Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit anti-dsRed | Takara Bio | Cat # 6324960 |
| Goat anti-Rabbit546 | ThermoFisher | Cat # A11010; RRID:AB_2534077 |
| Bacterial and virus strains | ||
| Aeromonas veronii ZOR0001 | Karen Guillemin lab | BioProject Accession: PRJNA205572 |
| Aeromonas veronii ZOR0001; dTomato | Karen Guillemin lab | NA |
| Aeromonas veronii ZOR0001; dTomato, aTc-mbpG | This study | NA |
| Aeromonas veronii ZOR0001; dTomato, aTc-mbpD | This study | NA |
| Aeromonas veronii ZOR0001; dTomato, aTc-empty | This study | NA |
| Aeromonas veronii ZOR0001 MB1 | This study | NA |
| Aeromonas veronii ZOR0001 MB1; dTomato | This study | NA |
| Aeromonas veronii ZOR0001 MB1; dTomato, aTc-mucA | This study | NA |
| Aeromonas veronii ZOR0001 MB2 | This study | NA |
| Aeromonas veronii ZOR0001 MB2; dTomato | This study | NA |
| Aeromonas veronii ZOR0001 MB3 | This study | NA |
| Aeromonas veronii ZOR0001 MB3; dTomato | This study | NA |
| Aeromonas veronii ZOR0001 MB4 | This study | NA |
| Aeromonas veronii ZOR0001 MB4; dTomato | This study | NA |
| Escherichia coli S17 | Karen Guillemin lab | NA |
| E. coli SM10 pTNS2 | Karen Guillemin lab | NA |
| E. coli SM10 pTn7xTS-dTomato | Karen Guillemin lab | Addgene #117391 |
| Chemicals, peptides, and recombinant proteins | ||
| Type III porcine gastric mucin | Sigma | Cat # M1778 |
| N-acetylglucosamine (GlcNAc) | Chem-Impex | Cat #1426 |
| D-Galactose (Gal) | Sigma-Aldrich | Cat # G0625 |
| N-acetylgalactosamine. (GalNAc) | Chem-Impex | Cat # 21629 |
| Sialic Acid (SA) | Sigma-Aldrich | Cat # 1612619 |
| L-Fucose (Fuc) | Chem-Impex | Cat # 736 |
| D-Glucose (Glu) | Acros | Cat # 170080010 |
| pNP-B-D-GlcNAc | GoldBio | Cat # N-230; CAS: 3459-18-5 |
| pNP-B-D-Gal | GoldBio | Cat # N-290; CAS: 3150-24-1 |
| pNP-B-D-GalNAc | GoldBio | Cat # N-200; CAS: 14948-96-0 |
| pNP-A-L-Fuc | GoldBio | Cat # N-250; CAS: 10231-84-2 |
| Anhydrotetracycline (aTc) | Takara | Cat # 631310 |
| Yeast Nitrogen Base without Amino Acids | Research Products International | Cat # Y20040 |
| CSM-URA | Sunrise Science | Cat # 1004-100 |
| Critical commercial assays | ||
| QIAquick PCR Purification | QIAGEN | Cat # 28106 |
| QIAprep Spin Miniprep Kit | QIAGEN | Cat # 27104 |
| QIAGEN DNeasy Blood & Tissue Kit | QIAGEN | Cat # 69506 |
| RNeasy | QIAGEN | Cat # 74104 |
| Zymoprep Yeast Plasmid Miniprep II | Zymo Research | Cat # D2004 |
| Cyclic-di-GMP Assay | Lucerna Technologies | Cat # 200-100 |
| Deposited data | ||
| Raw Sequence Reads | This study | SRA Accession: PRJNA988826 |
| Experimental models: Organisms/strains | ||
| AB X Tu wild type zebrafish; Danio rerio | Univ. of Oregon Zebrafish facility | NA |
| MPX:GFP reporter zebrafish; Tg(BACmpx:GFP)i114 | Guillemin lab (Renshaw et al, 2006) | NA |
| Myd88 mutant zebrafish, myd88−/−, Danio rerio | Guillemin lab (Troll et al, 2018) | NA |
| Oligonucleotides | ||
| See supplemental Table S3 | This study | NA |
| Recombinant DNA | ||
| pYTn7xTS | This study | NA |
| pYTn7xTS-dTomato, aTc-empty | This study | NA |
| pYTn7xTS-dTomato, aTc-mbpG | This study | NA |
| pYTn7xTS-dTomato, aTc-mbpD | This study | NA |
| pYTn7xTS-dTomato, aTc-mucA | This study | NA |
| pYTn7xTS-dTomato, aTc-PDE | This study | NA |
| Software and algorithms | ||
| Prism 9 | Dotmatics | https://www.graphpad.com |
| SnapGene | Dotmatics | https://www.snapgene.com |
| breseq | Deatherage and Barrick, 2014 | https://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing |
| Fiji | ImageJ | https://imagej.net/software/fiji/downloads |
| Identification of bacterial cells and clusters in 3D light sheet fluorescence images | Parthasarathy Lab University of Oregon | https://github.com/rplab/Bacterial_Automated_Pipeline |
| Other | ||
| WGA-FITC | Vector Laboratories | Cat #FL-1021; RRID:AB_2336866 |
| Prolong Diamond antifade | ThermoFisher | Cat #P36966 |
| MS-222 (Tricaine) | Syndel | NA |