TABLE 1.

Overview of applications of IVET to isolate microbial genes upregulated in complex niches

Category and geneFunctionMicroorganismHost or environmentReference(s)
Auxotrophy-based selection
    purADe novo purine nucleotide biosynthesis Salmonella enterica Mouse 98, 156, 264
Pseudomonas aeruginosa Mouse 93
    purEKDe novo purine nucleotide biosynthesis Pseudomonas aeruginosa Burned tissue 92
Biofilm 67
Mouse 290
    thyADe novo thymidine nucleotide biosynthesis Salmonella enterica Mouse 156
    pyrBDe novo pyrimidine nucleotide biosynthesis Pseudomonas putida Phytophthora parasitica 140
    ura5Uracil biosynthesis Histoplasma capsulatum Mouse 226
    asdDiaminopimelate biosynthesis Pseudomonas aeruginosa Mouse 95
Pseudomonas putida Maize 63
Shigella flexneri Macrophage 244
    dapBDiaminopimelate biosynthesis Pseudomonas fluorescens Sugar beet 78, 302, 303
Pseudomonas fluorescens Bulk soil 245
Pseudomonas stutzeri Rice 224
    panBPantothenate biosynthesis Pseudomonas fluorescens Sugar beet 218
    trpEGTryptophan biosynthesis Ralstonia solanacearum Tomato 26
    galUGalactose metabolism Klebsiella pneumoniae Mouse 133
    inhAMycolic acid biosynthesis Mycobacterium tuberculosis Macrophage 56
    ribBAHRiboflavin biosynthesis Actinobacillus pleuropneumoniae Pig 76
Antibiotic resistance selection
    catChloramphenicol resistance Xanthomonas campestris Turnip 190
Burkholderia pseudomallei Macrophage 239
Shigella flexneri Macrophage 14
Escherichia coli Mouse 126, 191
Helicobacter pylori Mouse 8
Salmonella enterica Mouse 98, 157
Yersinia enterocolitica Mouse 83, 300
Streptococcus gordonii Rabbit 127, 191
Yersinia ruckeri Fish 65
    ermErythromycin resistance Lactobacillus reuteri Mouse 285
Streptococcus suis Pig 254
    tetTetracycline resistance Porphyromonas gingivalis Mouse 141, 298
    kanKanamycin resistance Pasteurella multocida Mouse 108
RIVET
    tnpRSite-specific recombinase Vibrio cholerae Rabbit/mouse 32, 137, 174, 191
Staphylococcus aureus Mouse 152
    creSite-specific recombinase Salmonella enterica Epithelial cells 5
Lactobacillus plantarum Mouse 24
    FLPSite-specific recombinase Candida albicans Mouse 262
System-specific selection
    bacAMembrane protein necessary for bacteroid differentiation Sinorhizobium meliloti Alfalfa 188
    hlyListeriolysin Listeria monocytogenes Mouse 55, 77
    metXWMethionine biosynthesis Pseudomonas syringae pv. syringaeBean 159
    hrcCComponent of TTSS Pseudomonas syringae pv. tomato Arabidopsis thaliana 16
    gfpGreen fluorescent protein Erwinia chrysanthemi Spinach 299