Plant-associated microbes (collectively the microbiome) are important contributors to plant health.  They are known to play roles in increasing yield via improving stress tolerance, promoting growth, and suppressing the activity of plant pathogens.  Fusarium head blight (FHB), caused by Fusarium graminearum (sensu stricto), is a devastating disease of wheat and barley in the US.  Managing FHB is challenging because FHB impacts on plant health and agronomic properties are strongly integrated and genetic resistance is incomplete. Here we report recent investigations of amplicon and metagenomic based microbial responses to the presence of FHB among wheat varieties with varying levels of genetic resistance, sensitive (S), moderate resistance (MR), and resistant (R). Using field trials across three locations we identified changes in bacterial community (16S rRNA gene amplicons) composition that were associated with environment and host-resistance level, but not maturity group or variety. In addition, we have identified important taxonomic groups that are differentially abundant in the presence of the pathogen. In our preliminary analysis of the full community analysis (metagenomic sequencing) we have found that bacteria in this system comprise 85% of the most abundant reads. Among the fungal taxa present Fusarium spp.  and Cercospora spp. are among the most abundant. Predictably, among the Fusarium spp. present F. graminearum shifts in abundance from 54% to > 90% corresponding with visual FHB ratings. Surprisingly, however, in fields with little to no visual FHB, F. graminearum is 1 of 8 Fusarium spp. present. Exploring the communities present we find that these communities are relatively simple, with just 289 bacteria identified (thus far) across samples. Of these, notable shifts in these communities occur among host resistance genotype (R, MR, S), even grown in the same field, with taxa like Sphingomonas exhibiting substantially reduced relative abundance in MR and R lines in the presence of Fusarium. Conversely, members of the genus Methylobacterium do not show a change in relative abundance across R, MR, or S hosts. Finally, we find shifts in particular members of these genera, which have previously been identified with suppression of FHB, across host genotype. Future investigations will add additional metagenomic sequences and fungal amplicon data to unravel pathogen-microbial community interactions associated with infection.