Metatranscriptomic analysis of arginine deiminase expression within dental microbiome species
Arginine catabolism through the bacterial arginine deiminase (ADS) metabolic pathway 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 pathway in the oral cavity and its relation to caries have focused on indirect measures of activity, or on specific bacterial groups (e.g., Streptococcus) 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 and in vitro citrulline quantification, to characterize the microbial community and ADS operon expression in healthy and late-stage cavitated teeth. We find that while ADS activity is higher for healthy teeth as measured by citrulline production and the number of reads mapping to the operon, ADS expression is not limited to bacteria found on teeth with no carious lesions. We identify multiple bacterial lineages with upregulated ADS activity on cavitated teeth that are distinct from those found on healthy teeth. However, upregulation of ADS genes on diseased teeth is primarily driven by samples that have a low abundance of Streptococcus mutans, suggesting an antagonistic relationship between this cariogenic taxon and ADS competent bacteria in these environments. Moreover, our dual metataxonomic and metatranscriptomic approach documents that species abundance is a critical normalization factor for gene expression data 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 development of a strain-specific, mixed-microbial probiotic may be a beneficial approach given the heterogeneity of taxa identified here across health groups.