Taxa showing a statistically significant difference by ANOVA (*p* < 0.05). Please see Supplementary Table S3 for standard errors of the means. Different superscripts in the same row indicate that groups are significantly different by the Tukey's range test for multiple pairwise comparisons.

**Figure 2.** Comparison of intestinal bacterial communities in hybrid striped bass for five dietary treatments (BP-F1, BP-E, BP-W, BP, and CON). Principal Coordinate Analysis (PCoA) was performed based on the Bray–Curtis distance matrix. The x and y axes correspond to Principal Components 1 (PCo1) and 2 (PCo2), respectively, which together explained 67.82% of the variance. The PERMANOVA test supported the separation of samples into different groups (*p* = 0.001), but differences between groups could not be resolved by pairwise comparisons (*p* > 0.05).

#### *3.4. OTU Composition Analysis*

Of the 1132 OTUs that were identified across all samples, the most abundant OTUs, defined as representing at least 1.0% of sequences in at least one set of samples, were further analyzed (Figure 3; Table 6). Eleven of these OTUs, one assigned to Proteobacteria and ten affiliated to Firmicutes, were found to vary across dietary treatments (*p* ≤ 0.05), and they exhibited composition patterns that were consistent with their respective taxonomic groups. For instance, SD\_McMs-00002 was the most highly represented OTU of the family *Enterobacteriaceae*, representing 79.0–95.8% of sequence reads from this taxonomic group across all samples, and it accordingly was most abundant in diets BP-F1 and BP-E. Five of the OTUs of interest were assigned to *Peptostreptococcaceae* (SD\_McMs-00001, SD\_McMs-00011, SD\_McMs-00012, SD\_McMs-00014, and SD\_McMs-00015), and their highest representation was in samples from diets BP and CON. SD\_McMs-00001 was the most abundant OTU from this group, representing 2.86–4.42-times the combined read abundances from the other four *Peptostreptococcaceae* OTUs in each sample. Of the remaining Firmicutes OTUs that varied across dietary treatments, three were assigned to *Streptococcaceae* (SD\_McMs-00007, SD\_McMs-00010, and SD\_McMs-00016). SD\_McMs-00007 and SD\_McMs-00016 were most closely related to *Lactococcus lactis*, and they were at their highest representation in diets BP-E and BP-W, while SD\_McMs-00010 was most closely related to *Streptococcus dysgalactiae,* and it was most abundant in diets BP and CON. LEfse analysis was also used to identify biomarkers for the dietary treatments tested in the study; these consisted of 55 OTUs for CON, 38 OTUs for BPP, 17 OTUs for BP-E, four OTUs for BP-F1, and two OTUs for BP-W (Supplementary Figure S1). The eleven abundant

OTUs identified as significantly different by Kruskal–Wallis (Table 6) were identified as biomarkers by LEfse.

**Figure 3.** Histogram showing the relative abundance of the most highly represented intestinal OTUs in hybrid striped bass for five dietary treatments. OTUs showing 97% sequence identity or greater to their closest relative are represented by the full species name, while OTUs showing less than 97% identity to their closest relative are represented by their assigned genus.


**Table 6.** Mean relative abundance of the main bacterial OTUs identified in hybrid striped bass. Abundance is presented as a percentage (%) of the total number of analyzed reads per sample.
