Standardized studies of the oral microbiome: From technology-driven to hypothesis-driven

OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients

The human oral microbiome has been associated with multiple inflammatory conditions including inflammatory bowel disease (IBD). Identifying functional changes in oral microbiome by metaproteomics helps understanding the factors driving dysbiosis related to intestinal diseases. However, enriching bacterial cells from oral samples (such as saliva and mouth rinse) rich in host proteins is challenging. Here, we present an Optimized Salivary MetaProteomic sample analysis workflow (OSaMPle) to enrich salivary bacteria and reduce host-derived interferences for in-depth analysis of the oral metaproteome. Compared to a conventional approach, OSaMPle improved the identification of bacterial peptides and proteins by 3.2 folds and 1.7 folds, respectively. Furthermore, applying OSaMPle to analyze mouth rinse samples from IBD patients revealed significant alterations in bacterial protein expressions under disease conditions. Specifically, proteins involved in the fatty acid elongation pathway in Peptostreptococcus were significantly less abundant in IBD patients, whereas proteins associated with the TCA cycle in Neisseria were significantly more abundant. The OSaMPle workflow is capable of processing small-volume oral samples and adaptable to high-throughput automation. It holds promise as a strategy for investigating the functional responses of oral microbiomes under disease conditions and identifying disease-associated microbes with their proteins, providing critical insights for detecting disease-related biomarkers within the oral microbiome.

The oral-gut microbiota axis: a link in cardiometabolic diseases

The oral-gut microbiota axis plays a crucial role in cardiometabolic health. This review explores the interactions between these microbiomes through enteric, hematogenous, and immune pathways, resulting in disruptions in microbial balance and metabolic processes. These disruptions contribute to systemic inflammation, metabolic disorders, and endothelial dysfunction, which are closely associated with cardiometabolic diseases. Understanding these interactions provides insights for innovative therapeutic strategies to prevent and manage cardiometabolic diseases.

Oral Microbiome Dysbiosis as a Risk Factor for Stroke: A Comprehensive Review

Stroke represents a significant global health burden, with a substantial impact on mortality, morbidity, and long-term disability. The examination of stroke biomarkers, particularly the oral microbiome, offers a promising avenue for advancing our understanding of the factors that contribute to stroke risk and for developing strategies to mitigate that risk. This review highlights the significant correlations between oral diseases, such as periodontitis and caries, and the onset of stroke. Periodontal pathogens within the oral microbiome have been identified as a contributing factor in the exacerbation of risk factors for stroke, including obesity, dyslipidemia, atherosclerosis, hypertension, and endothelial dysfunction. The alteration of the oral microbiome may contribute to these conditions, emphasizing the vital role of oral health in the prevention of cardiovascular disease. The integration of dental and medical health practices represents a promising avenue for enhancing stroke prevention efforts and improving patient outcomes.

Microbiota of Saliva: A Non-invasive Diagnostic Tool

Potential of salivary microbiota as a non-invasive diagnostic tool for various diseases are explained in the present review. Traditional diagnostic methods rely on blood, which has limitations in terms of collection and biomarker specificity. We discuss the concept of normal flora and how disruptions in oral microbiota can be indicative of diseases. Saliva, harboring a diverse microbial community, offers promise as a diagnostic biomarker source for oral and non-oral conditions. We delve into the role of microbial dysbiosis in disease pathogenesis and the prospects of using biological indicators like dysbiosis for diagnosis, prediction, and monitoring. This review also emphasizes the significance of saliva microbiota in advancing early disease detection and timely intervention. We addressed the following research question and objectives: Can the microbiota of saliva serve as a non-invasive diagnostic tool for the early detection and monitoring of both oral and non-oral diseases? To achieve this, we will explore the normal flora of microorganisms in the oral cavity, the impact of microbial dysbiosis, and the potential of using specific pathogenic microorganisms as biomarkers. Additionally, we will investigate the correlation between oral and non-oral diseases by analyzing total saliva or site-specific dental biofilms for signs of symbiosis or dysbiosis. This research seeks to contribute valuable insights into the development of a non-invasive diagnostic approach with broad applications in healthcare.

