| Criteria | H. pylori Strain 26695 | H. pylori Strain J99 | Remarks |
| Origin | Isolated from a UK patient with gastritis | Isolated from a US patient with duodenal ulcer | Different clinical outcomes and geographic origins provide distinct genetic features |
| Genome Sequencing | First complete H. pylori genome sequence (1997) | Second complete genome published (2000) | Both are reference strains; comparative genomics between the two revealed significant diversity |
| Genome Size | ~1.67 Mb | ~1.64 Mb | J99 has a slightly smaller genome |
| Cag Pathogenicity Island (cagPAI) | Present and intact | Present and intact | Both are cagA-positive and possess functional type IV secretion systems |
| CagA EPIYA Motifs | Western-type CagA with fewer EPIYA-C repeats | Also Western-type, but with differences in EPIYA motif structure | Differences in CagA domains may influence SHP2 binding and downstream signaling |
| VacA Genotype | s1/m1 genotype; active toxin | s1/m2 genotype; less vacuolating activity | 26695 VacA may be more cytotoxic in vitro |
| Type IV Secretion System | Functional | Functional | Both strains can deliver CagA into host cells |
| Natural Competence | Moderate | Competent, used in transformation studies | Both are transformable, although 26695 is often more standardized for genomic studies |
| Inflammatory Response | Triggers moderate IL-8 in gastric epithelial cells | Similar IL-8 secretion profile | Comparable pro-inflammatory capacity in vitro |
| Use in Research | Widely used for genetic, transcriptomic, and proteomic studies | Frequently used for comparative and evolutionary studies | 26695 is the archetype; J99 complements it in evolutionary and diversity studies |
| Mobile Elements/IS Elements | Contains several IS elements and plasticity zones | Fewer plasticity regions and fewer transposable elements | J99 considered more genetically stable in some contexts |
