Advanced knowledge about the importance of gut microbiota for human health has increased the interest towards using new bacteria — besides the traditionally used lactobacilli and bifidobacteria — as probiotics. Currently candidates for next generation probiotics (NGP) have been searched amongst the gut bacteria that are associated with health, including strains from the genera Bacteroides, Clostridium, Faecalibacterium and Akkermansia. Unlike Lactobacillus spp. and Bifidobacterium spp., NGP, especially Bacteroides spp. and Clostridium spp., seem to be more ambivalent regarding their potential to cause infectious diseases. Therefore thorough safety assessment of NGP strains is vital. One important aspect of the safety assessment, which is sometimes ignored, is the potential to carry and spread antibiotic resistance genes. Because of the technological challenges in the production and formulation of many NGP species, it is likely that these will mainly be sold as supplements. The suitability and safety of novel probiotics to target consumer groups and conditions need to be carefully selected to ensure that the health promoting effects can be obtained.