The main process for the construction of small genome microbe is as following: i)Making clear the whole genome data of the strain;ii)Analyzing the genome data by bioinformation analysis(Essential gene,Genome island and DNA replication origin et al.);iii)Constructing a markerless large DNA fragment deletion method;iv)Constructing the genome reduced strain;v)Testing and compare the cell growth and product synthesis of the genome reduced strain.We have completed the whole genome sequencing of the Bacillus amyloliquefaciens LL3 strain and have also analyzed the genome data by bioinformation analysis(Table 1).A markerless gene deletion method was constructed by combining a temperature-sensitive plasmid pKSV7 and a counter selectable marker(Figure 1.).We finally obtained a about 10%genome reduced Bacillus amyloliquefaciens strain by the gene markerless deletion method(Table 2).At the meantime,we also studied the synthesis of levan.Six extracellular protease genes(bpr,epr,mpr,vpr,nprE,aprE),together with tasA gene(encoding major biofilm matrix component TasA)and the pgsBCA cluster(for γ-PGA synthesis),were knocked-out in Bacillus amyloliquefaciensstrain to enhance the fructooligosaccharide production.The finally obtained strain could produce 43.3 g/L fructooligosaccharide under the optimized fermentation condition and its purity could reach to 98%.