We have encountered the same coloring problem when we isolated metagenome from earthworm gut. Repeated washing of the gut contents with PBS removed the colour

Thanks for the input, does your sample amplified through PCR?

I am working on metagenome from soil. I used the SDS-based method same as yours and my DNA was brown (Concentration is very high for DNA). I tried purification using PowerClean but the result is not very good (The concentration is low and PCR no amplification). So I tried with gel purification method,  it gave me better result.

Oh ya... Purification always causes loss of DNA. Maybe you can try to increase the amount of your sample (5g increased to 10g). Usually I prepare 4 to 6 tubes of sample and then combine all together after purification.

Just use the mobio powesoil kit to extract DNA, it usually works well.

Incase you already have the DNA but want to purify it, run a gel and elute from gel.

YOu can also quantify based on gel, which is more accurate than on nanodrop as compounds co-extracted can share the spectra with DNA giving an impression of higher yields.

Noted, thanks for the precious input Yen Teng Tai! It is always brownish using SDS based method, but so far this SDS-based method can extract DNA from my sample

Jay Siddharth, unfotunately Mobio Powersoil kit were not able to extract the DNA, the same applied to Mobio Powerfecal... those kit give low concentration of DNA

The only reason I can think of for a low yield is high genomic dna yield from host tissue.

can you try to shred the tissue using a scalpel or grind it using a motar pestle in liq N2. before going in for the kit.

The high mw DNA can clog the column and thus result in low yield. This is especially true for tissue associated bugs like in gut and lungs.

Hey your suggestion does make a sense..since the SDS-based DNA extraction doesn't utilize any column so there won't be any DNA clogging and I think It is very weird that Powersoil kit coudln't extract DNA from guts sample.

Since Powersoil kit were equipped with bead beating tube, never crossed in my mind to grind the sample with nitrogen liquid, but I will give it a try. Thanks a lot Jay!

In my samples of soil (avocado farm) I used for DNA extraction a manual protocole (Godon et al., 1997) and the purification solutions of the Qiagen DNA extraction kit. I obtained some DNA extractions clear and useful for PCRq and SSCP analyses. However, some DNA extraction were brownish and SSCP didn't worked. All samples, including brownish, worked good for PCRq  using 200 and 1000 as dilutions. Actually, I don't know how to remove the brown color from this samples for SSCP analyses without lost high DNA quantities.

The easiest in this case is to run the DNA on a gel and elute the bands from that. If done right you have about 80%  recovery.

Alternatively you can add PCR enhancers to overcome the humic acids or bile salts that have been co-extracted.

We've seen huge discrepancies between the concentration measured by a Nanodrop and the concentration measured by a Qubit when humics are present.  Humic acid and polysaccharides can greatly inflate the absorbance at 260 nm as well as at 230 nm. So once the humics are removed, a lot of the DNA can appear to be "lost."  However, when the Qubit reading before and after clean-up are compared we can see that most of the time the DNA was not lost but only the PCR inhibitors. One could also use an agarose gel.

One other thing to keep in mind with any kit involving a silica spin column is DNA will be lost if the fragments are more than 50 kb in size.  So make sure the input DNA is smaller than this.

Specifically working with Gut, make sure you mince the tissue well else you can have "blobs" of cell mass that clog the column and also reduce the efficiency of the column and also reduce DNA yield by sequestering the DNA: