This works for me
\documentclass{article}
\begin{document}
<<message=FALSE>>=
library("taxize")
@
Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum \textit{\Sexpr{comm2sci(commnames='Collared Flycatcher', db="itis")[[1]][2]}}
\end{document}
Does this give you what you want? Looks right in the output pdf for me.