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Additional file 10: Table S1. demographic information of the included patients. Table S2. overview of the used QuantiTect primers. Table S3. 90% confidence interval of the relative mucin mRNA expression levels of functional dyspepsia patients. Table S4. number of interactions within the bacterial communities of samples with different mucin phenotypes. Table S5. Analysis of interactions in bacterial communities associated with different mucin phenotypes. Table S6. Analysis of interactions in bacterial communities associated with different expression level of MUC13. Table S7. Differentially abundant metagenomic pathways.

Additional file 4. Unique protein-encoding genes in the highly virulent trout isolate genome. 374 genes were identified in the genome of the highly virulent F. columnare JIP P11/91 isolate while being absent in that of the non-virulent F. columnare ATCC 49512. Of these 374 genes, the 263 hypothetical genes were left out in the representation above. Genes marked in bold are also predicted to be involved in virulence when identifying them via Virulence Factor Database. *Gene locations are formatted as NODEn:s-e where n is a unique scaffold number, s and e are the gene’s start and end position respectively.

Additional file 2. Protein-encoding genes present only in the virulent F. columnare genomes. The latter 42 genes are only present in genomes of the highly virulent carp (04017018) and trout (JIPP11/91) and low virulent carp (CDI-A) F. columnare isolates that could cause tissue damage and mortality. These genes are not present in the genome of the non-virulent F. columnare trout isolate ATCC49512. Hypothetical genes (114) were not included here. Genes marked in bold are also predicted to be involved in virulence when identifying them via Virulence Factor Database.

Additional file 7. Characteristics of prophage regions in the four Flavobacterium columnare isolates. The prophage regions were identified in the genome of the reference isolate (ATCC49512) and the three newly assembled F. columnare isolates 04017018, CDI-A and JIP P11/91 via PHASTER. Prophage regions with scores less than 70 are incomplete.

Additional file 7. Characteristics of prophage regions in the four Flavobacterium columnare isolates. The prophage regions were identified in the genome of the reference isolate (ATCC49512) and the three newly assembled F. columnare isolates 04017018, CDI-A and JIP P11/91 via PHASTER. Prophage regions with scores less than 70 are incomplete.

Additional file 3. Unique protein-encoding genes in the highly virulent carp isolate genome. 80 genes were identified to be present in the genome of the highly virulent carp isolate 04017018 while absent in that of the low virulent carp isolate CDI-A. Of these 80 genes, the 62 hypothetical genes were left out in the representation above. Genes marked in bold are also predicted to be involved in virulence when identifying them via Virulence Factor Database. *Gene locations are formatted as NODEn:s-e where n is a unique scaffold number, s and e are the gene’s start and end position respectively.

Additional file 6. Unique single nucleotide variants (SNVs) present in gyrA of isolate CDI-A. The impact of the SNP (single nucleotide polymorphism) on protein activity/stability was predicted by comparison of amino acid characteristics, by using PredictSNP and I-Mutant Suite 3.0 tools, and by investigating which amino acids were present in the reference strain of F. columnare and of HV carp isolate 04017018, both of the latter not displaying acquired resistance towards fluoroquinolones, using BLAST and ConSurf.

Additional file 4. Unique protein-encoding genes in the highly virulent trout isolate genome. 374 genes were identified in the genome of the highly virulent F. columnare JIP P11/91 isolate while being absent in that of the non-virulent F. columnare ATCC 49512. Of these 374 genes, the 263 hypothetical genes were left out in the representation above. Genes marked in bold are also predicted to be involved in virulence when identifying them via Virulence Factor Database. *Gene locations are formatted as NODEn:s-e where n is a unique scaffold number, s and e are the gene’s start and end position respectively.

Additional file 5. Single nucleotide variants (SNVs) in gyrase genes of Flavobacterium columnare isolates. This table shows the SNVs present in the gyrase genes of F. columnare isolates CDI-A and 04017018 when compared to gyrase genes of the reference genome ATCC 49512. However, as only isolate CDI-A displayed phenotypic antimicrobial resistance towards both first- and second-generation quinolones, the unique SNVs in the gyrase genes of the latter isolate are highlighted in grey background. No SNVs were encountered in DNA gyrase subunit B (EC 5.99.1.3). Average read quality score of the bases supporting a variant was higher than 35 (which is considered very good quality).

Additional file 13. Classification of down-regulated H. suis genes in cases compared to controls according to their function.

Additional file 6. Plots of the principal component analysis (PCA) of the restricted set of differentially expressed features. First 2 components (PC1 and PC2) of a PCA, with percentages of variance associated with each axis. These plots show the separation between samples based on the main sources of variation found in the rlog-transformed data sets (padj ≤ 0.01, fold change ≥ 2). (A) PCA-plot for H. suis (134 differentially expressed features) (B) PCA-plot for H. heilmannii (143 differentially expressed features). Blue dots indicate control samples (i.e. unbound Helicobacter); red dots indicate cases (i.e. Helicobacter bound to MKN7 cells). In both PCA plots, the sample groups (i.e. case and control) are well separated, indicating that the main variability within each experiment came from biological differences between cases and controls.

Additional file 7. H. suis up-regulated genes with (72) and without (11) H. heilmannii homologs according to BLASTp.

Additional file 11. Classification of up-regulated H. suis genes in cases compared to controls according to their function.

Additional file 9. H. heilmannii up-regulated genes with (47) and without (13) H. suis homologs according to BLASTp.

Additional file 10. H. heilmannii down-regulated genes with (74) and without (9) H. suis homologs according to BLASTp.

Additional file 4. List of 83 significantly down-regulated H. heilmannii genes in cases compared to controls (with p adj ≤ 0.01; fold change ≤ -2).

Additional file 12. Classification of up-regulated H. heilmannii genes in cases compared to controls according to their function.

Additional file 5. Volcano plots of the comparisons (case versus control). Red dots represent significantly differentially expressed genes (padj ≤ 0.01, fold change ≥ 2) in MKN7-bound helicobacters (i.e. cases) compared to unbound helicobacters (i.e. controls). (A) Volcano plot of the comparison (case versus control) for H. suis. (B) Volcano plot of the comparison (case versus control) for H. heilmannii.

Additional file 1. List of 83 significantly up-regulated H. suis genes in cases compared to controls (with p adj ≤ 0.01; fold change ≥ 2).

Additional file 2. List of 51 significantly down-regulated H. suis genes in cases compared to controls (with p adj ≤ 0.01; fold change ≤ -2).

Additional file 8. H. suis down-regulated genes with (45) and without (6) H. heilmannii homologs according to BLASTp.

Additional file 14. Classification of down-regulated H. heilmannii genes in cases compared to controls according to their function.

Additional file 3. List of 60 significantly up-regulated H. heilmannii genes in cases compared to controls (with p adj ≤ 0.01; fold change ≥ 2).

Validation parameters for quantification of chlortetracycline (CTC), doxycycline (DOX), sulfadiazine (SDZ) and trimethoprim (TRIM) in pig feed and feces. (DOCX 15 kb)