Properties of Probiotics Kocuria SM1 and Rhodococcus SM2 Isolated from Fish Guts

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

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

Deciphering the dysbiosis caused in the fish microbiota by emerging contaminants and its mitigation strategies-A review

The primary barrier to nutrient absorption in fish is the intestinal epithelium, followed by a community of microorganisms known as the gut microbiota, which can be thought of as a hidden organ. The gastrointestinal microbiota of fish plays a key role in the upholding of overall health by maintaining the homeostasis and disease resistance of the host. However, emerging contaminants as the result of anthropogenic activities have significantly led to disruptions and intestinal dysbiosis in fish. Which probably results in fish mortalities and disrupts the balance of an ecosystem. Therefore, we comprehensively seek to compile the effects and consequences of emerging contaminations on fish intestinal microbiota. Additionally, the mitigation strategies including prebiotics, probiotics, plant-based diet, and Biofloc technology are being outlined. Biofloc technology (BFT) can treat toxic materials, i.e., nitrogen components, and convert them into a useful product such as proteins and demonstrated promising elevating technique for the fish intestinal bacterial composition. However, it remains unclear whether the bacterial isolate is primarily responsible for the BFT's removal of nitrate and ammonia and the corresponding removal mechanism. To answer this, real time polymerase chain reaction (RT-PCR) with metagenomics, transcriptomics, and proteomics techniques probably provides a possible solution.

Omics analysis revealed the possible mechanism of streptococcus disease outbreak in tilapia under high temperature

High temperature is a main cause to result in the outbreak of tilapia streptococcal disease. However, the underlying mechanisms are not well understood. In this study, we first confirmed that tilapia infected with Streptococcus agalactiae (S. agalactiae) had a higher mortality at high temperature (35 °C) than that at normal temperature (28 °C). Subsequently, the effects of high temperature on gene expression pattern of S. agalactiae and intestinal microbiota of tilapia were respectively detected by RNA-seq and 16S rDNA sequencing. RNA-seq identified 357 differentially expressed genes (DEGs) in S. agalactiae cultured at 28 °C and 35 °C. GO and KEGG analysis showed that these DEGs were highly involved in metabolic processes, including glucose, lipid and amino acid metabolisms, which indicates that S. agalactiae have stronger vitality and are likely to be more infectious under high temperature. Microbiota analysis revealed that high temperature could influence the bacterial community composition of tilapia intestine, accompanied by changes in intestinal structure. Compared to feed at 28 °C, the total bacterial species as well as pathogens, such as norank_f__Rhizobiales_Incertae_Sedis, Pseudorhodoplanes, Ancylobacter, in tilapia intestine were significantly increased at 35 °C, which may weaken the immune resistance of tilapia. Taken together, our results suggest that high temperature evoked tilapia susceptible to S. agalactiae should be the combined effect of enhanced S. agalactiae metabolism and dysregulated tilapia intestinal microbiota.

Whole genome analysis of host-associated lactobacillus salivarius and the effects on hepatic antioxidant enzymes and gut microorganisms of Sinocyclocheilus grahami

As a fish unique to Yunnan Province in China, Sinocyclocheilus grahami hosts abundant potential probiotic resources in its intestinal tract. However, the genomic characteristics of the probiotic potential bacteria in its intestine and their effects on S. grahami have not yet been established. In this study, we investigated the functional genomics and host response of a strain, Lactobacillus salivarius S01, isolated from the intestine of S. grahami (bred in captivity). The results revealed that the total length of the genome was 1,737,623 bp (GC content, 33.09%), comprised of 1895 genes, including 22 rRNA operons and 78 transfer RNA genes. Three clusters of antibacterial substances related genes were identified using antiSMASH and BAGEL4 database predictions. In addition, manual examination confirmed the presence of functional genes related to stress resistance, adhesion, immunity, and other genes responsible for probiotic potential in the genome of L. salivarius S01. Subsequently, the probiotic effect of L. salivarius S01 was investigated in vivo by feeding S. grahami a diet with bacterial supplementation. The results showed that potential probiotic supplementation increased the activity of antioxidant enzymes (SOD, CAT, and POD) in the hepar and reduced oxidative damage (MDA). Furthermore, the gut microbial community and diversity of S. grahami from different treatment groups were compared using high-throughput sequencing. The diversity index of the gut microbial community in the group supplemented with potential probiotics was higher than that in the control group, indicating that supplementation with potential probiotics increased gut microbial diversity. At the phylum level, the abundance of Proteobacteria decreased with potential probiotic supplementation, while the abundance of Firmicutes, Actinobacteriota, and Bacteroidota increased. At the genus level, there was a decrease in the abundance of the pathogenic bacterium Aeromonas and an increase in the abundance of the potential probiotic bacterium Bifidobacterium. The results of this study suggest that L. salivarius S01 is a promising potential probiotic candidate that provides multiple benefits for the microbiome of S. grahami.

