**Table 3.** Legend to Figure 3.


**Table 3.** *Cont.*



Based on the proteinogram analysis, 732 bacterial proteins were detected in the material collected from the control group (n = 18). Of these, 104 proteins had an emPAI value of 0 and were not included in the further analysis. Of the remaining 628 proteins, 52 were also present in the material from the study group. The remaining 576 proteins were present only in the material collected from the control group (their content in the material is shown in Figure 3A,C,E and Supplementary Figures S1A,C,E and S2–S5).

Based on proteomic data, the bacteria identified in both groups are presented in Tables 4 and 5.

Based on proteomic data, the bacteria identified in both groups, but significantly higher in the study group, are: *Actinopolyspora erythraea*, *Listeria costaricensis*, *E. coli*, *Methylobacterium*, *Acidobacteria bacterium*, *Bacteroidetes bacterium*, *Paenisporsarcina* sp., *Thiodiazotropha endolloripes* and *Clostridiales bacterium*. The tendency towards statistical significance also concerned *Klebsiella* sp.

**Figure 3.** Bar graphs showing the content of proteins present only in the material from the study group or control. Graph showing the content of proteins (in order of decreasing emPAI value) found only in the material from the control group: proteins 1–20 (**A**); proteins 21–40 (**C**); proteins 41–60 (**E**) or tested: proteins 1–20 (**B**); proteins 21–40 (**D**); proteins 41–60 (**F**). Expressions from Figure 3 are explained in Table 3.

In addition, bacteria that may be pathological were identified in the study group (although data insignificantly higher): *Splinomonas* sp., *Pseudoalteromonas*, *Stenoprophomonas maltophila*, *Pseudomonas cichorii*, *Enterococcus faecium*, *Deltaproteobacteria bacterium*, *Acinetobacter baumannii*, *Firmicutes bacterium*, *Microbacterium*, *Archangium gephora*, *Veillonella magna*, *Hyphomonas* sp., *Enterococcus faecium* and *Lactobacillus harbinensis*.

In turn, in the control group, statistically more often, based on proteomic data, the following were found: *Flavobacterial bacterium*, *Aureimonas* sp., *Bacillus cereus* and *Klebsiella* were on the verge of statistical significance, as well as *Pneumoniae*, *Enterococcus faecium* and *E. coli*.


**Table 4.** Proteins for which emPAI was significantly higher in the study group compared to the control group.

**Table 5.** Proteins for which emPAI was significantly higher in the control group compared to the study group.

