Intestinal microbiota composition is altered according to nutritional biorhythms in the leopard coral grouper (Plectropomus leopardus)

Synchronously sexual maturity in hermaphrodite fish as revealed by transcriptome analysis in Plectropomus leopardus

Leopard coral grouper (Plectropomus leopardus) is a type of hermaphrodite fish, but the mechanisms of gonadal development and gametogenesis remain unclear. In the present study, we performed histological observation and transcriptomic analysis during the process of sexual differentiation in P. leopardus. According to the histological results, sexual differentiation was completed at 15 months old, developed synchronously in male and female individuals at 2 years old, and matured synchronously at 3 years old. Comparative transcriptomic analyses showed that the gonadal had differentiated by 15 months old, with enrichment of pathways associated with cell proliferation, transcriptional metabolism, and germline stem cell differentiation. Furthermore, cilium movement and fatty acid anabolism, which are associated with spermatogenesis and oocyte growth, were significantly enriched at 3 years old. In addition, key genes associated with male and female sex differentiation, such as amh, dmrt1, dmrt2a, zp4, sox3, gdf9, and gsdf, were identified by weighted gene co-expression network analysis (WGCNA). Finally, the localization and expression of the key genes amh and sox3 were observed in different cell types within the testes and ovaries, reflecting the development of the testes and ovaries, respectively. All the evidence indicates that P. leopardus is a hermaphrodite and synchronously sexually mature fish. Our study complements the gonadal development patterns of hermaphroditic fish by providing new insights into the molecular mechanisms underlying sexual differentiation and sex change in hermaphroditic groupers.

Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper ( Plectropomus leopardus)

The leopard coral grouper ( Plectropomus leopardus) is a species of significant economic importance. Although artificial cultivation of P. leopardus has thrived in recent decades, the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data. In this study, we identified over 8.73 million single nucleotide polymorphisms (SNPs) through whole-genome resequencing of 326 individuals spanning six distinct groups. Furthermore, we categorized 226 individuals with high-coverage sequencing depth (≥14×) into eight clusters based on their genetic profiles and phylogenetic relationships. Notably, four of these clusters exhibited pronounced genetic differentiation compared with the other populations. To identify potentially advantageous loci for P. leopardus, we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity ( θπ) and fixation index ( F ST) in these four clusters. Using these high-coverage resequencing data, we successfully constructed the first haplotype reference panel specific to P. leopardus. This achievement holds promise for enabling high-quality, cost-effective imputation methods. Additionally, we combined low-coverage sequencing data with imputation techniques for a genome-wide association study, aiming to identify candidate SNP loci and genes associated with growth traits. A significant concentration of these genes was observed on chromosome 17, which is primarily involved in skeletal muscle and embryonic development and cell proliferation. Notably, our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs, showing potential for genetic selective breeding efforts. These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P. leopardus.

Distinct gut microbial communities and functional predictions in divergent ophiuroid species: host differentiation, ecological niches, and adaptation to cold-water habitats

IMPORTANCE

Gastrointestinal microorganisms are critical to the survival and adaptation of hosts, and there are few studies on the differences and functions of gastrointestinal microbes in widely distributed species. This study investigated the gut microbes of two ophiuroid species (Ophiura sarsii and its subspecies O. sarsii vadicola) in cold-water habitats of the Northern Pacific Ocean. The results showed that a combination of host and environmental factors shapes the intestinal microbiota of ophiuroids. There was a high similarity in microbial communities between the two groups living in different regions, which may be related to their similar ecological niches. These microorganisms played a vital role in the ecological success of ophiuroids as the foundation for their adaptation to cold-water environments. This study revealed the complex relationship between hosts and their gut microbes, providing insights into the role they play in the adaptation and survival of marine species.

Configuration of gut bacterial community profile and their potential functionality in the digestive tract of the wild and cultivated Indonesian shortfin elver-phase eels (Anguilla bicolor bicolor McClelland, 1844)

This study aimed to explore the bacteria present in the digestive tracts of wild and cultivated Indonesian shortfin eel during the elver phase. The eel has high export potential due to its vitamin and micronutrient content, but slow growth and vulnerability to collapse in farm conditions hinder its cultivation. The microbiota in the eel's digestive tract is crucial for its health, particularly during the elver phase. This study used Next Generation Sequencing to analyze the community structure and diversity of bacteria in the eels' digestive tracts, focusing on the V3-V4 regions of the 16S rRNA gene. Mothur software was used for data analysis and PAST v.3.26 was used to calculate alpha diversity. The results showed that Proteobacteria (64.18%) and Firmicutes (33.55%) were the predominant phyla in the digestive tract of cultivated eels, while Bacteroidetes (54.16%), Firmicutes (14.71%), and Fusobacteria (10.56%) were predominant in wild eels. The most prevalent genera in cultivated and wild elver were Plesiomonas and Cetobacterium, respectively. The microbiota in the digestive tract of cultivated eels was diverse despite uneven distribution. The KEGG database analysis revealed that the primary function of the microbiome was to facilitate the eel's absorption of nutrients by contributing significantly to the metabolism of carbohydrates and amino acids. This study's findings can aid in assessing eel health and improving eel farming conditions.

Starvation alters gut microbiome and mitigates off-flavors in largemouth bass (Micropterus salmoides)

The present study aimed to investigate the response of intestinal microbiota during 3 weeks' starvation of largemouth bass (Micropterus salmoides), an economically important freshwater fish, using 16S rRNA gene amplicon sequencing and PICRUSt2 predictive functional profiling. Overall, the microbiota was mainly represented by Mycoplasma, Pseudomonas, Acinetobacter, and Microbacterium in the initial group. This pattern contrasted with that of Cetobacterium and Aeromonas, which were major representative genera in the starved group. Significant differences in the richness and composition of intestinal microbial community induced by starvation were observed. Notably, earthy-musty off-flavor compounds (geosmin and 2-methylisoborneol) were significantly decreased during starvation, which were significantly correlated with the abundance of certain actinobacterial taxa, namely, Microbacterium and Nocardioides. Additionally, the functional pathways involved in synthesis of off-flavor compounds, protein digestion, fatty acid degradation, and biosynthesis of cofactors greatly decreased with starvation, indicating that microbiota modulated the specific metabolic pathway to adapt to food deprivation. These results emphasize that starvation can modulate diversity, community structure, and functions of the intestinal microbiota and mitigate the off-flavors, which has important implications for strategies to eliminate off-flavor odorants through the application of probiotics to manipulate the gut microbiome and ultimately enhance flesh quality of freshwater fish.

Gut microbiota communities of reciprocal hybrids from koi (Cyprinus carpio) and goldfish (Carassius auratus) are more similar to koi than goldfish

AIMS

To investigate the gut microbiota communities of reciprocal hybrids and inbred lines of koi (Cyprinus carpio) and goldfish (Carassius auratus), as well as the genetic effect of intestinal microbiota between hybrids and parents.

METHODS AND RESULTS

The reciprocal hybrids and inbred lines derived from the parents, koi and goldfish, were established. Then the bacterial 16S rRNA gene of intestinal contents was sequenced using Illumina Miseq PE300. Alpha diversity in the two types of hybrids was lower than inbred lines of koi or goldfish and was highest in goldfish, followed by koi. For beta diversity, microbial samples presented clear clusters and the two types of hybrids were more similar to koi than goldfish, indicating the gut microbiota of the reciprocal hybrids was more affected by koi. The dominant phyla were Proteobacteria, Actinobacteria and Firmicutes in koi, and Proteobacteria, Fusobacteria and Actinobacteria in goldfish, and Proteobacteria, Fusobacteria and Firmicutes in the reciprocal hybrids. In the case of Proteobacteria, the dominant classes were Alphaproteobacteria and Gammaproteobacteria in four fish. The dominant genera were norank_f_Rhizobiales_Incertae_Sedis and Plesiomonas in koi, Cetobacterium in goldfish, and Cetobacterium and ZOR0006 in the reciprocal hybrids. PICRUSt1 predictive function analysis showed that the reciprocal hybrids had lower abundance in the most functional categories than koi and goldfish.

CONCLUSIONS

The gut microbiota of reciprocal hybrids was more affected by koi. Two types of hybrids possessed the same dominated phyla and were different from the inbred lines of koi and goldfish.

SIGNIFICANCE AND IMPACT OF THE STUDY

It enhanced our understanding of gut microbiota of hybrid lines of goldfish and koi and provided a new perspective for the selective breeding of gut microbiota traits.

Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish

The microbial gut communities of fish are receiving increased attention for their relevance, among others, in a growing aquaculture industry. The members of these communities are often split into resident (long-term colonisers specialised to grow in and adhere to the mucus lining of the gut) and transient (short-term colonisers originated from food items and the surrounding water) microorganisms. Separating these two communities in small fish are impeded by the small size and fragility of the gastrointestinal tract. With the aim of testing whether it is possible to recover two distinct communities in small species of fish using a simple sampling technique, we used 16S amplicon sequencing of paired intestinal wall and digesta samples from three small Cyprinodontiformes fish. We examined the diversity and compositional variation of the two recovered communities, and we used joint species distribution modelling to identify microbes that are most likely to be a part of the resident community. For all three species we found that the diversity of intestinal wall samples was significantly lower compared to digesta samples and that the community composition between sample types was significantly different. Across the three species we found seven unique families of bacteria to be significantly enriched in samples from the intestinal wall, encompassing most of the 89 ASVs enriched in intestinal wall samples. We conclude that it is possible to characterise two different microbial communities and identify potentially resident microbes through separately analysing samples from the intestinal wall and digesta from small species of fish. We encourage researchers to be aware that different sampling procedures for gut microbiome characterization will capture different parts of the microbiome and that this should be taken into consideration when reporting results from such studies on small species of fish.

Stress responses of the intestinal digestion, antioxidant status, microbiota and non-specific immunity in Songpu mirror carp (Cyprinus carpio L.) under starvation

Songpu mirror carp, Cyprinus carpio L., is a new variety of common carp that has become an economically important freshwater fish in China. However, it remains unknown how its metabolism is regulated under starvation. Here, we investigated how intestinal digestion, antioxidant status, microbiota and immune activities were affected under starvation stress. The feeding regimes were designed as follows: ST0 comprised fish allowed to feed continuously; ST1 comprised fish starved for 1 week; ST2 comprised fish starved for 2 weeks; ST3 comprised fish starved for 3 weeks; ST4 comprised fish starved for 4 weeks. Our results showed a significant decrease in the level of intestinal amylase, lipase, and protease activities in the group ST4 (P < 0.05). Compared with the control group, intestinal antioxidant enzyme activities were significantly increased during short-term starvation. The gene expression levels of interleukin 1β (IL-1β), interleukin 8 (IL-8) and tumor necrosis factor-alpha (TNF-α) were elevated in the groups ST3 and ST4. We also detected the reduction in the expression levels of interleukin 10 (IL-10) and transforming growth factor β (TGF-β2) compared with those of the group ST0. Notably, the gut microbial composition was dominated by Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. The relative abundance of the dominant microbial phyla changed significantly under starvation stress. Taken together, our results suggest that starvation can induce the change of intestinal digestion, non-specific immunity and microbiota in Songpu mirror carp, and provide new insights into its habitat selection and adaptation to environmental changes.

A systematic review of advances in intestinal microflora of fish

Intestinal flora is closely related to the health of organisms and the occurrence and development of diseases. The study of intestinal flora will provide a reference for the research and treatment of disease pathogenesis. Upon hatching, fish begin to acquire a microbial community in the intestine. In response to the environment and the host itself, the fish gut eventually develops a unique set of microflora, with some microorganisms being common to different fish. The existence of intestinal microorganisms creates an excellent microecological environment for the host, while the fish symbiotically provides conditions for the growth and reproduction of intestinal microflora. The intestinal flora and the host are interdependent and mutually restrictive. This review mainly describes the formation of fish intestinal flora, the function of normal intestinal flora, factors affecting intestinal flora, and a series of fish models.

