Seaweed in Fish Feed Rewires the Gut Microbiome to Boost Amino Acid Metabolism

A seaweed supplement added to the feed of one of the world’s most farmed fish appears to work its magic not directly on the animal, but through the trillions of microbes living in its gut. In a study published in Advanced Biotechnology, researchers report that supplementing the diet of grass carp (Ctenopharyngodon idella) with macroalgae—particularly the brown seaweed Sargassum hemiphyllum—selectively enriches a gut bacterium called Shewanella, which in turn ramps up the fish’s amino acid metabolism and supports faster growth. The finding, drawn from an unusually complete integration of gene sequencing, genome reconstruction, and metabolite profiling, offers one of the clearest pictures yet of how a dietary intervention in aquaculture is translated into physiological benefit by the gut microbiome.

Grass carp were an obvious choice for the investigation. As the most heavily farmed freshwater fish globally by production volume, the species carries enormous economic weight, and its herbivorous feeding habit made the team suspect it would be well suited to exploiting macroalgae as a feed ingredient. The researchers, led by Xingxing An and Qingyun Yan of Sun Yat-sen University’s Southern Marine Science and Engineering Guangdong Laboratory in Zhuhai, together with collaborators from industry and Hunan Agricultural University, designed a controlled feeding trial to test whether three chemically distinct seaweeds would produce different microbial and metabolic outcomes.

The experimental design was straightforward but rigorous. Young grass carp weighing roughly 91 grams were randomly assigned to one of four iso-nitrogenous and iso-lipidic diets: a control feed, or feeds supplemented with 5 percent powder of Sargassum hemiphyllum, Asparagopsis taxiformis, or Gracilaria lemaneiformis. The fish were reared for 52 days in a recirculating aquaculture system at 25 to 28 degrees Celsius, fed to apparent satiation twice daily, with no mortality recorded across the entire experiment. At the end of the trial, the team measured growth indices, collected serum and liver samples for immune and antioxidant assays, and aseptically sampled intestinal contents and feces for microbiome and metabolome analysis.

The physiological results immediately singled out one seaweed. Fish receiving the Sargassum diet showed significantly greater body weight, viscerosomatic index, and hepatosomatic index than controls, along with a marked boost in hepatic superoxide dismutase activity, a key antioxidant enzyme. The Asparagopsis group gained significantly in body length and viscerosomatic index, while the Gracilaria group produced more modest changes. Taken together, Sargassum hemiphyllum delivered the most comprehensive benefits for growth and antioxidant defense, hinting that its characteristic sulfated polysaccharides—compounds previously associated with immunomodulatory and anti-inflammatory activity—might be driving a distinctive microbial response.

Sequencing of the 16S rRNA gene from intestinal samples revealed a dramatic restructuring of the gut community. In control fish, the phylum Spirochaetota dominated at nearly 38 percent of the community, with the genus Brevinema as the standout member. In all three macroalgae groups, Spirochaetota collapsed to less than 0.03 percent, while Pseudomonadota surged—reaching over 61 percent in the Asparagopsis group. To pinpoint which genera truly distinguished the dietary groups, the researchers applied a Random Forest machine-learning classifier combined with differential abundance testing. One genus rose above all others: Shewanella, whose relative abundance increased significantly in the Sargassum group compared with controls. Other notable players included Vibrio, Bacteroides, and Butyricicoccus, the latter significantly enriched in the Gracilaria group.

To understand what these shifts meant functionally, the team turned to shotgun metagenomics, generating more than 392 gigabases of sequence data from fecal samples. From this they reconstructed 150 high-quality metagenome-assembled genomes, or MAGs—essentially draft genomes of the community’s constituent organisms. Functional annotation showed that Pseudomonadota carried the most comprehensive amino acid metabolic network, including a serine and threonine degradation pathway absent from other taxa. Crucially, one Shewanella MAG, designated C3_bin52, harbored 2,488 KEGG orthologs, with more than 10 percent of them tied to amino acid metabolism, including complete biosynthetic pathways for essential and branched-chain amino acids. Genes for branched-chain amino acid transferase (ilvE) and tryptophan synthesis (trpA, trpB) were identified within its repertoire.

