Beneficial bacteria for aquaculture: nutrition, bacteriostasis and immunoregulation

Therapeutic mechanism of Cornus Officinalis Fruit Coreon on ALI by AKT/Nrf2 pathway and gut microbiota

BACKGROUND

Acute liver injury (ALI) often precipitates severe liver function impairment and is associated with high mortality rates. Traditional Chinese Medicine (TCM) has demonstrated efficacy in mitigating hepatic damage by exhibiting anti-inflammatory effects, enhancing antioxidant activity, and modulating gut microbiota (GM). Numerous studies have identified similar or identical bioactive compounds within the Cornus Officinalis Fruit Coreon(COFO) and its flesh. Notably, Cornus Officinalis has been shown to possess potent hepatoprotective properties. However, studies on the pharmacological effects and mechanism of action of COFO for hepatoprotection have received little attention.

PURPOSE

To elucidate the mechanisms underlying the COFO effect in ALI by integrating GM gene sequencing, quantifying Short-Chain Fatty Acids (SCFAs), and examining relevant signaling pathways.

MATERIALS AND METHODS

A rat model for carbon tetrachloride (CCl4)-induced ALI was established, and the best liver protective components of COFO were selected by pathological observation and biochemical determination. The therapeutic efficacy of COFO in mitigating liver injury was elucidated through an integrated approach that included network pharmacology, biochemical indexes, 16S rDNA sequencing analyses, short-chain fatty acids, Western blotting analysis of protein levels, and immunohistochemical evaluations.

RESULTS

Pharmacological evaluation established that the n-butanol fraction (CNBP) provided optimal hepatoprotective effects. Firstly, the chemical constituents of CNBP were characterized, and its principal anti-ALI targets, such as ALI, AKT1, TNF, and IL-6, were identified through network pharmacology analysis. Secondly, experimental validation revealed that CNBP may enhance the genetic diversity of the GM, augmenting the diversity of the microbial community, increasing the levels of three SCFAs, and activating key proteins in the AKT/Nrf2 signaling pathway (AKT1, TNF-α, IL-6, NF-κB p65, Nrf2, and HO-1). Consequently, CNBP exhibited hepatoprotective effects, with antioxidative and anti-inflammatory properties.

CONCLUSION

CNBP may mitigate GM-induced disturbances, augment the levels of three SCFAs, activate the AKT/Nrf2 signaling pathway, and exhibit antioxidant and anti-inflammatory effects, thereby conferring hepatoprotective benefits.

Evaluation of the Combined Administration of Chlorella fusca and Vibrio proteolyticus in Diets for Chelon labrosus: Effects on Growth, Metabolism, and Digestive Functionality

This study aimed to evaluate the combined effect of dietary Chlorella fusca and ethanol-inactivated Vibrio proteolyticus DCF12.2 (C + V diet) in Chelon labrosus juveniles, highlighting their nutritional, physiological, and morphological effects. The results showed that the combined dietary inclusion of C. fusca and V. proteolyticus significantly enhanced growth performance and feed utilization compared to the control group. The C + V diet increased the fish lipid quality index (FLQ), n-3 polyunsaturated fatty acids, and n-3/n-6 ratio, which might be beneficial in terms of human nutrition. The C + V diet considerably increased carbohydrate metabolic activity by statistically boosting plasma glucose. The dietary inclusion of C. fusca in conjunction with V. proteolyticus increased metabolic enzyme activity as well as intestinal absorption capacity compared to that found in the control group. In conclusion, the experimental diet was suitable for feeding C. labrosus, increasing their growth and the nutritional characteristics of the muscle and intestine, without causing tissue damage.

Effect of feed restriction and refeeding on body condition, digestive functionality and intestinal microbiota in rainbow trout (Oncorhynchus mykiss)

The aim of the present work was to investigate the influence of fasting and refeeding on body condition, gut physiology and microbiota in reared O. mykiss. Ninety-six fish were randomly allotted among three groups subjected to different feeding plan: C (control, fed for 5 weeks); R (restricted ration over 3 weeks followed by 2 weeks feeding); F (fasted over 3 weeks followed by 2 weeks feeding) in a well's fresh water flow-through rearing plan. Sampling occurred at 0, 1, 2, 4, 7, 14 days during the refeeding period. At day 0 and throughout the feeding period until day 14, the weight of the fish was significantly affected by the feeding restriction. Feed deprivation reduced significantly the viscerosomatic and hepatosomatic indexes. Brush border membrane enzymes' specific activity was modulated by feeding regimes until day 7, to level in all experimental groups at day 14. At the end of the restricted/fasted period, the microbiota of the C group was made up of 70% of Actinobacteria, 24% of Proteobacteria, 4.2% of Firmicutes and < 1% of Bacteroides, while the restricted and fasted group were characterized by a strong reduction of Actinobacteria, and a significant increase in Bacteroidetes and Firmicutes. The feed deprivation determined a dysbiosis, allowing the development of different commensal or pathogenic bacteria. In conclusion, the effects of 2 weeks of feed deprivation, excluding those related to body weight, are gradually mitigated by refeeding, which allows the restoration of digestive functions and a healthy intestinal microbiota.