Oral nitrate-reducing bacteria as potential probiotics for blood pressure homeostasis

Hypertension is a leading cause of morbidity and mortality worldwide and poses a major risk factor for cardiovascular diseases and chronic kidney disease. Research has shown that nitric oxide (NO) is a vasodilator that regulates vascular tension and the decrease of NO bioactivity is considered one of the potential pathogenesis of essential hypertension. The L-arginine-nitric oxide synthase (NOS) pathway is the main source of endogenous NO production. However, with aging or the onset of diseases, the function of the NOS system becomes impaired, leading to insufficient NO production. The nitrate-nitrite-NO pathway allows for the generation of biologically active NO independent of the NOS system, by utilizing endogenous or dietary inorganic nitrate and nitrite through a series of reduction cycles. The oral cavity serves as an important interface between the body and the environment, and dysbiosis or disruption of the oral microbiota has negative effects on blood pressure regulation. In this review, we explore the role of oral microbiota in maintaining blood pressure homeostasis, particularly the connection between nitrate-reducing bacteria and the bioavailability of NO in the bloodstream and blood pressure changes. This review aims to elucidate the potential mechanisms by which oral nitrate-reducing bacteria contribute to blood pressure homeostasis and to highlight the use of oral nitrate-reducing bacteria as probiotics for oral microbiota intervention to prevent hypertension.

Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.

The Effects of Drug Addiction and Detoxification on the Human Oral Microbiota

Drug addiction can powerfully and chronically damage human health. Detoxification contributes to health recovery of the body. It is well established that drug abuse is associated with poor oral health in terms of dental caries and periodontal diseases. We supposed that drug addiction and detoxification might have significant effects on the oral microbiota. To test the hypothesis, we assessed the effects of drug (heroin and methylamphetamine) addiction/detoxification on the oral microbiota based on 16S rRNA gene sequencing by an observational investigation, including 495 saliva samples from participants. The oral microbial compositions differed between non-users, current and former drug users. Lower alpha diversities were observed in current drug users, with no significant differences between non-users and former drug users. Heroin and METH addiction can cause consistent variations in several specific phyla, such as the enrichment of Acidobacteria and depletion of Proteobacteria and Tenericutes. Current drug users had significantly lower relative abundances of Neisseria subflava and Haemophilus parainfluenzae compared to non-users and former drug users. The result of random forest prediction model suggested that the oral microbiota has a powerful classification potential for distinguishing current drug users from non-users and former drug users. A cooccurrence network analysis showed that current drug users had more complex oral microbial networks and lower functional modularity. Overall, our study suggested that drug addiction may damage the balance of the oral microbiota. These results may have benefits for further understanding the effects of addiction-related oral microbiota on the health of drug users and promoting the microbiota to serve as a potential tool for accurate forensic identification. IMPORTANCE Drug addiction has serious negative consequences for human health and public security. The evidence indicates that drug abuse can cause poor oral health. In the current study, we observed that drug addiction caused oral microbial dysbiosis. Detoxication have positive effects on the recovery of oral microbial community structures to some extent. Understanding the effects of drug addiction and detoxification on oral microbial communities will promote a more rational approach for recovering the oral function and health of drug users. Furthermore, specific microbial species might be considered biomarkers that could provide information regarding drug abuse status for saliva left at crime scenes. To the best of our knowledge, this is the first report on the role of the oral microbiota in drug addiction and detoxification. Our findings give new clues to understand the association between drug addiction and oral health.

The sampling strategy of oral microbiome

There are multiple habitats in the oral cavity with bacteria, fungi, viruses, and protozoa residing in, which together constitute the oral micro-ecosystem. These microflorae in the oral cavity primarily include saliva, supragingival dental plaque, subgingival dental plaque, submucosal plaque around implants, plaque in root canals, and plaque on the mucosal surface. The interest and knowledge of the microbiome have dynamically increased with the advancement of technology. Therefore, a reliable, feasible, and practical sampling strategy for the oral microbiome is required for the investigation. This paper introduced the sampling strategy of oral microorganisms, consisting of sample collection, transport, processing, and storage. The materials and devices involved in this study are all commonly used in clinical practice or laboratory. The feasibility and reliability of the sampling methods described in this paper have been verified by multiple studies.