PGRP3 is a protein that helps the body recognize and respond to bacteria based on the essential structures of the bacteria. They are believed to act by helping to maintain a beneficial microbial community. These proteins can attach to bacteria and coat them. However, it is unknown which bacteria they bind to. Here we separated the PGRP3 coated bacteria from dental plaque samples collected from individuals with severe periodontitis and individuals who did not have a diagnosis of periodontitis (non-periodontitis). We used an antibody-based separation technique to purify PGRP3 coated bacteria to a high level of purity. We then sequenced the DNA of the separated bacteria to identify species. We found that samples obtained from non-periodontitis subjects did not have enough PGRP3 coated bacteria to allow for purification. However, the periodontitis samples had significant numbers of PGRP3 coated bacteria. We also identified the following species as PGRP3 highly coated, i.e., Porphyromonas gingivalis, Corynebacterium durum, Streptococcus mutans, and Neisseria. Sp. Species that are not coated with PGRP3 include the following, Leptotrichia wadei, Selenomonas artemidis, Prevotella salivae, and Leptotrichia shahii. While it appears that PGRP3 coats putative oral pathogens including Porphyromonas gingivalis and Streptococcus mutans, PGRP3 coating is noted in only one of the three Treponema species, suggesting a species-level specificity of PGRP3 binding.