Next Article in Journal
Spatial and Temporal Variability in Prevalence Rates of Members of the Borrelia burgdorferi Species Complex in Ixodes ricinus Ticks in Urban, Agricultural and Sylvatic Habitats in Slovakia
Previous Article in Journal
Distribution Patterns of Benthic Protist Communities Depending on Depth Revealed by Environmental Sequencing—From the Sublittoral to the Deep Sea
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Microorganisms
Volume 11
Issue 7
10.3390/microorganisms11071665
microorganisms-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Potential Oral Microbial Markers for Differential Diagnosis of Crohn’s Disease and Ulcerative Colitis Using Machine Learning Models

by
Sang-Bum Kang
1,†,
Hyeonwoo Kim
2,†,
Sangsoo Kim
2,
Jiwon Kim
2,
Soo-Kyung Park
3,4,
Chil-Woo Lee
4,
Kyeong Ok Kim
5,
Geom-Seog Seo
6,
Min Suk Kim
7,
Jae Myung Cha
8,
Ja Seol Koo
9 and
Dong-Il Park
3,4,*
1
Department of Internal Medicine, College of Medicine, Daejeon St. Mary’s Hospital, The Catholic University of Korea, Daejeon 34943, Republic of Korea
2
Department of Bioinformatics, Soongsil University, Seoul 06978, Republic of Korea
3
Division of Gastroenterology, Department of Internal Medicine and Inflammatory Bowel Disease Center, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 03181, Republic of Korea
4
Medical Research Institute, Kangbuk Samsung Hospital, School of Medicine, Sungkyunkwan University, Seoul 03181, Republic of Korea
5
Department of Internal Medicine, College of Medicine, Yeungnam University, Daegu 42415, Republic of Korea
6
Department of Internal Medicine, School of Medicine, Wonkwang University, Iksan 54538, Republic of Korea
7
Department of Human Intelligence and Robot Engineering, Sangmyung University, Cheonan-si 31066, Republic of Korea
8
Department of Internal Medicine, Kyung Hee University Hospital at Gangdong, Kyung Hee University College of Medicine, Seoul 05278, Republic of Korea
9
Division of Gastroenterology and Hepatology, Department of Internal Medicine, Ansan Hospital, Korea University College of Medicine, Ansan 15355, Republic of Korea
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Microorganisms 2023, 11(7), 1665; https://doi.org/10.3390/microorganisms11071665
Submission received: 1 June 2023 / Revised: 21 June 2023 / Accepted: 25 June 2023 / Published: 26 June 2023
(This article belongs to the Section Medical Microbiology)
Browse Figures
Review Reports Versions Notes

Abstract

:
Although gut microbiome dysbiosis has been associated with inflammatory bowel disease (IBD), the relationship between the oral microbiota and IBD remains poorly understood. This study aimed to identify unique microbiome patterns in saliva from IBD patients and explore potential oral microbial markers for differentiating Crohn’s disease (CD) and ulcerative colitis (UC). A prospective cohort study recruited IBD patients (UC: n = 175, CD: n = 127) and healthy controls (HC: n = 100) to analyze their oral microbiota using 16S rRNA gene sequencing. Machine learning models (sparse partial least squares discriminant analysis (sPLS-DA)) were trained with the sequencing data to classify CD and UC. Taxonomic classification resulted in 4041 phylotypes using Kraken2 and the SILVA reference database. After quality filtering, 398 samples (UC: n = 175, CD: n = 124, HC: n = 99) and 2711 phylotypes were included. Alpha diversity analysis revealed significantly reduced richness in the microbiome of IBD patients compared to healthy controls. The sPLS-DA model achieved high accuracy (mean accuracy: 0.908, and AUC: 0.966) in distinguishing IBD vs. HC, as well as good accuracy (0.846) and AUC (0.923) in differentiating CD vs. UC. These findings highlight distinct oral microbiome patterns in IBD and provide insights into potential diagnostic markers.

1. Introduction

Because IBD can cause irreversible damage to the digestive tract if left untreated, early diagnosis and treatment should be mandatory to control inflammation and potentially limit this damage [1,2,3]. To diagnose IBD in the early stages, it is crucial for physicians to conduct a careful and thorough evaluation, which includes history-taking, laboratory tests, endoscopy, and cross-sectional imaging [4,5,6].
IBD is a complex disorder that involves the interplay of several factors: genetics [7], the immune system, environmental factors, and the gut microbiome. Among these factors, dysbiosis, which refers to the imbalance of microbial communities, is believed to play a significant role in the pathogenesis of IBD [8,9]. However, the relationship between dysbiosis and IBD is currently complex and not fully understood. While there is a clear association between dysbiosis and IBD, it remains uncertain whether dysbiosis is a cause or a consequence of IBD [10]. Dysbiosis can occur not only in the gut, but also in the oral cavity, potentially influencing the function of the gut barrier and immune response. These factors play a crucial role in the development of chronic inflammation, which is a characteristic feature of IBD [11,12].
According to recent studies [13,14,15], exploring the oral microbiome as a potential diagnostic tool for IBD offers several advantages, including ease of sample collection, stability, and early detection compared to fecal microbiome analysis. These studies have revealed a connection between the oral microbiome and IBD, as individuals with IBD tend to harbor distinct bacterial profiles in their mouths compared to those without the condition [16].
However, it is important to acknowledge the limitations and challenges associated with analyzing the oral microbiome for IBD diagnosis. Saliva-based microbiome analysis is a complex process that can be influenced by numerous factors, making it difficult to identify clear, disease-specific patterns. Furthermore, the oral microbiome may not directly reflect the gut environment as accurately as the fecal microbiome, potentially providing less relevant information about the disease state. To overcome these challenges, microbial analysis utilizing algorithmic machine learning models can be beneficial. These models address issues such as data complexity, the requirement for large and high-quality datasets, and validation problems, as well as ethical and privacy considerations [17,18,19]. One statistical method commonly used in this context is sparse partial least squares discriminant analysis (sPLS-DA), which aims to establish a linear relationship between two datasets while performing variable selection. This approach can help identify the most important microbial species for predicting the disease outcome [20].
The aim of this study was to assess the microbial patterns in saliva and identify differences between healthy controls and patients with IBD. Additionally, the study aimed to utilize a machine learning model, specifically sPLS-DA, to identify subgroups within IBD, such as CD and UC.

