1
|
Liu Q, Shi K, Bai Y, Yang F, Lei C, Wang X, Hu Y, Wang S, Wang R, Yu Y, Liu X, Yu X, Zhang L, Tang L, Li S, Meng Q. Biology of tongue coating in different disease stages of RA and its value in disease progression. Microb Pathog 2024; 191:106644. [PMID: 38616001 DOI: 10.1016/j.micpath.2024.106644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/04/2024] [Accepted: 04/10/2024] [Indexed: 04/16/2024]
Abstract
OBJECTIVE To assess and compare the composition of tongue coating microbiota among patients at different stages of rheumatoid arthritis (RA). METHODS A total of 47 patients diagnosed with RA, as per the American College of Rheumatology criteria, and 10 healthy individuals were enrolled in this study. The RA patients were stratified considering their Disease Activity Score 28 (DAS28), a composite measure based on the 28 tender and swollen joint count and erythrocyte sedimentation rate (ESR). The study population was further categorized into active phase group (LMH group) and inactive phase group (RE group) according to their DAS28 values. DNA extraction was extracted from tongue coating samples. Subsequently, the V3-V4 16S rDNA region was selectively amplified and sequenced through high-throughput 16S rDNA analysis. The resulting data were then utilized to ascertain the microbial contents. RESULTS Significant variations were observed in the tongue coating microbiota of patients with RA during active and inactive phases, in comparison to healthy individuals (p < 0.05). At the genus level, the presence of Prevotellan, Veillonella, Rothia, and Neisseria in RA patients was notably more evident than in the healthy control (HC) group. These disparities find support in existing research on gut and oral microbiota. During the active phase of RA, the relative abundance of Veillonella, Rothia, and Neisseria in the tongue coating microbiota of patients was significantly higher than in those with inactive RA. These findings underscore the need for further and in-depth research on the potential impact of these microorganisms on the progression of RA disease. CONCLUSION The results substantiate the hypothesis that tongue coating microbes actively contribute to the progression of RA.
Collapse
Affiliation(s)
- Qian Liu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Kangle Shi
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, China.
| | - Yunjing Bai
- Department of Rheumatism and Immunology, Seventh Medical Center of PLA General Hospital, Beijing, China
| | - Fangyan Yang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Cong Lei
- School of Basic Medicine, Heilongjiang University of Chinese Medicine, China
| | - Xiaocong Wang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Ying Hu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Shiyao Wang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Ruikun Wang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yuefan Yu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaoyu Liu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China; Department of Nephropathy and Endocrinology, Dongzhimen Hospital of Beijing University of Chinese Medicine, Beijing, China
| | - Xinping Yu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Lingling Zhang
- Department of Rheumatology and Clinical Immunology, Beijing Shijitan Hospital, Capital Medical University, China
| | - Ling Tang
- Nursing Department, DongFang Hospital of Beijing University of Chinese Medicine, China
| | - Suqian Li
- Department of Rheumatism, DongFang Hospital of Beijing University of Chinese Medicine, China
| | - Qinggang Meng
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China.
| |
Collapse
|
2
|
Yang J, Ding D, Zhang X, Gu H. A comparative analysis of soil physicochemical properties and microbial community structure among four shelterbelt species in the northeast China plain. Microbiol Spectr 2024; 12:e0368323. [PMID: 38376351 PMCID: PMC10986494 DOI: 10.1128/spectrum.03683-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024] Open
Abstract
Conducting studies that focus on the alterations occurring in the soil microbiome within protection forests in the northeast plain is of utmost importance in evaluating the ecological rehabilitation of agricultural lands in the Mollisols region. Nevertheless, the presence of geographic factors contributes to substantial disparities in the microbiomes, and thus, addressing this aspect of influence becomes pivotal in ensuring the credibility of the collected data. Consequently, the objective is to compare the variations in soil physicochemical properties and microbial community structure within the understory of diverse shelterbelt species. In this study, we analyzed the understory soils of Juglans mandshurica (Jm), Fraxinus mandschurica (Fm), Acer mono (Am), and Betula platyphylla (Bp) from the same locality. We employed high-throughput sequencing technology and soil physicochemical data to investigate the impact of these different tree species on soil microbial communities, chemical properties, and enzyme activities in Mollisols areas. Significant variations in soil nutrients and enzyme activities were observed among tree species, with soil organic matter content ranging from 49.1 to 67.7 g/kg and cellulase content ranging from 5.3 to 524.0 μg/d/g. The impact of tree species on microbial diversities was found to be more pronounced in the bacterial community (Adnoism: R = 0.605) compared to the fungal community (Adnoism: R = 0.433). The linear discriminant analysis effect size (LEfSe) analysis revealed a total of 5 (Jm), 3 (Bp), and 6 (Am) bacterial biomarkers, as well as 2 (Jm), 6 (Fm), 4 (Bp), and 1 (Am) fungal biomarker at the genus level (LDA3). The presence of various tree species was observed to significantly alter the relative abundance of specific microbial community structures, specifically in Gammaproteobacteria, Ascomycota, and Basidiomycota. Furthermore, environmental factors, such as pH, total potassium, and available phosphorus were important factors influencing changes in bacterial communities. We propose that Fm be utilized as the primary tree species for establishing farmland protection forests in the northeastern region, owing to its superior impact on enhancing soil quality. IMPORTANCE The focal point of this study lies in the implementation of a controlled experiment conducted under field conditions. In this experiment, we deliberately selected four shelterbelts within the same field, characterized by identical planting density, and planting year. This deliberate selection effectively mitigated the potential impact of extraneous factors on the three microbiomes, thereby enhancing the reliability and validity of our findings.
Collapse
Affiliation(s)
- Jia Yang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Dang Ding
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Xiuru Zhang
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Huiyan Gu
- School of Forestry, Northeast Forestry University, Harbin, China
| |
Collapse
|
3
|
Lei C, Xu Y, Zhang S, Huang C, Qin J. The role of microbiota in gastric cancer: A comprehensive review. Helicobacter 2024; 29:e13071. [PMID: 38643366 DOI: 10.1111/hel.13071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/19/2024] [Accepted: 03/25/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Gastric cancer (GC) continues to pose a significant global threat in terms of cancer-related fatalities. Despite notable advancements in medical research and therapies, further investigation is warranted to elucidate its underlying etiology and risk factors. Recent times have witnessed an escalated emphasis on comprehending the role of the microbiota in cancer development. METHODS This review briefly delves into recent developments in microbiome-related research pertaining to gastric cancer. RESULTS According to studies, the microbiota can influence GC growth by inciting inflammation, disrupting immunological processes, and generating harmful microbial metabolites. Furthermore, there is ongoing research into how the microbiome can impact a patient's response to chemotherapy and immunotherapy. CONCLUSION The utilization of the microbiome for detecting, preventing, and managing stomach cancer remains an active area of exploration.
Collapse
Affiliation(s)
- Changzhen Lei
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yitian Xu
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shaopeng Zhang
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Huang
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Qin
- Department of General Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
4
|
Yang J, He J, Jia L, Gu H. Integrating metagenomics and metabolomics to study the response of microbiota in black soil degradation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 899:165486. [PMID: 37442461 DOI: 10.1016/j.scitotenv.2023.165486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 07/15/2023]
Abstract
As the largest commercial food production base and ecological security barrier, land degradation in black soil areas seriously threatens the global food supply and natural ecosystems. Therefore, determining the response of soil microbiota is crucial to restoring degraded soils. This study combined metagenomics and metabolomics to investigate the effect of different degrees of soil degradation on microbial community composition and metabolic function in black soils. It was found that alpha diversity in degraded soils (Shannon: 22.3) was higher than in nondegraded soil (ND) (Shannon: 21.8), and the degree of degradation significantly altered the structure and composition of soil microbial communities. The results of LEfSe analysis obtained 9 (ND), 7 (lightly degraded, LD), 10 (moderately degraded, MD), and 1 (severely degraded, SD) biomarkers in four samples. Bradyrhizobium, Sphingomonas, and Ramlibacter were significantly affected by soil degradation and can be considered biomarkers of ND, MD, and SD, respectively. Soil nutrient and enzyme activities decreased significantly with increasing black soil degradation, soil organic matter (SOM) content decreased from 11.12 % to 1.97 %, and Sucrase decreased from 23.53 to 6.59 mg/g/d. In addition, C was the critical driver affecting microbial community structure, contributing 61.2 % to differences in microbial community distribution, and microbial altering relative abundance which participle in the carbon cycle to respond to soil degradation. Metabolomic analyses indicated that soil degradation significantly modified the soil metabolite spectrum, and the metabolic functions of most microorganisms responding to soil degradation were adversely affected. The combined multi-omics analysis further indicated that biomarkers dominate in accumulating metabolites. These findings confirmed that due to their role in the composition and functioning of these degraded soils, these biomarkers could be employed in strategies for managing and restoring degraded black soils.
Collapse
Affiliation(s)
- Jia Yang
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Jianhu He
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Lin Jia
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Huiyan Gu
- School of Forestry, Northeast Forestry University, Harbin 150040, China.
| |
Collapse
|
5
|
Chen J, Nie S, Qiu X, Zheng S, Ni C, Yuan Y, Gong Y. Leveraging existing 16S rRNA microbial data to identify diagnostic biomarker in Chinese patients with gastric cancer: a systematic meta-analysis. mSystems 2023; 8:e0074723. [PMID: 37787561 PMCID: PMC10654077 DOI: 10.1128/msystems.00747-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/11/2023] [Indexed: 10/04/2023] Open
Abstract
IMPORTANCE Gastric cancer is a significant and growing health problem in China. Studies have revealed significant differences in gastric microbiota between patients with gastric cancer and non-cancerous patients, suggesting that microbiota may play a role in tumorigenesis. In this meta-analysis, existing 16S rRNA microbial data were analyzed to find combinations consisting of five genera, which had good efficacy in distinguishing gastric cancer from non-cancerous patients in multiple types of samples. These results lend support to the use of microbial markers in detecting gastric cancer. Moreover, these biomarkers are plausible candidates for further mechanistic research into the role of the microbiota in tumorigenesis.
Collapse
Affiliation(s)
- Jijun Chen
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of Cancer Etiology and Prevention, Liaoning Education Department, The First Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of GI Cancer Etiology and Prevention, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Siru Nie
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of Cancer Etiology and Prevention, Liaoning Education Department, The First Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of GI Cancer Etiology and Prevention, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xunan Qiu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of Cancer Etiology and Prevention, Liaoning Education Department, The First Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of GI Cancer Etiology and Prevention, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Shuwen Zheng
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of Cancer Etiology and Prevention, Liaoning Education Department, The First Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of GI Cancer Etiology and Prevention, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Chuxuan Ni
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of Cancer Etiology and Prevention, Liaoning Education Department, The First Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of GI Cancer Etiology and Prevention, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of Cancer Etiology and Prevention, Liaoning Education Department, The First Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of GI Cancer Etiology and Prevention, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yuehua Gong
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of Cancer Etiology and Prevention, Liaoning Education Department, The First Hospital of China Medical University, Shenyang, Liaoning, China
- Key Laboratory of GI Cancer Etiology and Prevention, The First Hospital of China Medical University, Shenyang, Liaoning, China
| |
Collapse
|
6
|
Cho H, Ren Z, Divaris K, Roach J, Lin BM, Liu C, Azcarate-Peril MA, Simancas-Pallares MA, Shrestha P, Orlenko A, Ginnis J, North KE, Zandona AGF, Ribeiro AA, Wu D, Koo H. Selenomonas sputigena acts as a pathobiont mediating spatial structure and biofilm virulence in early childhood caries. Nat Commun 2023; 14:2919. [PMID: 37217495 PMCID: PMC10202936 DOI: 10.1038/s41467-023-38346-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 04/21/2023] [Indexed: 05/24/2023] Open
Abstract
Streptococcus mutans has been implicated as the primary pathogen in childhood caries (tooth decay). While the role of polymicrobial communities is appreciated, it remains unclear whether other microorganisms are active contributors or interact with pathogens. Here, we integrate multi-omics of supragingival biofilm (dental plaque) from 416 preschool-age children (208 males and 208 females) in a discovery-validation pipeline to identify disease-relevant inter-species interactions. Sixteen taxa associate with childhood caries in metagenomics-metatranscriptomics analyses. Using multiscale/computational imaging and virulence assays, we examine biofilm formation dynamics, spatial arrangement, and metabolic activity of Selenomonas sputigena, Prevotella salivae and Leptotrichia wadei, either individually or with S. mutans. We show that S. sputigena, a flagellated anaerobe with previously unknown role in supragingival biofilm, becomes trapped in streptococcal exoglucans, loses motility but actively proliferates to build a honeycomb-like multicellular-superstructure encapsulating S. mutans, enhancing acidogenesis. Rodent model experiments reveal an unrecognized ability of S. sputigena to colonize supragingival tooth surfaces. While incapable of causing caries on its own, when co-infected with S. mutans, S. sputigena causes extensive tooth enamel lesions and exacerbates disease severity in vivo. In summary, we discover a pathobiont cooperating with a known pathogen to build a unique spatial structure and heighten biofilm virulence in a prevalent human disease.
