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McKinnon Reish H, Dewey L, Kirschman LJ. A host of issues: pseudoreplication in host-microbiota studies. Appl Environ Microbiol 2024; 90:e0103324. [PMID: 39082810 PMCID: PMC11337823 DOI: 10.1128/aem.01033-24] [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] [Indexed: 08/22/2024] Open
Abstract
Pseudoreplication compromises the validity of research by treating non-independent samples as independent replicates. This review examines the prevalence of pseudoreplication in host-microbiota studies, highlighting the critical need for rigorous experimental design and appropriate statistical analysis. We systematically reviewed 115 manuscripts on host-microbiota interactions. Our analysis revealed that 22% of the papers contained pseudoreplication, primarily due to co-housed organisms, whereas 52% lacked sufficient methodological details. The remaining 26% adequately addressed pseudoreplication through proper experimental design or statistical analysis. The high incidence of pseudoreplication and insufficient information underscores the importance of methodological reporting and statistical rigor to ensure reproducibility of host-microbiota research.
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Affiliation(s)
- Hannah McKinnon Reish
- Department of Biology, Southeast Missouri State University, Cape Girardeau, Missouri, USA
| | - Lindsey Dewey
- Department of Biology, Southeast Missouri State University, Cape Girardeau, Missouri, USA
- Deparment of Biology, University of Dayton, Dayton, Ohio, USA
| | - Lucas J. Kirschman
- Department of Biology, Southeast Missouri State University, Cape Girardeau, Missouri, USA
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2
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Casarin RCV, Silva RVCD, Paz HEDS, Stolf CS, Carvalho LM, Noronha MF, Sallum AW, Monteiro MDF. Metatranscriptomic analysis shows functional alterations in subgingival biofilm in young smokers with periodontitis: a pilot study. J Appl Oral Sci 2024; 32:e20240031. [PMID: 39166556 PMCID: PMC11364450 DOI: 10.1590/1678-7757-2024-0031] [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: 01/27/2024] [Accepted: 06/24/2024] [Indexed: 08/23/2024] Open
Abstract
OBJECTIVE This study aimed to assess the influence of smoking on the subgingival metatranscriptomic profile of young patients affected by stage III/IV and generalized periodontal disease. METHODOLOGY In total, six young patients, both smokers and non-smokers (n=3/group), who were affected by periodontitis were chosen. The STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guidelines for case-control reporting were followed. Periodontal clinical measurements and subgingival biofilm samples were collected. RNA was extracted from the biofilm and sequenced via Illumina HiSeq. Differential expression analysis used Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and differentially expressed genes were identified using the Sleuth package in R, with a statistical cutoff of ≤0.05. RESULTS This study found 3351 KEGGs in the subgingival biofilm of both groups. Smoking habits altered the functional behavior of subgingival biofilm, resulting in 304 differentially expressed KEGGs between groups. Moreover, seven pathways were modulated: glycan degradation, galactose metabolism, glycosaminoglycan degradation, oxidative phosphorylation, peptidoglycan biosynthesis, butanoate metabolism, and glycosphingolipid biosynthesis. Smoking also altered antibiotic resistance gene levels in subgingival biofilm by significantly overexpressing genes related to beta-lactamase, permeability, antibiotic efflux pumps, and antibiotic-resistant synthetases. CONCLUSION Due to the limitations of a small sample size, our data suggest that smoking may influence the functional behavior of subgingival biofilm, modifying pathways that negatively impact the behavior of subgingival biofilm, which may lead to a more virulent community.
