*3.3. Taxonomic Diversity of Gut Microbiota*

We observed a low taxonomic diversity of the bacteria living in the digestive tract of *Daphnia* compared to typical diversity of the bacteria living in the lake waters and bacteria from the *Daphnia* digestive tracts described in other studies, e.g., in [61,75]. The gut microbiota was mainly represented by the bacteria belonging to three phyla—Actinobacteriota, Firmicutes, and Proteobacteria—with the predominance of Proteobacteria and Firmicutes (Figure 7a,b). The presence of each of the stressors, especially the high concentration of NPs, increased the Firmicutes' participation (Figure 7a,b). This effect was also apparent with the increasing concentrations of enrofloxacin (Figure 5). Despite the clear effect of both stressors on their own—the Firmicutes share the increase—the pattern was similar in the presence of single and combined stressors, which suggest a negative interaction between their effects (Figure 7a,b). The Bray–Curtis-based NMDS analyses at the family level did not show any apparent group of similar variants (Figure 8), which suggests the different taxonomic composition within phylum Firmicutes, whose relative abundance increased after adding both stressors. However, it revealed that the variants with the combined effect of both stressors and with high concentrations of each of the stressors on its own are further away from the control than the other variants (i.e., with low concentrations of each of the stressors on its own and combined).

**Figure 7.** The relative abundances of the top three dominant bacteria phyla present in the gut of *D. magna* (**a**) from the control variant (Cont.) and from variants of a single or combined low, medium, and high density of polystyrene NPs (Nl = 103, Nm = 106, and Nh = 109 particles L<sup>−</sup>1, respectively) and low and high concentration of enrofloxacin (El = 10 and Eh = 100 ng L<sup>−</sup>1, respectively), as well as (**b**) from the control variant (Cont.) and from variants of a single or combined the mean density of polystyrene NPs (Nmean for the combined data from Nl, Nm, and Nh) and the mean concentration of enrofloxacin (Emean for the combined data from El and Eh).

**Figure 8.** The graphical results of the Bray–Curtis-based NMDS analysis of sequence data, binned by taxonomic assignment to family. The figure shows the relative distances between the gut microbiota of *D. magna* from the control (Cont.) variant, and from variants of the combination of two variables: (1) NPs in low, medium, and high concentrations (Nl, Nm, Nh, respectively) and (2) enrofloxacin in low and high concentrations (El and Eh, respectively).

No significant correlation between the taxonomic profile (at the family level) and the Eco Plate-based metabolic profile was observed (Mantel Correlation, R = 0.153, *p* = 0.2052, permutation *n* = 9999).
