Exploring how dietary filamentous fungi and feeding duration modulate gut microbial composition in rainbow trout
Imagine if the secret to sustainable fish farming wasn't in the water, but in the trillions of microorganisms living inside the fish themselves. This isn't science fiction—it's the cutting edge of aquaculture research, where scientists are discovering how alternative feed ingredients can transform fish health from the inside out.
At the forefront of this research is a remarkable story about rainbow trout (Oncorhynchus mykiss), one of the world's most popular farmed fish species. With aquaculture being the fastest-growing animal food sector globally, scientists face increasing pressure to find sustainable alternatives to traditional fishmeal. What they're discovering is that the microscopic world within the fish gut—the microbiome—holds the key to unlocking more efficient, sustainable farming practices. Recent breakthroughs reveal that something as unusual as filamentous fungi can dramatically reshape this hidden microbial ecosystem, with profound implications for fish health, growth, and the future of sustainable seafood 1 2 .
Aquaculture is expanding rapidly to meet global protein demands
Research focuses on replacing traditional fishmeal with innovative ingredients
The fish gut microbiome represents an entire ecosystem teeming with bacteria, fungi, and other microorganisms living in the gastrointestinal tract. Think of it as an extra organ that plays crucial roles in digestion, immunity, and overall health. These microbial communities help break down food, produce essential vitamins, protect against pathogens, and even influence the host's stress response .
In healthy fish, certain bacterial phyla typically dominate this internal landscape. Firmicutes, Proteobacteria, Bacteroidetes, and Fusobacteria represent the major players across most fish species, though their proportions vary depending on species, environment, and diet 3 8 . When this microbial community falls out of balance—a state known as dysbiosis—fish become more susceptible to disease and may experience reduced growth and poor feed conversion 2 .
What makes the gut microbiome particularly fascinating is its plasticity—its ability to change in response to various factors, with diet being among the most powerful influencers 4 . Just as human gut bacteria respond to different dietary patterns, fish gut microbiomes undergo significant shifts when their feed changes.
This relationship has become increasingly important as aquaculture seeks alternatives to traditional fishmeal. Fishmeal production faces sustainability challenges, driving research into novel protein sources like plant proteins, insect meals, and microbial proteins 6 . Each of these alternatives interacts differently with the fish gut microbiome, potentially unlocking benefits or creating challenges for fish health.
Filamentous fungi are thread-like fungi that grow in branching networks called hyphae. While some species cause food spoilage, others have been safely used in food production for centuries. The species used in the featured study—Neurospora intermedia—is actually a food-grade fungus isolated from traditional fermented foods in Indonesia 1 .
The potential of filamentous fungi extends beyond basic nutrition—they may actively shape the gut environment in beneficial ways. The fungal cell wall contains chitin and chitosan, polysaccharides with known immunomodulatory and antimicrobial properties 9 . These compounds may selectively encourage the growth of beneficial bacteria while suppressing potential pathogens.
Additionally, fungi may serve as prebiotics—substances that induce the growth or activity of beneficial microorganisms. The concept is simple: by feeding the fish, we're also feeding their microbial inhabitants, and some feed ingredients provide better "meals" for these gut bacteria than others.
To understand exactly how filamentous fungi affect the rainbow trout gut microbiome, researchers at the Swedish University of Agricultural Sciences conducted a meticulously designed 30-day feeding trial 1 . Their study aimed to answer two fundamental questions: How does dietary inclusion of filamentous fungi affect gut microbial composition? And how long do these changes take to manifest?
The researchers investigated not just whether fungi inclusion mattered, but whether how the fungi were processed (preconditioned with heat treatment versus non-preconditioned) made a difference to their effects on the gut microbiome.
The experimental design followed these key steps:
300 rainbow trout (average weight 127.8 ± 19.8 g) were distributed across 15 tanks in a controlled aquatic facility with consistent temperature (11°C) and oxygen levels 1 .
Neurospora intermedia biomass was cultivated in a bubble column bioreactor using glucose and yeast extract as primary nutrients, then harvested, washed, and dried at 70°C 1 .