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Affiliation(s)
- Renato Corrêa Viana Casarin
- Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba, Departamento de Prótese e Periodontia, Piracicaba, Brasil
| | - Rafaela Videira Clima da Silva
- Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba, Departamento de Prótese e Periodontia, Piracicaba, Brasil
| | - Hélvis Enri de Sousa Paz
- Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba, Departamento de Prótese e Periodontia, Piracicaba, Brasil
| | - Camila Schmidt Stolf
- Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba, Departamento de Prótese e Periodontia, Piracicaba, Brasil
| | - Lucas Miguel Carvalho
- Universidade Estadual de Campinas, Centro de Pesquisas em Engenharias e Ciências Computacionais, Campinas, Brasil
| | - Melline Fontes Noronha
- University of Illinois at Chicago, Research Resource Center, Research Informatics Core, Illinois, USA
| | - Antonio Wilson Sallum
- Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba, Departamento de Prótese e Periodontia, Piracicaba, Brasil
| | - Mabelle de Freitas Monteiro
- Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba, Departamento de Prótese e Periodontia, Piracicaba, Brasil
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3
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Lu KYF, Alqaderi H, Bin Hasan S, Alhazmi H, Alghounaim M, Devarajan S, Freire M, Altabtbaei K. Sputum production and salivary microbiome in COVID-19 patients reveals oral-lung axis. PLoS One 2024; 19:e0300408. [PMID: 39052548 PMCID: PMC11271936 DOI: 10.1371/journal.pone.0300408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
SARS-CoV-2, a severe respiratory disease primarily targeting the lungs, was the leading cause of death worldwide during the pandemic. Understanding the interplay between the oral microbiome and inflammatory cytokines during acute infection is crucial for elucidating host immune responses. This study aimed to explore the relationship between the oral microbiome and cytokines in COVID-19 patients, particularly those with and without sputum production. Saliva and blood samples from 50 COVID-19 patients were subjected to 16S ribosomal RNA gene sequencing for oral microbiome analysis, and 65 saliva and serum cytokines were assessed using Luminex multiplex analysis. The Mann-Whitney test was used to compare cytokine levels between individuals with and without sputum production. Logistic regression machine learning models were employed to evaluate the predictive capability of oral microbiome, salivary, and blood biomarkers for sputum production. Significant differences were observed in the membership (Jaccard dissimilarity: p = 0.016) and abundance (PhILR dissimilarity: p = 0.048; metagenomeSeq) of salivary microbial communities between patients with and without sputum production. Seven bacterial genera, including Prevotella, Streptococcus, Actinomyces, Atopobium, Filifactor, Leptotrichia, and Selenomonas, were more prevalent in patients with sputum production (p<0.05, Fisher's exact test). Nine genera, including Prevotella, Megasphaera, Stomatobaculum, Selenomonas, Leptotrichia, Veillonella, Actinomyces, Atopobium, and Corynebacteria, were significantly more abundant in the sputum-producing group, while Lachnoanaerobaculum was more prevalent in the non-sputum-producing group (p<0.05, ANCOM-BC). Positive correlations were found between salivary IFN-gamma and Eotaxin2/CCL24 with sputum production, while negative correlations were noted with serum MCP3/CCL7, MIG/CXCL9, IL1 beta, and SCF (p<0.05, Mann-Whitney test). The machine learning model using only oral bacteria input outperformed the model that included all data: blood and saliva biomarkers, as well as clinical and demographic variables, in predicting sputum production in COVID-19 subjects. The performance metrics were as follows, comparing the model with only bacteria input versus the model with all input variables: precision (95% vs. 75%), recall (100% vs. 50%), F1-score (98% vs. 60%), and accuracy (82% vs. 66%).