Dead or alive: microbial viability treatment reveals both active and inactive bacterial constituents in the fish gut microbiota

AIMS

This study evaluated the microbial viability of fish gut microbiota in both digesta (faecal) and mucosal samples using a modified propidium monoazide (PMA) protocol, followed by 16S ribosomal RNA (rRNA) gene sequencing.

METHODS AND RESULTS

Digesta and gut mucosal samples from farmed yellowtail kingfish (Seriola lalandi) were collected and a modified PMA treatment was applied prior to DNA extraction to differentiate both active and nonviable microbial cells in the samples. All samples were then sequenced using a standard 16S rRNA approach. The digesta and mucosal samples contained significantly different bacterial communities, with a higher diversity observed in digesta samples. In addition, PMA treatment significantly reduced the microbial diversity and richness of digesta and mucosal samples and depleted bacterial constituents typically considered to be important within fish, such as Lactobacillales and Clostridales taxa.

CONCLUSIONS

These findings suggest that important bacterial members may not be active in the fish gut microbiota. In particular, several beneficial lactic acid bacteria (LAB) were identified as nonviable bacterial cells, potentially influencing the functional potential of the fish microbiota.

SIGNIFICANCE AND IMPACTS OF THE STUDY

Standardizing the methods for characterizing the fish microbiota are paramount in order to compare studies. In this study, we showed that both sample type and PMA treatment influence the bacterial communities found in the fish gut microbiota. Our findings also suggest that several microbes previously described in the fish gut may not be active constituents. As a result, these factors should be considered in future studies to better evaluate the active bacterial communities associated with the host.

Cross-Talk Between Intestinal Microbiota and Host Gene Expression in Gilthead Sea Bream (Sparus aurata) Juveniles: Insights in Fish Feeds for Increased Circularity and Resource Utilization

New types of fish feed based on processed animal proteins (PAPs), insect meal, yeast, and microbial biomasses have been used with success in gilthead sea bream. However, some drawback effects on feed conversion and inflammatory systemic markers were reported in different degrees with PAP- and non-PAP-based feed formulations. Here, we focused on the effects of control and two experimental diets on gut mucosal-adherent microbiota, and how it correlated with host transcriptomics at the local (intestine) and systemic (liver and head kidney) levels. The use of tissue-specific PCR-arrays of 93 genes in total rendered 13, 12, and 9 differentially expressed (DE) genes in the intestine, liver, and head kidney, respectively. Illumina sequencing of gut microbiota yielded a mean of 125,350 reads per sample, assigned to 1,281 operational taxonomic unit (OTUs). Bacterial richness and alpha diversity were lower in fish fed with the PAP diet, and discriminant analysis displayed 135 OTUs driving the separation between groups with 43 taxa correlating with 27 DE genes. The highest expression of intestinal pcna and alpi was achieved in PAP fish with intermediate values in non-PAP, being the pro-inflammatory action of alpi associated with the presence of Psychrobacter piscatorii. The intestinal muc13 gene was down-regulated in non-PAP fish, with this gene being negatively correlated with anaerobic (Chloroflexi and Anoxybacillus) and metal-reducing (Pelosinus and Psychrosinus) bacteria. Other inflammatory markers (igm, il8, tnfα) were up-regulated in PAP fish, positively correlating the intestinal igm gene with the inflammasome activator Escherichia/Shigella, whereas the systemic expression of il8 and tnfα was negatively correlated with the Bacilli class in PAP fish and positively correlated with Paracoccus yeei in non-PAP fish. Overall changes in the expression pattern of il10, galectins (lgals1, lgals8), and toll-like receptors (tlr2, tlr5, tlr9) reinforced the anti-inflammatory profile of fish fed with the non-PAP diet, with these gene markers being associated with a wide range of OTUs. A gut microbiota-liver axis was also established, linking the microbial generation of short chain fatty acids with the fueling of scd1- and elovl6-mediated lipogenesis. In summary, by correlating the microbiome with host gene expression, we offer new insights in the evaluation of fish diets promoting gut and metabolism homeostasis, and ultimately, the health of farmed fish.

