Tilapia species are among the most cultivated fish worldwide due to their biological advantages but face several challenges, including environmental impact and disease outbreaks. Feed additives, such as probiotics, prebiotics, and other microorganisms, have emerged as strategies to protect against pathogens and promote immune system activation and other host responses, with consequent reductions in antibiotic use. Because these additives also influence tilapia’s gut microbiota and positively affect the tilapia culture, we assume it is a flexible annex organ capable of being subject to significant modifications without affecting the biological performance of the host. Therefore, we evaluated the effect of probiotics and other additives ingested by tilapia on its gut microbiota through a meta-analysis of several bioprojects studying the tilapia gut microbiota exposed to feed additives (probiotic, prebiotic, biofloc). A total of 221 tilapia gut microbiota samples from 14 bioprojects were evaluated. Alpha and beta diversity metrics showed no differentiation patterns in relation to the control group, either comparing additives as a group or individually. Results also revealed a control group with a wide dispersion pattern even when these fish did not receive additives. After concatenating the information, the tilapia gut core microbiota was represented by four enriched phyla including Proteobacteria (31%), Fusobacteria (23%), Actinobacteria (19%), and Firmicutes (16%), and seven minor phyla Planctomycetes (1%), Chlamydiae (1%), Chloroflexi (1%), Cyanobacteria (1%), Spirochaetes (1%), Deinococcus Thermus (1%), and Verrucomicrobia (1%). Finally, results suggest that the tilapia gut microbiota is a dynamic microbial community that can plastically respond to feed additives exposure with the potential to influence its taxonomic profile allowing a considerable optimal range of variation, probably guaranteeing its physiological function under different circumstances.

Probiotics in aquaculture hold promise for enhancing fish health and growth. Due to their increased specificity and affinity for their host, indigenous probiotics may offer isolated and potentially amplified benefits. This study investigated the effects of Lactococcus lactis PH3-05, previously isolated from adults of tropical gar (Atractosteus tropicus), on the growth, survival, digestive enzyme activity, intestinal morphology, expression of barrier and immune genes, and intestinal microbiota composition in the larvae of tropical gar. Larvae were fed with live L. lactis PH3-05 concentrations of 10⁴, 10⁶, and 10⁸ CFU/g for 15 days alongside a control diet without probiotics. Higher concentrations of L. lactis PH3-05 (10⁶ and 10⁸ CFU/g) positively influenced larval growth, increasing hepatocyte area and enterocyte height. The 10⁶ CFU/g dose significantly enhanced survival (46%) and digestive enzyme activity. Notably, the 10⁸ CFU/g dose stimulated increased expression of muc-2 and il-10 genes, suggesting enhanced mucosal barrier function and anti-inflammatory response. Although L. lactis PH3-05 did not significantly change the diversity, structure, or Phylum level composition of intestinal microbiota, which was constituted by Proteobacteria, Bacteroidota, Chloroflexi, and Firmicutes, an increase in Lactobacillus abundance was observed in fish fed with 10⁶ CFU/g, suggesting enhanced probiotic colonization. These results demonstrate that administering L. lactis PH3-05 at 10⁶ CFU/g promotes growth, survival, and digestive health in A. tropicus larvae, establishing it as a promising indigenous probiotic candidate for aquaculture applications.

This work aimed to determine the presence of bacterial pathogens in fish with a clinical picture suggestive of infectious disease in Nile tilapia reared in Chiapas, Mexico. Blood and viscera samples were taken from healthy and diseased animals from commercial farms. Clinical and pathological examinations of each individual were performed and samples were collected for bacteriological studies. The bacterial isolates were identified and characterized by culture, biochemical tests, antibiogram, challenge tests and 16S rRNA sequencing. Staphylococcus haemolyticus and Providencia vermicola were isolated from various diseased organisms. The clinical picture caused by Staphylococcus haemolyticus was characterized by appetite disorders, neurological signs, nodulation or ulceration in different areas and congestion or enlargement of internal organs. Providenciosis in juvenile specimens caused a characteristic picture of hemorrhagic septicemia. Challenge tests performed in healthy organisms revealed that both infections caused higher mortality rates in fish (p < 0.05) compared with non-infected specimens, with 100% survival. There was 100% mortality for animals infected with P. vermicola after three days post infection and 45% for those infected with S. haemolyticus. The isolation and identification of two pathogens involved in an infection process were achieved and cataloged as potential causal agents of disease outbreaks in tilapia farming in Mexico. This is the first report of possible bacterial infection caused by S. haemolyticus and P. vermicola in tilapia farms, which are two uncommon but potentially emerging pathogens for the species.

The intestinal microbiota of fish is predominantly composed of prokaryotic microorganisms, with research historically focused on bacteria. In contrast, the role of microeukaryotic organisms in the fish gut remains largely unexplored. This review synthesizes current knowledge on the diversity, ecology, and potential functions of intestinal microeukaryotes, particularly fungi and protozoans, in teleost fish. Fungi, especially Ascomycota and Basidiomycota phyla members, are consistently identified across species and may contribute to digestion, immune modulation, and microbial homeostasis. Protists, though often viewed as pathogens, also exhibit potential commensal or immunoregulatory roles, including the modulation of bacterial communities through grazing. Other eukaryotic taxa, including metazoan parasites, microalgae, and zooplankton, are commonly found as transient or diet-derived members of the gut ecosystem. While many of these organisms remain poorly characterized, emerging evidence suggests they may play essential roles in host physiology and microbial balance. The review highlights the need for improved detection methodologies, functional studies using gnotobiotic and in vitro models, and multi-kingdom approaches to uncover fish gut microeukaryotes’ ecological and biotechnological potential.

Microbial communities, mainly those with probiotic characteristics, positively affect the culture of diverse organisms, including shrimp. In this study, three diets containing different types of probiotics were evaluated on the composition and diversity of the microbial community in the water column and gut of Litopenaeus vannamei, as well as on the expression of genes related to the immune system and resistance of the organisms after being challenged with WSSV and Vibrio parahaemolyticus. Results showed that probiotics affected the microbial community structure in water and shrimp. The expression of beta-glucan binding protein and prophenoloxidase increased in the treatments with probiotics compared to the control before and after the challenge. Overall the survival of shrimp was higher in all the treatments than in control. Results suggest that using probiotics in BFT systems could provide an extra benefit for these kinds of systems.