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Affiliation(s)
- Korina Yun-Fan Lu
- Harvard School of Dental Medicine, Boston, Massachusetts, United States of America
| | - Hend Alqaderi
- Tufts University School of Dental Medicine, Boston, Massachusetts, United States of America
- Dasman Diabetes Institute, Dasman, Kuwait
| | | | - Hesham Alhazmi
- Harvard School of Dental Medicine, Boston, Massachusetts, United States of America
- Department of Preventive Dentistry, Division of Pediatric Dentistry, Umm Al-Qura University, Mekkah, Saudi Arabia
| | | | | | - Marcelo Freire
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, California, United States of America
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, California, United States of America
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4
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Szymanski EA, Turner M. Metaphors as design tools for microbial consortia: An analysis of recent peer-reviewed literature. Microb Biotechnol 2024; 17:e14366. [PMID: 38009763 PMCID: PMC10832539 DOI: 10.1111/1751-7915.14366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/25/2023] [Accepted: 10/22/2023] [Indexed: 11/29/2023] Open
Abstract
Single engineered microbial species cannot always conduct complex transformations, while complex, incompletely defined microbial consortia have heretofore been suited to a limited range of tasks. As biodesigners bridge this gap with intentionally designed microbial communities, they will, intentionally or otherwise, build communities that embody particular ideas about what microbial communities can and should be. Here, we suggest that metaphors-ideas about what microbial communities are like-are therefore important tools for designing synthetic consortia-based bioreactors. We identify a range of metaphors currently employed in peer-reviewed microbiome research articles, characterizing each through its potential structural implications and distinctive imagery. We present this metaphor catalogue in the interest of, first, making metaphors visible as design choices, second, enabling deliberate experimentation with them towards expanding the potential design space of the field, and third, encouraging reflection on the goals and values they embed.
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Affiliation(s)
| | - Marie Turner
- Department of EnglishColorado State UniversityFort CollinsColoradoUSA
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5
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Molli VLP, Kissa J, Baraniya D, Gharibi A, Chen T, Al-Hebshi NN, Albandar JM. Bacteriome analysis of Aggregatibacter actinomycetemcomitans-JP2 genotype-associated Grade C periodontitis in Moroccan adolescents. FRONTIERS IN ORAL HEALTH 2023; 4:1288499. [PMID: 38033462 PMCID: PMC10682098 DOI: 10.3389/froh.2023.1288499] [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: 09/05/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023] Open
Abstract
Background Grade C (previously aggressive) periodontitis (GCP) in adolescents is prevalent in certain parts of Africa where it is associated with JP2 genotype, a highly virulent strain of Aggregatibacter actinomycetemcomitans. The aim of this study was to characterize the subgingival bacteriome in Moroccan subjects with GCP positive to A. actinomycetemcomitans JP2 genotype. Methods Subgingival plaque samples were collected from shallow and deep pockets of 8 subjects with GCP (17.2 ± 1.5 years) and from gingival sulci of 13 controls with no periodontitis (14.6 ± 1.1 years). Identification and genotyping of A. actinomycetemcomitans was performed using PCR analysis of the ltx operon, while bacteriome profiling was done by 16S rRNA gene sequencing (V1-V3 region). Groups were compared in terms of microbial diversity, abundances, and dysbiosis. Results The shallow and deep pocket sites from GCP cases had a significantly altered microbial composition compared to controls. Species associated with health included Haemophilus parainfluenzae, Lautropia mirabilis, Streptococcus spp., Gemella spp., and Rothia spp. While known periodontal pathogens, including Porphyromonas gingivalis, Tannerella forsythia, Treponema spp. and Fretibacterium spp., were significantly enriched in GCP, non-conventional taxa, including Pseudomonas oral taxon C61 and Enterobacter cloacae were more abundant and showed stronger association with the disease. Less significant differences in abundances of individual taxa were observed between shallow and deep pockets. Overall dysbiosis measured in terms of Subgingival Microbial Dysbiosis Index (SMDI) differentiated between GCP and no-periodontitis with 95% accuracy. Conclusions The results suggest that several periodontal pathogens involved in the adult-type periodontitis also play a role in JP2 genotype-associated GCP. The potential role of non-conventional taxa in the pathogenesis of GCP warrants further investigation.