The exposome paradigm to predict environmental health in terms of systemic homeostasis and resource balance based on NMR data science

The environment, from microbial ecosystems to recycled resources, fluctuates dynamically due to many physical, chemical and biological factors, the profile of which reflects changes in overall state, such as environmental illness caused by a collapse of homeostasis. To evaluate and predict environmental health in terms of systemic homeostasis and resource balance, a comprehensive understanding of these factors requires an approach based on the "exposome paradigm", namely the totality of exposure to all substances. Furthermore, in considering sustainable development to meet global population growth, it is important to gain an understanding of both the circulation of biological resources and waste recycling in human society. From this perspective, natural environment, agriculture, aquaculture, wastewater treatment in industry, biomass degradation and biodegradable materials design are at the forefront of current research. In this respect, nuclear magnetic resonance (NMR) offers tremendous advantages in the analysis of samples of molecular complexity, such as crude bio-extracts, intact cells and tissues, fibres, foods, feeds, fertilizers and environmental samples. Here we outline examples to promote an understanding of recent applications of solution-state, solid-state, time-domain NMR and magnetic resonance imaging (MRI) to the complex evaluation of organisms, materials and the environment. We also describe useful databases and informatics tools, as well as machine learning techniques for NMR analysis, demonstrating that NMR data science can be used to evaluate the exposome in both the natural environment and human society towards a sustainable future.

Beyond classic concepts in thyroid homeostasis: Immune system and microbiota

It has long been known that thyroid hormones have implications for multiple physiological processes and can lead to serious illness when there is an imbalance in its metabolism. The connections between thyroid hormone metabolism and the immune system have been extensively described, as they can participate in inflammation, autoimmunity, or cancer progression. In addition, changes in the normal intestinal microbiota involve the activation of the immune system while triggering different pathophysiological disorders. Recent studies have linked the microbiota and certain bacterial fragments or metabolites to the regulation of thyroid hormones and the general response in the endocrine system. Even if the biology and function of the thyroid gland has attracted more attention due to its pathophysiological importance, there are essential mechanisms and issues related to it that are related to the interplay between the intestinal microbiota and the immune system and must be further investigated. Here we summarize additional information to uncover these relationships, the knowledge of which would help establish new personalized medical strategies.

Plant and Animal-Type Feedstuff Shape the Gut Microbiota and Metabolic Processes of the Chinese Mitten Crab Eriocheir sinensis

In animals, growth and development are strongly correlated with the gut microbiota and metabolic profiles. In this study, gut microbiome communities, metabolic profiles, and growth performance of Eriocheir sinensis under three dietary feed types based on waterweed plants only, freshwater snails only, and waterweed plants combined with freshwater snails were studied by using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry. Results indicated that different feed types dramatically affected the growth performances of E. sinensis by altering the gut microbiota and metabolic profiles. Aquatic plants, such as waterweeds, played essential roles in shaping gut microbiome communities, and the optimal Bacteroides-to-Firmicutes ratio might strongly promote growth performance. Waterweed plants also helped decrease maleficent Proteobacteria caused by excess animal-type feedstuff, such as freshwater snails, and might have positive roles in antibacterial functions in gut. A diet based on waterweeds only resulted in lipid metabolism disorders, which significantly retarded the growth of E. sinensis. In summary, E. sinensis cultured with a diet of waterweeds and freshwater snails showed superior growth performance due to their healthy gut microbiota and metabolic homeostasis. Our findings unveiled the roles of aquatic plants and animal-type food such as freshwater snail in shaping the gut microbiota and metabolic processes and provided guidance for the aquaculture of E. sinensis in future.

Could the gut microbiota community in the coral trout Plectropomus leopardus (Lacepède, 1802) be affected by antibiotic bath administration?

