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Characterization of oral and gut microbiome and plasma metabolomics in COVID-19 patients after 1-year follow-up

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Military Medical Research 2023年第2期10卷 162-174页

作者： Guang-Ying Cui Ben-Chen Rao Zhao-Hai Zeng Xue-Mei Wang Tong Ren Hai-Yu Wang Hong Luo Hong-Yan Ren Chao Liu Su-Ying Ding Jun-Jie Tan Zhen-Guo Liu Ya-Wen Zou Zhi-Gang Ren Zu-Jiang Yu Department of Infectious Diseases the First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052China Gene Hospital of Henan Province/Precision Medicine Center the First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052China Department of Infectious Diseases Guangshan County People’s HospitalGuangshan CountyXinyang 465450HenanChina Department of Breast Surgery Affiliated Cancer Hospital of Zhengzhou UniversityZhengzhou 450052China Shanghai Mobio Biomedical Technology Co. LtdShanghai 201111China Health Management Center the First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052China

Background:Due to the outbreak and rapid spread of coronavirus disease 2019(COVID-19),more than 160 million patients have become convalescents worldwide to date.Significant alterations have occurred in the gut and oral microbiome and metabonomics of patients with COVID-19.However,it is unknown whether their characteristics return to normal after the 1-year recovery.Methods:We recruited 35 confirmed patients to provide specimens at discharge and 1 year later,as well as 160healthy controls.A total of 497 samples were prospectively collected,including 219 tongue-coating,129 stool and 149 plasma samples.Tongue-coating and stool samples were subjected to 16S rRNA sequencing,and plasma samples were subjected to untargeted metabolomics testing.Results:The oral and gut microbiome and metabolomics characteristics of the 1-year convalescents were restored to a large extent but did not completely return to normal.In the recovery process,the microbial diversity gradually increased.Butyric acid-producing microbes and Bifidobacterium gradually increased,whereas lipopolysaccharideproducing microbes gradually decreased.In addition,sphingosine-1-phosphate,which is closely related to the inflammatory factor storm of COVID-19,increased significantly during the recovery process.Moreover,the predictive models established based on the microbiome and metabolites of patients at the time of discharge reached high efficacy in predicting their neutralizing antibody levels one year later.Conclusions:This study is the first to characterize the oral and gut microbiome and metabonomics in 1-year convalescents of COVID-19.The key microbiome and metabolites in the process of recovery were identified,and provided new treatment ideas for accelerating recovery.And the predictive models based on the microbiome and metabolomics afford new insights for predicting the recovery situation which benefited affected individuals and healthcare.

关键词： Coronavirus disease 2019(COVID-19) Gut microbiome oral microbiome Plasma metabonomics Convalescents Individual outcomes Patient stratifcation Predictive Preventive and personalized medicine(3PM)

Alterations in the human oral microbiome in cholangiocarcinoma

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Military Medical Research 2023年第5期10卷 726-729页

作者： Ben-Chen Rao Gui-Zhen Zhang Ya-Wen Zou Tong Ren Hong-Yan Ren Chao Liu Zu-Jiang Yu Zhi-Gang Ren Department of Infectious Diseases the First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052China Jinan Microecological Biomedicine Shandong Laboratory Jinan 250000China Gene Hospital of Henan Province Precision Medicine Centerthe First Affiliated Hospital of Zhengzhou Univer‑sityZhengzhou 450052China Department of Pharmacy the First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052China Shanghai Mobio Biomedical Technology Co. Ltd.Shanghai 201111China

Dear Editor,Alterations in the human microbiome are closely related to various hepatobiliary diseases.Gut microbial dysbiosis has been found in patients with cholangiocarcinoma(CCA)[1].However,the characteristics of o... 详细信息

关键词： Cholangiocarcinoma oral microbiome Diagnostic biomarker Random forest model 16S rRNA MiSeq sequencing

oral microbiome and risk of malignant esophageal lesions in a high-risk area of China:A nested case-control study

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Chinese Journal of Cancer Research 2020年第6期32卷 742-754页

作者： Fangfang Liu Mengfei Liu Ying Liu Chuanhai Guo Yunlai Zhou Fenglei Li Ruiping Xu Zhen Liu Qiuju Deng Xiang Li Chaoting Zhang Yaqi Pan Tao Ning Xiao Dong Zhe Hu Huanyu Bao Hong Cai Isabel Dos Santos Silva Zhonghu He Yang Ke Key Laboratory of Carcinogenesis and Translational Research(Ministry of Education/Beijing) Laboratory of GeneticsPeking University Cancer Hospital&InstituteBeijing 100142China Novogene Co. LtdBeijing 100080China Hua County People's Hospital Anyang 456400China Anyang Cancer Hospital Anyang 455000China Department of Non-communicable Disease Epidemiology London School of Hygiene&Tropical MedicineLondon WC1E 7HTUK

Objective:We aimed to prospectively evaluate the association of oral microbiome with malignant esophageal lesions and its predictive potential as a biomarker of risk.Methods:We conducted a case-control study nested within a population-based cohort with up to 8 visits of oral swab collection for each subject over an 11-year period in a high-risk area for esophageal cancer in China.The oral microbiome was evaluated with 16 S ribosomal RNA(rRNA)gene sequencing in 428 pre-diagnostic oral specimens from 84 cases with esophageal lesions of severe squamous dysplasia and above(SDA)and 168 matched healthy controls.DESeq analysis was performed to identify taxa of differential abundance.Differential oral species together with subject characteristics were evaluated for their potential in predicting SDA risk by constructing conditional logistic regression models.Results:A total of 125 taxa including 37 named species showed significantly different abundance between SDA cases and controls(all P0.84.Conclusions:The oral microbiome may play an etiological and predictive role in esophageal cancer,and it holds promise as a non-invasive early warning biomarker for risk stratification for esophageal cancer screening programs.

关键词： Early warning biomarker esophageal squamous cell carcinoma oral microbiome risk prediction

Alterations in the oral microbiome in HIV infection:causes,effects and potential interventions

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Chinese Medical Journal 2021年第23期134卷 2788-2798页

作者： Shuang Li Bin Su Qiu-Shui He Hao Wu Tong Zhang Beijing Key Laboratory for HIV/AIDS Research Clinical and Research Center for Infectious DiseasesBeijing Youan HospitalCapital Medical UniversityBeijing 100069China Institute of Biomedicine Research Center for Infections and ImmunityUniversity of TurkuTurku 20520Finland.

A massive depletion of CD4+T lymphocytes has been described in early and acute human immunodeficiency virus(HIV)infection,leading to an imbalance between the human microbiome and immune responses.In recent years,a growing interest in the alterations in gut microbiota in HIV infection has led to many studies;however,only few studies have been conducted to explore the importance of oral microbiome in HIV-infected individuals.Evidence has indicated the dysbiosis of oral microbiota in people living with HIV(PLWH).Potential mechanisms might be related to the immunodeficiency in the oral cavity of HIV-infected individuals,including changes in secretory components such as reduced levels of enzymes and proteins in saliva and altered cellular components involved in the reduction and dysfunction of innate and adaptive immune cells.As a result,disrupted oral immunity in HIV-infected individuals leads to an imbalance between the oral microbiome and local immune responses,which may contribute to the development of HIV-related diseases and HIV-associated non-acquired immunodeficiency syndrome comorbidities.Although the introduction of antiretroviral therapy(ART)has led to a significant decrease in occurrence of the opportunistic oral infections in HIV-infected individuals,the dysbiosis in oral microbiome persists.Furthermore,several studies with the aim to investigate the ability of probiotics to regulate the dysbiosis of oral microbiota in HIV-infected individuals are ongoing.However,the effects of ART and probiotics on oral microbiome in HIV-infected individuals remain unclear.In this article,we review the composition of the oral microbiome in healthy and HIV-infected individuals and the possible effect of oral microbiome on HIV-associated oral diseases.We also discuss how ART and probiotics influence the oral microbiome in HIV infection.We believe that a deeper understanding of composition and function of the oral microbiome is critical for the development of effective preventive and therapeutic strategies for HIV infection

关键词： HIV oral microbiome Antiretroviral therapy Probiotics Intervention

The oral microbiome of pregnant women facilitates gestational diabetes discrimination

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Journal of Genetics and Genomics 2021年第1期48卷 32-39页

作者： Xiaoqing Li Jiayong Zheng Xiuling Ma Bing Zhang Jinyang Zhang Wenhuan Wang Congcong Sun Yeping Wang Jianqiong Zheng Haiying Chen Jiejing Tao Hai Wang Fengyi Zhang Jinfeng Wang Hongping Zhang Wenzhou People’s Hospital/Wenzhou Maternal and Child Health Care Hospital/The Third Clinical Institute Affiliated to Wenzhou Medical University Wenzhou 325000China Computational Genomics Lab Beijing Institutes of Life ScienceChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

The oral microbiota plays an important role in the development of various diseases,whereas its association with gestational diabetes mellitus (GDM) remains largely unclear.The aim of this study is to identify biomarkers from the oral microbiota of GDM patients by analyzing the microbiome of the saliva and dental plaque samples of 111 pregnant women.We find that the microbiota of both types of oral samples in GDM patients exhibits differences and significantly varies from that of patients with periodontitis or dental caries.Using bacterial biomarkers from the oral microbiota,GDM classification models based on support vector machine and random forest algorithms are constructed.The area under curve (AUC) value of the classification model constructed by combination of Lautropia and Neisseria in dental plaque and Streptococcus in saliva reaches 0.83,and the value achieves a maximum value of 0.89 by adding clinical features.These findings suggest that certain bacteria in either saliva or dental plaque can effectively distinguish women with GDM from healthy pregnant women,which provides evidence of oral microbiome as an informative source for developing noninvasive biomarkers of GDM.

关键词： Gestational diabetes mellitus oral microbiome Saliva Dental plaque Classification model

oral Hygiene in the Presence of Orthodontic Therapy

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Journal of Biosciences and Medicines 2024年第2期12卷 98-110页

作者： Emmanuel John Aryeetey Hicham Benyahia Fatima Zaoui Faculty of Dental Medicine Mohammed University in Rabat Rabat Morocco

Orthodontic treatment offers great advantages in improving facial and smile aesthetics, self-confidence and the function of the stomatognathic apparatus. The pursuit of these advantages makes use of orthodontic appliances that could be fixed or removable. However, it’s worth stating that these appliances interfere with tooth brushing, making it more difficult to brush teeth effectively. Orthodontics appliances therefore promote the accumulation of dental plaque, which results in both quantitative and qualitative changes in the oral microbiota, hence, exposing patients to several adverse effects such as White spot lesions, dental caries, periodontal pathologies and halitosis. For this reason, oral assessment of patients before, during and after treatment is necessary as well as oral hygiene instructions and motivation. Orthodontists therefore, should educate patients on oral and periodontal hygiene in order to control dental and periodontal complications. Prescriptions of plaque control materials adapted to each patient are done in order to optimize the final result and minimize unwanted complications.

关键词： Orthodontic Treatment oral microbiome oral Hygiene Periodontitis Gingivitis Orthodontic Fixed Appliances Orthodontic Removable Appliances White Spot Lesions (WSL)

Commensal microbiota in the digestive tract:a review of its roles in carcinogenesis and radiotherapy

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Cancer Biology & Medicine 2022年第1期19卷 43-55页

作者： Jiali Dong Yuan Li Huiwen Xiao Ming Cui Saijun Fan Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine Institute of Radiation MedicineChinese Academy of Medical Sciences and Peking Union Medical CollegeTianjin 300192China Department of Microbiology College of Life SciencesNankai UniversityTianjin 300071China

The human microflora is a complex ecosystem composed of diverse microorganisms mainly distributed in the epidermal and mucosal habitats of the entire body,including the mouth,lung,intestines,skin,and vagina.These microbial communities are involved in many essential functions,such as metabolism,immunity,host nutrition,and diseases.Recent studies have focused on the microbiota associated with cancers,particularly the oral and intestinal microbiota.Radiotherapy,the most effective cytotoxic modality available for solid tumors,contributes to the treatment of cancer patients.Mounting evidence supports that the microbiota plays pivotal roles in the efficacy and prognosis of tumor radiotherapy.Here,we review current research on the microbiota and cancer development,and describe knowledge gaps in the study of radiotherapy and the microbiota.Better understanding of the effects of the microbiome in tumorigenesis and radiotherapy will shed light on future novel prevention and treatment strategies based on modulating the microbiome in cancer patients.

关键词： oral microbiome gut microbiome cancer radiotherapy

microbiome and colorectal carcinogenesis:Linked mechanisms and racial differences

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World Journal of Gastrointestinal Oncology 2022年第2期14卷 375-395页

作者： Sofia C Tortora Vimal M Bodiwala Andrew Quinn Laura A Martello Shivakumar Vignesh Department of Medicine and Division of Gastroenterology&Hepatology SUNY Downstate Health Sciences UniversityBrooklynNY 11203United States

Various studies have shown the interplay between the intestinal microbiome,environmental factors,and genetic changes in colorectal cancer(CRC)development.In this review,we highlight the various gut and oral microbiota associated with CRC and colorectal adenomas,and their proposed molecular mechanisms in relation to the processes of“the hallmarks of cancer”,and differences in microbial diversity and abundance between race/ethnicity.Patients with CRC showed increased levels of Bacteroides,Prevotella,Escherichia coli,enterotoxigenic Bacteroides fragilis,Streptococcus gallolyticus,Enterococcus faecalis,Fusobacterium nucleatum(F.nucleatum)and Clostridium difficile.Higher levels of Bacteroides have been found in African American(AA)compared to Caucasian American(CA)patients.Pro-inflammatory bacteria such as F.nucleatum and Enterobacter species were significantly higher in AAs.Also,AA patients have been shown to have decreased microbial diversity compared to CA patients.Some studies have shown that using microbiome profiles in conjunction with certain risk factors such as age,race and body mass index may help predict healthy colon vs one with adenomas or carcinomas.Periodontitis is one of the most common bacterial infections in humans and is more prevalent in Non-Hispanic-Blacks as compared to Non-Hispanic Whites.This condition causes increased systemic inflammation,immune dysregulation,gut microbiota dysbiosis and thereby possibly influencing colorectal carcinogenesis.Periodontal-associated bacteria such as Fusobacterium,Prevotella,Bacteroides and Porphyromonas have been found in CRC tissues and in feces of CRC patients.Therefore,a deeper understanding of the association between oral and gastrointestinal bacterial profile,in addition to identifying prevalent bacteria in patients with CRC and the differences observed in ethnicity/race,may play a pivotal role in predicting incidence,prognosis,and lead to the development of new treatments.

关键词： Colorectal cancer oral microbiome Gut microbiome Hallmarks of cancer Racial/ethnic microbial diversity

Effect of Salivary Antimicrobial Factors on Microbial Composition of Tongue Coating in Patients with Coronary Heart Disease with Phlegm-Stasis Syndrome

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World Journal of Traditional Chinese Medicine 2022年第1期8卷 123-130页

作者： Juan Ye Ke-Lei Su Yue-Hua Xu Yang Yang Qian Zhou Wei Gao Xue-Ting Cai Qing-Yun Wei Meng Cao Peng Cao Affiliated Hospital of Integrated Traditional Chinese and Western Medicine Nanjing University of Chinese Medicine Department of Pharmacology School of PharmacyNanjing University of Chinese MedicineNanjing 210023 Institute of Comparative Medicine College of Veterinary MedicineJiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesJoint International Research Laboratory of Agriculture and Agri-Product SafetyThe Ministry of Education of ChinaYangzhou UniversityYangzhou225009China

Objective: Phlegm-stasis syndrome is one of the most common traditional Chinese medicine(TCM) syndromes and found in 59% of patients with coronary heart disease(CHD) in routine TCM clinical practice in China. One of the diagnostic criteria of phlegm-stasis syndrome is its characteristic white-greasy and thin tongue coating. We have previously reported that different types of tongue coating have different microbiome characteristics that can be used as diagnostic markers. However, the microbial characteristics of tongue coating of CHD patients with phlegm-stasis syndrome, including coating feature and underlying reason of formation, have rarely been reported. Herein, we examined the characteristic microbiome of tongue coating, and discussed the cause of tongue coating formation via salivary proteins in patients with phlegm-stasis syndrome. Methods: We examined white-greasy and thin tongue coatings obtained from 10 patients with CHD having phlegm-stasis syndrome(n = 10), and compared with those of patients with almost no coating – patients with Qi-Yin deficiency syndrome(n = 10) – and healthy controls(n = 10). 16S r RNA sequencing of tongue coating microbiome and isobaric tags for relative and absolute quantitation(i TRAQ)-based quantitative analysis of salivary proteins were used to detect tongue coating and salivary protein separately. Salivary levels of s Ig A, lysozyme, and amylase were detected by ELISA. Results: We identified Candidatus_Saccharimonas and Candidate_division_TM7_norank as the prominent members of tongue coating in patients with CHD having phlegm-stasis syndrome. Salivary proteins involved in biological processes, pentose phosphate pathway, and complement and coagulation cascades were among the differentially expressed proteins identified in patients with CHD having phlegm-stasis syndrome on i TRAQ analysis. Moreover, the formation of microbiota in tongue coating was associated with salivary s Ig A, lysozyme, and saliva flow rate. Conclusions: We explored the characteristics of microbial composit

关键词： Coronary heart disease oral microbiome salivary proteins traditional Chinese medicine syndrome tongue diagnosis