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Host-associated microbiota can influence host phenotypic variation, fitness and potential to adapt to local environmental conditions. In turn, both host evolutionary history and the abiotic and biotic environment can influence the diversity and composition of microbiota. Yet, to what extent environmental and host-specific factors drive microbial diversity remains largely unknown, limiting our understanding of host-microbiome interactions in natural populations. Here, we compared the intestinal microbiota between two phylogenetically related fishes, the three-spined stickleback (Gasterosteus aculeatus) and the nine-spined stickleback (Pungitius pungitius) in a common landscape. Using amplicon sequencing of the V3-V4 region of the bacterial 16S rRNA gene, we characterised the α and β diversity of the microbial communities in these two fish species from both brackish water and freshwater habitats. Across eight locations, α diversity was higher in the nine-spined stickleback, suggesting a broader niche use in this host species. Habitat was a strong determinant of β diversity in both host species, while host species only explained a small fraction of the variation in gut microbial composition. Strong habitat-specific effects overruled effects of geographic distance and historical freshwater colonisation, suggesting that the gut microbiome correlates primarily with local environmental conditions. Interestingly, the effect of habitat divergence on gut microbial communities was stronger in three-spined stickleback than in nine-spined stickleback, possibly mirroring the stronger level of adaptive divergence in this host species. Overall, our results show that microbial communities reflect habitat divergence rather than colonisation history or dispersal limitation of host species.

Dietary polyphenols improve gut health either through their direct effects on the intestinal barrier and antioxidant and immune systems of the host or through the action of metabolites produced by the microbiota. We have focused on phenolic acids like gallic acid and curcumin, stilbenes like resveratrol, and flavonoids such as quercetin, daidzein, and anthocyanins that can chelate metals and scavenge free radicals to prevent or treat intestinal inflammation and brain disorders. Although polyphenols undergo both phase I and II metabolisms, only a tiny fraction of the catabolites is bioavailable. The gut microbiota catabolizes these compounds to produce beneficial metabolites for the host.Fish can be suitable models for obtaining in-depth knowledge about the absorption and metabolism of polyphenols, and their breakdown by the gut microbiota. Gathering such knowledge along with their effects on the immune system could reveal the effectiveness of bioactive compounds like polyphenols in tackling intestine and brain disorders.

Alginate oligosaccharides (AOS) are natural bioactive compounds with anti-inflammatory properties. We performed a feeding trial employing a zebrafish (Danio rerio) model of soybean-induced intestinal inflammation. Five groups of fish were fed different diets: a control (CT) diet, a soybean meal (SBM) diet, a soybean meal+β-glucan (BG) diet and 2 soybean meal+AOS diets (alginate products differing in the content of low molecular weight fractions - AL, with 31% < 3kDa and AH, with 3% < 3kDa). We analyzed the intestinal transcriptomic and plasma metabolomic profiles of the study groups. In addition, we assessed the expression of inflammatory marker genes and histological alterations in the intestine. Dietary algal β-(1, 3)-glucan and AOS were able to bring the expression of certain inflammatory genes altered by dietary SBM to a level similar to that in the control group. Intestinal transcriptomic analysis indicated that dietary SBM changed the expression of genes linked to inflammation, endoplasmic reticulum, reproduction and cell motility. The AL diet suppressed the expression of genes related to complement activation, inflammatory and humoral response, which can likely have an inflammation alleviation effect. On the other hand, the AH diet reduced the expression of genes, causing an enrichment of negative regulation of immune system process. The BG diet suppressed several immune genes linked to the endopeptidase activity and proteolysis. The plasma metabolomic profile further revealed that dietary SBM can alter inflammation-linked metabolites such as itaconic acid, taurochenodeoxycholic acid and enriched the arginine biosynthesis pathway. The diet AL helped in elevating one of the short chain fatty acids, namely 2-hydroxybutyric acid while the BG diet increased the abundance of a vitamin, pantothenic acid. Histological evaluation revealed the advantage of the AL diet: it increased the goblet cell number and length of villi of the intestinal mucosa. Overall, our results indicate that dietary AOS with an appropriate amount of < 3kDa can stall the inflammatory responses in zebrafish.

Algae feeds and fish gut microbiota have been given importance in the past few years because of the necessity to rely on sustainable ingredients in aquafeeds and the link of host-associated microbes to organismal health. But little is known about the potential of algae, particularly of micro- and macroalgae combination, to shape the intestinal bacterial communities. Hence, in the present work, the 16S rRNA gene sequencing technique was employed to unravel the effects of the seaweed Gracilaria gracilis and the microalga Nannochloropsis oceanica - included either singly or in combination in the diets of European seabass - on the diversities and composition of the gut bacterial communities. Results indicated that 8% inclusion of either G. gracilis (GRA) or N. oceanica (NAN) led to a reduction in the gut microbial diversity. On the other hand, inclusion of the micro- and macroalga in a blend (NANGRA) mitigated these plausible effects on the intestinal bacterial communities. The core microbiota of European seabass was composed of both beneficial (Lactobacillus and Cetobacterium) and potentially pathogenic (Flavobacterium) bacteria. The GRA diet was associated with a lower abundance of carbohydrate degraders and also promoted the growth of bacteria capable of outcompeting fish pathogens (Sulfitobacter and Methylobacterium). On the other hand, the NAN diet led to a higher representation of the genus Bacillus, with probiotic potential, accompanied by a decrease in Vibrio, a genus encompassing several fish pathogenic species. These findings demonstrate the ability of micro- and macroalgae to modulate the gut microbiota of European seabass, with plausible implications to host gut homeostasis.