Gut microbiota in fish plays an important role in the nutrient digestion, immune responses and disease resistance. To understand the effect of fluoroquinolone antibiotic bath administration on fish gut microbiota, the gut microbiota community in the coral trout Plectropomus leopardus (Lacepède, 1802) was studied after enrofloxacin bathing treatment at two concentrations (5 and 10 mg/L) and 0 mg/L as control. A total of 90 fish were used in this study, and three replicates were used for each treatment. After a 24‐hr bath, the gut bacterial composition was analyzed using high‐throughput Illumina sequencing. The results indicated that the richness, diversity and the dominant bacterial taxa of P. leopardus gut bacteria were not affected by enrofloxacin bathing (p > .05). Proteobacteria and Firmicutes were the dominant phyla, and Exiguobacterium, Citrobacter, Vibrio, Acinetobacter, Pseudomonas were the dominant genus. The findings in the present study provide an understanding on the relationship between fish gut bacteria community and antibiotic bath administration. The findings of this study are instructive on the antibiotic bath administration applied for the management of P. leopardus health in aquaculture.

Lactobacillus acidophilus and L. plantarum improve health status, modulate gut microbiota and innate immune response of marron (Cherax cainii)

This study aimed to investigate the combined effects of two most potent probiotic bacteria Lactobacillus acidophilus and Lactobacillus plantarum on overall health and immune status of freshwater crayfish, marron under laboratory conditions. A total of 36 marron were distributed into six different tanks and two different feeding groups, control and probiotic-fed group. After acclimation, control group was fed with basal diet while probiotic group was fed 109 CFU/mL per kg of bacterial supplemented feed for 60 days. The results showed no significant differences in weight gain, however, probiotic feed significantly enhanced some hemolymph parameters and biochemical composition of tail muscle. Histology data revealed better hepatopancreas health and higher microvilli counts in the marron gut fed probiotic diet. The probiotic bacteria triggered significant shift of microbial communities at different taxa level, mostly those reported as beneficial for crayfish. The probiotic diet also enriched the metabolic functions and genes associated with innate immune response of crayfish. Further correlation analysis revealed significant association of some taxa with increased activity for hemolymph and immune genes. Therefore, dietary Lactobacillus supplementation can modulate the overall health and immunity as well as gut microbial composition and interaction network between gut microbiota and immune system in crayfish.

Next-generation sequencing reveals significant variations in bacterial compositions across the gastrointestinal tracts of the Indian major carps, rohu (Labeo rohita), catla (Catla catla) and mrigal (Cirrhinus cirrhosis)

Bacterial communities strongly influence the digestion, health and immune status of fish. This study investigates the microbial distribution of the anterior, middle and distal gut sections of three economically important carp species in Bangladesh, rohu, catla and mrigal (commonly known as Indian major carps), using 16S rRNA-based Illumina sequencing technology. The alpha-diversity measurement with one-way ANOVA indicated high species richness, Shannon and Simpson indices in the middle and distal gut, while the anterior gut of IMCs had the lowest diversity. At the phylum level, there was high abundance of Proteobacteria in the GITs of rohu and mrigal, whereas Fusobacteria was dominant in the anterior and middle guts of catla. At the genus level, diverse microbial communities were identified across the three GIT sections, with six indicator genera found in rohu, catla and mrigal, as revealed by linear discriminant analysis (LDA) at a 0·05 level of significance. Of the 218 genera identified, only 33 were common across the anterior, middle and distal guts of all three species. Bacterial diversity was significantly higher (P < 0·05) in mrigal, followed by catla and rohu, respectively. Alongside the common bacteria Aeromonas, Enterobacter and Serratia, the overwhelming abundance of Cetobacterium, Shewanella and Plesiomonas warrants further investigation. SIGNIFICANCE AND IMPACT OF THE STUDY: This study investigates the microbial communities of the gastrointestinal tracts (GITs) of three Indian major carp (IMC) species-rohu, catla and mrigal, obtained from a polyculture pond under the same feeding regime. Diverse microbial communities were found, with significantly different relative abundances and diversities of phyla and genera. The results provide valuable information on GIT microbial communities that may be useful for nutrition and health management in IMCs.