2. Materials and Methods

2.1. Study Population and Sample Collection

We recruited two cohorts of patients—one with CD and the other with UC—as well as a cohort of healthy controls for our study. The patients with CD were included from 15 tertiary hospitals in South Korea as part of a multicenter, retrospective case–control study [21]. For the ulcerative colitis (UC) multiomics study, a prospective multicenter study was established in Korea in 2020. A total of 14 university hospitals participated in this study and collected clinical data and biological specimens, including blood, stool, tissue, and saliva samples, from UC patients. From the outpatients who underwent screening by colonoscopy between June 2020 and December 2020, we selected 100 individuals who agreed to participate in the study and provide saliva samples to form the healthy control group.
Saliva samples (2 mL) were collected using a saliva collection kit (Cat. PDX-026; PDXen Biosystems Co., Daejeon, Republic of Korea) after lightly rinsing the mouth twice with mineral water, and they were transported and stored at room temperature (15–30 °C).

2.2. DNA Extraction, PCR Amplification, and 16S rRNA Gene Sequencing

Details of the sample preparation and sequencing have been published in [22]. In summary, the samples underwent centrifugation at 15,000 rpm for 20 min at 4 °C to separate the cellular pellet from the cell-free supernatant. Subsequently, DNA extraction from the cellular pellet was carried out using the QIAamp DNA Microbiome Kit (Qiagen, Valencia, CA, USA), following the manufacturer’s protocol.
The V3-4 region of the 16S rRNA gene was amplified using the 341F (5′-TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCT ACG GGN GGC WGC AG-3′) and 805R (5′-GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGA CTA CHV GGG TAT CTA ATC C-3′) primers, which included Illumina adaptor overhang sequences. The amplicons generated through PCR were purified using a magnetic-bead-based clean-up system (Agen-court AMPure XP Beckman CoulterTM, Brea, CA, USA). Indexed libraries were prepared using Nextera technology, which involves limited-cycle PCR, and the libraries were subsequently cleaned up and pooled at equimolar concentrations. Paired-end sequencing was performed on the Illumina MiSeq platform using a 2 × 300 bp protocol, following the manufacturer’s instructions.

2.3. 16S rRNA Gene Sequencing Data Analysis

The raw sequence data underwent quality filtering using FASTP (version 0.23.2, https://github.com/OpenGene/fastp, accessed on 16 August 2022) to remove sequences with low quality (quality score < 20) and reads shorter than 150 base pairs. Taxonomic assignments of the trimmed sequencing reads were performed using Kraken2 against the SILVA reference database (Release 138.1, https://www.arb-silva.de/documentation/release-138/, accessed on 20 September 2022), with default parameters. The Bioconductor R package phyloseq (version 1.38.0) was employed to analyze the microbiome profile data. Sequences that were not classified as bacteria or lacked annotation at the phylum level were filtered out. Samples with less than 20,000 reads and rarely observed phylotypes were excluded from the subsequent analysis. The alpha diversity indices of the samples were calculated using the Bioconductor R package microbiome (version 1.16.0). Using Mothur (version 1.48.0), we performed calculations of beta diversity indices and conducted permutational multivariate analysis of variance (PERMANOVA) tests based on distance matrices to assess the microbiome composition differences between different phenotypes.

2.4. Machine Learning for Diagnosis Model

Before the machine learning model’s development, log normalization with a pseudocount of 1 was performed to reduce the difference by sequencing depth for each sample, and ANCOM-BC (version 1.4.0) was used to correct the sequencing batch effects for all samples processed in different periods.
For performing principal component analysis (PCA) and developing the diagnosis models, we utilized the Bioconductor R package mixOmics (version 6.18.1). Specifically, we employed sparse partial least squares discriminant analysis (sPLS-DA), which offers computational efficiency and generates interpretable results through graphical outputs. The feature selection and parameter optimization process followed a general procedure. To determine the optimal number of components, we assessed the performance of the PLS-DA model using 50 repeated fivefold cross-validations (5-CVs) and monitored the overall error rate trend across the CVs. Subsequently, tuning processes were conducted to simultaneously select the optimal number of components and the optimal features for each component. The final sparse PLS-DA model was defined as the one that yielded the lowest overall error rate, indicating the best predictive performance.
To assess the performance of the machine learning models, we repeated the abovementioned process 100 times by randomly splitting the samples into 70% training and 30% validation sets. Using the 100 trained sPLS-DA models, the phenotypes of the corresponding validation sets were predicted, and the average performance was measured.

3. Results

In our study, we performed 16S rRNA sequencing on saliva samples collected from a total of 402 individuals, which included three different disease phenotypes: Crohn’s disease (CD: n = 127), ulcerative colitis (UC: n = 175), and healthy controls (HC: n = 100). The baseline demographics and clinical characteristics of the patients can be found in Table 1.
During the sequencing process, a total of 54,553,630 paired-end reads were generated. After applying quality trimming, we observed an average of 121,689 paired-end reads that were retained for each sample. Taxonomy assignment and subsequent phylotyping analysis allowed us to identify 2711 phylotypes within the bacterial kingdom. These phylotypes were annotated with specific phylum information and were observed more than 10 times in our dataset.
In the subsequent analysis, we focused on 398 samples that had paired-end read counts exceeding 20,000. These samples were selected to ensure sufficient data quality and were used to investigate the microbial patterns and associations related to the different disease phenotypes.

3.1. Diversity Analysis

The alpha diversity analysis revealed that HC individuals had a significantly richer microbiome compared to the UC patients (p < 0.01) and the CD patients (p < 0.05), as shown in Figure 1a–c. However, there were no significant differences in alpha diversity indices between CD and UC, except for Chao1.
In all three beta diversity principal coordinates analysis (PCoA) plots of the phylotype distribution, the HC samples were stretched along PCoA2 (Figure 1d–f). While some IBD samples overlapped with HC, the others were spread far along PCoA1.
These results from the beta diversity analysis align with the taxonomic distribution depicted in Figure 2. The Lachnospiraceae family was the most abundant family across all three groups. Although the HC group exhibited a significantly lower abundance of the Flavobacteriaceae family compared to IBD, no substantial taxonomic differences were observed among the IBD subgroups at the family level. The top 10 family groups are listed based on their abundance.