Collapse
Affiliation(s)
- Hunyong Cho
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhi Ren
- Biofilm Research Laboratories, Center for Innovation & Precision Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kimon Divaris
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jeffrey Roach
- UNC Information Technology Services and Research Computing, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bridget M Lin
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chuwen Liu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Andrea Azcarate-Peril
- UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Miguel A Simancas-Pallares
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Poojan Shrestha
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alena Orlenko
- Artificial Intelligence Innovation Lab, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jeannie Ginnis
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Apoena Aguiar Ribeiro
- Division of Diagnostic Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Di Wu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Hyun Koo
- Biofilm Research Laboratories, Center for Innovation & Precision Dentistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Orthodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
7
|
Yuan L, Yang L, Zhang S, Xu Z, Qin J, Shi Y, Yu P, Wang Y, Bao Z, Xia Y, Sun J, He W, Chen T, Chen X, Hu C, Zhang Y, Dong C, Zhao P, Wang Y, Jiang N, Lv B, Xue Y, Jiao B, Gao H, Chai K, Li J, Wang H, Wang X, Guan X, Liu X, Zhao G, Zheng Z, Yan J, Yu H, Chen L, Ye Z, You H, Bao Y, Cheng X, Zhao P, Wang L, Zeng W, Tian Y, Chen M, You Y, Yuan G, Ruan H, Gao X, Xu J, Xu H, Du L, Zhang S, Fu H, Cheng X. Development of a tongue image-based machine learning tool for the diagnosis of gastric cancer: a prospective multicentre clinical cohort study. EClinicalMedicine 2023; 57:101834. [PMID: 36825238 PMCID: PMC9941057 DOI: 10.1016/j.eclinm.2023.101834] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Tongue images (the colour, size and shape of the tongue and the colour, thickness and moisture content of the tongue coating), reflecting the health state of the whole body according to the theory of traditional Chinese medicine (TCM), have been widely used in China for thousands of years. Herein, we investigated the value of tongue images and the tongue coating microbiome in the diagnosis of gastric cancer (GC). METHODS From May 2020 to January 2021, we simultaneously collected tongue images and tongue coating samples from 328 patients with GC (all newly diagnosed with GC) and 304 non-gastric cancer (NGC) participants in China, and 16 S rDNA was used to characterize the microbiome of the tongue coating samples. Then, artificial intelligence (AI) deep learning models were established to evaluate the value of tongue images and the tongue coating microbiome in the diagnosis of GC. Considering that tongue imaging is more convenient and economical as a diagnostic tool, we further conducted a prospective multicentre clinical study from May 2020 to March 2022 in China and recruited 937 patients with GC and 1911 participants with NGC from 10 centres across China to further evaluate the role of tongue images in the diagnosis of GC. Moreover, we verified this approach in another independent external validation cohort that included 294 patients with GC and 521 participants with NGC from 7 centres. This study is registered at ClinicalTrials.gov, NCT01090362. FINDINGS For the first time, we found that both tongue images and the tongue coating microbiome can be used as tools for the diagnosis of GC, and the area under the curve (AUC) value of the tongue image-based diagnostic model was 0.89. The AUC values of the tongue coating microbiome-based model reached 0.94 using genus data and 0.95 using species data. The results of the prospective multicentre clinical study showed that the AUC values of the three tongue image-based models for GCs reached 0.88-0.92 in the internal verification and 0.83-0.88 in the independent external verification, which were significantly superior to the combination of eight blood biomarkers. INTERPRETATION Our results suggest that tongue images can be used as a stable method for GC diagnosis and are significantly superior to conventional blood biomarkers. The three kinds of tongue image-based AI deep learning diagnostic models that we developed can be used to adequately distinguish patients with GC from participants with NGC, even early GC and precancerous lesions, such as atrophic gastritis (AG). FUNDING The National Key R&D Program of China (2021YFA0910100), Program of Zhejiang Provincial TCM Sci-tech Plan (2018ZY006), Medical Science and Technology Project of Zhejiang Province (2022KY114, WKJ-ZJ-2104), Zhejiang Provincial Research Center for Upper Gastrointestinal Tract Cancer (JBZX-202006), Natural Science Foundation of Zhejiang Province (HDMY22H160008), Science and Technology Projects of Zhejiang Province (2019C03049), National Natural Science Foundation of China (82074245, 81973634, 82204828), and Chinese Postdoctoral Science Foundation (2022M713203).
Collapse
Key Words
- AFP, alpha fetoprotein
- AG, atrophic gastritis
- AI, artificial intelligence
- APINet, attentive pairwise interaction neural network
- AUC, area under the curve
- Artificial intelligence
- BC, breast cancer
- CA, carbohydrate antigen
- CEA, carcinoembryonic antigen
- CRC, colorectal cancer
- DT, decision tree learning
- EC, esophageal cancer
- GC, gastric cancer
- Gastric cancer
- HBPC, hepatobiliary pancreatic carcinoma
- HC, healthy control
- KNN, K-nearest neighbours
- LC, lung cancer
- NGC, non-gastric cancers
- PCoA, principal coordinates analysis
- SG, superficial gastritis
- SVM, support vector machine
- TCM, traditional Chinese medicine
- Tongue coating microbiome
- Tongue images
- Traditional Chinese medicine
- TransFG, transformer architecture for fine-grained recognition
Collapse
Affiliation(s)
- Li Yuan
- Department of Gastric Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Zhejiang Provincial Research Center for Upper Gastrointestinal Tract Cancer, Zhejiang Cancer Hospital, Hangzhou, 310022, China
- Zhejiang Key Lab of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Lin Yang
- Artificial Intelligence and Biomedical Images Analysis Lab, School of Engineering, Westlake University, China
| | - Shichuan Zhang
- Artificial Intelligence and Biomedical Images Analysis Lab, School of Engineering, Westlake University, China
| | - Zhiyuan Xu
- Department of Gastric Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Zhejiang Provincial Research Center for Upper Gastrointestinal Tract Cancer, Zhejiang Cancer Hospital, Hangzhou, 310022, China
- Zhejiang Key Lab of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Jiangjiang Qin
- Department of Gastric Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Zhejiang Provincial Research Center for Upper Gastrointestinal Tract Cancer, Zhejiang Cancer Hospital, Hangzhou, 310022, China
- Zhejiang Key Lab of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Yunfu Shi
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China
- Oncology Department, Tongde Hospital of Zhejiang Province, Hangzhou, 310012, China
| | - Pengcheng Yu
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yi Wang
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Zhehan Bao
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yuhang Xia
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jiancheng Sun
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325099, China
| | - Weiyang He
- Department of Gastrointestinal Surgery, Sichuan Cancer Hospital, Chengdu, 610042, China
| | - Tianhui Chen
- Department of Gastric Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xiaolei Chen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325099, China
| | - Can Hu
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yunlong Zhang
- Artificial Intelligence and Biomedical Images Analysis Lab, School of Engineering, Westlake University, China
| | - Changwu Dong
- College of Traditional Chinese Medicine, Anhui University of Traditional Chinese Medicine, HeFei, 230038, China
| | - Ping Zhao
- Department of Gastrointestinal Surgery, Sichuan Cancer Hospital, Chengdu, 610042, China
| | - Yanan Wang
- College of Traditional Chinese Medicine, Anhui University of Traditional Chinese Medicine, HeFei, 230038, China
| | - Nan Jiang
- College of Traditional Chinese Medicine, Anhui University of Traditional Chinese Medicine, HeFei, 230038, China
| | - Bin Lv
- Department of Gastroenterology, First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yingwei Xue
- Gastrointestinal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Baoping Jiao
- Department of General Surgery, Shanxi Cancer Hospital, Taiyuan, 030013, China
| | - Hongyu Gao
- Gastrointestinal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Kequn Chai
- Oncology Department, Tongde Hospital of Zhejiang Province, Hangzhou, 310012, China
| | - Jun Li
- Department of General Surgery, Shanxi Cancer Hospital, Taiyuan, 030013, China
| | - Hao Wang
- Gastrointestinal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Xibo Wang
- Gastrointestinal Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Xiaoqing Guan
- Department of Gastric Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xu Liu
- Department of Gastrointestinal Surgery, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Gang Zhao
- Department of Gastrointestinal Surgery, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Zhichao Zheng
- Department of Gastric Surgery, Cancer Hospital of China Medical University (Liaoning Cancer Hospital and Institute), Shenyang, 110042, China
| | - Jie Yan
- Department of Gastric Surgery, Cancer Hospital of China Medical University (Liaoning Cancer Hospital and Institute), Shenyang, 110042, China
| | - Haiyue Yu
- Department of Gastric Surgery, Cancer Hospital of China Medical University (Liaoning Cancer Hospital and Institute), Shenyang, 110042, China
| | - Luchuan Chen
- Department of Gastrointestinal Surgery, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, 350014, China
| | - Zaisheng Ye
- Department of Gastrointestinal Surgery, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, 350014, China
| | - Huaqiang You
- Department of Gastroenterology, Yuhang District People's Hospital, Hangzhou, 311199, China
| | - Yu Bao
- Department of Gastrointestinal Surgery, Sichuan Cancer Hospital, Chengdu, 610042, China
| | - Xi Cheng
- Department of Gastrointestinal Surgery, Sichuan Cancer Hospital, Chengdu, 610042, China
| | - Peizheng Zhao
- Department of Health Management Center, Yueyang Central Hospital, Yueyang, 414000, China
| | - Liang Wang
- Department of Endoscopy Center, Kecheng District People's Hospital, Quzhou, 324000, China
| | - Wenting Zeng
- Department of General Surgery, Shanxi Cancer Hospital, Taiyuan, 030013, China
| | - Yanfei Tian
- Department of Gastric Surgery, Cancer Hospital of China Medical University (Liaoning Cancer Hospital and Institute), Shenyang, 110042, China
| | - Ming Chen
- Department of Endoscopy Center, Shandong Cancer Hospital, Shandong, 250117, China
| | - You You
- Department of Health Management Center, Zigong Fourth People's Hospital, Zigong, 643099, China
| | - Guihong Yuan
- Department of Gastroenterology, Hainan Cancer Hospital, Hainan, 570312, China
| | - Hua Ruan
- Department of Chinese Surgery, Linping District Hospital of Traditional Chinese Medicine, Hangzhou, 311100, China
| | - Xiaole Gao
- The First Affiliated Hospital of Henan University of Science and Technology, Zhengzhou, 450062, China
| | - Jingli Xu
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Handong Xu
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Lingbin Du
- Department of Gastric Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Shengjie Zhang
- Department of Gastric Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Huanying Fu
- Department of Gastric Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Xiangdong Cheng
- Department of Gastric Surgery, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institutes of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Zhejiang Provincial Research Center for Upper Gastrointestinal Tract Cancer, Zhejiang Cancer Hospital, Hangzhou, 310022, China
- Zhejiang Key Lab of Prevention, Diagnosis and Therapy of Upper Gastrointestinal Cancer, Zhejiang Cancer Hospital, Hangzhou, 310022, China
- Corresponding author. Department of Gastric surgery, Zhejiang Cancer Hospital, Banshan Road 1#, Hangzhou, Zhejiang, 310022, China.