Dietary supplementation of black soldier fly (Hermetica illucens) meal modulates gut microbiota, innate immune response and health status of marron (Cherax cainii, Austin 2002) fed poultry-by-product and fishmeal based diets

The present study aimed to evaluate the dietary supplementary effects of black soldier fly (Hermetia illucens) (BSF) meal on the bacterial communities in the distal gut, immune response and growth of freshwater crayfish, marron (Cherax cainii) fed poultry-by-product meal (PBM) as an alternative protein source to fish meal (FM). A total of 64 marron were randomly distributed into 16 different tanks with a density of four marron per tank. After acclimation, a 60-days feeding trial was conducted on marron fed isonitrogenouts and isocalorific diets containing protein source from FM, PBM, and a combination of FM + BSF and PBM + BSF. At the end of the trial, weight gain and growth of marron were found independent of any dietary treatment, however, the two diets supplemented with BSF significantly (P < 0.05) enhanced haemolymph osmolality, lysozyme activity, total haemocyte counts, and protein and energy contents in the tail muscle. In addition, the analysis of microbiota and its predicted metabolic pathways via 16s rRNA revealed a significantly (P < 0.05) higher bacterial activity and gene function correlated to biosynthesis of protein, energy and secondary metabolites in PBM + BSF than other dietary groups. Diets FM + BSF and PBM + BSF were seen to be associated with an up-regulation of cytokine genes in the intestinal tissue of marron. Overall, PBM + BSF diet proved to be a superior diet in terms of improved health status, gut microbiota and up-regulated expression of cytokine genes for marron culture.

Gut Microbiota and Energy Homeostasis in Fish

The microorganisms within the intestinal tract (termed gut microbiota) have been shown to interact with the gut-brain axis, a bidirectional communication system between the gut and the brain mediated by hormonal, immune, and neural signals. Through these interactions, the microbiota might affect behaviors, including feeding behavior, digestive/absorptive processes (e.g., by modulating intestinal motility and the intestinal barrier), metabolism, as well as the immune response, with repercussions on the energy homeostasis and health of the host. To date, research in this field has mostly focused on mammals. Studies on non-mammalian models such as fish may provide novel insights into the specific mechanisms involved in the microbiota-brain-gut axis. This review describes our current knowledge on the possible effects of microbiota on feeding, digestive processes, growth, and energy homeostasis in fish, with emphasis on the influence of brain and gut hormones, environmental factors, and inter-specific differences.

Genetic Effects on the Gut Microbiota Assemblages of Hybrid Fish From Parents With Different Feeding Habits

Gut microbiota play critical roles in host nutrition and metabolism. However, little is known about the genetic effects on the gut microbiota assemblages because a suitable model for investigation is lacking. In the present study, we established the reciprocal hybrid fish lineages derived from the parents with different feeding habits, namely, herbivorous blunt snout bream (Megalobrama amblycephala, BSB, 2n = 48) and carnivorous topmouth culter (Culter alburnus, TC, 2n = 48). We investigated the genetic effects on gut microbiota assemblages by using 16S rRNA gene sequencing. The results showed that the gut characteristics (structure, relative gut length, relative gut mass, and Zihler’s index) differed between the two types of hybrids and the two parents. In particular, a strong correlation between genotype and gut microbial assemblages indicated that host genetic (subgenome) significantly altered the gut microbial communities. In addition, the microbial structures (composition and abundance) in the two types of hybrids were more similar to those in BSB parent (P > 0.05) than to those in TC parent (P < 0.05), and the cellulase contents in the gut (produced by gut microbes) also showed the similar results. The results suggested that the host genomic interaction (mainly subgenome domination) had a sizeable effect on shaping the gut microbiota assemblages in reciprocal hybrid fish. This study enriches our understanding of the relationship between host genetic and gut microbiota assemblages, and provides insight into gut microbiota and metabonomics.