Microbiome Dynamics in Teleost Fish Gut Ecosystems

Teleost fish possess complex and dynamic gut ecosystems in which diverse microbial communities interact with their hosts to influence nutrition, immunity and development. These assemblages are shaped by a combination of host‐intrinsic factors—such as genetics, developmental stage and trophic level—and extrinsic drivers including habitat characteristics, water microbiota and dietary inputs. Community assembly follows processes of environmental filtering within the gut ‘island’ alongside stochastic colonisation from the surrounding aquatic environment. Resulting shifts in community structure can alter the production of bioactive metabolites, including short‐chain fatty acids, modulate mucosal immunity and affect energy homeostasis. Understanding these dynamics is critical for wild‐population conservation under changing environmental conditions and for optimisation of aquaculture practices. Advances in high-throughput sequencing and multi-omic approaches have revealed functional potential within core and transient microbiota, offering opportunities to manipulate gut communities through probiotics, prebiotics and tailored feed formulations. Such interventions promise to improve disease resistance, growth performance and stress tolerance, supporting sustainable fisheries and food security on a global scale.

Research from Nature Portfolio

Recent studies have explored how microbiome diversity correlates with host phenotypic variation in teleosts with low genetic diversity, revealing that environmental factors dominate community composition while epigenetic and microbial profiles jointly contribute to traits such as vision and behaviour. Foundational work has also demonstrated that trophic level exerts a strong influence on gut community structure and metabolic enzyme activities, with carnivorous and herbivorous species harbouring distinct assemblages adapted to protein or polysaccharide digestion and producing differential short‐chain fatty acid profiles. These insights underline the role of the gut microbiome in dietary adaptation and metabolic capacity across teleost lineages.

Microbiome Dynamics in Teleost Fish Gut Ecosystems publication trend

The graph below shows the total number of articles in microbiome dynamics in teleost fish gut ecosystems across all publications each year (not limited to Nature Index journals).

Technical terms

Alpha diversity: species richness and evenness within a single microbial community.

Phylosymbiosis: parallelism between host phylogeny and microbiome composition, indicative of co-evolutionary relationships.

Short-chain fatty acids: microbial fermentation products that serve as energy substrates and signalling molecules for the host.

Environmental filtering: selective process by which host gut conditions favour certain microbial taxa over others.

References

1. Microbiome and epigenetic variation in wild fish with low genetic diversity. Nature Communications (2024).
2. The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels. Scientific Reports (2016).
3. Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome. Microbiome (2023).
4. The intestinal digesta microbiota of tropical marine fish is largely uncultured and distinct from surrounding water microbiota. npj Biofilms and Microbiomes (2024).
5. Environmental filtering decreases with fish development for the assembly of gut microbiota. Environmental Microbiology (2016).
6. Gut Microbiota and Energy Homeostasis in Fish. Frontiers in Endocrinology (2019).
7. Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries. Frontiers in Microbiology (2014).