3.2. Multi-Class Machine Learning Model Based on PLS-DA

To identify the main sources of variation, we conducted an initial analysis using principal component analysis (PCA) on the normalized log-transformed abundance values of the saliva microbiome data obtained from ANCOM-BC. The PCA results revealed the presence of two clusters; however, these clusters were not associated with the disease phenotype, consistent with the findings from the beta diversity PCoA plots. Specifically, there was no clear separation or clustering of the HC, CD, and UC samples along the first two principal components of the data (Figure 3a).
To develop a diagnostic model, we initially constructed a partial least squares discriminant analysis (PLS-DA) model capable of classifying the multi-class phenotypes. We examined the sample plot generated from this model (Figure 3b). While the plot displayed a slightly improved clustering of samples based on their phenotypes compared to the PCA plot, it remained challenging to distinguish between the three phenotypes using a single model alone.
Nevertheless, we proceeded to develop a multi-class machine learning model using the sparse PLS-DA method. The entire dataset was divided into training and test sets using a balanced split scheme, with 70% of the samples assigned to the training set (CD: n = 87, UC: n = 122, HC: n = 69) and 30% assigned to the test set (CD: n = 37, UC: n = 53, HC: n = 30). This process was repeated 100 times with different splits to ensure robustness.
In each run, we applied PLS-DA to the training set, determining the optimal number of components based on the trend of the overall error rate. Feature selection was performed through tuning processes to identify the most relevant components and phylotypes. The final sPLS-DA model for each run was defined using these optimal components and phylotypes. The performance of each model was then evaluated using the corresponding test set.
Table 2 presents the performance metrics from the 100 runs. Overall, the multi-class model demonstrated good classification of the healthy control (HC) group, but it did not perform as well for the IBD phenotypes.

3.3. Hierarchical Diagnosis Models Based on PLS-DA and sPLS-DA

In the previous step, it was observed that the multi-class model did not perform optimally in distinguishing all three phenotypes. To improve the accuracy of classification, we made the decision to develop two separate diagnostic models: one model for distinguishing between IBD and HC samples, and another model for classifying IBD samples into CD or UC. By employing these two models in a hierarchical manner, it becomes possible to classify an input sample into one of the three phenotypic classes.

3.3.1. Development of a Prediction Model That Classifies IBD vs. HC

The binary classification dataset was generated by combining the CD and UC classes into a single IBD class, while keeping the HC class unchanged. This merging operation was performed separately for both the training set (70%: HC, n = 69; IBD, n = 209) and the test set (30%: HC, n = 30; IBD, n = 90). The entire machine learning process, including model training and evaluation, was applied to each of the 100 different splits described earlier. Table S1 displays the top 10 genera that were selected with high frequency in the final models. The performance of the models was then averaged across these splits to obtain an overall assessment of their effectiveness.
A sample plot from one of the 100 final models demonstrated a clear separation between IBD and HC samples, although there was some overlap observed (Figure 4a). To evaluate the performance of each model, we predicted the phenotypes of individuals in the respective test sets. The classification of IBD versus HC achieved a mean accuracy of 0.908 (0.808–0.967), sensitivity of 0.919 (0.8–1), specificity of 0.974 (0.633–1), precision of 0.957 (0.887–1), and AUC of 0.967 (0.916–0.995) (Table 3). The AUROC plot of the test set prediction results for one of the 100 models is shown in Figure 4b. These performance metrics indicate that the models achieved high accuracy in distinguishing between IBD and HC samples.

3.3.2. Development of a Prediction Model That Classifies CD vs. UC

For the development of the model that distinguishes IBD samples into CD or UC, we kept only the CD and UC samples from the original 100 splits of the training (70%: CD, n = 87; UC, n = 122) and test (30% CD, n = 37; UC, n = 53) sets. Using this subset of data, sPLS-DA models were constructed for each split following the same procedure as described earlier. In Table S2, the top 10 genera, which were chosen with high frequency in the final models, are presented. This entire process was repeated 100 times, and the average performance was evaluated.
A representative PLS projection plot showed a clear distinction between CD and UC individuals (Figure 5a). This indicates that the model was able to effectively differentiate between the two subtypes of IBD based on the microbiome data.
To assess the performance of the trained sPLS-DA models, the phenotypes of individuals in the corresponding test sets were predicted. The classification results from the 100 test sets showed a mean accuracy of 0.846 (0.744–0.922), sensitivity of 0.82 (0.595–0.973), specificity of 0.864 (0.679–0.962), precision of 0.812 (0.646–0.936), and AUC of 0.923 (0.829–0.978) (Table 4). Figure 5b displays the AUROC plot illustrating the prediction results of the test set from one of the 100 models. These performance metrics demonstrate that the models were capable of classifying IBD into CD and UC with a considerable level of accuracy.

3.3.3. Evaluation of the Hierarchical Model

The two models were combined into a hierarchical model that classifies an input sample into three classes. In the first step, the samples are classified as either IBD or HC. Only the samples classified as IBD in the first step are further classified into CD or UC. We evaluated the performance of this model using the test sets. The results presented in Table 5 indicate that the mean accuracy, HC sensitivity, HC precision, CD sensitivity, CD precision, UC sensitivity, and UC precision were 0.803 (0.658–0.892), 0.875 (0.633–1), 0.791 (0.581–1), 0.791 (0.595–0.919), 0.792 (0.6–0.968), 0.77 (0.547–0.925), and 0.833 (0.682–0.932), respectively.

