Effect of sialidase inhibitors on a plaque community biofilm model

The oral microbiome is a diverse ecosystem that plays a critical role in health and disease and contains numerous bacterial species capable of metabolizing host-derived glycans, particularly sialic acids. Sialidase enzymes can be produced by both commensal and pathogenic bacteria influencing biofilm formation and host interactions. To investigate how sialidase activity might influence the oral microbiome, we conducted a series of <i>in vitro</i> polymicrobial biofilm experiments and assessed community composition using 16S rRNA sequencing. As a first step, we tested modified Oxford Nanopore Technology (ONT) primers using an in-house sequencing workflow and compared them to the standard Illumina MiSeq primers. Through <i>in silico</i> and <i>in vitro</i> assessments, we identified primer bias in the standard ONT 16S primers and designed human oral microbiome (HOM) modified primers (HOM_27F-YM/1492R-D) to improve taxonomic resolution, achieving results comparable to the gold-standard Illumina 16S primers particularly for key oral genera. These HOM-optimized primers had an overall lower error rate (3.4%) and generated community profiles that closely matched those produced by Illumina. We then used the same ONT workflow and modified 16S primers to evaluate the effects of the sialidase inhibitors oseltamivir and 2,3-dehydro-2-deoxy-<i>N</i>-acetylneuraminic acid on hydroxyapatite-coated minimum biofilm eradication concentration assay plate-derived plaque biofilms from a whole-plaque community model. Inhibitor-treated biofilms exhibited differences in relative abundance depending on the inhibitor combination used, with increased abundance of <i>Streptococcus</i> with oseltamivir alone and <i>Fusobacterium</i> with both inhibitors combined (Kruskal-Wallis cutoff=0.05, LDA>2). These findings demonstrate that ONT-based 16S sequencing with HOM-modified primers suggests that sialidase activity can modulate microbial community structure in plaque biofilms.