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- Erwinia herbicola
- Erwinia rhapontici
- Erwinia salicis
- Erwinia spp.
- Erysipelothrix monocytogenes
- Erysipelothrix rhusiopathiae
- Erysipelothrix spp.
- Escherichia coli
- Escherichia coli acr
- Escherichia spp.
- Eubacterium
- Eubacterium aerofaciens
- Eubacterium alactolyticum
- Eubacterium brachy
- Eubacterium combesii
- Eubacterium contortum
- Eubacterium lentum
- Eubacterium limosum
- Eubacterium moniliforme
- Eubacterium nodatum
- Eubacterium saburreum
- Eubacterium spp.
- Eubacterium sulci
- Eubacterium tenue
- Eubacterium timidum
- Eubacterium yurii
- Eubacterium lentum
- Eupenicillium ochrosalmoneum
- Exiguobacterium acetylicum
- Exophiala dermatitidis
- Exophiala jeanselmei
- Exophiala spinifera
- Exophiala werneckii
- Exserohilum turcicum