Editorial: Innovative Approaches to Modulate Fish Gut Microbiota for Disease Management in Aquaculture

Yuniel Méndez-Martínez¹ANGEL ISIDRO CAMPA^2*Antonio Luna-González^3*

• ¹Universidad Tecnica Estatal de Quevedo, Quevedo, Ecuador
• ²Centro de Investigación Biológica del Noroeste (CIBNOR), La Paz, Mexico
• ³Instituto Politecnico Nacional Centro Interdisciplinario de Investigacion para el Desarrollo Integral Regional Sinaloa, Guasave, Mexico

Over the past decade, targeted modulation of the gut microbiome has moved from a theoretical promise to a pragmatic strategy for improving animal health and performance while reducing antibiotic use in aquaculture. Against this backdrop, this Research Topic brings together six contributions that, from complementary perspectives, address nutrition, phytobiotics, environmental microbial ecology, abiotic stress and emerging pathogens, with the aim of advancing management grounded in the microbial ecosystems of the host and its environment. Indeed, multiple reviews indicate that probiotics, prebiotics and synbiotics are plausible alternatives for reducing antibiotic pressure and preventing bacterial infections in fish and crustaceans (Hoseinifar et al., 2018). Below, we synthesise these contributions, highlighting key findings, limitations and research priorities.It is worth emphasising that diet remodels the intestinal ecosystem, yet the host also exhibits resilience.In this regard, in a 60 day bioassay in Sparus aurata, Ruiz et al. documented that an abrupt change from a commercial feed to a wild shrimp-based diet initially increased diversity (Shannon) and altered bacterial community structure; however, by 40-60 days, communities converged and a stable core 34 was maintained, with implications for substituting marine ingredients with 35 sustainable alternatives without compromising intestinal homeostasis evidence of adaptation and 36 resilience. Thus, fish appear to possess ecological buffering mechanisms that favour post-shift 37 stabilisation, opening the way for eco-efficient diets, a transition period is respected and 38 functional effects are validated via metabolomic and immunomodulatory assessments. 39An additional study in a herbivorous carp provides an integrated view of fishmeal inclusion levels, gut 40 microbiota and product quality. In a trial with 0, 3 and 6% inclusion, Wang et al. found significant 41 improvements in growth and intestinal morphology at 3-6%, alongside distinct shifts in the intestinal 42 community (NMDS separation; indicator taxa) and changes in muscle volatile compounds; notably, 43 6% was associated with denser fibres and a superior aroma profile, whereas 3% optimised the growth-44 intestine balance. Taken together, these results support balanced formulations that simultaneously 45 weigh performance, intestinal health and fillet attributes. However, it remains to be clarified whether 46 the modulated taxa play probiotic or risk roles and how they connect to digestive efficiency and 47 immune robustness. This line of evidence aligns with syntheses describing diet and macronutrients as 48 primary modulators of the structure and function of the fish gut microbiome (Zhang et al., 2025). 49In parallel, phytobiotics are emerging as a low-impact alternative to reinforce the three pillars: growth, 50 immunity and microbial resilience. In Labeo rohita, Yadav et al. evaluated a Prosopis cineraria 51 (khejri) seed extract over 60 days followed by a challenge with Aeromonas hydrophila. 52 Supplementation (optimum 5 g kg⁻¹) improved growth, activated digestive and antioxidant enzymes, 53 increased serum proteins and reduced post-challenge mortality, evidencing an immunostimulatory 54 effect with potential to lessen antibiotic pressure in intensive systems. As a next step, it would be 55 valuable to map direct changes in the intestinal microbiota associated with the extract (e.g., increases 56 in lactic-acid bacteria or butyrate producers) and to verify reproducibility at commercial scale. The 57 biological plausibility of these effects is supported by reviews detailing the mechanisms of action of 58 probiotics and phytogenic additives contribute competition for adhesion sites, competitive exclusion, 59bacteriocin production and modulation of immune responses in disease prevention (Hoseinifar et al., 60 2018). 61It has been documented that fish microbial health is not explained solely by the intestinal lumen. 62Evidence suggests that modulating the environmental microbiome is equally decisive. In Litopenaeus 63 vannamei ponds, Huang et al. showed that adding oyster shells as substrates promotes nitrifying 3 biofilms (dominated by Nitrospira), accelerates the conversion of nitrite to nitrate, and improves 65 growth and survival ecological, low-cost bioengineering intervention that reduces nitrogenous 66 toxins and displaces potential opportunists in the water column. Accordingly, integrating "natural 67 bioreactors" within the production unit can reinforce the effects of functional diets, co-creating healthy 68 microbial landscapes in the fish and their surroundings. 69It is also important to emphasise that host physiology under abiotic stress conditions the stability of the 70 microbiome and the health risk. In Apostichopus japonicus, Cui et al. evaluated six common stressors 71 (thermal, hyposalinity, ammonia, nitrite, crowding, fasting) and observed performance declines and 72 consistent dysbiosis: decreases in the Bacteroidota:Proteobacteria and Firmicutes:Proteobacteria 73 ratios; enrichment of Vibrionaceae or Shewanellaceae depending on the stressor; and destabilisation 74 of microbial ecological networks. Notably, Verrucomicrobia emerged as a cross-cutting stress 75 biomarker. Although the model is an echinoderm, the mechanistic logic of stress, dysbiosis, and 76 susceptibility is transferable to fish and suggests the value of microbiome-based early-warning systems 77 to trigger corrective actions (stocking density, water quality, prebiotics/probiotics) before clinical 78 collapse. At the innovation frontier, it has further been proposed to move towards synthetic microbiotas 79 and the genetic engineering of commensal microbes as routes to precision therapies and pathogen 80 control, always within robust biosafety and regulatory frameworks (Martínez-Porchas et al., 2025). 81Finally, to understand the microbial adversary with genomic resolution, it is necessary to complement 82 modulation tactics. In Siniperca chuatsi, Chen et al. isolated a highly virulent strain of Nocardia 83 seriolae (LD50 = 3.89 × 10⁴ CFU.mL -1 ), describing multiorgan granulomatous lesions and an 8.12-Mb 84 genome harbouring 403 virulence genes and multiple resistance determinants; the susceptibility profile 85 included enrofloxacin, doxycycline and florfenicol, among others. Beyond the specific case, these data 86 lay the groundwork for molecular surveillance, early diagnosis, and the design of strategies that explore 87 whether probiotic consortia or environmental manipulations can compete with or inhibit opportunistic 88 pathogens. 89 Taken together, the six studies in this collection converge on a clear message: a shift from reactive 90 health management to ecosystem-based prevention, in which diet, additives, environment, stress 91 management and genomic surveillance are articulated to favour functional, robust microbiotas. 92 Immediate priorities include: (a) standardising designs and metrics (including omics) for comparability 93 across species and environments; (b) validating, at farm scale, the cost-benefit of phytobiotics, 94 probiotics and pro-biofilm substrates; (c) exploring fish the environment synergies (e.g., diets plus