Dolosigranulum pigrum Cooperation and Competition in Human Nasal Microbiota

Abstract

Multiple epidemiological studies identify <i>Dolosigranulum pigrum</i> as a candidate beneficial bacterium based on its positive association with health, including negative associations with nasal/nasopharyngeal colonization by the pathogenic species <i>Staphylococcus aureus</i> and <i>Streptococcus pneumoniae</i> Using a multipronged approach to gain new insights into <i>D. pigrum</i> function, we observed phenotypic interactions and predictions of genomic capacity that support the idea of a role for microbe-microbe interactions involving <i>D. pigrum</i> in shaping the composition of human nasal microbiota. We identified <i>in vivo</i> community-level and <i>in vitro</i> phenotypic cooperation by specific nasal <i>Corynebacterium</i> species. Also, <i>D. pigrum</i> inhibited <i>S. aureus</i> growth <i>in vitro</i>, whereas robust inhibition of <i>S. pneumoniae</i> required both <i>D. pigrum</i> and a nasal <i>Corynebacterium</i> together. <i>D. pigrum</i> l-lactic acid production was insufficient to account for these inhibitions. Genomic analysis of 11 strains revealed that <i>D. pigrum</i> has a small genome (average 1.86 Mb) and multiple predicted auxotrophies consistent with <i>D. pigrum</i> relying on its human host and on cocolonizing bacteria for key nutrients. Further, the accessory genome of <i>D. pigrum</i> harbored a diverse repertoire of biosynthetic gene clusters, some of which may have a role in microbe-microbe interactions. These new insights into <i>D. pigrum</i>'s functions advance the field from compositional analysis to genomic and phenotypic experimentation on a potentially beneficial bacterial resident of the human upper respiratory tract and lay the foundation for future animal and clinical experiments.<b>IMPORTANCE</b><i>Staphylococcus aureus</i> and <i>Streptococcus pneumoniae</i> infections cause significant morbidity and mortality in humans. For both, nasal colonization is a risk factor for infection. Studies of nasal microbiota identify <i>Dolosigranulum pigrum</i> as a benign bacterium present when adults are free of <i>S. aureus</i> or when children are free of <i>S. pneumoniae</i> Here, we validated these <i>in vivo</i> associations with functional assays. We found that <i>D. pigrum</i> inhibited <i>S. aureus</i><i>in vitro</i> and, together with a specific nasal <i>Corynebacterium</i> species, also inhibited <i>S. pneumoniae</i> Furthermore, genomic analysis of <i>D. pigrum</i> indicated that it must obtain key nutrients from other nasal bacteria or from humans. These phenotypic interactions support the idea of a role for microbe-microbe interactions in shaping the composition of human nasal microbiota and implicate <i>D. pigrum</i> as a mutualist of humans. These findings support the feasibility of future development of microbe-targeted interventions to reshape nasal microbiota composition to exclude <i>S. aureus</i> and/or <i>S. pneumoniae</i>.