How to cluster the 16s DNA obtained from metagenomic sequenc

I have a question. When I obtained the 16s rDNA from metagenomic sequencing, can I use the cluster command in Mothur? Or the cluster command Mothur can be used only for 16s rRNA genes by PCR?
I have tried with 10 different sequences from the same 16s rDNA (but different V region) of a strain, it seems that the 10 sequences were clustered into 10 OTU. It is strange.
Can you help me with this.

Unless you have an overlapping region between your reads, I don’t think it’s a good idea. It’s not really strange that different fragments of the same gene cluster into different OTUs - if I understand correctly you’ve essentially chopped a gene into pieces and then are comparing each piece to each other and seeing that they’re different.

You could try to use the phylotype command to group your reads, I think that’s about as good as you’ll get.

Thanks for chiming in, you’re exactly right. One added point. Relative to shotgun sequencing, it is incredibly cheap to sequence 16S amplicons. So why not just do the analysis the right way instead of bootstrapping shotgun sequencing to do something that it’s really bad at?