Aug 2026· Microorganisms· Vol 14· 0 citations· 177 references
Medicine
Abstract
Aquaculture is central to global food security, but intensification of production has increased disease risk and environmental pressure. The gut microbiome of aquatic organisms is now recognized as a key mediator of host physiology, nutrition, immunity, and pathogen resistance, making it a promising alternative to antimicrobial-based disease control. This review summarizes current knowledge on the composition, assembly, and functional roles of the gut microbiome in fish and crustaceans of aquacultural importance. Major bacterial phyla include Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria, Actinobacteria, and Verrucomicrobia. Community structure is shaped by environment, diet, host age, genetics, stress, and stochastic processes, with differences between marine and freshwater systems. The microbiome contributes to immune defense through short-chain fatty acid production, Toll-like receptor signaling, cytokine regulation, mucosal immunoglobulin responses, antimicrobial peptide and bacteriocin production, and competitive exclusion of pathogens. It also supports productivity by improving nutrient assimilation, vitamin and enzyme synthesis, and feed conversion. Probiotics, prebiotics, and synbiotics are discussed as strategies for targeted microbiome modulation, although unstable colonization and the lack of standardized protocols remain major challenges. Overall, targeted microbiome manipulation offers a promising route toward sustainable, antimicrobial-reduced aquaculture.
Abalone are economically, ecologically and culturally significant marine molluscs, with both wild and farmed populations under pressure due to intrinsic and extrinsic stressors. Abalone performance and health are centred on a highly specialized digestive system supported by a diverse gut microbiome, which enables nutrient assimilation, polysaccharide digestion, immune regulation and disease resistance. This review consolidates our current understanding of the abalone gut microbiome regulation by examining the interactions among host digestive physiology, microbial diversity and function, dietary influences and environmental conditions. Based on a systematic evaluation of sequencing‐based studies published between 2015 and 2025 and spanning 14 abalone species, a shared core gut microbiome was identified, primarily composed of genera including
Mycoplasma, Psychrilyobacter
and
Vibrio
. This review also evaluates microbiome‐related symbiosis and dysbiosis, with emphasis on how diet and environmental stress reshape microbial functions linked to growth, immunity and disease susceptibility. Finally, current methodological limitations and major knowledge gaps are outlined, particularly the need for mechanistic and multi‐omics approaches, standardized sampling and longitudinal surveys. As microbiome research progresses, these insights can be translated into practice, moving abalone aquaculture and fisheries beyond reactive management toward precision strategies that ultimately enhance animal health, productivity and long‐term ecological sustainability.
Jin-Cheng Guo, Leonie Venter, Donnabella C. Lacap‐Bugler et al.· Aquaculture, Fish and Fisher...· 2 citations
The review highlights the need to integrate multi-omics datasets, computational modelling, and precision livestock technologies to develop robust, scalable, and economically viable microbiome management strategies for sustainable livestock production, environmental stewardship, and overall global food security.
Shalu Singh, Yashesh Singh, Jagjiwan Ram et al.· Archives of Current Research...· 0 citations
The gut microbiome of rainbow trout plays a crucial role in fish nutrition, immune function and stress resistance, making it a key factor in aquaculture sustainability. This review systematizes metagenomic data that enable the distinction between resident and transient microbial communities and the identification of a core microbiome. At the phylum level, the core is predominantly composed of Bacillota, Pseudomonadota, Actinomycetota, Bacteroidota, and Mycoplasmatota, with additional phyla detected depending on the gut region and methodological approach. Diet-induced changes are often rapid and reversible: insect meal and certain probiotics increase the abundance of beneficial Bacillota and suppress opportunists. Unlike dietary shifts, chronic stressors—particularly elevated temperatures and antibiotic treatment—can override these benefits, causing a persistent alpha diversity reduction, overgrowth of Pseudomonadata, and depletion of key commensals. The autochthonous mucosal microbial community is more resilient to short-term fluctuations but can be irreversibly altered by prolonged stress or antimicrobial therapy, leading to dysbiosis and reduced colonization resistance. A holistic understanding of host–microbe–environment interactions is essential for establishing dynamic reference ranges for a “healthy” microbiome. Such knowledge would enable early detection of dysbiosis and support the rational development of functional feeds and probiotics in commercial trout farming.
A. Tsekova, N. Kantserova, L. Lysenko et al.· Veterinary Sciences· 0 citations
Antibiotics have transformed the management of infectious diseases but often have unintended adverse effects on the commensal intestinal microbiota. Loss of diversity in the gut microbiota, the disruption that is most evident after antibiotic exposure, has been identified as a key driver of metabolic homeostasis, immune regulation, and disease susceptibility. This review aims to study current evidence for indirect and long-lasting effects of antibiotics on the gut microbiome and to highlight clinical consequences. Specifically, this review focuses on four interrelated aspects of antibiotic-induced gut ecosystem disturbances: i) reduction in gut microbial diversity and diversity with reduced systemic ecological resilience accompanied by species richness depletion associated with accumulation of noncontributing operational taxonomic units to activities relevant to the host, corresponding to incompleteness in microbiome recovery; ii) loss or gain in metabolic activity for microbial metabolites such as short-chain fatty acids and enteric bile acids along with impairment of microbial vitamin synthesis; iii) polarization of mucosal and systemic immune responses regulating inflammation through microbiome-mediated mechanisms directed toward changes in T cell differentiation; and finally, iv) dysbiosis that increases susceptibility to recurrent infections by opportunistic microbes showing emerging resistance against antibiotics. Emerging evidence indicates that such perturbations driven by the antibiotics themselves can outlive treatment, especially after broad-spectrum antibiotic administration, and threaten intestinal barrier integrity and immune homeostasis. These results demonstrate that antibiotics-induced dysbiosis is a system-wide disruption involving tightly coupled microbial, metabolic, and immune pathways. This review also emphasizes the need for antimicrobial stewardship and strengthens the implementation of microbiome-targeted strategies to mitigate long-term adverse health events and improve infection resilience.
Maryam Al-saedi, Zainab H. Al-mohammadawy, Zainab A. Hasan et al.· Journal of Advanced Biotechn...· 0 citations
The gut microbiota plays an important role in nutrient utilization, intestinal homeostasis, immune regulation, and production performance in poultry. Its composition and functional activity are shaped by complex interactions among host species, developmental stage, intestinal segment, diet, genetic background, and rearing environment. This review summarizes current knowledge of the poultry gut microbiota, with particular emphasis on its roles in nutrition, metabolism, and production performance. We first examine microbial composition and spatial distribution across major poultry species, including broiler chickens, laying hens, ducks, geese, and turkeys, and discuss the factors contributing to interspecies and interstudy variation. We then evaluate how dietary components, including fiber, protein, amino acids, and lipids, modulate microbial communities and metabolic pathways. Particular attention is given to microbial fermentation, short-chain fatty acid production, microbial nitrogen metabolism, bile acid transformation, and host-microbiota signaling, which collectively influence nutrient utilization, intestinal barrier function, immune homeostasis, and metabolic regulation. The potential of microbiota-targeted strategies, including probiotics, prebiotics, synbiotics, dietary fiber manipulation, reduced-protein diets, and emerging microbial interventions, to improve feed efficiency, growth performance, carcass characteristics, meat quality, and resilience to environmental stress is also discussed. In addition, the implications of gut microbiota regulation for nitrogen utilization, ammonia emissions, animal welfare, and antibiotic-free production are considered. Despite substantial progress, the translation of microbiome research into practical applications remains limited by inconsistent experimental designs, methodological heterogeneity, insufficient functional validation, and a lack of causal evidence. Integrating multi-omics approaches with controlled intervention studies and standardized experimental frameworks will be essential for defining causal microbiota-host interactions and developing precision microbiota-based strategies. Overall, a functional understanding of the diet-microbiota-host axis may provide new opportunities to improve poultry productivity, health, and sustainability.
The pursuit of sustainable and efficient animal production systems has intensified global interest in microbiota-targeted nutritional strategies. This review synthesizes current research on prebiotics and probiotics, selectively utilized microbial substrates and beneficial live microorganisms, respectively, that confer health benefits, across major livestock and aquaculture sectors, including poultry, swine, ruminants, fish, and shrimp. It examines the fundamental role of host-specific gut microbiomes in regulating health and productivity and elucidates how prebiotics, alone or in synergistic formulations with probiotics, modulate these microbial communities. Mechanisms of action involve enhanced nutrient digestibility, improved intestinal morphology and barrier integrity, selective stimulation of beneficial bacteria (e.g., Lactobacillus, Bifidobacterium), suppression of pathogens (e.g., Escherichia coli, Salmonella, Vibrio), and potentiation of innate and humoral immune responses. Consistent evidence demonstrates that microbiota-targeted interventions improve key zootechnical indicators, including weight gain, feed conversion ratio, and carcass quality, while enhancing animal welfare and resilience to environmental and physiological stressors. A pivotal finding is their ability to reduce reliance on antimicrobial agents, addressing antibiotic resistance and aligning with consumer demand for ethical and natural production systems. Furthermore, this review highlights the valorisation of agro-industrial by-products (e.g., fruit pomace, cereal brans) and novel substrates such as Hermetia illucens (black soldier fly) as functional, cost-effective sources that embed animal nutrition within a circular bioeconomy framework. By integrating multidisciplinary findings from terrestrial and aquatic species, this review concludes that microbiota-based functional nutrition is indispensable for advancing next-generation sustainable animal production, uniting productivity, environmental stewardship, and animal welfare while supporting safe, ethical, and climate-resilient food systems worldwide. Probiotic and prebiotic integration in swine, poultry, cattle, and aquaculture systems. Supports animal health, feed efficiency, and sustainable by-product use, aligning with SDG 2 and SDG 12. Repurposing agro-industrial residues as novel prebiotics closes the resource loop, reinforcing the circular economy.
João Victor dos Anjos Almeida, Julia Memrava Cabrera, Mauro de Medeiros Oliveira et al.· Brazilian Journal of Microbi...· 1 citation
We use cookies to run the site and, with your consent, for analytics and to show ads.
See our Cookie Policy.
