The mediating roles of the oral microbiome in saliva and subgingival sites between e-cigarette smoking and gingival inflammation

A unified web cloud computing platform MiMedSurv for microbiome causal mediation analysis with survival responses

In human microbiome studies, mediation analysis has recently been spotlighted as a practical and powerful analytic tool to survey the causal roles of the microbiome as a mediator to explain the observed relationships between a medical treatment/environmental exposure and a human disease. We also note that, in a clinical research, investigators often trace disease progression sequentially in time; as such, time-to-event (e.g., time-to-disease, time-to-cure) responses, known as survival responses, are prevalent as a surrogate variable for human health or disease. In this paper, we introduce a web cloud computing platform, named as microbiome mediation analysis with survival responses (MiMedSurv), for comprehensive microbiome mediation analysis with survival responses on user-friendly web environments. MiMedSurv is an extension of our prior web cloud computing platform, named as microbiome mediation analysis (MiMed), for survival responses. The two main features that are well-distinguished are as follows. First, MiMedSurv conducts some baseline exploratory non-mediational survival analysis, not involving microbiome, to survey the disparity in survival response between medical treatments/environmental exposures. Then, MiMedSurv identifies the mediating roles of the microbiome in various aspects: (i) as a microbial ecosystem using ecological indices (e.g., alpha and beta diversity indices) and (ii) as individual microbial taxa in various hierarchies (e.g., phyla, classes, orders, families, genera, species). To illustrate its use, we survey the mediating roles of the gut microbiome between antibiotic treatment and time-to-type 1 diabetes. MiMedSurv is freely available on our web server ( http://mimedsurv.micloud.kr ).

A general kernel machine regression framework using principal component analysis for jointly testing main and interaction effects: Applications to human microbiome studies

The effect of a treatment on a health or disease response can be modified by genetic or microbial variants. It is the matter of interaction effects between genetic or microbial variants and a treatment. To powerfully discover genetic or microbial biomarkers, it is crucial to incorporate such interaction effects in addition to the main effects. However, in the context of kernel machine regression analysis of its kind, existing methods cannot be utilized in a situation, where a kernel is available but its underlying real variants are unknown. To address such limitations, I introduce a general kernel machine regression framework using principal component analysis for jointly testing main and interaction effects. It begins with extracting principal components from an input kernel through the singular value decomposition. Then, it employs the principal components as surrogate variants to construct three endogenous kernels for the main effects, interaction effects, and both of them, respectively. Hence, it works with a kernel as an input without knowing its underlying real variants, and also detects either the main effects, interaction effects, or both of them robustly. I also introduce its omnibus testing extension to multiple input kernels, named OmniK. I demonstrate its use for human microbiome studies.

The Effects of Nicotine Pouches and E-Cigarettes on Oral Microbes: A Pilot Study

It remains uncertain whether nicotine pouches and electronic cigarettes alter the oral environment and result in a high presence of periodontopathogenic bacteria in saliva, compared to that among cigarette users or non-tobacco users. In this study, saliva samples were collected from respondents using nicotine pouches, electronic cigarettes, and conventional cigarettes, alongside a control group of non-tobacco users. Polymerase chain reaction was used to identify clinical isolates of the following periodontal bacteria: Porphyromonas gingivalis, Tannerella forsythia, Prevotella intermedia, Fusobacterium nucleatum, Fusobacterium periodonticum, Porphyromonas endodontalis, and Rothia mucilaginosa. The presence of some periodontal pathogens was detected in the saliva samples from users of nicotine pouches, electronic cigarettes, and conventional cigarettes but not in samples taken from the control group. Therefore, the initial results of this pilot study suggest that the presence of periodontopathogenic bacteria in the saliva of nicotine pouch and electronic cigarette users could alter the oral microbiome, leading to periodontal diseases. However, further quantitative investigation is needed.

Oral Microbiota Linking Associations of Dietary Factors with Recurrent Oral Ulcer

Recurrent oral ulcer (ROU) is a prevalent and painful oral disorder with implications beyond physical symptoms, impacting quality of life and necessitating comprehensive management. Understanding the interplays between dietary factors, oral microbiota, and ROU is crucial for developing targeted interventions to improve oral and systemic health. Dietary behaviors and plant-based diet indices including the healthful plant-based diet index (hPDI) were measured based on a validated food frequency questionnaire. Saliva microbial features were profiled using 16S rRNA gene amplicon sequencing. In this cross-sectional study of 579 community-based participants (aged 22-74 years, 66.5% females), 337 participants had ROU. Participants in the highest tertile of hPDI exhibited a 43% lower prevalence of ROU (odds ratio [OR] = 0.57, 95%CI: 0.34-0.94), compared to the lowest tertile, independent of demographics, lifestyle, and major chronic diseases. Participants with ROU tended to have lower oral bacterial richness (Observed ASVs, p < 0.05) and distinct bacterial structure compared to those without ROU (PERMANOVA, p = 0.02). The relative abundances of 16 bacterial genera were associated with ROU (p-FDR < 0.20). Of these, Olsenella, TM7x, and unclassified Muribaculaceae were identified as potential mediators in the association between hPDI and ROU (all p-mediations < 0.05). This study provides evidence of the intricate interplays among dietary factors, oral microbiota, and ROU, offering insights that may inform preventive and therapeutic strategies targeting diets and oral microbiomes.

