Aldehyde-induced DNA-protein crosslinks- DNA damage, repair and mutagenesis.

Aldehyde exposure has been shown to lead to the formation of DNA damage comprising of DNA-protein crosslinks (DPCs), base adducts and interstrand or intrastrand crosslinks. DPCs have recently drawn more attention because of recent advances in detection and quantification of these adducts. DPCs are highly deleterious to genome stability and have been shown to block replication forks, leading to wide-spread mutagenesis. Cellular mechanisms to prevent DPC-induced damage include excision repair pathways, homologous recombination, and specialized proteases involved in cleaving the covalently bound proteins from DNA. These pathways were first discovered in formaldehyde-treated cells, however, since then, various other aldehydes have been shown to induce formation of DPCs in cells. Defects in DPC repair or aldehyde clearance mechanisms lead to various diseases including Ruijs-Aalfs syndrome and AMeD syndrome in humans. Here, we discuss recent developments in understanding how aldehydes form DPCs, how they are repaired, and the consequences of defects in these repair pathways.

HIV Infection and Exposure Increases Cariogenic Taxa, Reduces Taxonomic Turnover, and Homogenizes Spatial Differentiation for the Supragingival Microbiome.

Background: The oral microbiome comprises distinct microbial communities that colonize diverse ecological niches across the oral cavity, the composition of which are influenced by nutrient and substrate availability, host genetics, diet, behavior, age, and other diverse host and environmental factors. Unlike other densely populated human-associated microbial ecosystems (e.g., gut, urogenital), the oral microbiome is regularly and directly exposed to the external environment and is therefore likely less stable over time. Cross sectional studies of the oral microbiome capture a glimpse of this temporal dynamism, yet a full appreciation of the relative stability, robusticity, and spatial structure of the oral environment is necessary to understand the role of microbial communities in promoting health or disease. Results: Here we investigate the spatial and temporal stability of the oral microbiome over three sampling time points in the context of HIV infection and exposure. Individual teeth were sampled from a cohort of 565 Nigerian children with varying levels of tooth decay severity (i.e., caries disease). We collected 1,960 supragingival plaque samples and characterized the oral microbiome using a metataxonomic approach targeting an approximately 478 bp region of the bacterial rpoC gene. We found that both infection and exposure to HIV have significant effects on the stability of the supragingival plaque microbiome at both the spatial and temporal scale. Specifically, we detect (1) significantly lower taxonomic turnover of the oral community among exposed and infected children compared to unexposed children, (2) we find that HIV infection homogenizes the oral community across the anterior and posterior dentition, and (3) that impaired immunity (i.e., low CD4 count) and low taxonomic turnover over time in children living with HIV is associated with higher frequency of cariogenic taxa including Streptococcus mutans. Conclusions: Our results document substantial community fluctuations over time in children unexposed to HIV independent of oral health status. This suggests that the oral community, under typical conditions, rapidly adapts to environmental perturbations to maintain homeostasis and that long-term taxonomic rigidity is a signal of community dysfunction, potentially leading to a higher incidence of oral disease including caries.

Supragingival mycobiome of HIV-exposed-but-uninfected children reflects a stronger correlation with caries-free-associated taxa compared to HIV-infected or uninfected children.

IMPORTANCE: Globally, caries is among the most frequent chronic childhood disease, and the fungal component of the microbial community responsible is poorly studied despite evidence that fungi contribute to increased acid production exacerbating enamel demineralization. HIV infection is another global health crisis. Perinatal HIV exposure with infection are caries risk factors; however, the caries experience in the context of perinatal HIV exposure without infection is less clear. Using high-throughput amplicon sequencing, we find taxonomic differences that become pronounced during late-stage caries. Notably, we show a stronger correlation with health-associated taxa for HIV-exposed-but-uninfected children when compared to unexposed and uninfected children. This aligns with a lower incidence of caries in primary teeth at age 6 or less for exposed yet uninfected children. Ultimately, these findings could contribute to improved risk assessment, intervention, and prevention strategies such as biofilm disruption and the informed design of pro-, pre-, and synbiotic oral therapies.

Optimization and Evaluation of the 30S-S11 rRNA Gene for Taxonomic Profiling of Oral Streptococci.

Dental caries is a multifactorial disease driven by interactions between the highly complex microbial biofilm community and host factors like diet, oral hygiene habits, and age. The oral streptococci are one of the most dominant members of the plaque biofilm and are implicated in disease but also in maintaining oral health. Current methods used for studying the supragingival plaque community commonly sequence portions of the16S rRNA gene, which often cannot taxonomically resolve members of the streptococcal community past the genus level due to their sequence similarity. The goal of this study was to design and evaluate a more reliable and cost-effective method to identify oral streptococci at the species level by applying a new locus, the 30S-S11 rRNA gene, for high-throughput amplicon sequencing. The study results demonstrate that the newly developed single-copy 30S-S11 gene locus resolved multiple amplicon sequence variants (ASVs) within numerous species, providing much improved taxonomic resolution over 16S rRNA V4. Moreover, the results reveal that different ASVs within a species were found to change in abundance at different stages of caries progression. These findings suggest that strains of a single species may perform distinct roles along a biochemical spectrum associated with health and disease. The improved identification of oral streptococcal species will provide a better understanding of the different ecological roles of oral streptococci and inform the design of novel oral probiotic formulations for prevention and treatment of dental caries. IMPORTANCE The microbiota associated with the initiation and progression of dental caries has yet to be fully characterized. Although much insight has been gained from 16S rRNA hypervariable region DNA sequencing, this approach has several limitations, including poor taxonomic resolution at the species level. This is particularly relevant for oral streptococci, which are abundant members of oral biofilm communities and major players in health and caries disease. Here, we develop a new method for taxonomic profiling of oral streptococci based on the 30S-S11 rRNA gene, which provides much improved resolution over 16S rRNA V4 (resolving 10 as opposed to 2 species). Importantly, 30S-S11 can resolve multiple amplicon sequence variants (ASVs) within species, providing an unprecedented insight into the ecological progression of caries. For example, our findings reveal multiple incidences of different ASVs within a species with contrasting associations with health or disease, a finding that has high relevance toward the informed design of prebiotic and probiotic therapy.