| |
Collapse
|
8
|
Ma C, Zhang P, Du S, Li Y, Li S. Construction of Tongue Image-Based Machine Learning Model for Screening Patients with Gastric Precancerous Lesions. J Pers Med 2023; 13:jpm13020271. [PMID: 36836505 PMCID: PMC9968136 DOI: 10.3390/jpm13020271] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/25/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Screening patients with precancerous lesions of gastric cancer (PLGC) is important for gastric cancer prevention. The accuracy and convenience of PLGC screening could be improved with the use of machine learning methodologies to uncover and integrate valuable characteristics of noninvasive medical images related to PLGC. In this study, we therefore focused on tongue images and for the first time constructed a tongue image-based PLGC screening deep learning model (AITongue). The AITongue model uncovered potential associations between tongue image characteristics and PLGC, and integrated canonical risk factors, including age, sex, and Hp infection. Five-fold cross validation analysis on an independent cohort of 1995 patients revealed the AITongue model could screen PLGC individuals with an AUC of 0.75, 10.3% higher than that of the model with only including canonical risk factors. Of note, we investigated the value of the AITongue model in predicting PLGC risk by establishing a prospective PLGC follow-up cohort, reaching an AUC of 0.71. In addition, we developed a smartphone-based app screening system to enhance the application convenience of the AITongue model in the natural population from high-risk areas of gastric cancer in China. Collectively, our study has demonstrated the value of tongue image characteristics in PLGC screening and risk prediction.
Collapse
Affiliation(s)
- Changzheng Ma
- Institute of TCM-X/MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Peng Zhang
- Institute of TCM-X/MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Shiyu Du
- Department of Gastroenterology, China-Japan Friendship Hospital, Chaoyang District, Beijing 100029, China
| | - Yan Li
- Department of Traditional Chinese Medicine, Yijishan Hospital of Wannan Medical College, Wuhu 241000, China
| | - Shao Li
- Institute of TCM-X/MOE Key Laboratory of Bioinformatics, Bioinformatics Division, BNRist/Department of Automation, Tsinghua University, Beijing 100084, China
- Correspondence:
| |
Collapse
|
9
|
Zhang Y, Zhao H, Guo Y, Meng Y, Yu S, Pan B, Zhai X. Relationship between thick or greasy tongue-coating microbiota and tongue diagnosis in patients with primary liver cancer. Front Microbiol 2022; 13:903616. [PMID: 36643409 PMCID: PMC9835093 DOI: 10.3389/fmicb.2022.903616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 09/20/2022] [Indexed: 12/30/2022] Open
Abstract
Tongue diagnosis is a unique aspect of traditional Chinese medicine for diagnosing diseases before determining proper means of treatment, but it also has the disadvantage of relying on the subjective experience of medical practitioners and lack objective basis. The purpose of this article is to elucidate tongue-coating microbiota and metabolic differences in primary liver cancer (PLC) patients with thick or greasy tongue coatings. Tongue-coating samples were analyzed in 60 PLC patients (30 PLC with thick or greasy tongue-coating patients and 30 PLC with tongue-coating neither thick nor greasy) and 25 healthy controls (HC) using 16S rRNA gene sequencing technology. As compared to healthy individuals, tongue coatings of patients with PLC had elevated levels of Firmicutes and Actinobacteria. The abundance of Fusobacteria, SR1_Absconditabacteria_, and Spirochaete were higher in tongue coatings of healthy controls compared to samples in patients with PLC. In addition to site-specific differences, higher abundances of Fusobacteria and Actinobacteria were observed in thick or greasy tongue-coating patients as compared to non-thick and greasy tongue-coating patients. The inferred metagenomic pathways enriched in the PLC tongue-coating patients were mainly those involved in replication, recombination, and repair of protein. We also identify a tongue-coating microbiome signature to discriminate HC and PLC, including 15 variables on genus level. The prediction performance of the signature showed well in the training and validation cohorts. This research illustrates specific clinical features and bacterial structures in PLC patients with different tongue coatings, which facilitates understanding of the traditional tongue diagnosis.
Collapse
Affiliation(s)
- Yuren Zhang
- Department of Traditional Chinese Medicine, Changhai Hospital, Naval Military Medical University, Shanghai, China,Department of Gastroenterology, Shanghai Jiading Hospital of Traditional Chinese Medicine, Shanghai, China
| | - Hetong Zhao
- Department of Traditional Chinese Medicine, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Yuyu Guo
- Department of Traditional Chinese Medicine, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Yongbin Meng
- Department of Traditional Chinese Medicine, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Shasha Yu
- Department of Traditional Chinese Medicine, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Bo Pan
- Department of Traditional Chinese Medicine, Changhai Hospital, Naval Military Medical University, Shanghai, China
| | - Xiaofeng Zhai
- Department of Traditional Chinese Medicine, Changhai Hospital, Naval Military Medical University, Shanghai, China,*Correspondence: Xiaofeng Zhai
| |
Collapse
|
10
|
Zhu X, Ma Y, Guo D, Men J, Xue C, Cao X, Zhang Z. A Framework to Predict Gastric Cancer Based on Tongue Features and Deep Learning. MICROMACHINES 2022; 14:53. [PMID: 36677112 PMCID: PMC9865689 DOI: 10.3390/mi14010053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/05/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Gastric cancer has become a global health issue, severely disrupting daily life. Early detection in gastric cancer patients and immediate treatment contribute significantly to the protection of human health. However, routine gastric cancer examinations carry the risk of complications and are time-consuming. We proposed a framework to predict gastric cancer non-invasively and conveniently. A total of 703 tongue images were acquired using a bespoke tongue image capture instrument, then a dataset containing subjects with and without gastric cancer was created. As the images acquired by this instrument contain non-tongue areas, the Deeplabv3+ network was applied for tongue segmentation to reduce the interference in feature extraction. Nine tongue features were extracted, relationships between tongue features and gastric cancer were explored by using statistical methods and deep learning, finally a prediction framework for gastric cancer was designed. The experimental results showed that the proposed framework had a strong detection ability, with an accuracy of 93.6%. The gastric cancer prediction framework created by combining statistical methods and deep learning proposes a scheme for exploring the relationships between gastric cancer and tongue features. This framework contributes to the effective early diagnosis of patients with gastric cancer.
Collapse
Affiliation(s)
- Xiaolong Zhu
- Key Laboratory of Instrumentation Science & Dynamic Measurement, School of Instrument and Electronics, North University of China, Taiyuan 030051, China
| | - Yuhang Ma
- Key Laboratory of Instrumentation Science & Dynamic Measurement, School of Instrument and Electronics, North University of China, Taiyuan 030051, China
| | - Dong Guo
- Shanxi University of Chinese Medicine, Taiyuan 030051, China
| | - Jiuzhang Men
- Shanxi University of Chinese Medicine, Taiyuan 030051, China
| | - Chenyang Xue
- Key Laboratory of Instrumentation Science & Dynamic Measurement, School of Instrument and Electronics, North University of China, Taiyuan 030051, China
| | - Xiyuan Cao
- Key Laboratory of Instrumentation Science & Dynamic Measurement, School of Instrument and Electronics, North University of China, Taiyuan 030051, China
| | - Zhidong Zhang
- Key Laboratory of Instrumentation Science & Dynamic Measurement, School of Instrument and Electronics, North University of China, Taiyuan 030051, China
| |
Collapse
|
11
|
Li C, Xu S, Xiang C, Xu S, Zhou Q, Zhang J. The gut microbiota of silkworm are altered by antibiotic exposure. FEBS Open Bio 2022; 12:2203-2212. [PMID: 36287136 PMCID: PMC9714379 DOI: 10.1002/2211-5463.13502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/12/2022] [Accepted: 10/25/2022] [Indexed: 01/25/2023] Open
Abstract
In recent years, antibiotics have frequently been detected in soil, lakes, and rivers. Antibiotic residues in the environment may alter microbial structure and cause bacterial resistance, but their effect on interactions among host microbiota is still poorly understood. To investigate this issue, here we used silkworm (Bombyx mori) fed on antibiotic-treated mulberry leaf as a model to explore the effects of antibiotic exposure on gut bacteria and fungi. We observed that elimination of fungi significantly reduced bacterial richness and diversity in silkworm intestine after exposure to the antifungal amphotericin B, while the elimination of bacteria dramatically increased the richness and diversity of fungi after exposure to the antibacterial ampicillin-streptomycin. Thus, antibiotic-treated mulberry leaf significantly altered the community structure of microbiota in the gut of silkworm. Clearance of gut bacteria enhanced the correlation between gut fungi and leaf-derived fungi, while clearance of gut fungi promoted abnormal proliferation of gut bacteria. These data provide a simple model to explore the comprehensive effect of diet-derived bacteria, fungi, and antibiotics on gut microbiota.
Collapse
Affiliation(s)
- Chengxu Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life SciencesNanjing Normal UniversityChina,Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Shuo Xu
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicalChina
| | - Chunjie Xiang
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicalChina
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life SciencesNanjing Normal UniversityChina
| | - Qihai Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life SciencesNanjing Normal UniversityChina
| | - Junfeng Zhang
- School of Medicine & Holistic Integrative MedicineNanjing University of Chinese MedicalChina
| |
Collapse
|
12
|
Hua Z, Shen R, Lu B, Li M, Zhou P, Wu J, Dong W, Zhou Q, Zhang J. Weifuchun alters tongue flora and decreases serum trefoil factor I levels in gastric intestinal metaplasia: A CONSORT-compliant article. Medicine (Baltimore) 2022; 101:e31407. [PMID: 36397419 PMCID: PMC9666156 DOI: 10.1097/md.0000000000031407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 09/29/2022] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE To explore the molecular mechanisms of Weifuchun in the treatment of gastric intestinal metaplasia (GIM), we designed a preclinical pilot study to examine potential markers of disease progression based on alterations in the tongue flora. METHODS Total 27 patients with GIM were treated with Weifuchun for 4 weeks and 26 volunteers as controls. Tongue coating bacteria were profiled using 16S rDNA high-throughput sequencing. Serum pepsinogen I and II levels were detected using the latex immunoturbidimetric assay. The levels of serum trefoil factor I was detected by ELISA. Microplate-based quantification was used to detect serum total bile acid (TBA). RESULTS After treatment, the relative abundance of 4 dominant tongue coating genera (Granulicatella, Gemella, Lachnoanaerobaculum, and Neisseria) increased significantly wheras Alloprevotella, [Eubacterium] nodatum group, Prevotell, and Ruminococcaceae UCG-014 decreased (P < .05). The results showed that Alloprevotella and 3 rare tongue coating genera (Lautropia, Treponema 2, and Aliihoeflea) might be potential markers or target flora for the treatment of GIM. Kyoto encyclopedia of genes and genomes (KEGG) function prediction analysis showed that Weifuchun may regulate bile secretion and folate biosynthesis in patients with GIM. The level of serum trefoil factor I decreased significantly in response to Weifuchun treatment, which was consistent with the decrease in folate biosynthesis predicted by KEGG. CONCLUSION Weifuchun may restore the balance of tongue flora by decreasing the levels of serum trefoil factor I, thereby providing a new way to measuring the underlying effectiveness and potential mechanisms of action of this traditional Chinese medicinal compound in the treatment of GIM.
Collapse
Affiliation(s)
- Zhaolai Hua
- Institute of Tumor Prevention and Control, People’s Hospital of Yangzhong City, Yangzhong, China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Rui Shen
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medical, Nanjing, China
| | - Bin Lu
- Department of Oncology, People’s Hospital of Yangzhong City, Yangzhong, China
| | - Meifeng Li
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medical, Nanjing, China
| | - Ping Zhou
- Institute of Tumor Prevention and Control, People’s Hospital of Yangzhong City, Yangzhong, China
| | - Juan Wu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medical, Nanjing, China
| | - Wei Dong
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medical, Nanjing, China
| | - Qihai Zhou
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, China
| | - Junfeng Zhang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medical, Nanjing, China
| |
Collapse
|
13
|
Jiang X, Cheng H, Zhang N, Xu S, An L, Yan L, Niu F, Jia B. Study on syndrome rules of stagnated heat in liver and stomach of non-erosive reflux disease based on microecology of tongue coating. Medicine (Baltimore) 2022; 101:e31618. [PMID: 36343090 PMCID: PMC9646630 DOI: 10.1097/md.0000000000031618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
INTRODUCTION At present, the pathogenesis of non-erosive reflux disease (NERD) is still unclear, and proton pump inhibitors are the main treatment drug. However, the effect is limited. Traditional Chinese medicine treatment of NERD has advantages. Stagnated heat in liver and stomach syndrome is the most important traditional Chinese medicine syndrome type of this disease. Tongue diagnosis is an important basis for the diagnosis of stagnated heat in liver and stomach syndrome. The microecology of tongue coating suggests the occurrence and development of disease. The purpose of this study aims to clarify the regular changes of tongue coating microecology in stagnated heat in liver and stomach syndrome of NERD. METHODS AND ANALYSIS This is a cross-sectional clinical trial. This study is divided into NERD stagnated heat in liver and stomach syndrome group, qi stagnation, and phlegm obstruction syndrome control group and normal control group, with 20 cases in each group. Tongue coating samples will be collected from 3 groups, and 16SrRNA gene sequencing technology will be used to detect the genome of tongue coating flora in patients with NERD with stagnated heat in liver and stomach syndrome, control group with qi stagnation and phlegm obstruction syndrome and normal control group. The main outcome measures are the distribution, diversity, and richness of the tongue flora in patients and healthy controls. DISCUSSION The results of this study will clarify the internal relationship between NERD stagnated heat in liver and stomach syndrome and the microecological changes in tongue coating.
Collapse
Affiliation(s)
- Xinqi Jiang
- Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Hongjie Cheng
- Fangshan Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Naiwei Zhang
- Fangshan Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Shanshan Xu
- Fangshan Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Libao An
- Fangshan Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Ling Yan
- Fangshan Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Fang Niu
- Fangshan Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
| | - Boyi Jia
- Fangshan Hospital, Beijing University of Chinese Medicine, Beijing, People’s Republic of China
- * Correspondence: Boyi Jia, Fangshan Hospital, Beijing University of Chinese Medicine, No. 4, Chengguan Jianbao Road, Fangshan District, Beijing 102488, People’s Republic of China (e-mail: )
| |
Collapse
|
14
|
Yuan Z, Liu Q, Pang Z, Fallah N, Liu Y, Hu C, Lin W. Sugarcane Rhizosphere Bacteria Community Migration Correlates with Growth Stages and Soil Nutrient. Int J Mol Sci 2022; 23:ijms231810303. [PMID: 36142216 PMCID: PMC9499485 DOI: 10.3390/ijms231810303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
Plants and rhizosphere bacterial microbiota have intimate relationships. As neighbors of the plant root system, rhizosphere microorganisms have a crucial impact on plant growth and health. In this study, we sampled rhizosphere soil of sugarcane in May (seedling), July (tillering), September (elongation) and November (maturity), respectively. We employ 16S rRNA amplicon sequencing to investigate seasonal variations in rhizosphere bacteria community structure and abundance, as well as their association with soil edaphic factors. The results demonstrate that soil pH, total nitrogen (TN) and available nitrogen (AN) decrease substantially with time. Rhizosphere bacteria diversity (Shannon) and the total enriched OTUs are also significantly higher in July relative to other months. Bacteria OTUs and functional composition exhibit a strong and significant correlation with soil temperature (Tem), suggesting that Tem was the potential determinant controlling rhizosphere bacteria diversity, enriched OTUs as well as functional composition. Redundancy analysis (RDA) point toward soil total potassium (TK), pH, TN, Tem and AN as principal determinant altering shifting bacteria community structure. Variation partitioning analysis (VPA) analysis further validate that a substantial proportion of variation (70.79%) detected in the rhizosphere bacteria community structure was attributed to edaphic factors. Mfuzz analysis classified the bacterial genera into four distinct clusters, with cluster two exhibiting a distinct and dramatic increase in July, predominantly occupied by Allocatelliglobosispora. The stochastic forest model found the key characteristic bacterial populations that can distinguish the four key growth periods of sugarcane. It may help us to answer some pending questions about the interaction of rhizosphere microorganisms with plants in the future.
Collapse
Affiliation(s)
- Zhaonian Yuan
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Province and Ministry Co-Sponsored Collaborative Innovation Center of Sugar Industry, Nanning 530000, China
- Correspondence:
| | - Qiang Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yueming Liu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agricultural, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chaohua Hu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agro-Ecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|
15
|
Saliva microbiome, dietary, and genetic markers are associated with suicidal ideation in university students. Sci Rep 2022; 12:14306. [PMID: 35995968 PMCID: PMC9395396 DOI: 10.1038/s41598-022-18020-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 08/03/2022] [Indexed: 11/09/2022] Open
Abstract
Here, salivary microbiota and major histocompatibility complex (MHC) human leukocyte antigen (HLA) alleles were compared between 47 (12.6%) young adults with recent suicidal ideation (SI) and 325 (87.4%) controls without recent SI. Several bacterial taxa were correlated with SI after controlling for sleep issues, diet, and genetics. Four MHC class II alleles were protective for SI including DRB1*04, which was absent in every subject with SI while present in 21.7% of controls. Increased incidence of SI was observed with four other MHC class II alleles and two MHC class I alleles. Associations between these HLA alleles and salivary bacteria were also identified. Furthermore, rs10437629, previously associated with attempted suicide, was correlated here with SI and the absence of Alloprevotella rava, a producer of an organic acid known to promote brain energy homeostasis. Hence, microbial-genetic associations may be important players in the diathesis-stress model for suicidal behaviors.
Collapse
|
16
|
Jiao J, Zheng Y, Zhang Q, Xia D, Zhang L, Ma N. Saliva microbiome changes in thyroid cancer and thyroid nodules patients. Front Cell Infect Microbiol 2022; 12:989188. [PMID: 36034695 PMCID: PMC9403763 DOI: 10.3389/fcimb.2022.989188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
Objective Thyroid disease has been reported to associate with gut microbiota, but the effects of thyroid cancer and thyroid nodules on the oral microbiota are still largely unknown. This study aimed to identify the variation in salivary microbiota and their potential association with thyroid cancer and thyroid nodules. Methods We used 16S rRNA high-throughput sequencing to examine the salivary microbiota of thyroid cancer patients (n = 14), thyroid nodules patients (n = 9), and healthy controls (n = 15). Results The alpha-diversity indices Chao1 and ACE were found to be relatively higher in patients with thyroid cancer and thyroid nodules compared to healthy controls. The beta diversity in both the thyroid cancer and thyroid nodules groups was divergent from the healthy control group. The genera Alloprevotella, Anaeroglobus, Acinetobacter, unclassified Bacteroidales, and unclassified Cyanobacteriales were significantly enriched in the thyroid cancer group compared with the healthy control group. In contrast, the microbiome of the healthy controls was mainly composed of the genera Haemophilus, Lautropia, Allorhizobium Neorhizobium Pararhizobium Rhizobium, Escherichia Shigella, and unclassified Rhodobacteraceae. The thyroid nodules group was dominated by genre uncultured Candidatus Saccharibacteria bacterium, unclassified Clostridiales bacterium feline oral taxon 148, Treponema, unclassified Prevotellaceae, Mobiluncus, and Acholeplasma. In contrast, the genera unclassified Rhodobacteraceae and Aggregatibacter dominated the healthy control group. The study also found that clinical indicators were correlated with the saliva microbiome. Conclusion The salivary microbiota variation may be connected with thyroid cancer and thyroid nodules.
Collapse
Affiliation(s)
- Junjun Jiao
- Hospital of Stomatology, Jilin University, Changchun, China
| | - Youli Zheng
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin, China
| | - Qingyu Zhang
- Hospital of Stomatology, Jilin University, Changchun, China
| | - Degeng Xia
- Hospital of Stomatology, Jilin University, Changchun, China
| | - Li Zhang
- Hospital of Stomatology, Jilin University, Changchun, China
- *Correspondence: Ning Ma, ; Li Zhang,
| | - Ning Ma
- Hospital of Stomatology, Jilin University, Changchun, China
- *Correspondence: Ning Ma, ; Li Zhang,
| |
Collapse
|
17
|
Microbial Characteristics of Common Tongue Coatings in Patients with Precancerous Lesions of the Upper Gastrointestinal Tract. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:7598427. [PMID: 35480154 PMCID: PMC9038387 DOI: 10.1155/2022/7598427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 03/10/2022] [Accepted: 03/12/2022] [Indexed: 12/24/2022]
Abstract
The tongue coating (TC) microbiota, a crucial component of the tongue coating, illustrates a huge microbial percentage of the body that mostly includes actinobacteria, bacteroides, firmicutes, and fusobacteria. The TC microbiota is closely related to the development of upper gastrointestinal malignancies, such as oral, gastric, and esophageal cancer. Nonetheless, the microbiological characteristics of common TCs in individuals with precancerous lesions of the upper gastrointestinal tract are still unclear. Herein, we designed a case-control study, recruiting 153 PLUGT patients with four different types of TCs, including 47 white-thin, 19 white-thick, 47 yellow-thin, and 40 yellow-thick, as well as 47 volunteers as controls. To analyze microbial characteristics, 16S rRNA microbiome approaches were used. An enzyme-linked immunosorbent assay (ELISA) was employed to assess serum IL-17A and total bile acid (TBA). According to the obtained results, Leptotrichia was found to be a promising biomarker for thin as well as thick yellow coatings. In comparison to the control TC microbiota, 39 different genera developed commensal networks in common TCs. Lachnoanaerobaculum and pseudonocardia were the most striking core bacteria. Lachnoanaerobaculum positively correlated with Leptotrichia in W-thin and Y-thick coatings, with actinomyces and methylobacterium in Y-thin coatings, with Campylobacter in Y-thick coatings, and with Bradyrhizobium in W-thick and Y-thick coatings. Serum IL-17A levels were greater in cases with W-thin coating than in controls, and serum IL-17A was positively linked with Parvimonas in patients with W-thick or Y-thin coating. In Y-thin coating, the oral dominating bacteria Streptococcus was negatively linked with serum TBA. Taken together, the promoted bacteria were found to be synergistically proliferative in the TCs of PLUGT patients. The diverse TCs had distinct bacterial commensal networks, whereas the common TCs were linked by specific bacteria to serum IL-17A and TBA.
Collapse
|
18
|
Guo XJ, Jiang T, Ma XX, Hu XJ, Huang JB, Cui LT, Cui J, Yao XH, Shi YL, Li J, Guo ZL, Lou JD, Liang MC, Fu HY, Yuan P, Liu JY, Tu LP, Xu JT. Relationships Between Diurnal Changes of Tongue Coating Microbiota and Intestinal Microbiota. Front Cell Infect Microbiol 2022; 12:813790. [PMID: 35433494 PMCID: PMC9008461 DOI: 10.3389/fcimb.2022.813790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/02/2022] [Indexed: 11/29/2022] Open
Abstract
The oral cavity and the intestine are the main distribution locations of human digestive bacteria. Exploring the relationships between the tongue coating and gut microbiota, the influence of the diurnal variations of the tongue coating microbiota on the intestinal microbiota can provide a reference for the development of the disease diagnosis and monitoring, as well as the medication time. In this work, a total of 39 healthy college students were recruited. We collected their tongue coating microbiota which was collected before and after sleep and fecal microbiota. The diurnal variations of tongue coating microbiota are mainly manifested on the changes in diversity and relative abundance. There are commensal bacteria in the tongue coating and intestines, especially Prevotella which has the higher proportion in both sites. The relative abundance of Prevotella in the tongue coating before sleep has a positive correlation with intestinal Prevotella; the r is 0.322 (p < 0.05). Bacteroides in the intestine had the most bacteria associated with the tongue coating and had the highest correlation coefficient with Veillonella in the oral cavity, which was 0.468 (p < 0.01). These results suggest that the abundance of the same flora in the two sites may have a common change trend. The SourceTracker results show that the proportion of intestinal bacteria sourced from tongue coating is less than 1%. It indicates that oral flora is difficult to colonize in the intestine in healthy people. This will provide a reference for the study on the oral and intestinal microbiota in diseases.
Collapse
Affiliation(s)
- Xiao-jing Guo
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Tao Jiang
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Xu-xiang Ma
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Xiao-juan Hu
- Shanghai Collaborative Innovation Center of Health Service in Traditional Chinese Medicine (TCM), Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Jing-bin Huang
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Long-tao Cui
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Ji Cui
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Xing-hua Yao
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Yu-lin Shi
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Jun Li
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Zhi-ling Guo
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Jin-di Lou
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Meng-chen Liang
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Hong-yuan Fu
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Pei Yuan
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Jia-yi Liu
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Li-ping Tu
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
- *Correspondence: Li-ping Tu, ; Jia-tuo Xu,
| | - Jia-tuo Xu
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
- *Correspondence: Li-ping Tu, ; Jia-tuo Xu,
| |
Collapse
|
19
|
Cui J, Hou S, Liu B, Yang M, Wei L, Du S, Li S. Species composition and overall diversity are significantly correlated between the tongue coating and gastric fluid microbiomes in gastritis patients. BMC Med Genomics 2022; 15:60. [PMID: 35300688 PMCID: PMC8932003 DOI: 10.1186/s12920-022-01209-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 03/01/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND In traditional Chinese medicine, it is believed that the "tongue coating is produced by fumigation of stomach gas", and that tongue coating can reflect the health status of humans, especially stomach health. Therefore, studying the relationship between the microbiome of the tongue coating and the gastric fluid is of great significance for understanding the biological basis of tongue diagnosis. METHODS This paper detected the microbiomes of the tongue coating and the gastric fluid in 35 gastritis patients using metagenomic sequencing technology, systematically constructed the microbial atlas of tongue coating and gastric juice, and first described the similar characteristics between the two sites. RESULTS There was a significant correlation between tongue coating and gastric juice in terms of microbial species composition and overall diversity. In terms of species composition, it was found that the two sites were dominated by five phyla, namely, Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria, and that most of the gastric microbial species could be detected from the patient's own tongue coating. In terms of overall diversity, a significant correlation was found between the alpha diversity of the tongue coating microbiome and the gastric juice microbiome. Furthermore, in terms of abundance, 4 classes, 2 orders, 4 families, 18 genera and 46 species were found to significantly correlate between the tongue coating and the gastric fluid. CONCLUSIONS The results provide microbiome-based scientific evidence for tongue diagnosis, and offer a new perspective for understanding the biological basis of tongue diagnosis.
Collapse
Affiliation(s)
- Jiaxing Cui
- Institute of TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRist / Department of Automation, Tsinghua University, Beijing, 100084, China.,China Industrial Control Systems Cyber Emergency Response Team, Beijing, 100040, China
| | - Siyu Hou
- Institute of TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRist / Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Bing Liu
- Beijing Lotus BioMedical Technology Co., Ltd., Beijing, 102206, China
| | - Mingran Yang
- Institute of TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRist / Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, 510060, China
| | - Shiyu Du
- China-Japan Friendship Hospital, Beijing, 100029, China.
| | - Shao Li
- Institute of TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRist / Department of Automation, Tsinghua University, Beijing, 100084, China. .,School of Life Sciences and Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.
| |
Collapse
|
20
|
Chao X, Zhang L, Hongqin L, Ziwei W, Dechuan L, Weidong D, Lu X, Haitao C, Bo Z, Haixing J, Qinghua Y. Faeces from malnourished colorectal cancer patients accelerate cancer progression. Clin Nutr 2022; 41:632-644. [DOI: 10.1016/j.clnu.2022.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 12/10/2021] [Accepted: 01/03/2022] [Indexed: 12/23/2022]
|
21
|
Retnakumar R, Nath AN, Nair GB, Chattopadhyay S. Gastrointestinal microbiome in the context of Helicobacter pylori infection in stomach and gastroduodenal diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 192:53-95. [DOI: 10.1016/bs.pmbts.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
22
|
Reitano E, de’Angelis N, Gavriilidis P, Gaiani F, Memeo R, Inchingolo R, Bianchi G, de’Angelis GL, Carra MC. Oral Bacterial Microbiota in Digestive Cancer Patients: A Systematic Review. Microorganisms 2021; 9:2585. [PMID: 34946186 PMCID: PMC8707512 DOI: 10.3390/microorganisms9122585] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/04/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023] Open
Abstract
The relation between the gut microbiota and human health is increasingly recognized. Recently, some evidence suggested that dysbiosis of the oral microbiota may be involved in the development of digestive cancers. A systematic review was conducted according to the PRISMA guidelines to investigate the association between the oral microbiota and digestive cancers. Several databases including Medline, Scopus, and Embase were searched by three independent reviewers, without date restriction. Over a total of 1654 records initially identified, 28 studies (2 prospective cohort studies and 26 case-controls) were selected. They investigated oral microbiota composition in patients with esophageal squamous cell carcinoma (n = 5), gastric cancer (n = 5), colorectal cancer (n = 9), liver carcinoma (n = 2), and pancreatic cancer (n = 7). In most of the studies, oral microbiota composition was found to be different between digestive cancer patients and controls. Particularly, oral microbiota dysbiosis and specific bacteria, such as Fusobacterium nucleatum and Porphyromonas gingivalis, appeared to be associated with colorectal cancers. Current evidence suggests that differences exist in oral microbiota composition between patients with and without digestive cancers. Further studies are required to investigate and validate oral-gut microbial transmission patterns and their role in digestive cancer carcinogenesis.
Collapse
Affiliation(s)
- Elisa Reitano
- Division of General Surgery, Department of Translational Medicine, Maggiore della Carità Hospital, University of Eastern Piedmont, 28100 Novara, Italy;
| | - Nicola de’Angelis
- Unit of Digestive and HPB Surgery, CARE Department, Henri Mondor Hospital, AP-HP, 94010 Créteil, France; (N.d.); (G.B.)
- Faculté de Santé, Université Paris Est, UPEC, 94010 Créteil, France
| | - Paschalis Gavriilidis
- Department of HBP Surgery, University Hospitals Coventry and Warwickshire NHS Trust, Clifford Bridge Road, Coventry CV2 2DX, UK;
| | - Federica Gaiani
- Gastroenterology and Endoscopy Unit, Department of Medicine and Surgery, University Hospital of Parma, 43126 Parma, Italy;
- Microbiome Research Hub, University of Parma, 43126 Parma, Italy
| | - Riccardo Memeo
- Unit of HPB Surgery, General Regional University Hospital F. Miulli, Acquaviva delle Fonti, 72021 Bari, Italy;
| | - Riccardo Inchingolo
- Unit of Interventional Radiology, General Regional Hospital F. Miulli, Acquaviva delle Fonti, 72021 Bari, Italy;
| | - Giorgio Bianchi
- Unit of Digestive and HPB Surgery, CARE Department, Henri Mondor Hospital, AP-HP, 94010 Créteil, France; (N.d.); (G.B.)
| | - Gian Luigi de’Angelis
- Gastroenterology and Endoscopy Unit, Department of Medicine and Surgery, University Hospital of Parma, 43126 Parma, Italy;
| | - Maria Clotilde Carra
- Service of Odontology, Department of Periodontology, Rothschild Hospital, AP-HP, Université de Paris, U.F.R. of Odontology-Garanciere, 75006 Paris, France;
| |
Collapse
|
23
|
Oral health and gastrointestinal neoplasia: Narrative review. Cir Esp 2021; 99:716-723. [PMID: 34776408 DOI: 10.1016/j.cireng.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/12/2021] [Indexed: 11/20/2022]
Abstract
The oral cavity represents the gateway to the complex digestive system, so the knowledge of the exact mechanisms that link them is vitally important. Recently, oral and dental pathologies have been studied as potential risk factors for pathologies linked to lifestyle habits. Therefore, it could be considered as an interesting preventive way. We conducted a narrative review with a thorough bibliographic search on MEDLINE and SCOPUS, including international studies related to oral healthcare and gastrointestinal neoplasms, published between 2015 and 2020. The primary aim of this revision is to analyze the association between oral healthcare and carcinogenic gastrointestinal processes, providing a possible future preventive strategy for dental care. Moreover, we intend to raise awareness about the importance of oral healthcare as a new paradigm and study variable in the global health care system.
Collapse
|
24
|
Ali Mohammed MM, Al Kawas S, Al-Qadhi G. Tongue-coating microbiome as a cancer predictor: A scoping review. Arch Oral Biol 2021; 132:105271. [PMID: 34610507 DOI: 10.1016/j.archoralbio.2021.105271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/16/2021] [Accepted: 09/19/2021] [Indexed: 01/10/2023]
Abstract
OBJECTIVE The tongue microbiome has emerged as a non-invasive diagnostic and tracking prognostic tool in the detection of diseases mainly cancer. This scoping review aimed to identify the association between tongue microbiome and pre-cancer or cancer lesions. DESIGN A comprehensive electronic database search including PubMed, Web of Science, and Scopus was undertaken up to March 2021, without language or date restrictions. This review was conducted following the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) guideline. All observational studies that compared microbial community on the dorsal surface of the tongue between cancer or precancerous cases and healthy controls using NGS techniques were included. RESULTS Of 274 records identified, nine studies were eligible to be included. Despite the inconsistent observations in terms of diversity and richness, most studies reported alteration in bacterial communities between pre-cancer or cancer cases and control groups. The bacterial profile among cases was so far correlated at the phylum level with a noticeable diverse degree at the genus level. The majority of included studies reported a higher abundance of certain kinds of microorganisms as compared to healthy participants including Firmicutes, Fusobacteria and Actinobacteria at phyla level as well as Streptococcus, Actinomyces, Leptotrichia, Campylobacter, and Fusobacterium at the genus level. CONCLUSION The alteration of the tongue microbial community has been associated with several diseases mainly cancer. So, the tongue microbiome may serve as a promising diagnostic tool or as a long-term monitor in precancerous or cancer cases.
Collapse
Affiliation(s)
- Marwan Mansoor Ali Mohammed
- Department of Oral and Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, United Arab Emirates.
| | - Sausan Al Kawas
- Department of Oral and Craniofacial Health Sciences, College of Dental Medicine, University of Sharjah, United Arab Emirates.
| | - Gamilah Al-Qadhi
- Department of Basic Dental Sciences, Faculty of Dentistry, University of Science and Technology, Yemen.
| |
Collapse
|
25
|
Pang S, Zhao S, Bai X, Song N, Wang S, Yu J, Zhang J, Ding X. Variations of tongue coating microbiota in children with Henoch-Schönlein purpura nephritis. Microb Pathog 2021; 160:105192. [PMID: 34534642 DOI: 10.1016/j.micpath.2021.105192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/30/2021] [Accepted: 09/09/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Variations in the oral microbiota have been significantly correlated with the progress of autoimmune diseases, such as immunoglobulin A nephropathy and Henoch-Schönlein purpura (HSP). However, there is no report outlining the character of tongue coating microbiota variations in children with Henoch-Schönlein purpura nephritis (HSPN). METHOD A total of 20 children with HSPN and 14 healthy controls were recruited for this research. Tongue coating samples of two groups were collected for 16S rRNA gene sequencing. The diversity, principal component analysis (PCA), nonmetric multidimensional scaling (NMDS), partial least squares discriminant analysis (PLS-DA), and linear discriminant analysis (LDA) effect size (LEfSe) were performed. Microbial function was assessed using the PICRUST. RESULTS The ACE and Chao indices were greatly lower in the HSPN group than in the HG (P = 0.001). The Shannon and Simpson indices were dramatically reduced in children with HSPN compared with those in the healthy controls (P = 0.005). Bacteroidales, Selenomonadales, Lactobacillales, Fusobacteriales, Neisseriales, and Actinomycetales composed more than 80% of all sequences, while Bacteroidales was the most generous order in both groups. PCA, NMDS and PLS-DA showed a marked difference between the control and HSPN groups. LEfSe analysis showed alteration of tongue coating microbiota in the HSPN group. There were 30 metabolic functions significantly differed between the two groups. CONCLUSIONS Children with HSPN have substantially various tongue coating microbiota compared to healthy controls. Even though this research does not indicate causality, it is beneficial to enhance the possibility for coming microbial-based treatments to enhance the clinical effects of HSPN in children.
Collapse
Affiliation(s)
- Shuang Pang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Shuan Zhao
- Department of Nephrology, Zhongshan Hospital, Fudan University; Shanghai Institute of Kidney and Dialysis; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Medical Center of Kidney Disease, Shanghai, 200433, China
| | - Xiaohong Bai
- Department of Pediatrics, Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, 110032, China
| | - Nana Song
- Department of Nephrology, Zhongshan Hospital, Fudan University; Shanghai Institute of Kidney and Dialysis; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Medical Center of Kidney Disease, Shanghai, 200433, China
| | - Shengzhi Wang
- Department of Pediatrics, Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, 110032, China
| | - Jiawei Yu
- Department of Nephrology, Zhongshan Hospital, Fudan University; Shanghai Institute of Kidney and Dialysis; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Medical Center of Kidney Disease, Shanghai, 200433, China
| | - Jun Zhang
- Department of Pediatrics, Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, Shenyang, 110032, China.
| | - Xiaoqiang Ding
- Department of Nephrology, Zhongshan Hospital, Fudan University; Shanghai Institute of Kidney and Dialysis; Shanghai Key Laboratory of Kidney and Blood Purification; Shanghai Medical Center of Kidney Disease, Shanghai, 200433, China.
| |
Collapse
|
26
|
Xu S, Xiang C, Wu J, Teng Y, Wu Z, Wang R, Lu B, Zhan Z, Wu H, Zhang J. Tongue Coating Bacteria as a Potential Stable Biomarker for Gastric Cancer Independent of Lifestyle. Dig Dis Sci 2021; 66:2964-2980. [PMID: 33044677 DOI: 10.1007/s10620-020-06637-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/23/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Gastric cancer (GC) is one of the most common cancers, and the noninvasive diagnostic methods for monitoring GC are still lacking. Growing evidence shows that human microbiota has potential value for identifying digestive diseases. AIMS The present study aimed to explore the association of the tongue coating microbiota with the serum metabolic features and inflammatory cytokines in GC patients and seek a potential, noninvasive biomarker for diagnosing GC. METHODS The tongue coating microbiota was profiled by 16S rRNA and 18S rRNA genes sequencing technology in the original population with 181 GC patients and 112 healthy controls (HCs). Propensity score matching method was used to eliminate potential confounders including age, gender, and six lifestyle factors and a matching population with 66 GC patients and 66 HCs generated. Serum metabolomics profiling was performed by ultra-performance liquid chromatography tandem quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) in the matching population. Random forest model was constructed for the diagnosis of GC. RESULTS Linear discriminant analysis effect size (LEfSe) revealed that the differential bacterial taxa between GC patients and HCs in the matching population were similar to that in the original population, while the differential fungal taxa between GC patients and HCs dramatically changed before and after PSM. By random forest analysis, the combination of six bacterial genera (Peptostreptococcus, Peptococcus, Porphyromonas, Megamonas, Rothia, and Fusobacterium) was the optimal predictive model to distinguish GC patients from HCs effectively, with an area under the curve (AUC) value of 0.85. The model was verified with a high predictive potential (AUC = 0.76 to 0.96). In the matching population, eighteen specific HCs-enriched bacterial genera (Porphyromonas, Parvimonas, etc.) had negative correlations with lysophospholipids metabolites, and three of them had also negative correlations with serum IL-17α. CONCLUSIONS The alteration of tongue coating microbiota had a possible linkage with the inflammations and metabolome, and the tongue coating bacteria could be a potential noninvasive biomarker for diagnosing GC, which might be independent of lifestyle.
Collapse
Affiliation(s)
- Shuo Xu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Chunjie Xiang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Juan Wu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Yuhao Teng
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Zhenfeng Wu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Ruiping Wang
- Department of Oncology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Bin Lu
- Department of Oncology, Yangzhong People's Hospital, Yangzhong, 212200, Jiangsu, China
| | - Zhen Zhan
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Huangan Wu
- Shanghai Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- Shanghai Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No. 110 Ganhe Road, Shanghai, 200000, China
| | - Junfeng Zhang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China.
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, No. 138 Xianlin Road, Nanjing, 210000, China.
| |
Collapse
|
27
|
Wang J, Wang Y, Li Z, Gao X, Huang D. Global Analysis of Microbiota Signatures in Four Major Types of Gastrointestinal Cancer. Front Oncol 2021; 11:685641. [PMID: 34422640 PMCID: PMC8375155 DOI: 10.3389/fonc.2021.685641] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/20/2021] [Indexed: 12/19/2022] Open
Abstract
The gut microbiota has been previously linked with tumorigenesis and gastrointestinal cancer progression; however, intra-tumor microbiota analysis has just emerged and deserves increasing attention. Based on the public databases of The Cancer Microbiome Atlas (TCMA) and The Cancer Genome Atlas (TCGA), this study identified the tissue/organ microbial signatures generated from 443 biosamples of four major gastrointestinal cancer types, including esophageal carcinoma (ESCA), which further includes esophageal adenocarcinoma (EAD) and esophageal squamous cell carcinoma (ESCC), stomach adenocarcinoma (STAD), colon adenocarcinoma (COAD), and rectum adenocarcinoma (READ). According to partial least squares discrimination analysis (PLS-DA), the profile differences in microbial communities between the tumor and normal samples were not particularly noticeable across the four cancer cohorts, whereas paired comparison analyses revealed several specific differences in bacteria between tumor and normal samples in the EAD, STAD, and COAD samples. The taxa classified from the phylum to genus level revealed a trend of distinguishable microbial profiles between upper and lower gastrointestinal tumors. The Bacteroidetes/Firmicutes ratio in lower gastrointestinal tract tumors was nearly three times that in upper gastrointestinal tract tumors. We also determined the relative tissue/organ-prevalent microbes for each of the four cohorts at the order and genus levels. Microbe Alistipes, Blautia, Pasteurellales, and Porphyromonas compositions were correlated with the clinical characteristics of patients with gastrointestinal cancer, particularly colorectal cancer. Taken together, our findings indicate that microbial profiles shift across different gastrointestinal cancer types and that microbial colonization is highly site-specific. Composition of specific microbes can be indicative of cancer stage or disease progression. Overall, this study indicates that the microbial community and abundance in human tissues can be determined using publicly available data, and provides a new perspective for intra-tissue/organ microbiota research.
Collapse
Affiliation(s)
- Jihan Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, China
| | - Yangyang Wang
- School of Electronics and Information, Northwestern Polytechnical University, Xi'an, China
| | - Zhenzhen Li
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, China
| | - Xiaoguang Gao
- School of Electronics and Information, Northwestern Polytechnical University, Xi'an, China
| | - Dageng Huang
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
28
|
Hao Y, Zhang R, Morris R, Cheng F, Zhu Z, Xu Y, Wang Y. Metabolome and microbiome alterations in tongue coating of gastric precancerous lesion patients. Expert Rev Gastroenterol Hepatol 2021; 15:949-963. [PMID: 33252275 DOI: 10.1080/17474124.2021.1850259] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Objective: This paper seeks to provide mechanistic insight into the pathological transition through the analysis of metabolites and microorganisms in the tongue coating of gastric precancerous lesions (GPL) patients.Methods: GC-TOF-MS and UHPLC-QE-MS metabolomics, combined with 16S rRNA microbiome techniques, were performed to explore the changes in metabolites and microorganisms in the tongue coating of GPL patients.Results: When compared with 15 controls, 133 metabolites were found to be differentially expressed in 60 GPL cases, of which could be divided into ten categories. Among them, most of the differentially expressed metabolites identified were lipids or lipid-like molecules. These metabolites were implicated in 6 metabolic pathways including glycine, serine and threonine metabolism, arginine and proline metabolism, sphingolipid metabolism, valine, leucine and isoleucine degradation, arachidonic acid metabolism, and tyrosine metabolism. The relative abundances of Alloprevotella, Solobacterium, Rothia, Eikenella, and Aggregatibacter in the GPL group increased significantly relative to the controls and were associated with lipids and lipid-like molecules, organic nitrogen compounds, organic oxygen compounds, phenylpropanoids and polyketides, and organoheterocyclic compounds, respectively.Conclusions: Compared with healthy people, the changes of tongue coating metabolites in GPL patients were mainly characterized by alterations in lipid metabolism and were associated with localized changes in the microbiome.
Collapse
Affiliation(s)
- Yiming Hao
- Shanghai Key Laboratory of Health Identification and Assessment/Laboratory of TCM Four Diagnostic Information, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Renling Zhang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Robert Morris
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USA
| | - Feng Cheng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, USA
| | - Zhujing Zhu
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yifeng Xu
- Shanghai Key Laboratory of Health Identification and Assessment/Laboratory of TCM Four Diagnostic Information, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yiqin Wang
- Shanghai Key Laboratory of Health Identification and Assessment/Laboratory of TCM Four Diagnostic Information, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| |
Collapse
|
29
|
Wei LQ, Cheong IH, Yang GH, Li XG, Kozlakidis Z, Ding L, Liu NN, Wang H. The Application of High-Throughput Technologies for the Study of Microbiome and Cancer. Front Genet 2021; 12:699793. [PMID: 34394190 PMCID: PMC8355622 DOI: 10.3389/fgene.2021.699793] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/21/2021] [Indexed: 12/14/2022] Open
Abstract
Human gut microbiome research, especially gut microbiome, has been developing at a considerable pace over the last decades, driven by a rapid technological advancement. The emergence of high-throughput technologies, such as genomics, transcriptomics, and others, has afforded the generation of large volumes of data, and in relation to specific pathologies such as different cancer types. The current review identifies high-throughput technologies as they have been implemented in the study of microbiome and cancer. Four main thematic areas have emerged: the characterization of microbial diversity and composition, microbial functional analyses, biomarker prediction, and, lastly, potential therapeutic applications. The majority of studies identified focus on the microbiome diversity characterization, which is reaching technological maturity, while the remaining three thematic areas could be described as emerging.
Collapse
Affiliation(s)
- Lu Qi Wei
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Io Hong Cheong
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang Huan Yang
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Guang Li
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zisis Kozlakidis
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Lei Ding
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ning Ning Liu
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Centre for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
30
|
Chen H, Li Q, Li M, Liu S, Yao C, Wang Z, Zhao Z, Liu P, Yang F, Li X, Wang J, Zeng Y, Tong X. Microbial characteristics across different tongue coating types in a healthy population. J Oral Microbiol 2021; 13:1946316. [PMID: 34367522 PMCID: PMC8317956 DOI: 10.1080/20002297.2021.1946316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background The physical appearance of tongue coatings is vital for traditional Chinese medicine (TCM) to diagnose health and disease status. The microbiota of different tongue coatings could also influence coating formation and be further associated with specific diseases. Previous studies have focused on bacteria from different tongue coatings in the context of specific diseases, but the normal variations in healthy individuals remain unknown.Aim: We examined the tongue microbiota by metagenomics in 94 healthy individuals classified into eight different tongue types.Results: The overall composition of the tongue coating microbiome is not drastically different among different coating types, similar to the findings of previous studies in healthy populations. Further analysis revealed microbiota characteristics of each coating type, and many of the key bacteria are reported to be implicated in diseases. Moreover, further inclusion of diabetic patients revealed disease-specific enrichment of Capnocytophaga, even though the same tongue coatings were studied.Conclusions: This work revealed the characteristic compositions of distinctive tongue coatings in a healthy population, which serves as a basis for understanding the tongue coating formation mechanism and provides a valuable reference to further investigate disease-specific tongue coating bacterial markers.
Collapse
Affiliation(s)
- Hairong Chen
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Qingwei Li
- Departments of Endocrinology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Min Li
- Departments of Endocrinology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Sheng Liu
- Departments of Endocrinology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chensi Yao
- Departments of Endocrinology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zixiong Wang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhuoya Zhao
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ping Liu
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fan Yang
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xinjian Li
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yixin Zeng
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xiaolin Tong
- Departments of Endocrinology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| |
Collapse
|
31
|
Salliss ME, Maarsingh JD, Garza C, Łaniewski P, Herbst-Kralovetz MM. Veillonellaceae family members uniquely alter the cervical metabolic microenvironment in a human three-dimensional epithelial model. NPJ Biofilms Microbiomes 2021; 7:57. [PMID: 34230496 PMCID: PMC8260719 DOI: 10.1038/s41522-021-00229-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 06/16/2021] [Indexed: 12/12/2022] Open
Abstract
Bacterial vaginosis (BV) is a gynecologic disorder characterized by a shift in cervicovaginal microbiota from Lactobacillus spp. dominance to a polymicrobial biofilm composed of diverse anaerobes. We utilized a well-characterized human three-dimensional cervical epithelial cell model in conjunction with untargeted metabolomics and immunoproteomics analyses to determine the immunometabolic contribution of three members of the Veillonellaceae family: Veillonella atypica, Veillonella montpellierensis and Megasphaera micronuciformis at this site. We found that Veillonella spp. infections induced significant elevation of polyamines. M. micronuciformis infections significantly increased soluble inflammatory mediators, induced moderate levels of cell cytotoxicity, and accumulation of cell membrane lipids relative to Veillonella spp. Notably, both V. atypica and V. montpellierensis infections resulted in consumption of lactate, a key metabolite linked to gynecologic and reproductive health. Collectively our approach and data provide unique insights into the specific contributions of Veillonellaceae members to the pathogenesis of BV and women's health.
Collapse
Affiliation(s)
- Mary E Salliss
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Jason D Maarsingh
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Camryn Garza
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
- Arizona State University, Tempe, AZ, USA
| | - Paweł Łaniewski
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Melissa M Herbst-Kralovetz
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA.
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA.
| |
Collapse
|
32
|
Noguera E, Sorribas M, Admella V, Biondo S. Oral health and gastrointestinal neoplasia: Narrative review. Cir Esp 2021; 99:S0009-739X(21)00178-0. [PMID: 34144811 DOI: 10.1016/j.ciresp.2021.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 11/15/2022]
Abstract
The oral cavity represents the gateway to the complex digestive system, so the knowledge of the exact mechanisms that link them is vitally important. Recently, oral and dental pathologies have been studied as potential risk factors for pathologies linked to lifestyle habits. Therefore, it could be considered as an interesting preventive way. We conducted a narrative review with a thorough bibliographic search on MEDLINE and SCOPUS, including international studies related to oral healthcare and gastrointestinal neoplasms, published between 2015 and 2020. The primary aim of this revision is to analyze the association between oral healthcare and carcinogenic gastrointestinal processes, providing a possible future preventive strategy for dental care. Moreover, we intend to raise awareness about the importance of oral healthcare as a new paradigm and study variable in the global health care system.
Collapse
Affiliation(s)
- Elisabet Noguera
- Grado de Odontología, Facultad de Medicina y Ciencias de la Salud, Universidad de Barcelona, Barcelona, España
| | - María Sorribas
- Servicio de Cirugía General y Digestiva, Hospital Universitario de Bellvitge, Universidad de Barcelona, IDIBELL (Instituto de Investigación Biomédica de Bellvitge), Hospitalet de Llobregat, Barcelona, España
| | - Víctor Admella
- Servicio de Cirugía General y Digestiva, Hospital Universitario de Bellvitge, Universidad de Barcelona, IDIBELL (Instituto de Investigación Biomédica de Bellvitge), Hospitalet de Llobregat, Barcelona, España
| | - Sebastiano Biondo
- Servicio de Cirugía General y Digestiva, Hospital Universitario de Bellvitge, Universidad de Barcelona, IDIBELL (Instituto de Investigación Biomédica de Bellvitge), Hospitalet de Llobregat, Barcelona, España.
| |
Collapse
|
33
|
Isolation and Characterization of Capnocytophaga bilenii sp. nov., a Novel Capnocytophaga Species Detected in a Gingivitis Subject. Pathogens 2021; 10:pathogens10050547. [PMID: 34062778 PMCID: PMC8147312 DOI: 10.3390/pathogens10050547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 11/25/2022] Open
Abstract
Capnocytophaga species are commensal gliding bacteria that are found in human and animal oral microbiota and are involved in several inflammatory diseases, both in immunocompromised and immunocompetent subjects. This study contributes to increased knowledge of this genus by characterizing a novel species isolated from a dental plaque sample in a male with gingivitis. We investigated morphological and chemotaxonomic characteristics using different growth conditions, temperature, and pH. Cellular fatty acid methyl ester (FAME) analysis was employed with gas chromatography/mass spectrometry (GC/MS). Phylogenetic analysis based on 16S rRNA, orthologous average nucleotide identity (OrthoANI), and digital DNA–DNA hybridization (dDDH) relatedness were performed. The Marseille-Q4570T strain was found to be a facultative aerobic, Gram-negative, elongated, round-tipped bacterium that grew at 25–56 °C and tolerated a pH of 5.5 to 8.5 and an NaCl content ranging from 5 to 15 g/L. The most abundant fatty acid was the branched structure 13-methyl-tetradecanoic acid (76%), followed by hexadecanoic acid (6%) and 3-hydroxy-15-methyl-hexadecanoic acid (4%). A 16S rDNA-based similarity analysis showed that the Marseille-Q4570T strain was closely related to Capnocytophaga leadbetteri strain AHN8855T (97.24% sequence identity). The OrthoANI and dDDH values between these two strains were, respectively, 76.81% and 25.6%. Therefore, we conclude that the Marseille-Q4570T strain represents a novel species of the genus Capnocytophaga, for which the name Capnocytophaga bilenii sp. nov. is proposed (=CSUR Q4570).
Collapse
|
34
|
Saadaoui M, Singh P, Al Khodor S. Oral microbiome and pregnancy: A bidirectional relationship. J Reprod Immunol 2021; 145:103293. [PMID: 33676065 DOI: 10.1016/j.jri.2021.103293] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/28/2021] [Accepted: 02/15/2021] [Indexed: 12/13/2022]
Abstract
The oral cavity contains the second most complex microbial population within the human body, with more than 700 bacterial organisms. Recent advances in Next Generation Sequencing technology have unraveled the complexities of the oral microbiome and provided valuable insights into its role in health and disease. The human oral microbiome varies dramatically during the different stages of life, including pregnancy. The total viable microbial counts in pregnant women are known to be higher compared to non-pregnant women, especially in the first trimester of pregnancy. A balanced oral microbiome is vital for a healthy pregnancy, as perturbations in the oral microbiome composition can contribute to pregnancy complications. On the other hand, physiological changes and differences in hormonal levels during pregnancy, increase susceptibility to various oral diseases such as gingivitis and periodontitis. A growing body of evidence supports the link between the composition of the oral microbiome and adverse pregnancy outcomes such as preterm birth, preeclampsia, low birth weight among others. This review aims to summarize the dynamics of oral microbiome during pregnancy and to discuss the relationship between a dysbiotic oral microbiome and pregnancy complications.
Collapse
Affiliation(s)
| | - Parul Singh
- Research Department, Sidra Medicine, Doha, Qatar
| | | |
Collapse
|
35
|
Jolivet-Gougeon A, Bonnaure-Mallet M. Screening for prevalence and abundance of Capnocytophaga spp by analyzing NGS data: A scoping review. Oral Dis 2020; 27:1621-1630. [PMID: 32738007 DOI: 10.1111/odi.13573] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 07/07/2020] [Accepted: 07/19/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Capnocytophaga spp. are commensal bacteria of the oral cavity and constitute a genus of the core microbiome. OBJECTIVE This genus is responsible for many local and systemic conditions in both the immunocompetent and immunocompromised patients, but its beneficial or deleterious role in the microbiota has been little explored. DESIGN Online databases were used to identify papers published from 1999 to 2019 based on next-generation sequencing (NGS) data to study comparative trials. Work using other identification methods, case reports, reviews, and non-comparative clinical trials was excluded. RESULTS AND CONCLUSION We selected 42 papers from among 668 publications. They showed a link between the abundance of Capnocytophaga spp. in the oral microbiota and various local pathologies (higher for gingivitis and halitosis; lower in active smokers, etc.) or systemic diseases (higher for cancer and carcinomas, IgA nephropathy, etc.). After discussing the limits inherent to the NGS techniques, we present several technical and biological hypotheses to explain the diversity of results observed between studies, as well as the links between the higher or lower abundance of Capnocytophaga spp and the appearance of local or systemic conditions and diseases.
Collapse
Affiliation(s)
- Anne Jolivet-Gougeon
- INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), Univ Rennes, Rennes, France
| | - Martine Bonnaure-Mallet
- INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), Univ Rennes, Rennes, France
| |
Collapse
|
36
|
Wang L, Xin Y, Zhou J, Tian Z, Liu C, Yu X, Meng X, Jiang W, Zhao S, Dong Q. Gastric Mucosa-Associated Microbial Signatures of Early Gastric Cancer. Front Microbiol 2020; 11:1548. [PMID: 32733423 PMCID: PMC7358557 DOI: 10.3389/fmicb.2020.01548] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022] Open
Abstract
Alterations in the microbiome are associated with the development of gastric cancer. Our study aimed to identify dysbiotic features in early gastric cancer (EC). The gastric microbiome was assessed in EC (n = 30), advanced gastric cancer (AC) (n = 30), and chronic gastritis (CG) (n = 60). The results demonstrated significant differences in the microbial profile and composition between EC and AC, suggesting alterations associated with gastric cancer progression. Linear discriminant analysis (LDA) effect size (LEfSe) analyses identified 32 bacterial genera that were associated with EC. Functional analyses of the gastric microbiome showed that the production of urease and synthesis of bacterial flagella were weakened in EC, while the glycolysis of fructose and hydrolysis of glycosides were enhanced. A classifier based on a random forest (RF) machine learning algorithm identified a microbial signature that distinguished EC from CG or AC with high accuracy. The correct identification of the signature was further validated in independent cohorts. This signature enriched of bacteria with varied abundance, high degree of bacterial interactions and carcinogenic potentials. Constrained principal coordinate analyses revealed that the presence of Helicobacter pylori and the cagA and vacA virulence genotypes influenced the structure of the gastric microbiome. To determine the impacts of host genetic variations on the gastric microbiome, six previously reported single nucleotide polymorphisms (SNPs) were examined. The minor allele of MUC1 rs4072037 was associated with an increased abundance of Ochrobactrum. The gastric microbiome altered in EC, which might be attributed in part to host genetic variations, H. pylori infection, bacterial virulence and environmental adaptations. The identified microbial signature could serve as biomarkers for clinical assessment of gastric cancer risk in high-risk patients.
Collapse
Affiliation(s)
- Lili Wang
- Central Laboratories, Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Yongning Xin
- Central Laboratories, Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Jianhua Zhou
- Central Laboratories, Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Zibin Tian
- Department of Gastroenterology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chenguang Liu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xinjuan Yu
- Central Laboratories, Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Xinying Meng
- Central Laboratories, Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Weina Jiang
- Central Laboratories, Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Shoufeng Zhao
- Central Laboratories, Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Quanjiang Dong
- Central Laboratories, Department of Gastroenterology, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| |
Collapse
|
37
|
Yan R, Guo Y, Gong Q, Chen M, Guo Y, Yang P, Huang H, Huang H, Huang W, Ma Z, Zheng Z, Tian D, Su M. Microbiological evidences for gastric cardiac microflora dysbiosis inducing the progression of inflammation. J Gastroenterol Hepatol 2020; 35:1032-1041. [PMID: 31783428 DOI: 10.1111/jgh.14946] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/11/2019] [Accepted: 11/17/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND AND AIM Nowadays, anti-inflammation treatment is a promising approach for preventing tumorigenesis, and human microflora is closely related to inflammation. This study aimed to investigate the gastric cardiac microbiome and identify inflammation-related microorganisms for gastric cardiac inflammation. METHODS We performed 16S rRNA sequencing on a total of 11 healthy individuals and 89 individuals with different degree of gastric cardiac inflammation. Immunohistochemistry was used for verifying candidate bacteria. Phylogenetic reconstruction of unobserved states (picrust) was used for predicting the pathways involved by cardiac microflora. RESULTS The resident phyla in normal were Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria, and the dominant genus in normal were Halomonas, shewanella, and Comamonas. In the progression of gastric cardiac inflammation, the diversity of cardiac microflora did not change (P > 0.05). However, the composition structure of cardiac microflora varied between healthy and inflamed tissues (P < 0.05). Meanwhile, there were 64 species parallel increased with inflammation degree, especially Helicobacter pylori, Lactobacillus spp. Additionally, inflammation-related species were detected (P < 0.05), including H. pylori, Acinetobacter ursingii, and Streptococcus agalactiae. Higher H. pylori colonization was positively related to the progression of cardiac inflammation (γ coefficient = 0.678, P < 0.001), and it also influenced the cardiac microbial community structure. Cardiac microflora also participated in DNA repair pathways and is affected by the relative abundance of H. pylori (P < 0.0001). CONCLUSIONS Cardiac microflora dysbiosis, especially the increasing of the relevant abundance of H. pylori, promotes the progression of cardiac inflammation.
Collapse
Affiliation(s)
- Ruijing Yan
- Institute of Clinical Pathology & Department of Pathology, Shantou University Medical College, Shantou, China
| | - Yi Guo
- Department of Endoscopy, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Qingyun Gong
- Institute of Clinical Pathology & Department of Pathology, Shantou University Medical College, Shantou, China
| | - Man Chen
- Department of Pathology, Chaozhou People's Hospital, Chaozhou, China
| | - Yuanning Guo
- Institute of Clinical Pathology & Department of Pathology, Shantou University Medical College, Shantou, China
| | - Peng Yang
- Institute of Clinical Pathology & Department of Pathology, Shantou University Medical College, Shantou, China
| | - Hao Huang
- Institute of Clinical Pathology & Department of Pathology, Shantou University Medical College, Shantou, China
| | - Haihua Huang
- Department of Pathology, the Second Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Wen Huang
- Department of Pathology, Chaozhou People's Hospital, Chaozhou, China
| | - Zikai Ma
- Department of Pathology, Puning Kangmei Hospital, Jieyang, China
| | - Zhijian Zheng
- Department of Pathology, Puning Overseas Chinese Hospital, Jieyang, China
| | - Dongping Tian
- Institute of Clinical Pathology & Department of Pathology, Shantou University Medical College, Shantou, China
| | - Min Su
- Institute of Clinical Pathology & Department of Pathology, Shantou University Medical College, Shantou, China
| |
Collapse
|
38
|
Mucosa microbiome of gastric lesions: Fungi and bacteria interactions. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 171:195-213. [PMID: 32475522 DOI: 10.1016/bs.pmbts.2020.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Many components of the gastric non-Helicobacter pylori microbiota have been identified recently thanks to advances in DNA sequencing techniques. Several lines of evidence support the hypothesis that the gastric microbiome is essential for gastric disorders such as gastric cancer. Microbial interactions impact the pathophysiology of various gastric disorders. This chapter provides an overview of recent findings regarding general gastric microbial community profiling, microbial interactions in the stomach, and microbial characteristics in various gastric disorders.
Collapse
|
39
|
Rodriguez RM, Hernandez BY, Menor M, Deng Y, Khadka VS. The landscape of bacterial presence in tumor and adjacent normal tissue across 9 major cancer types using TCGA exome sequencing. Comput Struct Biotechnol J 2020; 18:631-641. [PMID: 32257046 PMCID: PMC7109368 DOI: 10.1016/j.csbj.2020.03.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 12/26/2022] Open
Abstract
Identification of microbial composition directly from tumor tissue permits studying the relationship between microbial changes and cancer pathogenesis. We interrogated bacterial presence in tumor and adjacent normal tissue strictly in pairs utilizing human whole exome sequencing to generate microbial profiles. Profiles were generated for 813 cases from stomach, liver, colon, rectal, lung, head & neck, cervical and bladder TCGA cohorts. Core microbiota examination revealed twelve taxa to be common across the nine cancer types at all classification levels. Paired analyses demonstrated significant differences in bacterial shifts between tumor and adjacent normal tissue across stomach, colon, lung squamous cell, and head & neck cohorts, whereas little or no differences were evident in liver, rectal, lung adenocarcinoma, cervical and bladder cancer cohorts in adjusted models. Helicobacter pylori in stomach and Bacteroides vulgatus in colon were found to be significantly higher in adjacent normal compared to tumor tissue after false discovery rate correction. Computational results were validated with tissue from an independent population by species-specific qPCR showing similar patterns of co-occurrence among Fusobacterium nucleatum and Selenomonas sputigena in gastric samples. This study demonstrates the ability to identify bacteria differential composition derived from human tissue whole exome sequences. Taken together our results suggest the microbial profiles shift with advanced disease and that the microbial composition of the adjacent tissue can be indicative of cancer stage disease progression.
Collapse
Key Words
- BLCA, bladder carcinoma
- CESC, cervical & endocervical squamous cell carcinomas
- COAD, colon adenocarcinoma
- COREAD, colon and rectal adenocarcinoma TCGA cohorts
- Cancer microbiome
- Exome sequencing
- HNSC, head & neck squamous cell carcinoma
- L2FC, log 2 fold change
- LIHC, liver hepatocellular carcinoma
- LUAD, lung adenocarcinoma
- LUSC, lung squamous cell carcinoma
- Microbial landscape
- READ, rectal adenocarcinoma
- STAD, stomach adenocarcinoma
- TCGA
- TCGA, The Cancer Genome Atlas
Collapse
Affiliation(s)
- Rebecca M. Rodriguez
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii Mānoa, Honolulu, HI, United States
- Population Sciences in the Pacific Program-Cancer Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, United States
| | - Brenda Y. Hernandez
- Epidemiology, University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, United States
- Population Sciences in the Pacific Program-Cancer Epidemiology, University of Hawaii Cancer Center, Honolulu, HI, United States
| | - Mark Menor
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii Mānoa, Honolulu, HI, United States
| | - Youping Deng
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii Mānoa, Honolulu, HI, United States
| | - Vedbar S. Khadka
- Bioinformatics Core, Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii Mānoa, Honolulu, HI, United States
| |
Collapse
|
40
|
Ning Y, Yang G, Chen Y, Zhao X, Qian H, Liu Y, Chen S, Shi G. Characteristics of the Urinary Microbiome From Patients With Gout: A Prospective Study. Front Endocrinol (Lausanne) 2020; 11:272. [PMID: 32508748 PMCID: PMC7251145 DOI: 10.3389/fendo.2020.00272] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 04/14/2020] [Indexed: 12/19/2022] Open
Abstract
The role of host microbes in the pathogenesis of several diseases has been established, and altered microbiomes have been related to diseases. However, the variability of the urinary microbiome in individuals with gout has not been evaluated to date. Therefore, we conducted the present prospective study to characterize the urinary microbiome and its potential relation to gout. Urine samples from 30 patients with gout and 30 healthy controls were analyzed by Illumina MiSeq sequencing of the 16S rRNA hypervariable regions, and the microbiomes were compared according to alpha-diversity indices, complexity (beta diversity) with principal component analysis, and composition with linear discriminant analysis effect size. The most significantly different taxa at the phylum and genus levels were identified, and their potential as biomarkers for discriminating gout patients was assessed based on receiver operating characteristic (ROC) curve analysis. Compared with the healthy controls, there was a dramatic decrease in microbial richness and diversity in the urine of gout patients. The phylum Firmicutes and its derivatives (Lactobacillus_iners, Family_XI, and Finegoldia), the phylum Actinobacteria and its derivatives (unidentified_Actinobacteria, Corynebacteriales, Corynebacteriale, Corynebacterium_1, and Corynebacterium_tuberculostearicum), and the genera Prevotella and Corynebacterium_1 were significantly enriched in the urine of gout patients. ROC analysis indicated that the top five altered microbial genera could be reliable markers for distinguishing gout patients from healthy individuals. These findings demonstrate that there are specific alterations in the microbial diversity of gout patients. Thus, further studies on the causal relationship between gout and the urinary microbiome will offer new prospects for diagnosing, preventing, and treating gout.
Collapse
Affiliation(s)
- Yaogui Ning
- School of Medicine, Xiamen University, Xiamen, China
- Department of Intensive Care Unit, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Guomei Yang
- School of Medicine, Xiamen University, Xiamen, China
| | - Yangchun Chen
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Xue Zhao
- School of Medicine, Xiamen University, Xiamen, China
| | - Hongyan Qian
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Yuan Liu
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Shiju Chen
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, Xiamen, China
- *Correspondence: Shiju Chen
| | - Guixiu Shi
- Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, Xiamen, China
- Guixiu Shi
| |
Collapse
|
41
|
Abstract
Gastric cancer is the third deadliest cancer in the world, and the absolute number of cases is increasing every year due to aging and growing of high-risk populations. This disease is a consequence of the complex interaction of microbial agents, with environmental and host factors, resulting in the dysregulation of multiple oncogenic and tumor-suppressing signaling pathways. Despite the advances in our understanding of carcinogenesis, there are still reduced therapeutic options for patients with gastric cancer. In recent years, genomic analyses of gastric tumors have emphasized their molecular heterogeneity. The distinction of gastric cancer molecular subtypes may be a key to identify novel therapeutic targets, to predict patient outcome and response to therapy, and to guide early diagnosis strategies. In this review, we summarize the most recent updates on the relationship between microbial agents and gastric cancer, in particular, Helicobacter pylori, the non-H pylori microbiome, and Epstein-Barr virus. We also highlight the main advances made in the past year regarding the molecular characterization of gastric cancer, especially the signatures with potential clinical utility.
Collapse
Affiliation(s)
- M Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Ceu Figueiredo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Jose C Machado
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| |
Collapse
|