I am currently trying to detect bacterial 16S rRNA DNA in human tissue to ultimately sequence the results. I conducted PCR on diluted samples (original concentration of DNA was between 100-500ng/ul) and when I ran it through gel electrophoresis I got a very faint band for 16S; however, when I attempted to sequence it, the concentration was too low. 

I tried to then conduct PCR on the aforementioned PCR product without dilution to amplify the 16S target. I got a positive result (a clear, bright band) for my positive control (an E.coli sample); however, the other samples had a clear band at a shorter DNA template size (~200-400bp).

Is my 16S amplification being inhibited by the higher concentration of human DNA? 

What will be the best way to isolate only the 16S DNA template in order to conduct PCR and get enough 16S PCR product to conduct sequencing?

Any advice will be greatly appreciated!!

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