microbiota composition with function potentials in shrimp post-larvae gut.

RESULTS

We sequenced the 16S rRNA gene (V4) of gut samples to assess diversity and composition of the shrimp gut microbiome and used differential abundance and Tax4Fun2 analyses to identify the differences of taxonomy and predicted function between different treatment groups. The ingested probiotic bacteria (E. faecium) were tracked in gut microbiota of Tre and the shrimps here showed the best growth performance especially in survival ratio (SR). The distribution of SR across samples was similar to that in PCoA plot based on Bray-Curits and two subgroups generated (SL: SR < 70%, SH: SR ≥ 70%). The gut microbiota structure and predicted function were correlated with both treatment and SR, and SR was a far more important factor driving taxonomic and functional differences than treatment. Both Tre and SH showed a low and uneven community species and shorted phylogenetic distance. We detected a shift in composition profile at phylum and genus level and further identified ten OTUs as relevant taxa that both closely associated with treatment and SR. The partial least squares path model further supported the important role of relevant taxa related to shrimp survival ratio.

CONCLUSIONS

Overall, we found gut microbiota correlated to both shrimp survival and ingested probiotic bacteria (E. faecium). These correlations should not be dismissed without merit and will uncover a promising strategy for developing novel probiotics through certain consortium of gut microbiota.

Quantitative microbiological risk assessment of complex microbial community in Prawn farm wastewater and applicability of nanoparticles and probiotics for eliminating of antibiotic-resistant bacteria

The current review highlighted the quantitative microbiological risk assessment of Vibrio parahaemolyticus in Prawn farm wastewaters (PFWWs) and the applicability of nanoparticles for eliminating antibiotic-resistant bacteria (ARB). The high availability of the antibiotics in the environment and their transmission into human through the food-chain might cause unknown health effects. The aquaculture environments are considered as a reservoir for the antibiotic resistance genes (ARGs) and contributed effectively in the increasing of ABR. The metagenomic analysis is used to explore ARGs in the non-clinical environment. V. parahaemolyticus is among the pathogenic bacteria which are transmitted through sea food causing human acute gastroenteritis due to available thermostable direct hemolysin (tdh), adhesins, TDH related hemolysin (trh). The inactivation of pathogenic bacteria using nanoparticles act by disturbing the cell membrane, interrupting the transport system, DNA and mitochondria damage, and oxidizing the cellular component by reactive oxygen species (ROS). The chloramphenicol, nitrofurans, and nitroimidazole are among the prohibited drugs in fish and fishery product. The utilization of probiotics is the most effective and safe alternative for antibiotics in Prawn aquaculture. This review will ensure public understanding among the readers on how they can decrease the risk of the antimicrobial resistance distribution in the environment.

FeS2 nanoparticles decorated carbonized Luffa cylindrica as biofilm substrates for fabricating high performance biosensors

A high-performance microbial biosensor was fabricated with a reasonably designed biofilm substrate, where the aerogel of carbonized Luffa cylindrica (LC) was used as the scaffold for loading biofilm and FeS₂ nanoparticles (FeS₂NPs) were employed to modify this aerogel (FeS₂NPs/Gel_LC). The fabricated FeS₂NPs/Gel_LC exhibited a spring-like structure similar with that of the raw LC, which facilitated the linkage of the scaffold and promoted its mechanical strength, and further prolonged the service period of the as-prepared biosensor from few days to two months. Meanwhile, the introduced FeS₂NPs improved the microbial electron transfer of the biofilm and causing an increase in the sensor's signals from 155.0 ± 2.6 to 352.0 ± 17.1 nA and a decrease in the detection limit from 0.95 to 0.38 mg O L^-1 (S/N = 3) for the detection of glucose-glutamic acid (GGA). More important, the FeS₂NPs had been demonstrated to have the capability for modulating a persistent shift of the microbial community with organic pollutant biodegradability. Compared with the Gel_LC, the FeS₂NPs/Gel_LC exhibited a promising performance for measuring the synthetic sewage and real water samples in BOD assay and an increasing inhibition-ratio for detecting 3,5-dichlorophenol (DCP) in toxicity assay. Based on the vast resource and renewability of LC, this work pave a new avenue for developing high-performance microbial biosensors that are expected to be the engineering production.

White spot syndrome virus (WSSV) disturbs the intestinal microbiota of shrimp (Penaeus vannamei) reared in biofloc and clear seawater