4. Discussion

This study revealed distinct taxonomic distributions in saliva samples between IBD patients and healthy controls, as well as the ability to differentiate between patients with Crohn’s disease (CD) and ulcerative colitis (UC). Exploring the oral microbiome as a potential diagnostic tool for IBD offers several advantages over fecal microbiome analysis. Firstly, collecting oral samples is less invasive and generally more acceptable to patients compared to collecting fecal samples. Secondly, the oral microbiome exhibits greater stability over time and is less likely to be influenced by short-term dietary changes, potentially providing a more reliable marker of long-term microbial trends. Lastly, utilizing the oral microbiome for early IBD diagnosis allows for prompt intervention before significant gut damage occurs. Hence, we opted to utilize saliva samples instead of fecal samples in our study.
We successfully identified a total of 2711 phylotypes through taxonomic assignment of 16S rRNA sequencing data from saliva samples using Kraken2 and a series of filtering processes. The number of taxa classified in our study is sufficient to assess microbial diversity and compares favorably to previous studies [23,24]. Consistent with previous research [25,26], our findings indicate that the oral microbiome of IBD patients differs from that of healthy controls in terms of both alpha and beta diversity. Regarding alpha diversity analysis, we observed a significant difference in microbial richness between the healthy controls (HCs) and patients with ulcerative colitis (UC) (p < 0.01), as well as between HCs and patients with Crohn’s disease (CD) (p < 0.05). These results suggest that the oral microbiome of HC individuals is more diverse compared to those of UC and CD patients. Furthermore, our beta diversity analysis revealed heterogeneous microbiome profiles among IBD patients. While some IBD samples exhibited similarities to HC, others showed distinct differences. This indicates that the overall composition of the oral microbiome can vary significantly in patients with IBD, with some individuals displaying a profile closer to that of HC and others displaying a distinct microbial pattern. Overall, these findings provide valuable insights into the oral microbiome characteristics associated with IBD and highlight the complexity of the microbial changes observed in this condition.
The oral cavity indeed exhibits lower microbial diversity compared to the gut. The gut microbiota is known for its remarkable diversity, with hundreds to thousands of different bacterial species. In contrast, the oral cavity faces unique challenges, including exposure to air, fluctuations in temperature and pH, and limited availability of nutrients between meals. These factors contribute to a narrower range of microbes that can thrive in the oral environment [27]. Additionally, saliva contains antimicrobial compounds such as lysozyme and lactoferrin, which can restrict microbial growth. Despite its lower taxonomic diversity, the oral microbiome plays crucial roles in maintaining overall health and can contribute to disease development. It is an integral part of the human microbiota [28]. It is important to note that although the gut microbiota generally exhibits higher diversity, the oral microbiota can vary significantly between individuals and can be influenced by factors such as oral hygiene practices, diet, and tobacco smoking. These factors can further contribute to the interindividual variability observed in the oral microbiome composition.
Machine learning (ML) is a subfield of artificial intelligence (AI) that empowers computers to learn from data and make predictions or take actions without explicit programming. ML has found applications in various domains, including healthcare. In the context of IBD diagnosis, ML techniques can be utilized with diverse data sources, such as endoscopic images, histopathology slides, blood tests, fecal biomarkers, and electronic health records [29]. The gut microbiome, in particular, holds great promise as a valuable data source for ML-based approaches in IBD. It represents the complex interplay between the host and the environment, offering valuable insights into the pathogenesis and prognosis of the disease. By leveraging ML algorithms, researchers and clinicians can analyze and interpret the vast amounts of microbial data to identify patterns, biomarkers, and predictive models that aid in the diagnosis, treatment, and prognosis of IBD.
ML can be applied to analyze the microbiome data for IBD diagnosis. ML can be used to (1) classify samples into different microbiome groups based on their composition or function, (2) predict continuous outcomes based on the microbiome features, (3) group samples into clusters based on their microbiome similarity, (4) reduce the complexity and noise of high-dimensional microbiome data, and (5) discover associations between the microbiome and other variables of interest. Several studies [17,19,30,31,32] have evaluated the performance of ML models for microbiome analysis in IBD diagnosis using different datasets, methods, and metrics. Overall, ML models have demonstrated good accuracy, sensitivity, specificity, and area under the curve (AUC) for IBD diagnosis.
In our study, we employed sPLS-DA, which is a computationally efficient method that yields interpretable results through graphical outputs. sPLS-DA is particularly valuable in high-dimensional datasets, where numerous variables may be irrelevant or redundant. When applied to microbiome data, sPLS-DA can help identify a subset of microbial species that exhibit the highest predictive power for a specific outcome, such as disease status (e.g., IBD vs. healthy control). The key advantage of utilizing sPLS-DA in this context is its ability to handle high-dimensional data, effectively manage correlations, and identify the most significant microbial species for predicting the outcome.
While machine learning (ML) holds significant potential for improving the diagnosis of IBD patients based on their microbiome data, there are several challenges and limitations that must be addressed before widespread adoption of ML in clinical practice. Firstly, ML models rely on large and diverse datasets that accurately represent the target population, with well-annotated, standardized, and validated data. Without such robust datasets, the performance and generalizability of ML models can be compromised. Secondly, ML models often exhibit complexity and opaqueness, making it challenging to comprehend how they arrive at decisions and which features they prioritize. This lack of interpretability can hinder trust and acceptance from clinicians and patients, as well as impeding error identification and bias mitigation. Thirdly, ML models necessitate testing and validation on independent and external datasets that encompass diverse settings, populations, and scenarios. This ensures the robustness and reliability of the models in real-world applications. Lastly, the integration of ML models into existing clinical workflows and systems, such as electronic health records or mobile applications, is crucial. Furthermore, evaluating the clinical impact, cost-effectiveness, and user satisfaction of ML models is necessary to gauge their overall utility and practicality. Addressing these challenges and limitations will be pivotal in harnessing the full potential of ML for enhancing the diagnosis and management of IBD patients based on their microbiome data.
Hence, future research on ML for microbiome analysis in IBD diagnosis should focus on the following: (1) Developing and sharing high-quality datasets for microbiome analysis in IBD diagnosis that are large, diverse, standardized, and annotated. (2) Applying explainable AI techniques to enhance the transparency and interpretability of ML models for microbiome analysis in IBD diagnosis. (3) Conducting rigorous external validation and clinical trials to assess the performance and utility of ML models for microbiome analysis in IBD diagnosis. (4) Collaborating with multidisciplinary teams to design and implement user-friendly and clinically relevant ML solutions for microbiome analysis in IBD diagnosis.
As we found that sPLS-DA models with differently divided training sets were able to distinguish IBD vs. HC with high performance (average accuracy = 0.908, sensitivity = 0.919, precision = 0.957, AUC = 0.966) and distinguish CD vs. UC with average accuracy 0.846, sensitivity 0.82, precision 0.812, and AUC = 923 in the prediction of the corresponding test sets, our study employed machine learning techniques to identify potential oral microbial markers to distinguish not only IBD and HC, but also CD and UC. The distinctive microbial patterns associated with each disease can provide valuable insights for their differential diagnosis.
Machine learning has revolutionized how we analyze complex biological data, offering an unparalleled ability to detect patterns and correlations within highly multidimensional datasets [33]. In this study, we employed machine learning to discern between CD and UC, focusing on the oral microbiome. This strategy yielded promising results, suggesting potential for the application of such techniques in differential diagnosis. The success of this study is primarily premised on the growing evidence that the human microbiome—and particularly the oral microbiome—has implications for IBD.
However, it is important to acknowledge the limitations of our research. Firstly, we were not able to identify a specific strain that was consistently associated with IBD patients. This highlights the complexity of the oral microbiome and its interactions with the gut microbiome, which are still not fully understood. While our study identified potential microbial markers, further investigations are needed to elucidate their functional implications and the underlying mechanisms linking these oral microbial markers to the development of CD and UC. Additionally, although machine learning provided valuable insights in our study, its widespread adoption in routine clinical practice is hindered by the requirement for significant computational resources and expertise. Overcoming these challenges and refining these tools to enhance accessibility and ease of use will be crucial for their practical implementation [34,35]. Finally, although the purpose of this study was to assess the predictive performance of the saliva microbiome alone, it would be highly reasonable to improve the model’s performance by incorporating additional types of data, such as clinical data. Therefore, we intend to pursue this approach in future investigations.
In summary, while our research presents early promise for the use of oral microbial markers in the diagnosis and differentiation of IBD, there is a need for further research to address the limitations and fully explore the functional significance of these markers. Furthermore, efforts should be made to optimize machine learning techniques for clinical application in order to realize their potential in improving patient care.

5. Conclusions

Our study offers preliminary but promising evidence regarding the potential usefulness of oral microbial markers in diagnosing IBD compared to healthy controls, as well as in differentiating between CD and UC. The application of machine learning models has facilitated these advancements. The development of noninvasive diagnostic methods, based on these findings, could greatly enhance our ability to diagnose, distinguish, and effectively manage IBD. This, in turn, could pave the way for personalized medicine approaches in the field of IBD.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/microorganisms11071665/s1, Table S1: Top10 genera selected with high frequency in the IBD vs. HC sPLS-DA models. Table S2: Top10 genera selected with high frequency in the CD vs. UC sPLS-DA models.

Author Contributions

Conceptualization: D.-I.P.; data curation: C.-W.L., H.K., S.K., S.-B.K., S.-K.P., K.O.K., G.-S.S., M.S.K., J.M.C. and J.S.K.; funding acquisition: D.-I.P.; methodology: D.-I.P.; software: H.K. and S.K.; formal analysis: S.-B.K., H.K., J.K. and S.K.; resources: D.-I.P.; writing—original draft preparation: S.-B.K., H.K., and S.K.; writing—review and editing: S.-B.K., H.K., S.K. and D.-I.P.; project administration: D.-I.P. All authors have read and agreed to the published version of the manuscript.

Funding

This research was supported by a grant from the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health and Welfare of the Republic of Korea (grant number: HI23C0661), supported by a National Research Foundation (NRF) grant funded by the Korean government (NRF 2020R1A2B5B02002259) and by a grant from WooDuk Scholarship Foundation to the Korean Association for the Study of Intestinal Diseases for 2020.

Institutional Review Board Statement

This study was conducted in accordance with the Declaration of Helsinki and approved by the Institutional Review Board (or Ethics Committee) of Kangbuk Samsung Hospital and each center (protocol code: KBSMC 2016-07-029, date of approval: 18 October 2016).

Informed Consent Statement

Written informed consent has been obtained from the patients to publish this paper.

Data Availability Statement

The raw 16S rRNA amplicon sequences generated in this study have been deposited in the Korean Nucleotide Archive (KoNA) operated by the Korea Bioinformation Center (KOBIC) under accession code PRJKA230590.

Acknowledgments

S.K. and H.K. acknowledge that the computational resources were kindly provided by the Korea Institute of Science and Technology Information (GSDC and KREONET).