Resident microbial communities that can support various host functions play a key role in their development and health. In fishes, microbial symbionts are vertically transferred from the parents to their progeny. Such transfer of microbes in mouthbrooder fish species has not been reported yet. Here, we employed Nile tilapia (Oreochromis niloticus) to investigate the vertical transmission of microbes across generations using a 16S rRNA amplicon sequencing approach, based on the presence of bacteria in different generations. Our analysis revealed that the core microbiome in the buccal cavity and posterior intestine of parents shapes the gut microbiome of the progeny across generations. We speculate that the route of this transmission is via the buccal cavity. The identified core microbiome bacteria, namely Nocardioides, Propionibacterium, and Sphingomonas have been reported to play an essential role in the health and development of offspring. These core microbiome members could have specific functions in fish, similar to mammals.

Fish are widely exposed to higher microbial loads compared to land and air animals. It is known that the microbiome plays an essential role in the health and development of the host. The oral microbiome is vital in females of different organisms, including the maternal mouthbrooding species such as Nile tilapia (Oreochromis niloticus). The present study reports for the first time the microbial composition in the buccal cavity of female and male Nile tilapia reared in a recirculating aquaculture system. Mucus samples were collected from the buccal cavity of 58 adult fish (∼1 kg), and 16S rRNA gene amplicon sequencing was used to profile the microbial communities in females and males. The analysis revealed that opportunistic pathogens such as Streptococcus sp. were less abundant in the female buccal cavity. The power play of certain bacteria such as Acinetobacter, Acidobacteria (GP4 and GP6), and Saccharibacteria that have known metabolic advantages was evident in females compared to males. Association networks inferred from relative abundances showed few microbe–microbe interactions of opportunistic pathogens in female fish. The findings of opportunistic bacteria and their interactions with other microbes will be valuable for improving Nile tilapia rearing practices. The presence of bacteria with specific functions in the buccal cavity of female fish points to their ability to create a protective microbial ecosystem for the offspring.

In industrial animal production, breeding strategies are essential to produce offspring of better quality and vitality. It is also known that host microbiome has a bearing on its health. Here, we report for the first time the influence of crossbreeding strategy, inbreeding or outbreeding, on the buccal and intestinal bacterial communities in female Nile tilapia (Oreochromis niloticus). Crossbreeding was performed within a family and between different fish families to obtain the inbred and outbred study groups, respectively. The genetic relationship and structure analysis revealed significant genetic differentiation between the inbred and outbred groups. We also employed a 16S rRNA gene sequencing technique to understand the significant differences between the diversities of the bacterial communities of the inbred and outbred groups. The core microbiota composition in the mouth and the intestine was not affected by the crossbreeding strategy but their abundance varied between the two groups. Furthermore, opportunistic bacteria were abundant in the buccal cavity and intestine of the outbred group, whereas beneficial bacteria were abundant in the intestine of the inbred group. The present study indicates that crossbreeding can influence the abundance of beneficial bacteria, core microbiome and the inter-individual variation in the microbiome.

Prebiotics are substrates intended to sculpt gut microbial communities as they are selectively utilized by the microorganisms to exert beneficial health effects on hosts. Macroalga-derived oligosaccharides are candidate prebiotics, and herein, we determined the effects of Laminaria sp.-derived alginate oligosaccharide (AlgOS) on the distal intestinal microbiota of Atlantic salmon (Salmo salar). Using a high-throughput 16S rRNA gene amplicon sequencing technique, we investigated the microbiota harbored in the intestinal content and mucus of the fish offered feeds supplemented with 0.5 and 2.5% AlgOS. We found that the prebiotic shifts the intestinal microbiota profile; alpha diversity was significantly reduced with 2.5% AlgOS while with 0.5% AlgOS the alteration occurred without impacting the bacterial diversity. Beta diversity analysis indicated the significant differences between control and prebiotic-fed groups. The low supplementation level of AlgOS facilitated the dominance of Proteobacteria (including Photobacterium phosphoreum, Aquabacterium parvum, Achromobacter insolitus), and Spirochaetes (Brevinema andersonii) in the content or mucus of the fish, and few of these bacteria (Aliivibrio logei, A. parvum, B. andersonii, A. insolitus) have genes associated with butyrate production. The results indicate that the low inclusion of AlgOS can plausibly induce a prebiotic effect on the distal intestinal microbiota of Atlantic salmon. These findings can generate further interest in the potential of macroalgae-derived oligosaccharides for food and feed applications.