White spot syndrome virus (WSSV) is one of the most virulent pathogens afflicting shrimp farming. Understanding its influence on shrimp intestinal microbiota is paramount for the advancement of aquaculture, since gut dysbiosis can negatively impact shrimp development, physiology, and immunological response. Thereupon, the data presented herein assesses the influence of WSSV infection and different rearing systems on the intestinal microbiota of Penaeus vannamei. Our study aimed to describe and correlate the composition of shrimp (Penaeus vannamei) gut microbiota, when reared in biofloc and clear seawater, before and (48 h) after WSSV experimental infection. Shrimp were kept in two different systems (biofloc and clear seawater) and experimentally infected with WSSV. Intestine and water samples were characterized by 16S rRNA gene sequencing, before and after viral infection. We observed (i) WSSV induced higher mortality among shrimp reared in biofloc; (ii) WSSV led to a loss of intestinal microbiota heterogeneity, at the genus level, in shrimp kept in clear seawater; (iii) there was a prevalence of Cetobacterium and Bacillus in the intestine of shrimp from both systems; (iv) WSSV did not cause significant changes in intestinal microbiota diversity or richness; (v) regardless of the type of system and time of infection, intestinal microbiota was dissimilar to that of the surrounding water, despite being influenced by the type of system. Therefore, WSSV infection leads to punctual dysbiotic changes in shrimp microbiota, although the virus is sufficiently virulent to cause high mortalities even in well-managed systems, such as a balanced experimental biofloc system. KEY POINTS: • WSSV infection leads to a perturbed gut microbiota in shrimp. • WSSV infection greater impacts microbiota of shrimp reared in CSW than those in BFT. • WSSV infection caused higher mortality levels in shrimp reared in BFT than in CSW. • Rearing system influences shrimp gut microbiota composition. Graphical abstract.

Understanding the role of the shrimp gut microbiome in health and disease

With rapid increases in the global shrimp aquaculture sector, a focus on animal health during production becomes ever more important. Animal productivity is intimately linked to health, and the gut microbiome is becoming increasingly recognised as an important driver of cultivation success. The microbes that colonise the gut, commonly referred to as the gut microbiota or the gut microbiome, interact with their host and contribute to a number of key host processes, including digestion and immunity. Gut microbiome manipulation therefore represents an attractive proposition for aquaculture and has been suggested as a possible alternative to the use of broad-spectrum antibiotics in the management of disease, which is a major limitation of growth in this sector. Microbiota supplementation has also demonstrated positive effects on growth and survival of several different commercial species, including shrimp. Development of appropriate gut supplements, however, requires prior knowledge of the host microbiome. Little is known about the gut microbiota of the aquatic invertebrates, but penaeid shrimp are perhaps more studied than most. Here, we review current knowledge of information reported on the shrimp gut microbiota, highlighting the most frequently observed taxa and emphasizing the dominance of Proteobacteria within this community. We discuss involvement of the microbiome in the regulation of shrimp health and disease and describe how the gut microbiota changes with the introduction of several economically important shrimp pathogens. Finally, we explore evidence of microbiome supplementation and consider its role in the future of penaeid shrimp production.

Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota

The shrimp has become the most valuable traded marine product in the world, and its microbiota plays an essential role in its development and overall health status. Massive high-throughput sequencing techniques using several hypervariable regions of the 16S rRNA gene are broadly applied in shrimp microbiota studies. However, it is essential to consider that the use of different hypervariable regions can influence the obtained data and the interpretation of the results. The present study compares the shrimp microbiota structure and composition obtained by three types of amplicons: one spanning both the V3 and V4 hypervariable regions (V3V4), one for the V3 region only (V3), and one for the V4 region only (V4) using the same experimental and bioinformatics protocols. Twenty-four samples from hepatopancreas and intestine were sequenced and evaluated using the GreenGenes and silva reference databases for clustering and taxonomic classification. In general, the V3V4 regions resulted in higher richness and diversity, followed by V3 and V4. All three regions establish an apparent clustering effect that discriminates between the two analyzed organs and describe a higher richness for the intestine and a higher diversity for the hepatopancreas samples. Proteobacteria was the most abundant phyla overall, and Cyanobacteria was more common in the intestine, whereas Firmicutes and Actinobacteria were more prevalent in hepatopancreas samples. Also, the genus Vibrio was significantly abundant in the intestine, as well as Acinetobacter and Pseudomonas in the hepatopancreas suggesting these taxa as markers for their respective organs independently of the sequenced region. The use of a single hypervariable region such as V3 may be a low-cost alternative that enables an adequate description of the shrimp microbiota, allowing for the development of strategies to continually monitor the microbial communities and detect changes that could indicate susceptibility to pathogens under real aquaculture conditions while the use of the full V3V4 regions can contribute to a more in-depth characterization of the microbial composition.

Effect of Streptomyces probiotics on the gut microbiota of Litopenaeus vannamei challenged with Vibrio parahaemolyticus

This study assessed the intestinal microbiota of juveniles of the White shrimp Litopenaus vannamei, whose feed was enriched with three probiotic formulations: Streptomyces sp. RL8 (RL8); a mix of Lactobacillus graminis and Streptomyces spp. RL8 and N7 (Lac-Strep); and a mix of Bacillus spp. and Streptomyces spp. RL8 and N7 (Bac-Strep). The analysis was performed by sequencing the V3 region of the 16S rRNA gene of treated animals and the control group before and after Vibrio parahaemolyticus challenge. After challenge, the highest Shannon diversity indexes corresponded to RL8 and Bac-Strep (3.94 ± 0.11 and 3.39 ± 0.3, respectively) and the lowest to the control group (2.58 ± 0.26). The most abundant phyla before and after challenge were Proteobacteria, Actinobacteria, and Bacteroidetes. The principal component analysis and Statistical Analysis of Metagenomic Profiles (STAMP) showed that the gut microbiota of the groups RL8 and Bac-Strep after challenge was different from the other experimental groups, which was characterized by a higher bacterial diversity, as well as a significant stimulation of the Bacteriovorax population and other antimicrobial producing genera that protected shrimp from infection.