Meningococcal meningitis, caused by Neisseria meningitidis, is a serious bacterial infection characterized by inflammation of the membranes surrounding the brain. Meningococcal vaccines currently in use fail to protect against N. meningitidis strains belonging to serogroup B. A new vaccine, Bexsero^®, has recently been developed by Novartis for use against serogroup B meningococci. This vaccine contains five different protein components: fHbp, NHBA, NadA, GNA1030 and GNA2091. Although the vaccine has been designed to elicit the production of antibodies that kill N. meningitidis, it is possible the antibodies could also affect other beneficial bacteria living in or on the human body that express similar surface antigens. The goal of the current study was to assess this possibility by using bioinformatics approaches to search for the five vaccine antigen-encoding genes in all microorganisms represented in the Human Microbiome Project reference genome database. The fHbp gene was found in N. cinerea and N. polysaccharea, and the nhba gene was found in N. flavescens, N. lactamica and N. polysaccharea. Multiple species, including 15 nonpathogenic Neisseria species, contain genes similar to gna1030 and gna2091. Thus, the human microbiota includes organisms possessing genes with the capacity to encode proteins highly similar to those included in the Bexsero^® vaccine.