Probiotic legacy effects on gut microbial assembly in tilapia larvae

Microbiomes in the context of developing sustainable intensified aquaculture

With an ever-growing human population, the need for sustainable production of nutritional food sources has never been greater. Aquaculture is a key industry engaged in active development to increase production in line with this need while remaining sustainable in terms of environmental impact and promoting good welfare and health in farmed species. Microbiomes fundamentally underpin animal health, being a key part of their digestive, metabolic and defense systems, in the latter case protecting against opportunistic pathogens in the environment. The potential to manipulate the microbiome to the advantage of enhancing health, welfare and production is an intriguing prospect that has gained considerable traction in recent years. In this review we first set out what is known about the role of the microbiome in aquaculture production systems across the phylogenetic spectrum of cultured animals, from invertebrates to finfish. With a view to reducing environmental footprint and tightening biological and physical control, investment in "closed" aquaculture systems is on the rise, but little is known about how the microbial systems of these closed systems affect the health of cultured organisms. Through comparisons of the microbiomes and their dynamics across phylogenetically distinct animals and different aquaculture systems, we focus on microbial communities in terms of their functionality in order to identify what features within these microbiomes need to be harnessed for optimizing healthy intensified production in support of a sustainable future for aquaculture.

Effects of Dietary Supplementation with Bacillus amyloliquefaciens US573 on Intestinal Morphology and Gut Microbiota of European Sea Bass

Probiotics or direct-fed microbials (DFM) have proven strong potential for improving aquaculture sustainability. This study aims to evaluate the effects of dietary supplementation with the DFM Bacillus amyloliquefaciens US573 on growth performance, intestinal morphology, and gut microbiota (GM) of European sea bass. For this purpose, healthy fish were divided into two feeding trials in triplicate of 25 fish in each tank. The fish were fed with a control basal diet or a DFM-supplemented diet for 42 days. Results showed that, while no significant effects on growth performance were observed, the length and abundance of villi were higher in the DFM-fed group. The benefic effects of DFM supplementation included also the absence of cysts formation and the increase in number of goblet cells playing essential role in immune response. Through DNA metabarcoding analysis of GM, 5 phyla and 14 major genera were identified. At day 42, the main microbiome changes in response to B. amyloliquefaciens US573 addition included the significant decrease in abundance of Actinobacteria phylum that perfectly correlates with a decrease in Nocardia genus representatives which represent serious threat in marine and freshwater fish. On the contrary, an obvious dominance of Betaproteobacteria associated with the abundance in Variovorax genus members, known for their ability to metabolize numerous substrates, was recorded. Interestingly, Firmicutes, particularly species affiliated to the genus Sporosarcina with recent promising probiotic potential, were identified as the most abundant. These results suggest that B. amyloliquefaciens US573 can be effectively recommended as health-promoting DFM in European sea bass farming.

Gut microbiome modulation mediated by probiotics: Positive impact on growth and health status of Labeo rohita

The current study was targeted to determine the effect of probiotics on the growth, physiology, and gut microbiology of Labeo rohita fingerlings. One hundred and twenty fishes were divided into four dietary groups, each in triplicate for a feeding trial of 90 days. These treatments included T0 (control, basal diet) used as the reference, and three probiotic-supplemented diets represented as Tbc (Bacillus cereus), Tgc (Geotrichum candidum), and Tmc (B. cereus and G. candidum). The probiotics were supplemented at a level of 1 × 10⁹ CFU/g feed. Fishes nurtured on probiotic-added diet showed significantly high physiological improvement (p < 0.05) in terms of growth, feed utilization capacity, hematological profile, and digestive enzymes as compared to control. The fish were subjected to a challenge test after a 90-day feeding trial. The Tmc exhibited maximum fish growth when challenged by Staphylococcus aureus and showed fish survival when compared to control, in which fish mortality was examined. Fish gut microbial composition was modulated by probiotic treatments, especially in Tgc and Tmc as compared to control. The absence of opportunistic pathogens such as Staphylococcus saprophyticus and Sporobolomyces lactosus and detection of lower levels of Trichosporon and Cryptococcus in treated groups indicate the gut modulation driven by applied probiotics. The G. candidum QAUGC01 was retrieved in yeast metagenomics data, which might be due to the production of polyamines by them that facilitated adherence and consequent persistence. In conclusion, it can be suggested that the probiotic-supplemented diet could enhance fish growth and feed efficiency through community modulation and digestive enzymes, which could be a milestone in local aquaculture.

Research Progress of the Gut Microbiome in Hybrid Fish

Fish, including hybrid species, are essential components of aquaculture, and the gut microbiome plays a vital role in fish growth, behavior, digestion, and immune health. The gut microbiome can be affected by various internal and/or external factors, such as host development, diet, and environment. We reviewed the effects of diet and dietary supplements on intestinal microorganisms in hybrid fish and the difference in the gut microbiome between the hybrid and their hybrids that originate. Then, we summarized the role of the gut microbiome in the speciation and ecological invasion of hybrid fish. Finally, we discussed possible future studies on the gut microbiome in hybrid fish, including the potential interaction with environmental microbiomes, the effects of the gut microbiome on population expansion, and fish conservation and management.

Impact of early-life rearing history on gut microbiome succession and performance of Nile tilapia

Background

Fish gut microbial colonisation starts during larval stage and plays an important role in host’s growth and health. To what extent first colonisation could influence the gut microbiome succession and growth in later life remains unknown. In this study, Nile tilapia embryos were incubated in two different environments, a flow-through system (FTS) and a biofloc system (BFS); hatched larvae were subsequently cultured in the systems for 14 days of feeding (dof). Fish were then transferred to one common recirculating aquaculture system (RAS1, common garden, 15–62 dof), followed by a growth trial in another RAS (RAS2, growth trial, 63–105 dof). In RAS2, fish were fed with two types of diet, differing in non-starch polysaccharide content. Our aim was to test the effect of rearing environment on the gut microbiome development, nutrient digestibility and growth performance of Nile tilapia during post-larvae stages.

Results

Larvae cultured in the BFS showed better growth and different gut microbiome, compared to FTS. After the common garden, the gut microbiome still showed differences in species composition, while body weight was similar. Long-term effects of early life rearing history on fish gut microbiome composition, nutrient digestibility, nitrogen and energy balances were not observed. Still, BFS-reared fish had more gut microbial interactions than FTS-reared fish. A temporal effect was observed in gut microbiome succession during fish development, although a distinct number of core microbiome remained present throughout the experimental period.

Conclusion

Our results indicated that the legacy effect of first microbial colonisation of the fish gut gradually disappeared during host development, with no differences in gut microbiome composition and growth performance observed in later life after culture in a common environment. However, early life exposure of larvae to biofloc consistently increased the microbial interactions in the gut of juvenile Nile tilapia and might possibly benefit gut health.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00145-w.

Evaluation of probiotic characteristics and whole genome analysis of Pediococcus pentosaceus MR001 for use as probiotic bacteria in shrimp aquaculture

The development of non-antibiotic and environmentally friendly agents is a key consideration for health management in shrimp aquaculture. In this study, the probiotic potential in shrimp aquaculture of Pediococcus pentosaceus MR001, isolated from Macrobrachium rosenbergii, was investigated by means of feeding trial and genetic characterization. In the feeding trial, dietary supplementation with P. pentosaceus MR001 significantly increased weight gain and digestive enzyme activity (p < 0.05) in shrimp, Litopenaeus vannamei. The intestinal histology showed that shrimp given the probiotic diet had healthier guts than the control group. Also, the immune gene expression and the survival rate in the treatment group were significantly increased when compared with the control group. The genetic characteristics of P. pentosaceus strain MR001 were explored by performing whole-genome sequencing (WGS) using the HiSeq 2500 platform and PacBio system, revealing the complete circular genome of 1,804,896 bp. We also identified 1789 coding genes and subsequently characterized genes related to the biosynthesis of bacteriocins, stress resistance, and bile tolerance. Our findings suggest that insights in the functional and genetic characteristics of P. pentosaceus strain MR001 could provide opportunities for applications of such strain in shrimp diet supplementation.