Tapioca starch and skim milk support probiotic efficacy of Lactiplantibacillus plantarum post-fermentation medium against pathogens and cancer cells

The production of functional foods containing prebiotic ingredients is an area of particular interest and a very promising market with the potential to dominate the food industry. This study aims to explore the potential of starch-based prebiotic tapioca and skim milk, as low-cost and easily accessible food sources and as natural and "clean label" food ingredients on the probiotic activities of Lactiplantibacillus plantarum (formerly Lactobacillus plantarum). The results show that concomitant use of the modified tapioca starch and skim milk promotes the antibacterial and anti-cancer properties of L. plantarum post-fermentation media pointing out how the functionality of probiotic products can be regulated by growth supplements.

Effects of the potential probiotic Bacillus subtilis D1-2 on growth, digestion, immunity and intestinal flora in juvenile sea cucumber, Apostichopus japonicus

In the present study, a potential probiotic Bacillus subtilis D1-2 with antibacterial activity was isolated from the gut of Apostichopus japonicus. The purpose of this experiment was to assess the effect of B. subtilis D1-2 at different concentrations (C: 0 CFU/g, BL: 10⁵ CFU/g, BM: 10⁷ CFU/g and BH: 10⁹ CFU/g) on the growth performance, digestive enzyme activity, immune ability and intestinal flora of A. japonicus. After the 56-day feeding trial, the final body weight and weight gain rate of juvenile sea cucumber A. japonicus fed B. subtilis D1-2 were significantly increased, especially in the BM group. Additionally, the lipase activity of the intestine was significantly increased in the BM and BH groups. Enhanced immunity was also found in sea cucumbers supplemented with B. subtilis D1-2. Alpha diversity indices showed that the B. subtilis D1-2-supplemented groups had higher intestinal microbial richness and diversity than the control group. The beta diversity analysis indicated that the bacterial communities in the B. subtilis D1-2-supplemented groups were quite similar but different from the bacterial communities in the control group. Dietary supplementation with B. subtilis D1-2 increased the relative abundance of some potential probiotic-related genera, including Lactobacillus, Clostridium, Lactococcus, Bifidobacterium and Streptococcus. In conclusion, dietary addition of B. subtilis D1-2 could effectively promote the growth of A. japonicus, improve its digestion and immunity capacity to a certain extent, and actively regulate the intestinal microflora of A. japonicus.

Draft Genome Sequence of Lactococcus lactis Subsp. cremoris WA2-67: A Promising Nisin-Producing Probiotic Strain Isolated from the Rearing Environment of a Spanish Rainbow Trout (Oncorhynchus mykiss, Walbaum) Farm

Probiotics are a viable alternative to traditional chemotherapy agents to control infectious diseases in aquaculture. In this regard, Lactococcus lactis subsp. cremoris WA2-67 has previously demonstrated several probiotic features, such as a strong antimicrobial activity against ichthyopathogens, survival in freshwater, resistance to fish bile and low pH, and hydrophobicity. The aim of this manuscript is an in silico analysis of the whole-genome sequence (WGS) of this strain to gain deeper insights into its probiotic properties and their genetic basis. Genomic DNA was purified, and libraries prepared for Illumina sequencing. After trimming and assembly, resulting contigs were subjected to bioinformatic analyses. The draft genome of L. cremoris WA2-67 consists of 30 contigs (2,573,139 bp), and a total number of 2493 coding DNA sequences (CDSs). Via in silico analysis, the bacteriocinogenic genetic clusters encoding the lantibiotic nisin Z (NisZ) and two new bacteriocins were identified, in addition to several probiotic traits, such as the production of vitamins, amino acids, adhesion/aggregation, and stress resistance factors, as well as the absence of transferable antibiotic resistance determinants and genes encoding detrimental enzymatic activities and virulence factors. These results unveil diverse beneficial properties that support the use of L. cremoris WA2-67 as a probiotic for aquaculture.

