Intermittent Fasting Keeps Farmed Fish Guts Healthy, Multi-Omics Study Finds

When fish farmers skip meals, what happens inside a fish’s intestine turns out to be far more consequential than a simple matter of hunger. A new study of the Chu’s croaker (Nibea coibor), a commercially valuable croaker raised along the coast of Zhanjiang in China’s Guangdong Province, shows that the timing and rhythm of feeding can reshape the gut’s microscopic architecture, its resident bacterial communities, and the activity of hundreds of genes — with direct consequences for how fast the fish grow. The research, published in Advanced Biotechnology, offers one of the most detailed portraits yet of how feeding schedules translate into intestinal health in a farmed marine fish.

The research team, led by scientists at the Southern Marine Science and Engineering Guangdong Laboratory in Zhanjiang, compared four feeding strategies over a 21-day trial in juvenile croakers: normal daytime feeding, intermittent fasting with two days of feeding followed by one day without food, continuous fasting, and nighttime feeding. Each group was reared under identical conditions — 30-degree water, 27 parts per thousand salinity, and a standardized commercial diet offered at 2 percent of total biomass when feeding occurred. Afterward, the researchers dissected the fish’s intestines for histological examination, sequenced the gut microbiome using 16S rRNA gene sequencing, and profiled gene expression across the intestinal transcriptome.

The morphological results were striking. Fish subjected to continuous fasting showed markedly shortened intestinal villi — the finger-like projections that expand the absorptive surface of the gut — along with a sharp loss of goblet cells, the mucus-secreting cells that form a critical chemical barrier against pathogens. In contrast, intermittently fasted fish developed the tallest villi of any group, suggesting adaptive mucosal hyperplasia that maximizes nutrient uptake when food returns. This compensatory remodeling echoes patterns seen in Nile tilapia and even in mammalian models of fasting-refeeding, and it represents an evolutionarily conserved strategy for recovering from periods of scarcity.

Beneath the tissue level, the microbial ecosystem told its own story. Continuous fasting disrupted microbial homeostasis, enriching genera with troubling reputations: Vibrio, a well-documented destroyer of intestinal epithelium and driver of inflammation; Actinomyces, linked to metabolic disorders and inflammatory responses; Photobacterium, repeatedly associated with compromised health in stressed aquatic animals; and Akkermansia. The daytime-fed control group, by comparison, maintained higher relative abundances of Firmicutes and Bacteroidota — phyla central to digestive efficiency and immune balance — while keeping Proteobacteria in check. Linear discriminant analysis effect size, or LEfSe, further revealed that intermittent fasting enriched beneficial taxa including Parabacteroides and Bilophila, while continuous fasting preferentially boosted Flavonifractor.

The transcriptomic analysis added a molecular dimension to these observations. Continuous fasting triggered a broad transcriptional reprogramming, suppressing genes central to energy metabolism — pfkfb4, a master regulator of the glycolysis-lactate axis, and pla2g12b, involved in phospholipid metabolism — while downregulating rptor, a key component of the mTORC1 signaling pathway that governs epithelial renewal, and pecam1, an immune-related gene. Meanwhile, col1a, a collagen gene tied to structural integrity, was upregulated, likely reflecting tissue stress and repair responses. Quantitative reverse-transcription PCR confirmed these expression patterns across ten key genes, lending robustness to the sequencing data.

Intermittently fasted fish, by contrast, sustained healthy expression of the genes governing energy metabolism and barrier function. Rather than undergoing wholesale transcriptional reprogramming, these animals appeared to adapt primarily through their microbiota: the intermittently fasted group showed the highest microbial diversity and the most complex co-occurrence network among gut bacteria. The authors suggest this microbial stabilization fosters mucosal protection through ecological competition — beneficial communities crowding out potential pathogens — a mechanism that is metabolically cheaper for the host than constant genetic adjustment.

To tie these threads together, the team constructed a partial least squares path model integrating intestinal morphology, gene expression, microbial composition, serum biochemistry, and growth performance. The model, which showed good overall fit, revealed a clear cascade: gut microbiota significantly influenced host gene expression, gene expression shaped intestinal phenotype, and intestinal architecture — villus height and goblet cell density above all — emerged as the strongest direct positive driver of weight gain rate. Serum glucose, cortisol, and lactate, meanwhile, exerted a significant negative effect on growth. Microbes, in other words, do not determine growth directly; they act upstream, tuning the genetic programs that build the gut, which in turn sets the pace of growth.

Nighttime feeding produced a subtler picture. Compared with daytime feeding, the nocturnal schedule elicited only minor downregulation of energy metabolism genes and modest changes in muscularis thickness, without significant morphological damage or microbial disruption. This suggests that, over the three-week window of the experiment, circadian misalignment alone imposes limited costs on this species — a finding that contrasts with studies in species whose natural rhythms align more tightly with night feeding, such as darkbarbel catfish and Dabry’s sturgeon, where nocturnal schedules improved nutrient utilization.

The practical implications for aquaculture are considerable. Feed represents one of the largest operating costs in fish farming, and intermittent feeding schedules have already been shown to cut costs while preserving health in species like longfin yellowtail and neotropical catfish, and to trigger compensatory growth in Nile tilapia and Siberian sturgeon. This study adds a mechanistic foundation to that empirical record: the two-day feeding, one-day fasting cycle sustained villus height, goblet cell density, and microbial diversity simultaneously, positioning it as a promising protocol for Nibea coibor specifically. The findings also carry a warning — prolonged fasting, whether for cost savings or pre-slaughter management, risks metabolic depression, barrier dysfunction, and blooms of potentially pathogenic bacteria that could undermine both welfare and yield.

Beyond the fish farm, the work contributes to a growing appreciation of gut microbiota as a metabolic interface between diet and host physiology. By demonstrating that microbial communities can regulate intestinal architecture through host transcription — and that this cascade ultimately governs growth — the study provides a systemic framework that could guide feeding optimization across marine aquaculture. As the authors note, the intestine sits at the crossroads of absorption and microbial ecology, and it is precisely there that the economics of feeding schedules are converted into the biology of growth. For an industry under pressure to produce more protein with fewer resources, understanding that conversion may prove one of the most valuable tools available.

Subject of Research: Effects of feeding strategies on intestinal morphology, transcriptome, and microbiota in farmed Nibea coibor

Article Title: Integrated transcriptomic and microbiota analyses reveal growth-related intestinal responses to feeding strategies in Nibea coibor

Article References: Qu, Z., Zhou, J., Li, R., Min, Q., Yi, X., Zhuang, Z., Yuan, B., Ba, X., Zhao, N., & Zhang, B. (2025). Integrated transcriptomic and microbiota analyses reveal growth-related intestinal responses to feeding strategies in Nibea coibor. Advanced Biotechnology, 3(4), Article 37. https://doi.org/10.1007/s44307-025-00088-2

Image Credits: AI Generated

DOI: 10.1007/s44307-025-00088-2

Keywords: Nibea coibor, aquaculture, feeding strategies, intermittent fasting, gut microbiota, intestinal homeostasis, transcriptomics, 16S rRNA sequencing, goblet cells, villus height, PLS-PM, fish growth