Commensal non-pathogenic Neisseria spp. compete for mucosal niches alongside the pathogenic Neisseria meningitidis and Neisseria gonorrhoeae. Horizontal gene transfer, resulting from natural competence within the genus, has been seen to go from commensals to pathogens and reverse. Four distinct Neisseria spp. were isolated from the throats of two southwest London university students and have been assessed using a combination of microbiological and bioinformatics techniques. Three of the isolates have been identified as Neisseria subflava biovar perflava and one as Neisseria cinerea, using a combination of laboratory and different sequence-based strategies to support species assignments. Amongst identified strain-specific regions are secretion systems: a Type 6 Secretion System and a Type 4 Secretion System unlike that in other Neisseria spp. This investigation is the first to identify these systems in either the non-pathogenic or pathogenic Neisseria spp. In addition, the N. subflava biovar perflava possess previously unreported capsule loci sequences that indicate that these isolates may express one more more serogroups that have not previously been explored experimentally. As has been observed in other investigations, sequences have been identified in all four isolates that are similar to genes associated with virulence seen within the pathogens. These data from the four commensal isolates provides further evidence for a Neisseria spp. gene pool and highlights the presence of systems within the commensals with functions still to be explored.