Allison E. Mann

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 and in vitro citrulline 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 and denovo assembly 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.

Although a typical treatment option for metabolic disorders is synthetically derived formula diets, the effects have not been extensively studied, and may render other health consequences. Dietary fiber is essential to protect the gut from opportunistic pathogens and increase the population of commensal bacteria in the colon, which is the most densely populated area for microbiota in the human body. Previous research has demonstrated that diets high in fiber are crucial to human health, as they increase microbial diversity and short chain fatty acid production and allow for proper maintenance of gut tissue. Notably, evidence suggests that high-fiber diets improve cognition and provide neuroprotection, as the gut and brain are connected by the gut-brain axis. Conversely, previous studies in both human subjects and animals have shown that low-fiber diets are associated with decreased gut bacterial diversity, decreased short chain fatty acid production, increased gastrointestinal distress, and increased cognitive dysfunction and anxiety-like behavior. In the current, multidisciplinary study, we examined the effects of a synthetically derived, low-fiber, amino acid diet on anxiety-like behavior, locomotor activity, cognition, the gut microbiome, cytokines, colon length, and short-chain fatty acid production in male C57BL/6J mice. Mice were assigned to one of two diet conditions at post-natal day 21: a standard rodent diet or a synthetic diet analogous to the standard rodent diet, and continued consumption for 13 weeks. The results revealed that this synthetic diet altered locomotor activity. Additionally, by sequencing the 16S rRNA gene from fecal samples (collected weekly) in each group, we identified a decrease in bacterial diversity, and through PICRUSt2 analysis, we predicted changes in metabolic pathway activities. Furthermore, we saw a decrease in the production of short chain fatty acids and a shortening of the colon in mice consuming the synthetic diet. Finally, we measured TNF-α, IL-6, and IL-10 in serum, the hippocampus, and colon, and found that the synthetic diet significantly increased IL-6 production in the hippocampus. These results demonstrate the importance of a multidisciplinary approach to future diet and microbiome studies, as diet not only impacts the gut microbiome, but potentially cognitive and immune function as well.

Highly active antiretroviral treatment (HAART) has greatly reduced opportunistic infections in HIV-infected individuals. However, even with use of HAART, HIV-infected individuals are still at an increased risk of oral diseases, including dental caries. Dental caries development is associated with microbial community shifts leading to community dysbiosis. HIV infection can significantly alter the bacteriome and mycobiome composition in the oral cavity; however, these impacts have not been assessed for caries initiation and progression. The aim of this study was to characterize the mycobiome for supragingival plaque samples from HIV-infected (HI), HIV-exposed-but-uninfected (HEU), and HIV-unexposed-and-uninfected (HUU) children with and without caries. To accomplish this, ITS1 amplicons of 127 samples were sequenced. We found that HIV infection and exposure resulted in changes to the supragingival plaque mycobiome for both health and caries. Overall, a reduction in community diversity as caries progressed was observed, with HI children having the lowest diversity and HEU children the highest. \emphCandida albicans was the most abundant species identified, with 177 different ASVs. Two \emphC. albicans ASVs dominated the data (53.0% and 38.5% of all taxonomic assignments). The more frequent ASV dominated HI and HUU communities, whereas the second dominated HEU communities. HEU children also had the lowest abundance of \emphC. albicans and the highest number of health-associated taxa.