Results
In bats, we obtained on average 40278 (± 3719, n= 8) reads per
individual and in birds 71367 (± 26981, n= 10) (Supplementary
information: Table S1). From early on, we were able to detect that a
large percentage of the reads in the unclamped samples were allocated to
a few ASVs and, after performing the taxonomic assignment, we were
certain that those reads matched known sequences of chloroplasts and
mitochondria from publicly available databases. The chloroplast
sequences obtain form the bat samples were a 100% match with
chloroplast sequences obtained from chloroplast of Saguaro Columnar
cacti (GenBank Accession number: KT164771).
After filtering out the chloroplast and mitochondria assigned reads from
the data set, we found that, by using the PNA-DNA clamps, we were able
to retain a significantly larger portion of the reads after the
filtering step (Fig 4). Although the effectivity varied between
individual samples, we always detected an improvement of read coverage
available for downstream analyses while using the clamps compared with
the unclamped results in pairwise comparisons. On average, the
percentage of reads kept improved by 13-fold for the bat (with the
clamps cpPNA and mPNA) and by 34-fold for the bird (cPNA and mPNA)
(Table S1). The two extreme cases were the bat sample Lepto-195 with a
65-fold improvement and the bird sample MM-143195 with a 216-fold
improvement. The control samples, i.e. the bacterial mock community
without chloroplasts and mitochondria, showed no fold change indicating
that the use of the clamps did not affect the Zymo Mock community in any
way (Fig 4). These samples also confirmed that the use of the clamps
affected neither the read number nor the percentage of reads kept after
the subsequent filtering step.