Heterogeneous lineage-specific arginine deiminase expression within dental microbiome species

Abstract

Arginine catabolism by the bacterial arginine deiminase system (ADS) has anticariogenic properties through the production of ammonia, which modulates the pH of the oral environment. Given the potential protective capacity of the ADS pathway, the exploitation of ADS competent oral microbes through pre- or probiotic applications is a promising therapeutic target to prevent tooth decay. To date, most investigations of the ADS in the oral cavity and its relation to caries have focused on indirect measures of activity, or on specific bacterial groups, yet the pervasiveness and rate of expression of the ADS operon in diverse mixed microbial communities in oral health and disease remains an open question. Here we use a multivariate approach, combining ultra-deep metatranscriptomic sequencing with paired metataxonomic andin vitrocitrulline quantification to characterize the microbial community and ADS operon expression in healthy and late-stage cavitated teeth. While ADS activity is higher in healthy teeth, we identify multiple bacterial lineages with upregulated ADS activity on cavitated teeth that are distinct from those found on healthy teeth using both reference-based mapping anddenovoassembly methods. Our dual metataxonomic and metatranscriptomic approach demonstrates the importance of species abundance for gene expression data interpretation and that patterns of differential expression can be skewed by low abundance groups. Finally, we identify several potential candidate probiotic bacterial lineages within species that may be useful therapeutic targets for the prevention of tooth decay and propose that the development of a strain-specific, mixed-microbial probiotic may be a beneficial approach given the heterogeneity of taxa identified here across health groups.IMPORTANCETooth decay is the most common preventable chronic disease, globally affecting more than two billion people. The development of caries on teeth is primarily a consequence of acid production by cariogenic bacteria that inhabit the plaque microbiome. Other bacterial strains in the oral cavity may suppress or prevent tooth decay by producing ammonia as a byproduct of the arginine deiminase metabolic pathway, increasing the pH of the plaque biofilm. While the benefits of arginine metabolism on oral health have been extensively documented in specific bacterial groups, the prevalence and consistency of ADS activity among oral bacteria in a community context remains an open question. In the current study, we use a multi-omics approach to document the pervasiveness of expression of the ADS operon in both health and disease to better understand the conditions in which ADS activity may prevent tooth decay.

Shaping human gut community assembly and butyrate production by controlling the arginine dihydrolase pathway

“…The prevalence of the arc operon has been investigated in oral-associated microbial species and strains of select species [10][11][12] . To determine the prevalence of the arc operon across the human microbiome, we analyzed a metagenome-assembled genome dataset containing 154,723 microbial genomes assembled from 9,428 samples of the human microbiome 38 .…”

“…The arginine dihydrolase pathway (encoded by the arc operon or arginine deiminase system) is a specialized metabolic pathway that converts arginine into several products including ammonia, which could impact the gut community 8 . The arc operon has been shown to influence pH homeostasis in oral biofilms 9 and its prevalence has been studied in oral species 10 , strains of Escherichia coli 11 and Eggerthella lenta (E. lenta) 12 . Specifically in the gut, this pathway is harbored by diverse human gut species enabling utilization of arginine as an energy source under aerobic and anaerobic conditions [13][14][15] .…”