Germ Free Mouse Analysis

I have a single germ free mouse sample that I’m analyzing. I followed the Schloss SOP to process the sample and classify the sequences. When I got to classification, I only have 40 unique sequences, which is raising questions about how I analyzed the sample. I was trying to go back and run the processing steps without the unique.seqs. When I ran align.seqs, it still only used the unique sequences. Is there anyway that I can work around this? Or is there a better explanation beyond unique.seqs removes complexity (it’s hard for people to accept with just 1 sample)? I think that more germ free analysis will come my way in the future, so I’m wondering if there are any caveats to this analysis.

Well, how many total sequences do you have? What was your inoculum?

excuse my curriosity, but this really interests me since I m working with soils only. What exactly is a germ free mouse? The question is more like what germs you are looking for in germ free animal? If you somehow spike your animal with some bacteria, then you should be getting really low number of unique sequences( unique sequences = strains + noisy sequences generated by the amplicon pyrosequencing process) - Unless you inoculated them with complex bacteria community.

In your case you should be also interested what total number of sequences is. If you have, let’s say a thousand and more redundant sequences and 40 unique sequences then these numbers make perfect sense to me.