Time to integrate biotechnological approaches into fish gut microbiome research

Like for other vertebrates, the fish microbiome is critical to the health of its host and has complex and dynamic interactions with the surrounding environment. Thus, the study of the fish microbiome can benefit from the new prospects gained by innovative biotechnological applications in human and other animals, that include manipulation of the associated microbial communities (to improve the health, productivity, and sustainability of fish production), in vitro gut simulators, synthetic microbial communities, and others. Here, we summarize the current state of knowledge on such biotechnological approaches to better understand and engineer the fish microbiome, as well as to advance our knowledge on host-microbes interactions. A particular focus is given to the most recent strategies for fish microbiome manipulation to improve fish health, food safety and environmental sustainability.

Seasonal Dynamics Are the Major Driver of Microbial Diversity and Composition in Intensive Freshwater Aquaculture

Aquaculture facilities such as fishponds are one of the most anthropogenically impacted freshwater ecosystems. The high fish biomass reared in aquaculture is associated with an intensive input into the water of fish-feed and fish excrements. This nutrients load may affect the microbial community in the water, which in turn can impact the fish health. To determine to what extent aquaculture practices and natural seasonal cycles affect the microbial populations, we characterized the microbiome of an inter-connected aquaculture system at monthly resolution, over 3 years. The system comprised two fishponds, where fish are grown, and an operational water reservoir in which fish are not actively stocked. Clear natural seasonal cycles of temperature and inorganic nutrients concentration, as well as recurring cyanobacterial blooms during summer, were observed in both the fishponds and the reservoir. The structure of the aquatic bacterial communities in the system, characterized using 16S rRNA sequencing, was explained primarily by the natural seasonality, whereas aquaculture-related parameters had only a minor explanatory power. However, the cyanobacterial blooms were characterized by different cyanobacterial clades dominating at each fishpond, possibly in response to distinct nitrogen and phosphate ratios. In turn, nutrient ratios may have been affected by the magnitude of fish feed input. Taken together, our results show that, even in strongly anthropogenically impacted aquatic ecosystems, the structure of bacterial communities is mainly driven by the natural seasonality, with more subtle effects of aquaculture-related factors.

Exogenous enzymes and probiotics alter digestion kinetics, volatile fatty acid content and microbial interactions in the gut of Nile tilapia

Sustainable aquafeed production requires fishmeal replacement, leading to an increasing use of plant-derived ingredients. As a consequence, higher levels of antinutritional substances, such as non-starch polysaccharides and phytate, are present in aquafeeds, with negative effects on fish performance, nutrient digestibility and overall gut health. To alleviate these negative effects, providing exogenous digestive enzymes and/or probiotics can be an effective solution. In this study, we tested the effect of dietary supplementation of enzymes (phytase and xylanase) and probiotics (three strains of Bacillus amyloliquefaciens) on nutrient digestion kinetics and volatile fatty acid content along the gut, and the distal gut microbiome diversity in Nile tilapia. Chyme volatile fatty content was increased with probiotic supplementation in the proximal gut, while lactate content, measured for the first time in vivo in fish, decreased with enzymes along the gut. Enzyme supplementation enhanced crude protein, Ca and P digestibility in proximal and middle gut. Enzymes and probiotics supplementation enhanced microbial interactions as shown by network analysis, while increased the abundance of lactic acid bacteria and Bacillus species. Such results suggest that supplementation with exogenous enzymes and probiotics increases nutrient availability, while at the same time benefits gut health and contributes to a more stable microbiome environment.

