Microbial community profiling method has been improved substantially in the past three decades,from the electrophoresis dependent Ribosomal Intergenic Spacer analysis (RISA) and Denaturing Gradient Gel Electrophoresis (DGGE) analysis,to the electrophoresis independent Next Generation Sequencing (NGS),for instance.However,no matter how advanced the profiling method is,a DNA extraction method with high uniformity and representativeness of the microbial community samples is still the fundamental key to guarantee a preciseness analysis.A novel DNA extraction method (FC) was developed,using filter paper pre-absorbance treatment to magnify extraction material,and Chelex resin to absorb DNA contaminants,aimed to improve the uniformity and representativeness of the extracted DNA.The developed FC method was compared with commercial kit method using fresh compost material (K) and kit method using filter paper pre-absorbance material (FK) as well.DNA was tested by Bacteria-RISA (B-RISA) analysis to profile bacterial community structure.The BRISA bands were interpreted into fragment length,transferred to a data matrix,clustered and analyzed by Multivariate regression tree (MRT) method to interpret the interaction between composting days/chemical properties and bacterial community structure.The B-RISA gel results showed that the FC method had higher similarity of bacteria bands among triplicates,while K method showed less similarity among triplicates.This is consistence with the clustering analyses,that FC samples clustered according to the time and replicates,while K samples clustered with no pattern.Comparing FC,FK and K gels,the FC and FK method showed higher similarity than the K method,whereas the FK and K method showed less similarity.This suggested that the difference in between FC and K method was not because of the limitation of FC method,but because of the difference in the extraction material.Using limited material for DNA extraction,as in the commercial kit,may cause high randomness and less representativeness in the extracted DNA exhibited by the following profile procedure.Further MRT analysis showed compost samples processed by FC method could be divided into five groups by time,three groups by chemical properties,and NH4-N and total nitrogen (TN) was the primary and secondary chemical factor influenced bacteria community changing.In contract,due to the unclear profile pattern by the K method,compost samples could only be divided into two groups by time and three groups by chemical properties,whereas total carbon (TC) was both the primary and secondary chemical factor driving bacteria community variation.This difference highly implied that microbial profiling pattern might impact chemical vs.microbe interaction analysis substantially,and less representative microbial profiling likely lead the analysis to an inaccurate direction.Altogether,the present study provided a DNA extraction method with improved uniformity and representativeness of compost DNA,which could be used in combination with bacterial community profiling,for a better characterization of the interaction between environmental factors and bacterial community structures.