Probiotics for coral aquaculture: challenges and considerations

Globally, coral reefs are under pressure from climate change, with concerning declines in coral abundance observed due to increasing cumulative impacts. Active intervention measures that mitigate the declines are increasingly being applied to buy time for coral reefs as the world transitions to a low-carbon economy. One such mitigation strategy is coral restoration based on large-scale coral aquaculture to provide stock for reseeding reefs, with the added potential of selecting corals that better tolerate environmental stress. Application of probiotics during production and deployment, to modulate the naturally occurring bacteria associated with corals, may confer health benefits such as disease resistance, increased environmental tolerance or improved coral nutrition. Here, we briefly describe coral associated bacteria and their role in the coral holobiont, identify probiotics traits potentially beneficial to coral, and discuss current research directions required to develop, test and verify the feasibility for probiotics to improve coral aquaculture at industrial scales.

Aquaculture production of hatchling Hawaiian Bobtail Squid (Euprymna scolopes) is negatively impacted by decreasing environmental microbiome diversity

Aims

The Hawaiian Bobtail Squid (Euprymna scolopes) is a model organism for investigating host–symbiont relationships. The current scientific focus is on the microbiome within E. scolopes, while very little is known about the microbiome of the tanks housing E. scolopes. We examined the hypothesis that bacterial communities and geochemistry within the squid tank environment correlate with the production of viable paralarval squid.

Methods and Results

Total DNA was extracted from sediment and filtered water samples from ‘productive’ squid cohorts with high embryonic survival and paralarval hatching, ‘unproductive’ cohorts with low embryonic survival and paralarval hatching. As a control total DNA was extracted from environmental marine locations where E. scolopes is indigenous. Comparative analysis of the bacterial communities by the 16S rRNA gene was performed using next generation sequencing. Thirty‐eight differentially abundant genera were identified in the adult tank waters. The majority of the sequences represented unclassified, candidate or novel genera. The characterized genera included Aquicella, Woeseia and Ferruginibacter, with Hyphomicrobium and Rhizohapis were found to be more abundant in productive adult tank water. In addition, nitrate and pH covaried with productive cohorts, explaining 67% of the bacterial populations. The lower abundance of nitrate‐reducing bacteria in unproductive adult tank water could explain detected elevated nitrate levels.

Conclusions

We conclude that microbiome composition and water geochemistry can negatively affect E. scolopes reproductive physiology in closed tank systems, ultimately impacting host‐microbe research using these animals.

Significance and Impact of study

These results identify the tight relationship between the microbiome and geochemistry to E. scolopes. From this study, it may be possible to design probiotic counter‐measures to improve aquaculture conditions for E. scolopes.

Modulation of HMGB1 Release in APAP-Induced Liver Injury: A Possible Strategy of Chikusetsusaponin V Targeting NETs Formation

Acetaminophen (APAP), one of the most common antipyretic analgesics, which is safe at therapeutic dose, cause acute liver injury and even death at overdose. However, the mechanism of APAP-induced inflammation in liver injury is still controversial. Therefore, effective drug intervention is urgently needed. The aim of this study was to explore the inflammatory exact mechanism of APAP, especially on neutrophils, and to study the intervention effect of Chikusetsusaponin V (CKV) derived from Panax japonicus. Establishment of hepatotoxicity model of APAP in vitro and in vivo. In vitro, HepG2 cells, AML12 cells, primary mouse hepatocytes and neutrophils were used to mimic APAP-affected hepatocytes and neutrophil. In vivo, C57BL/6 mice were administrated overdose of APAP with or without neutrophil depletion or abolishing neutrophil extracellular traps (NETs) formation. In this study, APAP stimulation increased the level of HMGB1, IL-1β and Caspase-1 in mouse liver, especially hepatocytes, which had a synergistic effect with LPS/ATP combination. NETs were formatted at early stage of APAP or HMGB1-stimulated neutrophils’ damage. Conditioned mediums from APAP-treated hepatocytes induced more significant NETs than direct APAP stimulation. Neutrophil depletion or abolishing NETs formation decreased HMGB1 level, eventually blocked hepatocytes necrosis. CKV pretreatment interfered Caspase-1 activation and HMGB1 release in APAP-damaged hepatocytes. CKV also prevented NETs formation. These results indicate that the production of HMGB1 may depend on the activation of Caspase-1 and play a key role in liver inflammation caused by APAP. The cross-dialogue between hepatocytes and neutrophils can be mediated by HMGB1. Therefore, CKV has a positive intervention effect on NETs-related inflammation in APAP-damaged liver, targeting Caspase-1-HMGB1.

