Collect surgical swabs (if you got the chance to have a collaboration with a surgery departiment) or fecies and proceed an extraction for the DNA collection. To isolate bacteria you have to choose the species you are interested in and sow the sample on selective and specific agar media.

• McConkey for Enterobacteriaceae and other Gram negative
• CNA for Enterococcus spp and Other gram positive
• Shedler (canavanco and cna) for anaerobic flora (anaerobic incubation)
• ecc...

To normalize the 16S, I think it depends on what kind of procedure you will use, I guess you have to be more specific. What do you mean exacly?

You  can collect with a sterile swab fecies and make a pre-incubation in 6 ml of Brain heart infusion (BHI) for 24 hrs. After that time you can use selective or specific agar media to sow  the sample from de pre-incubation media.

-McCkonkey for Enterobacteriaceae

-XLD or Hektoen for Salmonella

-EMB(Levine) for Escherichia coli

About to normalize 16S, what procedure are you going to use? and what specific is you want to find.

You should be able to do a DNA extraction and isolate the bacterial DNA for sequencing from biopsy or stool samples, if you are looking at the community. Culturing would be far more difficult. If you want samples directly from different areas of the intestine, you would have to work with a surgical team. The alternative is to use stool samples, which are far easier to obtain. 

You can do qPCR from cells if you dilute them to a low concentration, but you have to be careful about what inhibitory things might be in the mix with your cells. 

Many thanks for all the answers. I do not want to culture the bacteria. I want to collect the bacteria and isolate genomic DNA from them. So I want to know how to collect these bacteria.

The best way to collect bacteria is isolate them on cultures, so you'll be able to identify them and isolate a single colony, then you can storage them on glicerol at -80°C (dissolves 4/5 colonies into a 1ml of Glicerol solution, be sure to melt them well cause glicerole is viscous, and then storage immediatly). 

Also you can use the isolated colonies to make a solution to operate immediatly a 

DNA extraction to have your qPCR procedure.

Hoping to be helpful, I wish you good work.

Collecting the bacteria is going to depend on where you want the bacteria from. Using stool samples is going to be the easiest and cheapest method, but you can't get bacteria only from a certain part of the intestine. If you are targeting a specific area, you are going to have to get biopsies, which would require surgery. 

DNA extraction from stool or intestinal samples is not very difficult. We use a Qiagen kit with an adapted protocol for our work using stool samples.