B. pumilus isolates have been used as probiotic or for other animal and human biotechnological or pharmaceutical applications by their ability to produce compounds with distinct biological activities, such as biosurfactant and antimicrobials (Handtke et al., 2014). Recently, phylogenetic affiliations supported on different genetic biomarkers analysis, underlined the reassignment of most B. pumilus as Bacillus safensis or Bacillus invictae (Branquinho et al., 2014). Additionally, some reports also associate B. pumilus group members with food poisoning (From et al., 2007). Currently, the absence of a resistance profile to antibiotics of human and veterinary importance and also of toxin encoding genes are pre-requisites specified by EFSA when their use is intended in the food sector.