Staphylococcus aureus biofilm is a major contamination concern in the food processing environment. S. aureus constructs complex biofilms with environmental species, but its inter-species interactions are not well. In this study, 16S rRNA metagenomic analysis was used to identify interactors for S. aureus biofilm formation. Fifty-six microbiota samples extracted from retail foods were employed to construct biofilms with S. aureus ATCC12600 on stainless steel. Then, the composition of the microbiota was analyzed by 16S rRNA metagenomic analysis and compared with the number of S. aureus cells in the biofilm. As a result, 22 genera, especially Serratia sp. and Enterobacter sp., were suggested to be remarkably effective inhibitors of S. aureus biofilm formation. Furthermore, Serratia sp. 19-SA-0058-001 was isolated, and its inhibitory effect was confirmed. The present study demonstrated efficient strategy to identify an interactor from complex microflora.

Bifidobacterium globosum is expected to be applied to foods as a probiotic, and a method to rapidly distinguish it from the related Bifidobacterium pseudolongum is necessary for product development and quality control. In this study, we evaluated existing methods of bacterial species classification for B. globosum/pseudolongum with the published whole-genomes. The results showed that the Polymerase Chain Reaction (PCR) - Restriction Fragment Length Polymorphism (RFLP) method by the restriction enzyme HaeIII for hsp60 genes and the sequence analysis of hsp60 and rpoB gene sequences could not accurately distinguish B. globosum/pseudolongum, and both species could be accurately distinguished by the sequence analysis of clpC gene sequences. The clpC gene sequence similarity was at least 97.9% in the same species and no more than 95.4% in different species. Therefore, we developed a novel method of RFLP by restriction enzyme BspT104I on PCR products of clpC genes to identify B. globosum/pseudolongum. This method was considered to be faster and more accurate than previously proposed methods for identification of B. globosum/pseudolongum. Thus, the method presented in this study enables efficient species classification and it is very useful in utilization of B. globosum/pseudolongum for foods.