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Affiliation(s)
- Vijaya Lakshmi Pavani Molli
- Department of Periodontology and Oral Implantology, Maurice H. Kornberg School of Dentistry, Temple University, Philadelphia, PA, United States
| | - Jamila Kissa
- Department of Periodontology, Faculty of Dental Medicine, University of Hassan II, Casablanca, Morocco
| | - Divyashri Baraniya
- Oral Microbiome Research Laboratory, Maurice H. Kornberg School of Dentistry, Temple University, Philadelphia, PA, United States
| | - Amina Gharibi
- Department of Periodontology, Faculty of Dental Medicine, University of Hassan II, Casablanca, Morocco
| | - Tsute Chen
- Department of Microbiology, Forsyth Institute, Cambridge, MA, United States
| | - Nezar N. Al-Hebshi
- Oral Microbiome Research Laboratory, Maurice H. Kornberg School of Dentistry, Temple University, Philadelphia, PA, United States
| | - Jasim M. Albandar
- Department of Periodontology and Oral Implantology, Maurice H. Kornberg School of Dentistry, Temple University, Philadelphia, PA, United States
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6
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Reuben RC, Beugnon R, Jurburg SD. COVID-19 alters human microbiomes: a meta-analysis. Front Cell Infect Microbiol 2023; 13:1211348. [PMID: 37600938 PMCID: PMC10433767 DOI: 10.3389/fcimb.2023.1211348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/23/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected a substantial portion of the world's population, and novel consequences of COVID-19 on the human body are continuously being uncovered. The human microbiome plays an essential role in host health and well-being, and multiple studies targeting specific populations have reported altered microbiomes in patients infected with SARS-CoV-2. Given the global scale and massive incidence of COVID on the global population, determining whether the effects of COVID-19 on the human microbiome are consistent and generalizable across populations is essential. Methods We performed a synthesis of human microbiome responses to COVID-19. We collected 16S rRNA gene amplicon sequence data from 11 studies sampling the oral and nasopharyngeal or gut microbiome of COVID-19-infected and uninfected subjects. Our synthesis included 1,159 respiratory (oral and nasopharyngeal) microbiome samples and 267 gut microbiome samples from patients in 11 cities across four countries. Results Our reanalyses revealed communitywide alterations in the respiratory and gut microbiomes across human populations. We found significant overall reductions in the gut microbial diversity of COVID-19-infected patients, but not in the respiratory microbiome. Furthermore, we found more consistent community shifts in the gut microbiomes of infected patients than in the respiratory microbiomes, although the microbiomes in both sites exhibited higher host-to-host variation in infected patients. In respiratory microbiomes, COVID-19 infection resulted in an increase in the relative abundance of potentially pathogenic bacteria, including Mycoplasma. Discussion Our findings shed light on the impact of COVID-19 on the human-associated microbiome across populations, and highlight the need for further research into the relationship between long-term effects of COVID-19 and altered microbiota.
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Affiliation(s)
- Rine Christopher Reuben
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Rémy Beugnon
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Leipzig Institute for Meteorology, Universität Leipzig, Leipzig, Germany
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Stephanie D. Jurburg
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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7
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Iniesta M, Chamorro C, Ambrosio N, Marín MJ, Sanz M, Herrera D. Subgingival microbiome in periodontal health, gingivitis and different stages of periodontitis. J Clin Periodontol 2023; 50:905-920. [PMID: 36792073 DOI: 10.1111/jcpe.13793] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 02/04/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023]
Abstract
AIM To characterize the subgingival microbiome in subjects with different periodontal health statuses. MATERIALS AND METHODS In this cross-sectional observational study, subgingival samples were harvested from Spanish subjects with different periodontal health statuses, based on the 2018 Classification of Periodontal and Peri-Implant Diseases and Conditions. Samples were processed using high-throughput sequencing technologies (Illumina MiSeq). Taxa differentially abundant were identified using Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC). α- and β-diversity metrics were calculated using q2-diversity in QIIME2. The analyses were adjusted for age, gender and smoking status. RESULTS The identified subgingival microbiome showed statistically significant differences among subjects, categorized into periodontal health, gingivitis and stages I-II and III-IV periodontitis (p < .05). In patients with severe (stages III-IV) periodontitis, the genera Filifactor and Fretibacterium were detected 24 times more frequently than in periodontally healthy subjects. Similarly, the genera Porphyromonas, Prevotella and Tannerella were detected four times more frequently (p < .05). The genera Granulicatella, Streptococcus, Paracoccus, Pseudomonas, Haemophilus, Actinobacteria, Bergeyella and Capnocytophaga were significantly associated with healthier periodontal status (p < .05). CONCLUSIONS Significant differences were detected in the subgingival microbiome among periodontal health, gingivitis and stages I-II or III-IV periodontitis, suggesting overlapping, yet distinguishable microbial profiles.
