There are some challenges for detecting microorganisms because of the high cost,long time and low accuracy of traditional methods.For example,methods based on polymerase chain reaction(PCR)are easily blocked with the existence of polymerase inhibiting compounds,such as humic acids.In addition,antibodies based methods are not robust for continual use and labor intensive.Meanwhile,mass spectrometry based methods are very expensive and not portable.Due to these problems,direct methods for identification of microorganisms are being sought by researchers.There are many reports about using Raman spectroscopy to study bacteria in the field of food safety,explosives detection and clinical diagnosis.Nowadays,due to cost factors,some manufacturers use nosiheptide prepared with fermentation to replace those prepared through chemical synthesis.We report a simple,low-cost and effective method for detection of microorganisms with photonic crystal and Surface Enhanced Raman Spectroscopy(SERS)(Fig.1).In this study,three different substrates has been used,they are Au nanoparticles(AuNPs)(Fig.2a and 2d)substrate,Ag-plated AuNPs substrate(Fig.2b)and Ag-plated photonic crystal substrate(Fig.2c).With the Ag-plated photonic crystal substrate,nosiheptide samples contain Streptomyces actuosus(Fig.2c)could be easily distinguished from those which dont contain(Fig.2d).Then this method could be used to separate nosiheptide samples prepared with fermentation from those prepared through chemical synthesis obviously.