The Immunostimulatory Effects of Commercial Feed Additives on Growth Performance, Non-specific Immune Response, Antioxidants Assay, and Intestinal Morphometry of Nile tilapia, Oreochromis niloticus

The main objective of the present research was to investigate the impacts of commercial immunostimulants on growth, non-specific immune response, antioxidant enzymes, and intestinal morphometry of Nile tilapia, Oreochromis niloticus. Fish (100 ± 6.5 g) were randomly divided into five groups in triplicates (150 fish in each replicate), stocked in 20 m² of aerated concrete ponds. The fish were fed on a control diet (30.0% crude protein) (control), and four experimental diets supplemented with Yeast Plus^®, Digestarom^®, and Biotronic^® Top³ at 1 kg ton^–1, and Sanolife PRO-F^® at 0.5 kg ton^–1. After the experimental period, the highest significant yield (kg m^–3), mean final weight (g fish^–1), average weight gain (g fish^–1), and specific growth rate (% body weight day^–1), were recorded in fish fed on the diet supplemented by Sanolife PRO-F, followed by Yeast Plus ponds. The lowest yield was recorded in the control group. However, the feed conversion ratio was significantly decreased with Sanolife PRO-F diet. Furthermore, the hematological analysis increased in the following ascending order: Sanolife PRO-F^®; Yeast Plus^®; Biotronic^® Top3 and finally Digestarom^® groups. The lowest concentrations of white blood cells, red blood cells, hematocrite, and hemoglobin (P ≤ 0.05) were observed in the control group. The levels of phagocytic activity and phagocytic index were significantly higher in fish fed with Sanolife PRO-F^® group (P ≤ 0.05). Likewise, serum lysozyme activity was significantly highest in Sanolife PRO-F (0.63 and 0.68 U/mL, after 0.5 min and 3 min, respectively). Levels of total serum proteins, globulin, Immunoglobulin M, catalase, and super oxide dismutase were significantly higher in fish fed with Sanolife PRO-F^® supplement. On the contrary, length measurement of the intestinal villus height/width, absorption area, crypt depth, and goblet cells, were significantly lower in the control group, whereas their highest values was observed in fish fed Sanolife PRO-F (P ≤ 0.05). Consequently, Sanolife PRO-F^® is recommended at a level of 0.5 kg ton^–1, to improve the growth performance, antioxidative capacity, and immune response of Nile tilapia.

Osmotic stress induces gut microbiota community shift in fish

Alteration of the gut microbiota plays an important role in animal health and metabolic diseases. However, little is known with respect to the influence of environmental osmolality on the gut microbial community. The aim of the current study was to determine whether the reduction in salinity affects the gut microbiota and identify its potential role in salinity acclimation. Using Oryzias melastigma as a model organism to perform progressive hypotonic transfer experiments, we evaluated three conditions: seawater control (SW), SW to 50% sea water transfer (SFW) and SW to SFW to freshwater transfer (FW). Our results showed that the SFW and FW transfer groups contained higher operational taxonomic unit microbiota diversities. The dominant bacteria in all conditions constituted the phylum Proteobacteria, with the majority in the SW and SFW transfer gut comprising Vibrio at the genus level, whereas this population was replaced by Pseudomonas in the FW transfer gut. Furthermore, our data revealed that the FW transfer gut microbiota exhibited a reduced renin-angiotensin system, which is important in SW acclimation. In addition, induced detoxification and immune mechanisms were found in the FW transfer gut microbiota. The shift of the bacteria community in different osmolality environments indicated possible roles of bacteria in facilitating host acclimation.