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Podolsky, D.K. Inflammatory Bowel Disease. N. Engl. J. Med. 2002, 347, 417–429. [Google Scholar] [CrossRef] [PubMed]
  2. Abreu, M.T. The pathogenesis of inflammatory bowel disease: Translational implications for clinicians. Curr. Gastroenterol. Rep. 2002, 4, 481–489. [Google Scholar] [CrossRef]
  3. Korzenik, J.R.; Podolsky, D.K. Evolving knowledge and therapy of inflammatory bowel disease. Nat. Rev. Drug Discov. 2006, 5, 197–209. [Google Scholar] [CrossRef] [PubMed]
  4. Noor, N.M.; Sousa, P.; Paul, S.; Roblin, X. Early Diagnosis, Early Stratification, and Early Intervention to Deliver Precision Medicine in IBD. Inflamm. Bowel Dis. 2021, 28, 1254–1264. [Google Scholar] [CrossRef] [PubMed]
  5. Moazzami, B.; Moazzami, K.; Rezaei, N. Early onset inflammatory bowel disease: Manifestations, genetics and diagnosis. Turk. J. Pediatr. 2019, 61, 637–647. [Google Scholar] [CrossRef]
  6. Na, S.-Y.; Moon, W. Recent advances in surveillance colonoscopy for dysplasia in inflammatory bowel disease. Clin. Endosc. 2022, 55, 726–735. [Google Scholar] [CrossRef]
  7. Khor, B.; Gardet, A.; Xavier, R.J. Genetics and pathogenesis of inflammatory bowel disease. Nature 2011, 474, 307–317. [Google Scholar] [CrossRef] [Green Version]
  8. Loftus, E.V.; Sandborn, W.J. Epidemiology of inflammatory bowel disease. Gastroenterol. Clin. N. Am. 2002, 31, 1–20. [Google Scholar] [CrossRef]
  9. Andres, P.G.; Friedman, L.S. Epidemiology and the Natural Course of Inflammatory Bowel Disease. Gastroenterol. Clin. N. Am. 1999, 28, 255–281. [Google Scholar] [CrossRef]
  10. Ni, J.; Wu, G.D.; Albenberg, L.; Tomov, V.T. Gut microbiota and IBD: Causation or correlation? Nat. Rev. Gastroenterol. Hepatol. 2017, 14, 573–584. [Google Scholar] [CrossRef] [Green Version]
  11. Elmaghrawy, K.; Hussey, S.; Moran, G.P. The Oral Microbiome in Pediatric IBD: A Source of Pathobionts or Biomarkers? Front. Pediatr. 2021, 8, 620254. [Google Scholar] [CrossRef] [PubMed]
  12. Qi, Y.; Wu, H.-M.; Yang, Z.; Zhou, Y.-F.; Jin, L.; Yang, M.-F.; Wang, F.-Y. New Insights into the Role of Oral Microbiota Dysbiosis in the Pathogenesis of Inflammatory Bowel Disease. Dig. Dis. Sci. 2021, 67, 42–55. [Google Scholar] [CrossRef]
  13. Xun, Z.; Zhang, Q.; Xu, T.; Chen, N.; Chen, F. Dysbiosis and Ecotypes of the Salivary Microbiome Associated With Inflammatory Bowel Diseases and the Assistance in Diagnosis of Diseases Using Oral Bacterial Profiles. Front. Microbiol. 2018, 9, 1136. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  14. Docktor, M.J.; Paster, B.J.; Abramowicz, S.; Ingram, J.; Wang, Y.E.; Correll, M.; Jiang, H.; Cotton, S.L.; Kokaras, A.S.; Bousvaros, A. Alterations in diversity of the oral microbiome in pediatric inflammatory bowel disease. Inflamm. Bowel Dis. 2012, 18, 935–942. [Google Scholar] [CrossRef] [PubMed]
  15. Somineni, H.K.; Weitzner, J.H.; Venkateswaran, S.; Dodd, A.; Prince, J.; Karikaran, A.; Sauer, C.G.; Abramowicz, S.; Zwick, M.; Cutler, D.J.; et al. Site- and Taxa-Specific Disease-Associated Oral Microbial Structures Distinguish Inflammatory Bowel Diseases. Inflamm. Bowel Dis. 2021, 27, 1889–1900. [Google Scholar] [CrossRef] [PubMed]
  16. Lam, G.; Albarrak, H.; McColl, C.J.; Pizarro, A.; Sanaka, H.; Gomez-Nguyen, A.; Cominelli, F.; da Silva, A.P.B. The Oral-Gut Axis: Periodontal Diseases and Gastrointestinal Disorders. Inflamm. Bowel Dis. 2022, izac241. [Google Scholar] [CrossRef]
  17. Manandhar, I.; Alimadadi, A.; Aryal, S.; Munroe, P.B.; Joe, B.; Cheng, X. Gut microbiome-based supervised machine learning for clinical diagnosis of inflammatory bowel diseases. Am. J. Physiol. Liver Physiol. 2021, 320, G328–G337. [Google Scholar] [CrossRef]
  18. Gubatan, J.; Levitte, S.; Patel, A.; Balabanis, T.; Wei, M.T.; Sinha, S.R. Artificial intelligence applications in inflammatory bowel disease: Emerging technologies and future directions. World J. Gastroenterol. 2021, 27, 1920–1935. [Google Scholar] [CrossRef]
  19. Kubinski, R.; Djamen-Kepaou, J.-Y.; Zhanabaev, T.; Hernandez-Garcia, A.; Bauer, S.; Hildebrand, F.; Korcsmaros, T.; Karam, S.; Jantchou, P.; Kafi, K.; et al. Benchmark of Data Processing Methods and Machine Learning Models for Gut Microbiome-Based Diagnosis of Inflammatory Bowel Disease. Front. Genet. 2022, 13, 784397. [Google Scholar] [CrossRef]
  20. Lê Cao, K.-A.; Boitard, S.; Besse, P. Sparse PLS discriminant analysis: Biologically relevant feature selection and graphical displays for multiclass problems. BMC Bioinform. 2011, 12, 253. [Google Scholar] [CrossRef] [Green Version]
  21. Park, S.-K.; Kim, S.; Lee, G.-Y.; Kim, S.-Y.; Kim, W.; Lee, C.-W.; Park, J.-L.; Choi, C.-H.; Kang, S.-B.; Kim, T.-O.; et al. Development of a Machine Learning Model to Distinguish between Ulcerative Colitis and Crohn’s Disease Using RNA Sequencing Data. Diagnostics 2021, 11, 2365. [Google Scholar] [CrossRef] [PubMed]
  22. Shin, S.Y.; Kim, S.; Choi, J.W.; Kang, S.-B.; Kim, T.O.; Seo, G.S.; Cha, J.M.; Chun, J.; Jung, Y.; Im, J.P.; et al. The Common and Unique Pattern of Microbiome Profiles among Saliva, Tissue, and Stool Samples in Patients with Crohn’s Disease. Microorganisms 2022, 10, 1467. [Google Scholar] [CrossRef] [PubMed]
  23. Molinero, N.; Taladrid, D.; Zorraquín-Peña, I.; de Celis, M.; Belda, I.; Mira, A.; Bartolomé, B.; Moreno-Arribas, M.V. Ulcerative Colitis Seems to Imply Oral Microbiome Dysbiosis. Curr. Issues Mol. Biol. 2022, 44, 1513–1527. [Google Scholar] [CrossRef] [PubMed]
  24. Ribaldone, D.G.; Brigo, S.; Mangia, M.; Saracco, G.M.; Astegiano, M.; Pellicano, R. Oral Manifestations of Inflammatory Bowel Disease and the Role of Non-Invasive Surrogate Markers of Disease Activity. Medicines 2020, 7, 33. [Google Scholar] [CrossRef]
  25. Amos, G.C.A.; Sergaki, C.; Logan, A.; Iriarte, R.; Bannaga, A.; Chandrapalan, S.; Wellington, E.M.H.; Rijpkema, S.; Arasaradnam, R.P. Exploring how microbiome signatures change across inflammatory bowel disease conditions and disease locations. Sci. Rep. 2021, 11, 18699. [Google Scholar] [CrossRef]
  26. Lin, H.; Das Peddada, S. Analysis of microbial compositions: A review of normalization and differential abundance analysis. npj Biofilms Microbiomes 2020, 6, 60. [Google Scholar] [CrossRef]
  27. López, R.L.; Burgos, M.J.G.; Gálvez, A.; Perez-Pulido, R. The human gastrointestinal tract and oral microbiota in inflammatory bowel disease: A state of the science review. Apmis 2016, 125, 3–10. [Google Scholar] [CrossRef]
  28. Abdelbary, M.M.H.; Hatting, M.; Bott, A.; Dahlhausen, A.; Keller, D.; Trautwein, C.; Conrads, G. The oral-gut axis: Salivary and fecal microbiome dysbiosis in patients with inflammatory bowel disease. Front. Cell. Infect. Microbiol. 2022, 12, 1010853. [Google Scholar] [CrossRef]
  29. Ahmad, H.A.; East, J.E.; Panaccione, R.; Travis, S.; Canavan, J.B.; Usiskin, K.; Byrne, M.F. Artificial intelligence in inflammatory bowel disease: Implications for clinical practice and future directions. Intest. Res. 2023. epub ahead of print. [Google Scholar] [CrossRef]
  30. Liñares-Blanco, J.; Fernandez-Lozano, C.; Seoane, J.A.; López-Campos, G. Machine Learning Based Microbiome Signature to Predict Inflammatory Bowel Disease Subtypes. Front. Microbiol. 2022, 13, 872671. [Google Scholar] [CrossRef]
  31. Zuo, W.; Wang, B.; Bai, X.; Luan, Y.; Fan, Y.; Michail, S.; Sun, F. 16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis. Sci. Rep. 2022, 12, 6421. [Google Scholar] [CrossRef]