Gut and Gill-Associated Microbiota of the Flatfish European Plaice (Pleuronectes platessa): Diversity, Metabolome and Bioactivity against Human and Aquaculture Pathogens

Similar to other marine holobionts, fish are colonized by complex microbial communities that promote their health and growth. Fish-associated microbiota is emerging as a promising source of bioactive metabolites. Pleuronectes platessa (European plaice, plaice), a flatfish with commercial importance, is common in the Baltic Sea. Here we used a culture-dependent survey followed by molecular identification to identify microbiota associated with the gills and the gastrointestinal tract (GIT) of P. platessa, then profiled their antimicrobial activity and metabolome. Altogether, 66 strains (59 bacteria and 7 fungi) were isolated, with Proteobacteria being the most abundant phylum. Gill-associated microbiota accounted for higher number of isolates and was dominated by the Proteobacteria (family Moraxellaceae) and Actinobacteria (family Nocardiaceae), whereas Gram-negative bacterial families Vibrionaceae and Shewanellaceae represented the largest group associated with the GIT. The EtOAc extracts of the solid and liquid media cultures of 21 bacteria and 2 fungi representing the diversity of cultivable plaice-associated microbiota was profiled for their antimicrobial activity against three fish pathogens, human bacterial pathogen panel (ESKAPE) and two human fungal pathogens. More than half of all tested microorganisms, particularly those originating from the GIT epithelium, exhibited antagonistic effect against fish pathogens (Lactococcus garvieae, Vibrio ichthyoenteri) and/or human pathogens (Enterococcus faecium, methicillin-resistant Staphylococcus aureus). Proteobacteria represented the most active isolates. Notably, the solid media extracts displayed higher activity against fish pathogens, while liquid culture extracts were more active against human pathogens. Untargeted metabolomics approach using feature-based molecular networking showed the high chemical diversity of the liquid extracts that contained undescribed clusters. This study highlights plaice-associated microbiota as a potential source of antimicrobials for the control of human and the aquaculture-associated infections. This is the first study reporting diversity, bioactivity and chemical profile of culture-dependent microbiota of plaice.

The Gut Microbiota of Healthy and Flavobacterium psychrophilum-Infected Rainbow Trout Fry Is Shaped by Antibiotics and Phage Therapies

In the aquaculture sector, there is an increased interest in developing environmentally friendly alternatives to antibiotics in the treatment and prevention of bacterial infections. This requires an understanding of the effects of different treatments on the fish microbiota as a measure for improving the fish health status. In this study, we focused on the freshwater pathogen Flavobacterium psychrophilum and investigated the effects of antibiotics (florfenicol) and phage therapies on the gut microbiota of healthy and infected rainbow trout fry (1–2 g). Florfenicol-coated feed was administered for 10 days, starting two days after the infection procedure. A two-component mix of phage targeting F. psychrophilum (FpV4 and FPSV-D22) was continuously delivered by feed with a prophylactic period of 12 days. Samples of the distal intestine were collected over time (day -1 and 1, 8, and 33 days post-infection) and analyzed by community analysis targeting the 16S rRNA gene (V3–V4 region). Results showed the dysbiosis effect caused both by the infection and by florfenicol administration. Shifts in the overall composition were detected by β-diversity analysis, and changes in specific populations were observed during taxonomic mapping. Measures of α-diversity were only affected in infected fish (large variation observed 1 and 8 dpi). These community alterations disappeared again when fish recovered from the infection and the antibiotic treatment was terminated (33 dpi). Interestingly, phage addition altered the microbiota of the fish independently of the presence of their target bacterium. The overall gut bacterial community in fish fed phage-treated feed was different from the controls at each time point as revealed by β-diversity analysis. However, it was not possible to identify specific bacterial populations responsible for these changes except for an increase of lactic acid bacteria 33 dpi. Overall, the results indicate that the administered phages might affect the complex network of phage-bacteria interactions in the fish gut. Nevertheless, we did not observe negative effects on fish health or growth, and further studies should be directed in understanding if these changes are beneficial or not for the fish health with an additional focus on the host immune response.

