Dolosigranulum pigrum Cooperation and Competition in Human Nasal Microbiota

Abstract

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

Quantifying Variation in Bacterial Reproductive Fitness: a High-Throughput Method

“…However, determining whether this was due to outcompeting the neighboring strain for nutrients, or if there was another metabolic interaction between the strains, was not an objective of our BaQFA experiments. It could still be hypothesized that with our BaQFA method, bacterial interactions might be quantified, as they have been described similarly in vivo and in vitro ( 8 , 9 ). Although we regard the results from our method validation work to only be of an exploratory nature, we could observe a substantially increased fitness in the methicillin-resistant JE2 strain compared to the methicillin-susceptible Cowan strain, suggesting a different baseline-fitness of the underlying USA300 background in JE2 compared to Cowan or the presence of compensatory mutations or other mechanisms of fitness gain.…”

First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies

“…In this step, the model-predicted phenotypes are compared with the experimental data [ 60 ]. Brugger et al predicted the biosynthesis, uptake, and degradation of amino acids, carbohydrates, polyamines, and enzyme cofactors in eleven D. pigrum strains by evaluating their genetic content [ 25 ]. COBRApy [ 61 ] was used for all evaluation steps.…”

“…We identified and removed four reactions without evidence in KEGG [ 37 ], BioCyc [ 51 ], or a significant hit in a BLAST search [ 62 ]. With these alterations, the model is now incapable of producing methionine, as Brugger et al observed in their study [ 25 ]. An ATP-binding cassette (ABC) transporter for the uptake of methionine is present in the model.…”

“…As the human nose is part of the upper respiratory tract, D. pigrum also plays a pivotal role in the human nasal microbiota [ 25 ]. Additionally to the negative association of D. pigrum with Streptococcus pneumoniae , it is also negatively associated with Staphylococcus aureus .…”

“…However, the overall mechanisms behind the inhibition remain unclear. Possible mechanisms include nutrient competition or the excretion of primary or secondary metabolites [ 25 ].…”