Sustainable plant-based diets promote rainbow trout gut microbiota richness and do not alter resistance to bacterial infection

Background

Farmed fish food with reduced fish-derived products are gaining growing interest due to the ecological impact of fish-derived protein utilization and the necessity to increase aquaculture sustainability. Although different terrestrial plant proteins could replace fishmeal proteins, their use is associated with adverse effects. Here, we investigated how diets composed of terrestrial vegetal sources supplemented with proteins originating from insect, yeast or terrestrial animal by-products affect rainbow trout (Onchorynchus mykiss) gut microbiota composition, growth performance and resistance to bacterial infection by the fish pathogen Flavobacterium psychrophilum responsible for frequent outbreaks in aquaculture settings.

Results

We showed that the tested regimes significantly increased gut bacterial richness compared to full vegetal or commercial-like diets, and that vegetal diet supplemented with insect and yeast proteins improves growth performance compared to full vegetal diet without altering rainbow trout susceptibility to F. psychrophilum infection.

Conclusion

Our results demonstrate that the use of insect and yeast protein complements to vegetal fish feeds maintain microbiota functions, growth performance and fish health, therefore identifying promising alternative diets to improve aquaculture’s sustainability.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00107-2.

The biological activities of postbiotics in gastrointestinal disorders

According to outcomes from clinical studies, an intricate relationship occurs between the beneficial microbiota, gut homeostasis, and the host's health status. Numerous studies have confirmed the health-promoting effects of probiotics, particularly in gastrointestinal diseases. On the other hand, the safety issues regarding the consumption of some probiotics are still a matter of debate, thus to overcome the problems related to the application of live probiotic cells in terms of clinical, technological, and economic aspects, microbial-derived biomolecules (postbiotics) were introducing as a potential alternative agent. Presently scientific literature confirms that the postbiotic components can be used as promising tools for both prevention and treatment strategies in gastrointestinal disorders with less undesirable side-effects, particularly in infants and children. Future head-to-head trials are required to distinguish appropriate strains of parent cells, optimal dosages of postbiotics, and assessment of the cost-effectiveness of postbiotics compared to alternative drugs. This review provides an overview of the concept and safety issues regarding postbiotics, with emphasis on their biological role in the treatment of some important gastrointestinal disorders.

Gnotobiotic rainbow trout (Oncorhynchus mykiss) model reveals endogenous bacteria that protect against Flavobacterium columnare infection

The health and environmental risks associated with antibiotic use in aquaculture have promoted bacterial probiotics as an alternative approach to control fish infections in vulnerable larval and juvenile stages. However, evidence-based identification of probiotics is often hindered by the complexity of bacteria-host interactions and host variability in microbiologically uncontrolled conditions. While these difficulties can be partially resolved using gnotobiotic models harboring no or reduced microbiota, most host-microbe interaction studies are carried out in animal models with little relevance for fish farming. Here we studied host-microbiota-pathogen interactions in a germ-free and gnotobiotic model of rainbow trout (Oncorhynchus mykiss), one of the most widely cultured salmonids. We demonstrated that germ-free larvae raised in sterile conditions displayed no significant difference in growth after 35 days compared to conventionally-raised larvae, but were extremely sensitive to infection by Flavobacterium columnare, a common freshwater fish pathogen causing major economic losses worldwide. Furthermore, re-conventionalization with 11 culturable species from the conventional trout microbiota conferred resistance to F. columnare infection. Using mono-re-conventionalized germ-free trout, we identified that this protection is determined by a commensal Flavobacterium strain displaying antibacterial activity against F. columnare. Finally, we demonstrated that use of gnotobiotic trout is a suitable approach for the identification of both endogenous and exogenous probiotic bacterial strains protecting teleostean hosts against F. columnare. This study therefore establishes an ecologically-relevant gnotobiotic model for the study of host-pathogen interactions and colonization resistance in farmed fish.

