Chimera checking conservativeness

Since large “candidate” bacterial phyla that are phylogenetically distant from all the ones we knew (and that dominate our databases) have been recently detected (e.g. Hug et al 2016)… are we sure the chimera checking is not tossing them away? As a consecuence of long phylogenetic distance…

Things like chimera.uchime use sequences from within the dataset - not an external reference - to find parents. So I suspect the likelihood of tossing CPR sequences as chimeras is low.

Pat