Isolation and Characterization of Competitive Exclusion Microorganisms from Animal Wastes-Based Composts against Listeria monocytogenes

AIM

To isolate the slow-growing or viable but non-culturable competitive exclusion (CE) microorganisms from composts and then verify the anti-Listeria monocytogenes activities of those CE isolates in compost.

METHODS AND RESULTS

CE strains were isolated from composts using double- or triple-layer agar methods, purified, and then characterized. Both compost extracts and solid compost samples were spiked with a cocktail of 3 L. monocytogenes strains which were co-inoculated with or without CE strain cocktail and incubated at both 22°C and 35°C for 168 h. Results indicated that the addition of resuscitation promoting factor (Rpf) promoted the growth of slow-growing species from composts. About 50% of the isolated CE strains (n=40) were identified as Bacillus spp., 17 strains can inhibit more than ten tested L. monocytogenes strains, and 9 strains were motile and competitive biofilm formers. In compost extracts, the growth potentials of L. monocytogenes were reduced up to 2.2 logs when co-culturing with CE strains. In compost samples, the addition of CE strains reduced L. monocytogenes population by ca. 1.3 log CFU/g at 22°C after 24 to 168 h incubation.

CONCLUSION

Our modified double/triple-layer agar procedure with Rpf as growth supplement coupled with spot-on-lawn testing can be a quick and efficient method for isolating CE candidates from composts. The efficacy of CE strains against L. monocytogenes in compost extracts and compost samples was affected by compost type, nutrient level, and incubation temperature.

SIGNIFICANCE AND IMPACT OF THE STUDY

Compost is a rich source of CE microorganisms and compost-adapted CE microorganisms have the potential as a biological agent to control L. monocytogenes in agricultural environments.

Impacts of benzo(a)pyrene exposure on scallop (Chlamys farreri) gut health and gut microbiota composition

The gut tissue interacts with nutrients and pollutants which can impact gut health. Gut microbiota is essential to the host health, but is also easily affected by external environment. However, little is known about the toxicological assessment of environmental contaminants on gut health and microbiota, especially in marine invertebrates. In this study, we first explored the effect of benzo(a)pyrene (BaP) on the gut health and gut microbiota of scallops (Chlamys farreri). The scallops were exposed to different concentrations (0, 0.4, 2 and 10 μg/L) of BaP for 21 days. The histological morphology, immune- and oxidative enzyme-related gene expression, and lipid peroxidation of the scallops were analyzed at 7, 14 and 21 days. The results revealed that BaP could impair intestinal barrier function, increasing the intestinal permeability of scallops. Moreover, immune and antioxidant responses were induced in the gut tissue. After a 21-day exposure to different concentrations of BaP, the intestinal microbial community was analyzed based on 16S rRNA sequencing. Our results suggested that BaP exposure altered the gut microbial diversity and composition in scallops. Many beneficial genera declined after BaP treatment, while the potential pathogens were increased, such as Mycoplasma and Tenacibaculum. A series of hydrocarbon-degrading bacteria were recognized in BaP-treated groups, such as Pseudomonas, Polaribacter, Amphritea and Kordiimonas. Interestingly, the degrading bacteria present varied after exposure to different concentrations of BaP. Overall, this study provides new insights into gut health and gut microbiota in marine invertebrates following exposure to persistent organic pollutants.

Characterisation of a potential probiotic strain Paracoccus marcusii KGP and its application in whey bioremediation

Whey, the main by-product obtained from the manufacture of cheese, which contains a very high organic load (mainly due to the lactose content), is not easily degradable and creates concern over environmental issues. Hydrolysis of lactose present in whey and conversion of whey lactose into valuable products such as bioethanol, sweet syrup, and animal feed offers the possibility of whey bioremediation. The increasing need for bioremediation in the dairy industry has compelled researchers to search for a novel source of β-galactosidase with diverse properties. In the present study, the bacterium Paracoccus marcusii KGP producing β-galactosidase was subjected to morphological, biochemical, and probiotic characterisation. The bacterial isolate was found to be non-pathogenic and resistant to low pH (3 and 4), bile salts (0.2%), salt (10%), pepsin (at pH 3), and pancreatin (at pH 8). Further characterisation revealed that the bacteria have a good auto-aggregation ability (40% at 24 h), higher hydrophobicity (chloroform-60%, xylene-50%, and ethyl acetate-40%) and a broad spectrum of antibiotic susceptibility. The highest growth of P. marcusii KGP was achieved at pH 7 and 28 °C, and the yeast extract, galactose, and MgSO₄ were the best for the growth of the bacterial cells. The bacterium KGP was able to utilise whey as a substrate for its growth with good β-galactosidase production potential. Furthermore, the β-galactosidase extracted from the isolate KGP could hydrolyse 47% whey lactose efficiently at 50 °C. The study thus reveals the potential application of β-galactosidase from P. marcusii KGP in whey bioremediation.

Community Structure of Protease-Producing Bacteria Cultivated From Aquaculture Systems: Potential Impact of a Tropical Environment

Protease-producing bacteria play vital roles in degrading organic matter of aquaculture system, while the knowledge of diversity and bacterial community structure of protease-producing bacteria is limited in this system, especially in the tropical region. Herein, 1,179 cultivable protease-producing bacterial strains that belonged to Actinobacteria, Firmicutes, and Proteobacteria were isolated from tropical aquaculture systems, of which the most abundant genus was Bacillus, followed by Vibrio. The diversity and relative abundance of protease-producing bacteria in sediment were generally higher than those in water. Twenty-one genera from sediment and 16 genera from water were identified, of which Bacillus dominated by Bacillus hwajinpoensis in both and Vibrio dominated by Vibrio owensii in water were the dominant genera. The unique genera in sediment or water accounted for tiny percentage may play important roles in the stability of community structure. Eighty V. owensii isolates were clustered into four clusters (ET-1-ET-4) at 58% of similarity by ERIC-PCR (enterobacterial repetitive intergenic consensus-polymerase chain reaction), which was identified as a novel branch of V. owensii. Additionally, V. owensii strains belonged to ET-3 and ET-4 were detected in most aquaculture ponds without outbreak of epidemics, indicating that these protease-producing bacteria may be used as potential beneficial bacteria for wastewater purification. Environmental variables played important roles in shaping protease-producing bacterial diversity and community structure in aquaculture systems. In sediment, dissolved oxygen (DO), chemical oxygen demand (COD), and salinity as the main factors positively affected the distributions of dominant genus (Vibrio) and unique genera (Planococcus and Psychrobacter), whereas temperature negatively affected that of Bacillus (except B. hwajinpoensis). In water, Alteromonas as unique genus and Photobacterium were negatively affected by NO₃ ^--N and NO₂ ^--N, respectively, whereas pH as the main factor positively affected the distribution of Photobacterium. These findings will lay a foundation for the development of protease-producing bacterial agents for wastewater purification and the construction of an environment-friendly tropical aquaculture model.

Main bacterial species causing clinical disease in ornamental freshwater fish in Brazil

Bacterial diseases are common in ornamental fish, more frequently associated with ubiquitous bacteria from the aquarium environment. The disease can lead to fish mortality and cause high economic losses if not rapidly controlled. The aim of this study was to identify the main causative bacterial agents of infection in ornamental fish with different clinical signs. A total of 126 freshwater fish, from 12 families and 38 species, with clinical signs were collected in a wholesaler in São Paulo, SP, Brazil. Samples were taken from the eye, skin ulcers, kidneys, and gills, plated on MacConkey, CHROMagar Orientation, and blood agar and incubated under aerobic and anaerobic conditions. Bacterial identification was performed by MALDI-TOF mass spectrometry. From the 126 studied animals, 112 were positive for bacterial isolation. Among the positive animals, 32.1% presented infection caused by a single bacterial species, while in the remaining 67.9%, two to six different bacterial species were identified. A total of 259 bacterial strains were obtained and classified among 46 bacterial species. The species of higher frequency were Aeromonas veronii (26.3%), Aeromonas hydrophilla (16.2%), Shewanella putrefaciens (7.3%), Citrobacter freundii (8.1%), Vibrio albensis (5.8%), and Klebsiella pneumoniae (4.2%). MALDI-TOF MS showed to be a rapid method for diagnosis of bacterial disease outbreaks in ornamental fish establishments.

Effects of Chitosan-Gentamicin Conjugate Supplement on Non-Specific Immunity, Aquaculture Water, Intestinal Histology and Microbiota of Pacific White Shrimp (Litopenaeus vannamei)

When the aquaculture water environment deteriorates or the temperature rises, shrimp are susceptible to viral or bacterial infections, causing a large number of deaths. This study comprehensively evaluated the effects of the oral administration of a chitosan-gentamicin conjugate (CS-GT) after Litopenaeus vannamei were infected with Vibrio parahaemolyticus, through nonspecific immunity parameter detection, intestinal morphology observation, and the assessment of microbial flora diversification by 16S rRNA gene sequencing. The results showed that the oral administration of CS-GT significantly increased total hemocyte counts and reduced hemocyte apoptosis in shrimp (p < 0.05). The parameters (including superoxide dismutase, glutathione peroxidase, glutathione, lysozyme, acid phosphatase, alkaline phosphatase, and phenoloxidase) were significantly increased (p < 0.05). The integrity of the intestinal epithelial cells and basement membrane were enhanced, which correspondingly alleviated intestinal injury. In terms of the microbiome, the abundances of Vibrio (Gram-negative bacteria and food-borne pathogens) in the water and gut were significantly reduced. The canonical correspondence analysis (CCA) showed that the abundances of Vibrio both in the water and gut were negatively correlated with CS-GT dosage. In conclusion, the oral administration of CS-GT can improve the immunity of shrimp against pathogenic bacteria and significantly reduce the relative abundances of Vibrio in aquaculture water and the gut of Litopenaeus vannamei.

In vitro assessment of potential probiotic characteristics of indigenous Lactococcus lactis and Weissella oryzae isolates from rainbow trout (Oncorhynchus mykiss Walbaum)

AIM

The objective of this study was to evaluate the probiotic potential of lactic acid bacteria (LAB) isolated from the intestinal ecosystem of rainbow trout.

METHODS AND RESULTS

Among LAB isolates, 10 of them were selected and screened for resistance to acid and bile salts, pancreatin, sodium chloride and temperature, hydrophobicity, growth profile and antimicrobial activity against fish pathogens. Then, biosafety assessments were investigated. Selected LAB tolerated to gastrointestinal physiological conditions, pancreatin and a range of sodium chloride and temperature. They also exhibited hydrophobicity and showed antagonistic activity against Streptococcus iniae and Yersinia ruckeri. Results of 16S rRNA gene sequencing showed that selected LAB belonged to the Lactococcus lactis (n = 5) and Weissella oryzae (n = 5) species. They exhibited no β-haemolytic activity, while six selected LAB were resistant to some antibiotics. None of them harboured virulence factors.

CONCLUSIONS

This study revealed probiotic characteristics of indigenous LAB isolated from the intestinal ecosystem of rainbow trout. However, further studies are required to confirm the effectiveness of these isolates as probiotics in aquaculture.

SIGNIFICANCE AND IMPACT OF THE STUDY

To the best of our knowledge, for the first time, the presence of probiotic candidates belonging to W. Oryzae was confirmed in fish intestinal microbiota.

Quorum Quenching Properties and Probiotic Potentials of Intestinal Associated Bacteria in Asian Sea Bass Lates calcarifer

Quorum quenching (QQ), the enzymatic degradation of N-acyl homoserine lactones (AHLs), has been suggested as a promising strategy to control bacterial diseases. In this study, 10 AHL-degrading bacteria isolated from the intestine of barramundi were identified by 16S rDNA sequencing. They were able to degrade both short and long-chain AHLs associated with several pathogenic Vibrio species (spp.) in fish, including N-[(RS)-3-Hydroxybutyryl]-l-homoserine lactone (3-oh-C₄-HSL), N-Hexanoyl-l-homoserine lactone (C₆-HSL), N-(β-Ketocaproyl)-l-homoserine lactone (3-oxo-C₆-HSL), N-(3-Oxodecanoyl)-l-homoserine lactone (3-oxo-C₁₀-HSL), N-(3-Oxotetradecanoyl)-l-homoserine lactone (3-oxo-C₁₄-HSL). Five QQ isolates (QQIs) belonging to the Bacillus and Shewanella genera, showed high capacity to degrade both synthetic AHLs as well as natural AHLs produced by Vibrio harveyi and Vibrio alginolyticus using the well-diffusion method and thin-layer chromatography (TLC). The genes responsible for QQ activity, including aiiA, ytnP, and aaC were also detected. Analysis of the amino acid sequences from the predicted lactonases revealed the presence of the conserved motif HxHxDH. The selected isolates were further characterized in terms of their probiotic potentials in vitro. Based on our scoring system, Bacillus thuringiensis QQ1 and Bacillus cereus QQ2 exhibited suitable probiotic characteristics, including the production of spore and exoenzymes, resistance to bile salts and pH, high potential to adhere on mucus, appropriate growth abilities, safety to barramundi, and sensitivity to antibiotics. These isolates, therefore, constitute new QQ probiotics that could be used to control vibriosis in Lates calcalifer.

Systematic evaluation of the gut microbiome of swamp eel (Monopterus albus) by 16S rRNA gene sequencing

Background

The swamp eel (Monopterus albus) is a commercially important farmed species in China. The dysbiosis and homeostasis of gut microbiota has been suggested to be associated with the swamp eel’s disease pathogenesis and food digestion. Although the contributions of gut microbiome in fish growth and health has been increasingly recognized, little is known about the microbial community in the intestine of the swamp eel (Monopterus albus).

Methods

The intestinal microbiomes of the five distinct gut sections (midgut content and mucosa, hindgut content and mucosa, and stools) of swamp eel were compared using Illumina MiSeq sequencing of the bacterial 16S rRNA gene sequence and statistical analysis.

Results

The results showed that the number of observed OTUs in the intestine decreased proximally to distally. Principal coordinate analysis revealed significant separations among samples from different gut sections. There were 54 core OTUs shared by all gut sections and 36 of these core OTUs varied significantly in their abundances. Additionally, we discovered 66 section-specific enriched KEGG pathways. These section-specific enriched microbial taxa (e.g., Bacillus, Lactobacillus) and potential function capacities (e.g., amino acid metabolism, carbohydrate metabolism) might play vital roles in nutrient metabolism, immune modulation and host-microbe interactions of the swamp eel.

Conclusions

Our results showed that microbial diversity, composition and function capacity varied substantially across different gut sections. The gut section-specific enriched core microbial taxa and function capacities may perform important roles in swamp eel’s nutrient metabolism, immune modulation, and host-microbe interactions. This study should provide insights into the gut microbiome of the swamp eel.

Sex, Age, and Bacteria: How the Intestinal Microbiota Is Modulated in a Protandrous Hermaphrodite Fish

Intestinal microbiota is key for many host functions, such as digestion, nutrient metabolism, disease resistance, and immune function. With the growth of the aquaculture industry, there has been a growing interest in the manipulation of fish gut microbiota to improve welfare and nutrition. Intestinal microbiota varies with many factors, including host species, genetics, developmental stage, diet, environment, and sex. The aim of this study was to compare the intestinal microbiota of adult gilthead sea bream (Sparus aurata) from three groups of age and sex (1-year-old males and 2- and 4-year-old females) maintained under the same conditions and fed exactly the same diet. Microbiota diversity and richness did not differ among groups. However, bacterial composition did, highlighting the presence of Photobacterium and Vibrio starting at 2 years of age (females) and a higher presence of Staphylococcus and Corynebacterium in 1-year-old males. The core microbiota was defined by 14 Operational Taxonomic Units (OTUs) and the groups that showed more OTUs in common were 2- and 4-year-old females. Discriminant analyses showed a clear separation by sex and age, with bacteria belonging to the phyla Firmicutes, Proteobacteria and Actinobacteria driving the separation. Pathway analysis performed with the inferred metagenome showed significant differences between 1-year-old males and 4-year-old females, with an increase in infection-related pathways, nitrotoluene degradation and sphingolipid metabolism, and a significant decrease in carbohydrate metabolism pathways with age. These results show, for the first time, how intestinal microbiota is modulated in adult gilthead sea bream and highlight the importance of reporting age and sex variables in these type of studies in fish.