Disentangling sequencing technology and biological age effects in canine gut microbiota profiling
Background. Short-read Illumina sequencing of hypervariable regions of the 16S rRNA gene and long-read Oxford Nanopore Technologies (ONT) sequencing of the full-length 16S gene are increasingly used to profile microbial communities. However, differences in sequencing chemistry, read length, and taxonomic assignment raise questions about the comparability of microbiome profiles generated by these platforms and about how platform-specific effects influence downstream biological interpretation.