Potential Pharmaceutical and Food Applications of Postbiotics: A Review

In recent decades, functional foods with ingredients comprising probiotics, prebiotics and postbiotics have been gaining a lot of attention from scientists. Probiotics and postbiotics are usually applied in pharmaceutical formulations and/or commercial food-based products. These bioactive agents can be associated with host eukaryotic cells and have a key role in maintaining and restoring host health. The review describes the concept of postbiotics, their quality control and potential applications in pharmaceutical formulations and commercial food-based products for health promotion, prevention of disease and complementary treatment. Despite the effectiveness of probiotic products, researchers have introduced the concept of postbiotic to optimize their beneficial effects as well as to meet the needs of consumers to provide a safe product. The finding of recent studies suggests that postbiotics might be appropriate alternative agents for live probiotic cells and can be applied in medical, veterinary and food practice to prevent and to treat some diseases, promote animal health status and develop functional foods. Presently scientific literature confirms that postbiotics, as potential alternative agents, may have superiority in terms of safety relative to their parent live cells, and due to their unique characteristics in terms of clinical, technological and economical aspects, can be applied as promising tools in the drug and food industry for developing health benefits, and therapeutic aims.

Potential in vivo delivery routes of postbiotics

Bioactive micro- and macro-molecules (postbiotics) derived from gut beneficial microbes are among natural chemical compounds with medical significance. Currently, a unique therapeutic strategy has been developed with an emphasis on the small molecular weight biomolecules that are made by the microbiome, which endow the host with several physiological health benefits. A large number of postbiotics have been characterized, which due to their unique pharmacokinetic properties in terms of controllable aspects of the dosage and various delivery routes, could be employed as promising medical tools since they exert both prevention and treatment strategies in the host. Nevertheless, there are still main challenges for the in vivo delivery of postbiotics. Currently, scientific literature confirms that targeted delivery systems based on nanoparticles, due to their appealing properties in terms of high biocompatibility, biodegradability, low toxicity, and significant capability to carry both hydrophobic and hydrophilic postbiotics, can be used as a novel and safe strategy for targeted delivery or/and release of postbiotics in various (oral, intradermal, and intravenous) in vivo models. The in vivo delivery of postbiotics are in their emerging phase and require massive investigation and randomized double-blind clinical trials if they are to be applied extensively as treatment strategies. This manuscript provides an overview of the various postbiotic metabolites derived from the gut beneficial microbes, their potential therapeutic activities, and recent progressions in the drug delivery field, as well as concisely giving an insight on the main in vivo delivery routes of postbiotics.

Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp (Penaeus monodon) with different growth performance

Understanding the correlation between shrimp growth and their intestinal bacteria would be necessary to optimize animal's growth performance. Here, we compared the bacterial profiles along with the shrimp's gene expression responses and metabolites in the intestines between the Top and the Bottom weight groups. Black tiger shrimp (Penaeus monodon) were collected from the same population and rearing environments. The two weight groups, the Top-weight group with an average weight of 36.82 ± 0.41 g and the Bottom-weight group with an average weight of 17.80 ± 11.81 g, were selected. Intestines were aseptically collected and subjected to microbiota, transcriptomic and metabolomic profile analyses. The weighted-principal coordinates analysis (PCoA) based on UniFrac distances showed similar bacterial profiles between the two groups, suggesting similar relative composition of the overall bacterial community structures. This observed similarity was likely due to the fact that shrimp were from the same genetic background and reared under the same habitat and diets. On the other hand, the unweighted-distance matrix revealed that the bacterial profiles associated in intestines of the Top-weight group were clustered distinctly from those of the Bottom-weight shrimp, suggesting that some unique non-dominant bacterial genera were found associated with either group. The key bacterial members associated to the Top-weight shrimp were mostly from Firmicutes (Brevibacillus and Fusibacter) and Bacteroidetes (Spongiimonas), both of which were found in significantly higher abundance than those of the Bottom-weight shrimp. Transcriptomic profile of shrimp intestines found significant upregulation of genes mostly involved in nutrient metabolisms and energy storage in the Top-weight shrimp. In addition to significantly expressed metabolic-related genes, the Bottom-weight shrimp also showed significant upregulation of stress and immune-related genes, suggesting that these pathways might contribute to different degrees of shrimp growth performance. A non-targeted metabolome analysis from shrimp intestines revealed different metabolic responsive patterns, in which the Top-weight shrimp contained significantly higher levels of short chain fatty acids, lipids and organic compounds than the Bottom-weight shrimp. The identified metabolites included those that were known to be produced by intestinal bacteria such as butyric acid, 4-indolecarbaldehyde and L-3-phenyllactic acid as well as those produced by shrimp such as acyl-carnitines and lysophosphatidylcholine. The functions of these metabolites were related to nutrient absorption and metabolisms. Our findings provide the first report utilizing multi-omics integration approach to investigate microbiota, metabolic and transcriptomics profiles of the host shrimp and their potential roles and relationship to shrimp growth performance.