Prevalent Bacterial Species and Novel Phylotypes in Advanced Noma Lesions

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Abstract
The purpose of this study was to determine the bacterial diversity in advanced noma lesions using culture-independent molecular methods. 16S ribosomal DNA bacterial genes from DNA isolated from advanced noma lesions of four Nigerian children were PCR amplified with universally conserved primers and spirochetal selective primers and cloned intoEscherichia coli. Partial 16S rRNA sequences of approximately 500 bases from 212 cloned inserts were used initially to determine species identity or closest relatives by comparison with sequences of known species or phylotypes. Nearly complete sequences of approximately 1,500 bases were obtained for most of the potentially novel species. A total of 67 bacterial species or phylotypes were detected, 25 of which have not yet been grown in vitro. Nineteen of the species or phylotypes, includingPropionibacterium acnes,Staphylococcusspp., and the opportunistic pathogensStenotrophomonas maltophiliaandOchrobactrum anthropiwere detected in more than one subject. Other known species that were detected includedAchromobacterspp.,Afipiaspp.,Brevundimonas diminuta,Capnocytophagaspp.,Cardiobacteriumsp.,Eikenella corrodens,Fusobacteriumspp.,Gemella haemoylsans, andNeisseriaspp. Phylotypes that were unique to noma infections included those in the generaEubacterium,Flavobacterium,Kocuria,Microbacterium, andPorphyromonasand the relatedStreptococcus salivariusand generaSphingomonasandTreponema. Since advanced noma lesions are infections open to the environment, it was not surprising to detect species not commonly associated with the oral cavity, e.g., from soil. Several species previously implicated as putative pathogens of noma, such as spirochetes andFusobacteriumspp., were detected in at least one subject. However, due to the limited number of available noma subjects, it was not possible at this time to associate specific species with the disease.