Take a very high quality picture of your gel image making sure remove bubbles and other debris from the gel. Then you'll want to run the gel image through software such as QualityOne (Biorad) to analyze the banding patterns between samples and determine their similarities/differences. You'll then input the numerical output into graphing software such as PAST to visualize the data. There are some good papers describing the process and settings you can use. 

You have to check the profile of received stripes. If they are different, then you have different microorganisms.

Take a very high quality picture of your gel image making sure remove bubbles and other debris from the gel. Then you'll want to run the gel image through software such as QualityOne (Biorad) to analyze the banding patterns between samples and determine their similarities/differences. You'll then input the numerical output into graphing software such as PAST to visualize the data. There are some good papers describing the process and settings you can use. 

Dear Elizabeth,

Thank you for the answer. Can you please suggest me few papers regarding this. ?

Not to plug my own work but I have a couple papers in which DGGE was used.  There is also this very helpful blog which should answer most of the questions you might have on DGGE.

http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2011.02235.x/full

http://ddgehelp.blogspot.dk/2005/11/dgge-guide.html

Bionumerics is also in interesting software for comparative and statistical analysis of DGGE profiles.

you can elute each band and then sequence it to know the representing genera on each band. you can also calculate  range weighted richness (Rr) value for each soil sample which shows the carrying capacity of the soil ecosystem. you can refer paper 

How to get more out of molecular fingerprints: practical tools for microbial ecology. (Marzorati et al.)

after running DGGE, You need to collect different bands from the gel. then, you will use PCR technique to sequence them. in the next stage, you will blast your sequences on NCBI to identify them and build phylogenetic trees which show you the relationship of the microbial system. After that, you need to design specific primers from the sequences and use them in FISH method. then, you will discover the percentages of the microbial compositions

Once you have taken a picture of good quality of the gel and cut bands for sequencing and identifying the microorganisms from your sample. The picture can be processed through software such as GelCompar II to obtain Shannon-Weiner diversity indexes and UPGMA clustering-trees, thus obtaining valuable information of diversity about your samples.

Sequencing will provide you with the phylogenetic relationships of your bands with other existing sequences in the GenBank. This may be done by direct sequencing or after cloning the DGGE fragments. For ecological indices, proceeding a MDS (Multidimensional scaling) analysis may also help you to visualize the level of similarity of individual bands in the whole band set.

You'd better to cut bands for sequencing. And then you could establish  phylogenetic tree and obtain Shannon diversity index and so on.

This is more accurate than the discuss from QualityOne.

Hi，which kind of DGGE marker you use? 

Hello Sir You can take help from this paper.

good luck.