  32. Ma, S.; Shungin, D.; Mallick, H.; Schirmer, M.; Nguyen, L.H.; Kolde, R.; Franzosa, E.; Vlamakis, H.; Xavier, R.; Huttenhower, C. Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin. Genome Biol. 2022, 23, 208. [Google Scholar] [CrossRef] [PubMed]
  33. Yin, J.; Sternes, P.R.; Wang, M.; Song, J.; Morrison, M.; Li, T.; Zhou, L.; Wu, X.; He, F.; Zhu, J.; et al. Shotgun metagenomics reveals an enrichment of potentially cross-reactive bacterial epitopes in ankylosing spondylitis patients, as well as the effects of TNFi therapy upon microbiome composition. Ann. Rheum. Dis. 2019, 79, 132–140. [Google Scholar] [CrossRef] [PubMed]
  34. Min, S.; Lee, B.; Yoon, S. Deep learning in bioinformatics. Brief. Bioinform. 2016, 18, 851–869. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  35. Ching, T.; Himmelstein, D.S.; Beaulieu-Jones, B.K.; Kalinin, A.A.; Do, B.T.; Way, G.P.; Ferrero, E.; Agapow, P.-M.; Zietz, M.; Hoffman, M.M.; et al. Opportunities and obstacles for deep learning in biology and medicine. J. R. Soc. Interface 2018, 15, 20170387. [Google Scholar] [CrossRef] [PubMed] [Green Version]
Microorganisms 11 01665 g001 550
Figure 1. Diversity plots. Alpha diversity indices (Chao1 (a), Shannon (b), and Pielou evenness (c)) of the microbial communities in the three disease phenotype groups are represented as violin plots. The Wilcoxon test was used to measure the significance of the alpha diversity differences between disease phenotypes. *, **, ****, and ns correspond to p < 0.05, p < 0.01, p < 0.0001, and non-significance, respectively. PCoA plots were based on three beta diversity indices: Jaccard dissimilarity (d), Bray−Curtis dissimilarity (e), and the Yue and Clayton measure of dissimilarity (f). F- and p-values were calculated by a PERMANOVA test with 1000 permutations.
Figure 1. Diversity plots. Alpha diversity indices (Chao1 (a), Shannon (b), and Pielou evenness (c)) of the microbial communities in the three disease phenotype groups are represented as violin plots. The Wilcoxon test was used to measure the significance of the alpha diversity differences between disease phenotypes. *, **, ****, and ns correspond to p < 0.05, p < 0.01, p < 0.0001, and non-significance, respectively. PCoA plots were based on three beta diversity indices: Jaccard dissimilarity (d), Bray−Curtis dissimilarity (e), and the Yue and Clayton measure of dissimilarity (f). F- and p-values were calculated by a PERMANOVA test with 1000 permutations.
Microorganisms 11 01665 g001
Microorganisms 11 01665 g002 550
Figure 2. Taxonomic composition bar plot of saliva samples from HC, CD, and UC groups at the family level.
Figure 2. Taxonomic composition bar plot of saliva samples from HC, CD, and UC groups at the family level.
Microorganisms 11 01665 g002
Microorganisms 11 01665 g003 550
Figure 3. Principal component analysis (a) and PLS−DA (b) plots of saliva microbiome data. Normalized log-transformed abundance values from ANCOM−BC were used.
Figure 3. Principal component analysis (a) and PLS−DA (b) plots of saliva microbiome data. Normalized log-transformed abundance values from ANCOM−BC were used.
Microorganisms 11 01665 g003
Microorganisms 11 01665 g004 550
Figure 4. (a) A representative PLS projection onto the subspace spanned by the two components of the sPLS−DA model developed for classifying IBD vs. HC. The ellipses for each class represent the 95% confidence levels of discrimination. (b) Area under the receiver operating characteristic curve (AUROC) for the predictions on the validation set of the representative model.
Figure 4. (a) A representative PLS projection onto the subspace spanned by the two components of the sPLS−DA model developed for classifying IBD vs. HC. The ellipses for each class represent the 95% confidence levels of discrimination. (b) Area under the receiver operating characteristic curve (AUROC) for the predictions on the validation set of the representative model.
Microorganisms 11 01665 g004
Microorganisms 11 01665 g005 550
Figure 5. (a) A representative PLS projection onto the subspace spanned by the two components of the sPLS−DA model developed for classifying CD and UC. The ellipses for each class represent the 95% confidence levels of discrimination. (b) Area under the receiver operating characteristic curve (AUROC) for the predictions on the test set of the representative model.
Figure 5. (a) A representative PLS projection onto the subspace spanned by the two components of the sPLS−DA model developed for classifying CD and UC. The ellipses for each class represent the 95% confidence levels of discrimination. (b) Area under the receiver operating characteristic curve (AUROC) for the predictions on the test set of the representative model.
Microorganisms 11 01665 g005
Table
Table 1. Baseline demographic and clinical characteristics of participants.
Table 1. Baseline demographic and clinical characteristics of participants.
CD (n = 127)UC (n = 175)HC (n = 100)
Age (year), mean ± SD37.6 ± 11.639.4 ± 15.637.4 ± 14.5
Male, n (%)97 (76.4)124 (70.9)50 (50)
BMI (kg/m2), mean ± SD20.8 ± 4.123 ± 3.1
Smoking status, n (%)
Current20 (15.7)23 (13.1)
Former5 (3.9)37 (21.1)
Never101 (79.5)112 (64)
Unknown1 (0.8)3 (1.7)
Disease location, n (%)Ileum, 28 (22)Proctitis, 69 (39.4)
Colon, 25 (19.7)Distal, 57 (32.6)
Ileocolon, 71 (55.9)Extensive, 45 (25.7)
Ileocolon + upper GI, 1 (0.8)
Unknown, 2 (1.6)Unknown, 4 (2.3)
SD, standard deviation; BMI, body mass index.
Table
Table 2. Evaluation metrics from prediction using multi-class models.
Table 2. Evaluation metrics from prediction using multi-class models.
AccurayCD Sens.CD Prec.UC Sens.UC Prec.HC Sens.HC Prec.AUC
Min.0.5250.4050.4420.3770.5740.6330.4760.650
1st Qu.0.6170.5950.5650.4910.6650.80.6190.759
Median0.6580.6760.6240.5280.7050.8670.6590.801
Mean0.6530.6660.6150.5320.70.850.6520.819
3rd Qu.0.6830.730.6590.5660.7380.90.6930.898
Max.0.7580.9190.8080.7550.85210.8390.968
Sens, sensitivity; Prec, precision. Evaluation metrics were calculated from each of 100 models.
Table
Table 3. Evaluation metrics from prediction using IBD vs. HC models.
Table 3. Evaluation metrics from prediction using IBD vs. HC models.
AccuracySensitivitySpecificityPrecisionAUC
Min.0.8080.80.6330.8870.916
1st Qu.0.8920.90.8330.9430.954
Median0.9080.9170.8670.9550.967
Mean0.9080.9190.9740.9570.966
3rd Qu.0.9250.9440.9330.9770.979
Max.0.9671110.995
Evaluation metrics were calculated from each of 100 models.
Table
Table 4. Evaluation metrics from prediction using CD vs. UC models.
Table 4. Evaluation metrics from prediction using CD vs. UC models.
AccuracySensitivitySpecificityPrecisionAUC
Min.0.7440.5950.6790.6460.829
1st Qu.0.8220.7840.830.7670.899
Median0.8440.8240.870.8160.928
Mean0.8460.820.8640.8120.923
3rd Qu.0.8780.8720.9060.8570.949
Max.0.9220.9730.9620.9360.978
Evaluation metrics were calculated from each of 100 models.
Table
Table 5. Evaluation metrics from prediction using hierarchical models.
Table 5. Evaluation metrics from prediction using hierarchical models.
AccurayCD Sens.CD Prec.UC Sens.UC Prec.HC Sens.HC Prec.
Min.0.6580.5950.60.5470.6820.6330.581
1st Qu.0.7830.730.7380.7170.7990.8330.741
Median0.80.7970.7950.7640.8370.8670.784
Mean0.8030.7910.7920.770.8330.8750.791
3rd Qu.0.8250.8650.8440.830.8670.9330.839
Max.0.8920.9190.9680.9250.93211
Sens, sensitivity; Prec, precision. Evaluation metrics were calculated from each of 100 models.
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