Environmental plasticity and colonisation history in the Atlantic salmon microbiome: A translocation experiment

Microbial communities associated with the gut and the skin are strongly influenced by environmental factors, and can rapidly adapt to change. Historical processes may also affect the microbiome. In particular, variation in microbial colonisation in early life has the potential to induce lasting effects on microbial assemblages. However, little is known about the relative extent of microbiome plasticity or the importance of historical colonisation effects following environmental change, especially for nonmammalian species. To investigate this we performed a reciprocal translocation of Atlantic salmon between artificial and semi-natural conditions. Wild and hatchery-reared fry were transferred to three common garden experimental environments for 6 weeks: standard hatchery conditions, hatchery conditions with an enriched diet, and simulated wild conditions. We characterized the faecal and skin microbiome of individual fish before and after the environmental translocation, using a BACI (before-after-control-impact) design. We found evidence of extensive microbiome plasticity for both the gut and skin, with the greatest changes in alpha and beta diversity associated with the largest changes in environment and diet. Microbiome richness and diversity were entirely determined by environment, with no detectable effects of fish origin, and there was also a near-complete turnover in microbiome structure. However, we also identified, for the first time in fish, evidence of historical colonisation effects reflecting early-life experience, including ASVs characteristic of captive rearing. These results have important implications for host adaptation to local selective pressures, and highlight how conditions experienced during early life can have a long-term influence on the microbiome and, potentially, host health.

Altered monocytic phenotypes are linked with systemic inflammation and may be linked to mortality in dialysis patients

The major causes for increased morbidity and mortality among chronic kidney disease patients are cardiovascular diseases and infection. A causal link between an activated immune system and aggravated atherosclerosis has been postulated that skews the system towards inflammatory responses. Previously, we demonstrated a positive association of pro-inflammatory cytokines with monocytic Y-box binding protein-1 (YB-1) expression and vessel wall infiltration in hemodialysis patients. Here, we question whether the responsiveness and cytokine repertoire of monocytes is altered by pre-activation and how this correlates with survival. EDTA whole blood from hemodialysis patients (n = 45) and healthy controls (n = 34) was collected and leukocytes challenged with LPS. The distribution of monocyte subsets, YB-1_acetyl content, and serum cytokine levels were determined. Compared to controls, dialysis patients have fewer classical (Mo1) and more intermediate (Mo2) and non-classical (Mo3) monocytes. In response to LPS, the Mo2 subset significantly increases (p < 0.001) in control subjects, but not in hemodialysis patients; increased CD86 expression indicates a positive response to LPS. Based on the changes within Mo2, subjects could be classified as responders or non-responders: 60% non-responders were seen in the dialysis cohort versus only 35% among healthy controls. YB-1 acetylation is higher in dialysis patients, independent of LPS stimulation. In this small cohort with 72 months follow-up period intracellular YB-1_acetyl levels, IL-6, uPAR, and IP10 correlated with excess mortality in the dialysis cohort. Changes in YB-1 acetylation and serum cytokines may, at a given time point, possibly predict the long-term outcome and thus provide a legacy effect in hemodialysis patients.

An examination of data from the American Gut Project reveals that the dominance of the genus Bifidobacterium is associated with the diversity and robustness of the gut microbiota

Bifidobacterium and Lactobacillus are beneficial for human health, and many strains of these two genera are widely used as probiotics. We used two large datasets published by the American Gut Project (AGP) and a gut metagenomic dataset (NBT) to analyze the relationship between these two genera and the community structure of the gut microbiota. The meta-analysis showed that Bifidobacterium, but not Lactobacillus, is among the dominant genera in the human gut microbiota. The relative abundance of Bifidobacterium was elevated when Lactobacillus was present. Moreover, these two genera showed a positive correlation with some butyrate producers among the dominant genera, and both were associated with alpha diversity, beta diversity, and the robustness of the gut microbiota. Additionally, samples harboring Bifidobacterium present but no Lactobacillus showed higher alpha diversity and were more robust than those only carrying Lactobacillus. Further comparisons with other genera validated the important role of Bifidobacterium in the gut microbiota robustness. Multivariate analysis of 11,744 samples from the AGP dataset suggested Bifidobacterium to be associated with demographic features, lifestyle, and disease. In summary, Bifidobacterium members, which are promoted by dairy and whole-grain consumption, are more important than Lactobacillus in maintaining the diversity and robustness of the gut microbiota.

Marked variations in gut microbiota and some innate immune responses of fresh water crayfish, marron (Cherax cainii, Austin 2002) fed dietary supplementation of Clostridium butyricum

This study aimed to investigate the effects of Clostridium butyricum as a dietary probiotic supplement in fishmeal based diet on growth, gut microbiota and immune performance of marron (Cherax cainii). Marron were randomly distributed into two different treatment groups, control and probiotic fed group. After 42 days of feeding trial, the results revealed a significant (P < 0.05) increase in growth due to increase in number of moults in marron fed probiotics. The probiotic diet also significantly enhanced the total haemocyte counts (THC), lysozyme activity in the haemolymph and protein content of the tail muscle in marron. Compared to control, the 16S rRNA sequences data demonstrated an enrichment of bacterial diversity in the probiotic fed marron where significant increase of Clostridium abundance was observed. The abundance for crayfish pathogen Vibrio and Aeromonas were found to be significantly reduced post feeding with probiotic diet. Predicted metabolic pathway revealed an increased activity for the metabolism and absorption of carbohydrate, degradation of amino acid, fatty acid and toxic compounds, and biosynthesis of secondary metabolites. C. butyricum supplementation also significantly modulated the expression level of immune-responsive genes of marron post challenged with Vibrio mimicus. The overall results suggest that C. butyricum could be used as dietary probiotic supplement in marron aquaculture.

Effects of dietary probiotic supplementation on the growth, gut health and disease resistance of juvenile Nile tilapia (Oreochromis niloticus)

This study investigated the effects of the Streptococcus agalactiae antagonizing probiotics Bacillus cereus NY5 and Bacillus subtilis as feed additives for Nile tilapia in terms of growth performance, intestinal health and resistance to S. agalactiae. A total of 720 apparently healthy juvenile Nile tilapia (0.20 ± 0.05 g) were randomly divided into 4 equal groups with 3 replicates for each group. Fish were fed a basal diet (control check group, CK group) supplemented with B. subtilis (1 × 10⁸ CFU/g feed, BS group), B. cereus NY5 (1 × 10⁸ CFU/g feed, BC group), and B. subtilis + B. cereus NY5 (0.5 × 10⁸ CFU/g feed of each probiotic, BS + BC group) for 6 wk, and the probiotic supplementation groups were then fed the basal diet for 1 wk to investigate the gut microbial community. The results of this study showed that BS + BC and BC treatments significantly increased weight gain (WG), feed conversion ratio (FCR) and S. agalactiae resistance in Nile tilapia (P < 0.05). Gut microvilli length and density and c-type lysozyme (lyzc) gene expression were significantly increased by probiotic supplementation (P < 0.05). The results of high-throughput sequencing showed that the B. cereus NY5 and B. subtilis + B. cereus NY5-supplemented feed resulted in a significant improvement in tilapia autochthonous gut bacterial communities and had a stimulation effect on a variety of potential probiotics after 6 wk of feeding. After cessation of probiotic administration for 1 wk, the gut bacteria of the fish in the BS + BC and BC groups had minor changes and maintained a stable state. Consequently, it was inferred that, as a feed supplement, B. cereus NY5 and the mixture of B. subtilis and B. cereus NY5 at 1 × 10⁸ CFU/g feed were able to promote growth and disease resistance, which may be associated with the supplement's effects on gut immune status, intestinal morphology, and intestinal microbial community composition.

Effects of Lactococcus lactis subsp. lactis JCM5805 on colonization dynamics of gut microbiota and regulation of immunity in early ontogenetic stages of tilapia

The administration of probiotics during early ontogenetic stages can be an effective way to manipulate the gut microbiota of animals. Specifically, the administration of probiotics can enhance gut-colonization success and regulate the immune response. In this study, the effects of early contact with probiotic Lactococcus lactis subsp. lactis JCM5805 on the gut microbial assembly of larvae Nile tilapia were examined. The effects of JCM5805 on IFNα expression through the TLR7 and TLR9-dependent signal transduction pathway as well as larval disease resistance were studied. Three days postfertilization, embryos were randomly allocated into nine 30 L tanks with a concentration of 20 eggs L^-1. Triplicate tanks were performed for each treatment. Treatments included a control group (C), a low probiotic concentration group (T1), where JCM5805 was added to the water at 1 × 10⁴ cfu ml^-1, and a high probiotic concentration group (T2), where JCM5805 was added to the water at 1 × 10⁸ cfu ml^-1. Probiotics were administered continuously for 15 days. qPCR was used to analyze transcript levels of the TLR7, TLR9, MyD88, IRF7 and IFNα genes using RNA extracted from whole embryos on day 5 and 10, and from the intestine of larvae on day 15. Transcription of these genes was also measured in the intestine, liver and spleen of larvae one month after the cessation of probiotic administration. The results showed that MyD88 and IRF7 were significantly elevated on days 5 and 10 in the T2 group. TLR9 and IFNα were also significantly elevated on days 5, 10 and 15 during probiotic application of T2 (P < 0.05). One month after the cessation of probiotics administration, no significant difference was observed in the expression of these genes (P > 0.05). The larvae were fed probiotics for 15 days and were infused with Streptococcus agalactiae strain WC1535 at a final concentration of 1 × 10⁶ cfu ml^-1. The survival rate of T2 was significantly higher than that of the C group (P < 0.05). Microbial characterization by Illumina HiSeq sequencing of 16S rRNA gene amplicons showed the significantly higher presence of JCM5805 in the guts of T2 after 15 days of probiotic continuous application. Although JCM5805 was below the detection level after the cessation of probiotic for 5 days, the gut microbiota of the exposed tilapia larvae in T2 remained clearly different from that of the control treatment after the cessation of probiotic administration. These data indicated that a high concentration of the probiotic strain JCM5805 upregulated the expression of IFNα via the TLR7/TLR9-Myd88 pathway and enhanced disease resistance of larvae. JCM5805 was only transiently detected and thus was not included in the stable larval microbiota. The early microbial exposure of tilapia larvae affects the gut microbiota at later life stages. However, whether the upregulation of related genes is related to the presence of JCM5805 strain in the intestine requires further verification.

Fish Gut Microbiome: Current Approaches and Future Perspectives

In recent years, investigations of microbial flora associated with fish gut have deepened our knowledge of the complex interactions occurring between microbes and host fish. The gut microbiome not only reinforces the digestive and immune systems in fish but is itself shaped by several host-associated factors. Unfortunately, in the past, majority of studies have focused upon the structure of fish gut microbiome providing little knowledge of effects of these factors distinctively and the immense functional potential of the gut microbiome. In this review, we have highlighted the recently gained insights into the diversity and functions of the fish gut microbiome. We have also delved on the current approaches that are being employed to study the fish gut microbiome with an aim to collate all the knowledge gained and make accurate conclusions for their application based perspectives. The literature reviewed indicated that the future research should shift towards functional microbiomics to improve the maximum sustainable yield in aquaculture.

Progress in the gut microbiota in exploring shrimp disease pathogenesis and incidence

It is now recognized that gut microbiota contributes indispensable roles in safeguarding host health. Shrimp is being threatened by newly emerging diseases globally; thus, understanding the driving factors that govern its gut microbiota would facilitate an initial step to reestablish and maintain a "healthy" gut microbiota. This review summarizes the factors that assemble the shrimp gut microbiota, which focuses on the current progresses of knowledge linking the gut microbiota and shrimp health status. In particular, I propose the exploration of shrimp disease pathogenesis and incidence based on the interplay between dysbiosis in the gut microbiota and disease severity. An updated research on shrimp disease toward an ecological perspective is discussed, including host-bacterial colonization, identification of polymicrobial pathogens and diagnosing disease incidence. Further, a simple conceptual model is offered to summarize the interplay among the gut microbiota, external factors, and shrimp disease. Finally, based on the review, current limitations are raised and future studies directed at solving these concerns are proposed. This review is timely given the increased interest in the role of gut microbiota in disease pathogenesis and the advent of novel diagnosis strategies.

Effects of dietary Lactobacillus rhamnosus JCM1136 and Lactococcus lactis subsp. lactis JCM5805 on the growth, intestinal microbiota, morphology, immune response and disease resistance of juvenile Nile tilapia, Oreochromis niloticus

The present study aimed to evaluate the individual and combined effects of Lactobacillus rhamnosus (LR) JCM1136 and Lactococcus lactis subsp. lactis (LL) JCM5805 on the growth, intestinal microbiota, intestinal morphology, immune response and disease resistance of juvenile Nile tilapia (Oreochromis niloticus). A total of 720 apparently healthy juvenile Nile tilapia (0.20 ± 0.05 g) were randomly divided into four equal groups. Fish were fed with a basal diet (CK) supplemented with JCM1136 (LR), JCM5805 (LL), and JCM1136 + JCM5805 (LR+LL) at 1 × 10⁸ CFU/g basal diet for 6 weeks, followed by a basal diet for 1 week. After 6 weeks of feeding, the LL treatment significantly increased the growth and feed utilization of Nile tilapia when compared with the CK. Light microscopy and transmission electron microscopy images of the midgut revealed that probiotic supplementation significantly increased gut microvilli length and microvilli density compared to CK. The transcript levels of several key immune-related genes in the mid-intestine and liver of fish were analyzed by means of quantitative polymerase chain reaction (qPCR) at the end of the sixth week. The results showed the following: when compared to CK group, fish in LR had significantly increased transcript levels of IFN-γ, lyzc, hsp70 and IL-1β in the intestine; LL fish showed significantly increased expressions of TNF-α, IFN-γ, lyzc, hsp70 and IL-1β in the intestine and liver; and intestine lyzc, hsp70 and IL-1β and liver TNF-α, IFN-γ, hsp70 and IL-1β were significantly increased in LR+LL fish. Following a 6-week period of being fed probiotics or a control diet, the tilapia were challenged with an intraperitoneal injection of 20 μl of the pathogenic Streptococcus agalactiae (WC1535) (1 × 10⁵ CFU/ml). The survival rates of the probiotic-fed groups were significantly higher than that of the CK group, and the LL group had the highest survival rate. High-throughput sequencing revealed a significantly higher presence of JCM5805 in the guts of LL fish during the period of probiotic application, but this was no longer detected in all LL samples 1 week post cessation of probiotic administration. Cessation of probiotic administration led to disorders of individual gut microbes within the LR and LL groups. Statistical analysis (LEfSe) demonstrated that three phyla, namely, Bacteroidetes, Fusobacteria and Actinobacteria were enriched in the CK group, while the abundance of Proteobacteria was greater in the probiotic-fed fish. At the genus level, Plesiomonas, which includes potential pathogens of fish, were significantly decreased in the probiotic-fed groups. In contrast, a significant increase of Rhizobium and Achromobacter, which can produce a variety of enzymes with cellulolytic and pectolytic activity, were observed in fish fed with probiotics, indicating that dietary probiotics were helpful in the propagation of some probiotic bacteria. Our data revealed that JCM1136 and JCM5805, as a feed additive at 10⁸ CFU/g feed, could improve intestinal morphology, enhance immune status and disease resistance, and affect the gut microbiota of tilapia; thus, these additives could be used as probiotics for juvenile Nile tilapia. JCM5805 was more effective than JCM1136 or the mixture of the two for promoting the growth, enhancing the immune status and disease resistance of tilapia.