The metabolomics data provided the physiological confirmation. Using ultra-high-performance liquid chromatography coupled to high-resolution mass spectrometry, the researchers profiled 947 metabolites in fecal samples and found clear separation between dietary groups. The Sargassum group stood out with 21 up-regulated metabolites, dominated by essential amino acids such as L-valine and L-threonine, the branched-chain amino acid leucine, and derivatives including 5-hydroxy-L-tryptophan and trans-cinnamic acid—a compound with documented antimicrobial activity against fish pathogens. Pathway enrichment confirmed that the Sargassum diet preferentially activated protein digestion and absorption and amino acid biosynthesis, whereas Asparagopsis skewed toward tyrosine and thyroid hormone pathways and Gracilaria toward nucleotide metabolism.

The statistical integration of all three data layers converged on Shewanella as the central hub. Spearman correlation analysis identified 78 significant microbiome-metabolite associations, and Shewanella displayed the highest connectivity, correlating positively with 22 metabolites, including L-valine and the aromatic amino acid derivative 2-hydroxycinnamic acid. A partial least squares path model, with a goodness-of-fit of 0.554, showed that Shewanella abundance was positively and significantly associated with amino acid metabolism (coefficient 0.655), which in turn correlated positively with growth performance (coefficient 0.596). In other words, the data support a causal-style chain: seaweed polysaccharides and free amino acids feed a microbial niche, Shewanella fills it, and its metabolic output enriches the host’s amino acid pool.

The biological plausibility of this axis is reinforced by what is already known about the genus. Shewanella species are metabolically versatile aquatic bacteria capable of dual pyruvate and lactate fermentation, degradation of complex polysaccharides such as alginate via thermostable lyases, and even biosynthesis of health-promoting omega-3 polyunsaturated fatty acids. Probiotic strains of Shewanella putrefaciens have previously been shown to improve growth and disease resistance in farmed fish. In fish-derived strains, roughly 8 percent of coding sequences are devoted to amino acid transport and metabolism—an extraordinary genomic commitment that aligns neatly with the metabolite patterns observed in the carp.

Beyond its mechanistic interest, the study carries practical weight for a rapidly growing industry under pressure to find sustainable alternatives to fishmeal and other conventional feed ingredients. Macroalgae cultivation requires no freshwater, arable land, or fertilizer, making seaweed-supplemented feeds an attractive sustainability proposition. The finding that different seaweeds steer the gut microbiome toward different functional outcomes—Sargassum toward amino acid metabolism and growth, Asparagopsis toward tyrosine pathways and suppression of the opportunistic pathogen Acinetobacter, Gracilaria toward butyrate-producing taxa and nucleotide metabolism—suggests that feed formulators could in principle select macroalgal species to elicit targeted microbial and metabolic effects. The authors caution that the specific functional roles of individual Shewanella species still require direct experimental validation, for example through isolation and gnotobiotic challenge studies. Even so, the work establishes a compelling diet-microbiome-metabolite framework for herbivorous aquaculture species and positions a once-obscure marine bacterium as a potential keystone of fish nutrition—one that farmers may one day cultivate deliberately, simply by choosing the right seaweed.

Subject of Research: Macroalgae supplementation modulates the gut microbiome and amino acid metabolism in grass carp

Article Title: Dietary macroalgae enhances amino acid metabolism via intestinal Shewanella in grass carp (Ctenopharyngodon idella)

Article References: An, X., Niu, S., Al, M. A., Su, E., Chen, L., He, H., Wang, Y., Zhang, S., Yang, Y., Wang, S., Wen, Z., Xu, B., Ming, Y., Zhu, W., Zhao, Z., Wu, K., Yang, Y., Xie, W., He, Z., & Yan, Q. (2025). Dietary macroalgae enhances amino acid metabolism via intestinal Shewanella in grass carp (Ctenopharyngodon idella). Advanced Biotechnology, 3(4), Article 36. https://doi.org/10.1007/s44307-025-00090-8

Image Credits: AI Generated

DOI: 10.1007/s44307-025-00090-8

Keywords: grass carp, macroalgae, gut microbiome, Shewanella, amino acid metabolism, aquaculture, metagenomics, metabolomics, Sargassum hemiphyllum, feed additives, metagenome-assembled genomes, fish nutrition