MDPI and ACS Style

Kang, S.-B.; Kim, H.; Kim, S.; Kim, J.; Park, S.-K.; Lee, C.-W.; Kim, K.O.; Seo, G.-S.; Kim, M.S.; Cha, J.M.; et al. Potential Oral Microbial Markers for Differential Diagnosis of Crohn’s Disease and Ulcerative Colitis Using Machine Learning Models. Microorganisms 2023, 11, 1665. https://doi.org/10.3390/microorganisms11071665

AMA Style

Kang S-B, Kim H, Kim S, Kim J, Park S-K, Lee C-W, Kim KO, Seo G-S, Kim MS, Cha JM, et al. Potential Oral Microbial Markers for Differential Diagnosis of Crohn’s Disease and Ulcerative Colitis Using Machine Learning Models. Microorganisms. 2023; 11(7):1665. https://doi.org/10.3390/microorganisms11071665

Chicago/Turabian Style

Kang, Sang-Bum, Hyeonwoo Kim, Sangsoo Kim, Jiwon Kim, Soo-Kyung Park, Chil-Woo Lee, Kyeong Ok Kim, Geom-Seog Seo, Min Suk Kim, Jae Myung Cha, and et al. 2023. "Potential Oral Microbial Markers for Differential Diagnosis of Crohn’s Disease and Ulcerative Colitis Using Machine Learning Models" Microorganisms 11, no. 7: 1665. https://doi.org/10.3390/microorganisms11071665

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop