During a previous study on the molecular interaction between commensal bacteria and host gut immunity, two novel bacterial strains, A911(T) and G707(T), were isolated from the gut of Drosophila melanogaster. In this study, these strains were characterized in a polyphasic taxonomic study using phenotypic, genetic, and chemotaxonomic analyses. We show that the strains represent novel species in the family Acetobacteraceae. Strain G707(T), a highly pathogenic organism, represents a new species in the genus Gluconobacter, "Gluconobacter morbifer" sp. nov. (type strain G707 = KCTC 22116(T) = JCM 15512(T)). Strain A911(T), dominantly present in the normal Drosphila gut community, represents a novel genus and species, designated "Commensalibacter intestini" gen. nov., sp. nov. (type strain A911 = KCTC 22117(T) = JCM 15511(T)).