Three experimental diets were formulated: Reference Diet (traditional fishmeal), Non-Preconditioned Diet (30% fungal biomass), and Preconditioned Diet (heat-treated fungal biomass) 1 .
Fish were fed twice daily for 30 days, with gut microbiota samples collected on days 0, 10, 20, and 30 for analysis 1 .
Using high-throughput DNA sequencing techniques, the researchers identified and quantified bacterial species present in the gut samples 1 .
| Diet Component | Reference Diet (RD) | Non-Preconditioned Diet (NPD) | Preconditioned Diet (PD) |
|---|---|---|---|
| Major protein source | Fishmeal | 70% RD + 30% fungi | 70% RD + 30% fungi |
| Processing | Standard pelleting | Mixed and pelleted | Heat-treated at 105°C for 5 min |
| Fungal inclusion | None | 30% N. intermedia | 30% N. intermedia |
Perhaps the most striking discovery was the temporal pattern of microbial changes. On day 0, all fish had similar gut communities, but by days 10 and 20, significant differences emerged between dietary groups. Surprisingly, by day 30, the gut communities had converged again, becoming similar regardless of diet 1 .
This suggests that gut microbiomes undergo an adjustment period after dietary changes before eventually stabilizing. The implication for research is profound: short-term feeding trials (less than 30 days) might capture temporary transition states rather than stable microbial profiles 1 .
While the overall microbial composition became similar by day 30, the journey there differed markedly between diets. The fungal-based diets led to distinct microbial patterns during the intermediate time points compared to the traditional fishmeal diet 1 .
Contrary to expectations, the preconditioning (heat treatment) of the fungal diet made surprisingly little difference to gut microbiome composition 1 . This suggests that the fungal biomass itself, rather than its processing method, drives most of the microbial changes observed.
| Bacterial Group | Day 0-10 Pattern | Day 20 Pattern | Day 30 Pattern |
|---|---|---|---|
| Peptostreptococcus | Higher abundance | Variable | Lower abundance |
| Streptococcus | Higher abundance | Variable | Lower abundance |
| Lactococcus lactis | Lower abundance | Increasing | Higher abundance |
| Overall diversity | Similar across diets | Significant differences | Similar across diets |
Understanding fish gut microbiomes requires specialized reagents and equipment. Here are key tools researchers use to unravel these complex microbial ecosystems:
Essential for obtaining high-quality DNA from gut samples for sequencing 5 .
Qiagen PowerSoil NucleoSpinTarget specific regions of bacterial DNA, allowing identification of different microbial species 5 .
515F/806REnable comprehensive profiling of complex microbial communities 3 .
Illumina MiSeq HiSeqUsed to cultivate filamentous fungal biomass under controlled conditions 1 .
Ensure consistent, timed feeding during experiments, reducing human error 1 .
The discovery that fungal-based diets modulate rainbow trout gut microbiomes—and that these changes follow a specific temporal pattern—has substantial implications for aquaculture and microbiome research.
From a practical perspective, this research supports the feasibility of using fungal biomass as a sustainable alternative to traditional fishmeal. The ability of fungi to influence gut communities without causing dysbiosis suggests they may be a safe and beneficial feed ingredient 1 9 .
The temporal findings offer important methodological guidance: feeding trials should extend for at least 30 days to allow gut microbiomes to stabilize before drawing conclusions about dietary effects 1 . This could explain inconsistencies in earlier studies that used shorter trial periods.
Looking ahead, researchers are now asking more nuanced questions: Do these microbial changes translate to measurable health benefits for fish? Can specific fungal strains be selected to promote particularly beneficial bacteria?
What's clear is that understanding the complex relationship between diet, gut microbes, and host health will be crucial for developing more sustainable, efficient aquaculture practices worldwide. As we face the challenge of feeding a growing global population, harnessing the power of these invisible microbial communities may be key to unlocking more sustainable fish farming methods.
The next time you enjoy a piece of farmed rainbow trout, remember that there's more to its story than what meets the eye—deep within its digestive tract, trillions of microorganisms have been working in harmony with their host, their composition and function potentially shaped by innovative feeding approaches that represent the future of sustainable aquaculture.