Antibiotic usage, along with disease management, remains one of the key challenges in aquaculture. Functional feed additives such as brewer’s yeast may provide a means to enhance microbial resilience and health of fish and reduce reliance on antibiotics. This study evaluated the impact of three commercial brewer’s yeast additives (Leiber GmbH) on the intestinal microbiota of mirror carp before and after oxytetracycline administration.
A 10-week trial was conducted, with two phases. In Phase 1, mirror carp juvenile (2.5 g) were fed a control diet (T1) or one of six yeast-supplemented diets: CeFi® Pro at 0.1% (T2) or 0.25% (T3), Brewers’ Yeast® at 0.1% (T4), 0.25% (T5), or 2.5% (T6), and YeaFi® BT at 2.5% (T7) for 9 weeks. In Phase 2, the same diets were also supplemented with oxytetracycline (at 75 mg kg⁻¹ biomass) for 1 week. Intestinal samples were taken for various analyses, including a full-length 16S rRNA gene metabarcoding.
At the phylum level, communities were dominated by Pseudomonadota, Fusobacteriota, Bacillota, and Bacteroidota (Fig. 1). In Phase 1, no significant difference (p > 0.05) was observed in the relative abundance of each phylum among different groups. Fusobacteriota relative abundance was consistently high (30-52%) across groups, followed by Pseudomonadota (14-34%) and Bacillota (6-35%).
After the antibiotic intervention, Fusobacteriota relative abundance expanded (62-80%) across all groups, with a significant increase (p < 0.05) observed in T1 and T2 compared to pre-antibiotic levels. Bacillota abundance was significantly reduced (p < 0.05) in T2 and T4. Bacteroidota relative abundance significantly increased (p = 0.012) in T5 compared to pre-antibiotic levels. Although no significant difference (p < 0.05) was observed, the relative abundance of Pseudomonadota declined overall in each treatment across the phases, mostly in T1 (from 33.8% in Phase 1 to 9.7% post antibiotic intervention).
At the genus level, a similar trend was also observed. Cetobacterium was the dominant genus, increasing from 30-52% (Phase 1) to 38-80% (Phase 2), with a significant difference (p < 0.05) observed in T1 and T2. In contrast, Culicoidibacter relative abundance in T4 and T7 pre-antibiotics (33% and 35%) declined sharply after antibiotic intervention (8% and 10%, respectively). Aeromonas persisted at moderate levels (5-13%) across all treatments and both phases, while other opportunistic genera, such as Acinetobacter, were significantly reduced post-antibiotics.
Analysis of similarity (ANOSIM) confirmed significant shifts (p < 0.05) between pre- and post-antibiotic communities in most treatments, with the strongest effects in T2 (R = 0.60) and T4 (R = 0.46).
Overall, brewer’s yeast supplementation modulated carp intestinal microbiota in a diet-specific manner. Treatments such as T4 (0.1% Brewers’ Yeast®) and T7 (2.5% YeaFi® BT) reduced the abundance of some genera, such as Culicoidibacter, after antibiotic intervention, while others, such as T2 (0.1% CeFi® Pro), enhanced Cetobacterium dominance.