Evaluation of the Microbiome Identification of Forensically Relevant Biological Fluids: A Pilot Study

In forensic sciences, body fluids, or biological traces, are a major source of information, and their identification can play a decisive role in criminal investigations. Currently, the nature of biological fluids is assessed using immunological, physico-chemical, mRNA and epigenetic methods, but these have limits in terms of sensitivity and specificity. The emergence of next-generation sequencing technologies offers new opportunities to identify the nature of body fluids by determining bacterial communities. The aim of this pilot study was to assess whether analysis of the bacterial communities in isolated and mixed biological fluids could reflect the situation observed in real forensics labs. Several samples commonly encountered in forensic sciences were tested from healthy volunteers: saliva, vaginal fluid, blood, semen and skin swabs. These samples were analyzed alone or in combination in a ratio of 1:1. Sequencing was performed on the Ion Gene StudioTM S5 automated sequencer. Fluids tested alone revealed a typical bacterial signature with specific bacterial orders, enabling formal identification of the fluid of interest, despite inter-individual variations. However, in biological fluid mixtures, the predominance of some bacterial microbiomes inhibited interpretation. Oral and vaginal microbiomes were clearly preponderant, and the relative abundance of their bacterial communities and/or the presence of common species between samples made it impossible to detect bacterial orders or genera from other fluids, although they were distinguishable from one another. However, using the beta diversity, salivary fluids were identified and could be distinguished from fluids in combination. While this method of fluid identification is promising, further analyses are required to consolidate the protocol and ensure reliability.

MiMultiCat: A Unified Cloud Platform for the Analysis of Microbiome Data with Multi-Categorical Responses

The field of the human microbiome is rapidly growing due to the recent advances in high-throughput sequencing technologies. Meanwhile, there have also been many new analytic pipelines, methods and/or tools developed for microbiome data preprocessing and analytics. They are usually focused on microbiome data with continuous (e.g., body mass index) or binary responses (e.g., diseased vs. healthy), yet multi-categorical responses that have more than two categories are also common in reality. In this paper, we introduce a new unified cloud platform, named MiMultiCat, for the analysis of microbiome data with multi-categorical responses. The two main distinguishing features of MiMultiCat are as follows: First, MiMultiCat streamlines a long sequence of microbiome data preprocessing and analytic procedures on user-friendly web interfaces; as such, it is easy to use for many people in various disciplines (e.g., biology, medicine, public health). Second, MiMultiCat performs both association testing and prediction modeling extensively. For association testing, MiMultiCat handles both ecological (e.g., alpha and beta diversity) and taxonomical (e.g., phylum, class, order, family, genus, species) contexts through covariate-adjusted or unadjusted analysis. For prediction modeling, MiMultiCat employs the random forest and gradient boosting algorithms that are well suited to microbiome data while providing nice visual interpretations. We demonstrate its use through the reanalysis of gut microbiome data on obesity with body mass index categories. MiMultiCat is freely available on our web server.

MiTree: A Unified Web Cloud Analytic Platform for User-Friendly and Interpretable Microbiome Data Mining Using Tree-Based Methods

The advent of next-generation sequencing has greatly accelerated the field of human microbiome studies. Currently, investigators are seeking, struggling and competing to find new ways to diagnose, treat and prevent human diseases through the human microbiome. Machine learning is a promising approach to help such an effort, especially due to the high complexity of microbiome data. However, many of the current machine learning algorithms are in a "black box", i.e., they are difficult to understand and interpret. In addition, clinicians, public health practitioners and biologists are not usually skilled at computer programming, and they do not always have high-end computing devices. Thus, in this study, we introduce a unified web cloud analytic platform, named MiTree, for user-friendly and interpretable microbiome data mining. MiTree employs tree-based learning methods, including decision tree, random forest and gradient boosting, that are well understood and suited to human microbiome studies. We also stress that MiTree can address both classification and regression problems through covariate-adjusted or unadjusted analysis. MiTree should serve as an easy-to-use and interpretable data mining tool for microbiome-based disease prediction modeling, and should provide new insights into microbiome-based diagnostics, treatment and prevention. MiTree is an open-source software that is available on our web server.

Comprehensive microbiome causal mediation analysis using MiMed on user-friendly web interfaces

It is a central goal of human microbiome studies to see the roles of the microbiome as a mediator that transmits environmental, behavioral, or medical exposures to health or disease outcomes. Yet, mediation analysis is not used as much as it should be. One reason is because of the lack of carefully planned routines, compilers, and automated computing systems for microbiome mediation analysis (MiMed) to perform a series of data processing, diversity calculation, data normalization, downstream data analysis, and visualizations. Many researchers in various disciplines (e.g. clinicians, public health practitioners, and biologists) are not also familiar with related statistical methods and programming languages on command-line interfaces. Thus, in this article, we introduce a web cloud computing platform, named as MiMed, that enables comprehensive MiMed on user-friendly web interfaces. The main features of MiMed are as follows. First, MiMed can survey the microbiome in various spheres (i) as a whole microbial ecosystem using different ecological measures (e.g. alpha- and beta-diversity indices) or (ii) as individual microbial taxa (e.g. phyla, classes, orders, families, genera, and species) using different data normalization methods. Second, MiMed enables covariate-adjusted analysis to control for potential confounding factors (e.g. age and gender), which is essential to enhance the causality of the results, especially for observational studies. Third, MiMed enables a breadth of statistical inferences in both mediation effect estimation and significance testing. Fourth, MiMed provides flexible and easy-to-use data processing and analytic modules and creates nice graphical representations. Finally, MiMed employs ChatGPT to search for what has been known about the microbial taxa that are found significantly as mediators using artificial intelligence technologies. For demonstration purposes, we applied MiMed to the study on the mediating roles of oral microbiome in subgingival niches between e-cigarette smoking and gingival inflammation. MiMed is freely available on our web server (http://mimed.micloud.kr).