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Affiliation(s)
- Margarita Iniesta
- ETEP (Etiology and Therapy of Periodontal and Peri-Implant Diseases) Research Group, School of Dentistry, Complutense University of Madrid, Madrid, Spain
| | - Cristina Chamorro
- ETEP (Etiology and Therapy of Periodontal and Peri-Implant Diseases) Research Group, School of Dentistry, Complutense University of Madrid, Madrid, Spain
| | - Nagore Ambrosio
- ETEP (Etiology and Therapy of Periodontal and Peri-Implant Diseases) Research Group, School of Dentistry, Complutense University of Madrid, Madrid, Spain
| | - María José Marín
- ETEP (Etiology and Therapy of Periodontal and Peri-Implant Diseases) Research Group, School of Dentistry, Complutense University of Madrid, Madrid, Spain
| | - Mariano Sanz
- ETEP (Etiology and Therapy of Periodontal and Peri-Implant Diseases) Research Group, School of Dentistry, Complutense University of Madrid, Madrid, Spain
| | - David Herrera
- ETEP (Etiology and Therapy of Periodontal and Peri-Implant Diseases) Research Group, School of Dentistry, Complutense University of Madrid, Madrid, Spain
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Zhao T, Chu Z, Chu CH, Dong S, Li G, Wu J, Tang C. Macrophages induce gingival destruction via Piezo1-mediated MMPs-degrading collagens in periodontitis. Front Immunol 2023; 14:1194662. [PMID: 37261355 PMCID: PMC10228731 DOI: 10.3389/fimmu.2023.1194662] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/03/2023] [Indexed: 06/02/2023] Open
Abstract
Macrophages are an integral part of the innate immune response in periodontal tissue and play a crucial role in the progression of periodontitis. Here we reported that macrophages also provoke periodontitis-induced gingival destruction through Piezol-mediated collagen degradation. We discovered that the PIEZO1 expression was markedly elevated in patients with periodontitis through transcriptomic profiling. Moreover, Piezo1 promoted macrophage polarization toward the M1 type in response to lipopolysaccharide (LPS) and induced production of proinflammatory cytokines, which in turn stimulated production of matrix metalloproteinases (MMPs) leading to collagen degradation. Our study suggests that Piezol might be a potential therapeutic target for treating periodontitis-induced gingival destruction.
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Affiliation(s)
- Tong Zhao
- Department of Dental Implantology and Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Oral Diseases, Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, China
| | - Zhuangzhuang Chu
- Department of Dental Implantology and Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Oral Diseases, Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, China
| | - Catherine Huihan Chu
- Key Laboratory of Oral Diseases, Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, China
- Department of Dental Orthodontic, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shuo Dong
- Department of Dental Implantology and Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Oral Diseases, Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, China
| | - Guoqing Li
- Department of Dental Implantology and Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Oral Diseases, Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, China
| | - Jin Wu
- Department of Dental Implantology and Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Oral Diseases, Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, China
| | - Chunbo Tang
- Department of Dental Implantology and Prosthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China
- Key Laboratory of Oral Diseases, Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, China
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9
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Mangal U, Noh K, Lee S, Cha JK, Song JS, Cha JY, Lee KJ, Kim KM, Kwon JS, Choi SH. Multistability and hysteresis in states of oral microbiota: Is it impacting the dental clinical cohort studies? J Periodontal Res 2023; 58:381-391. [PMID: 36641544 DOI: 10.1111/jre.13098] [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: 09/12/2022] [Revised: 12/06/2022] [Accepted: 01/03/2023] [Indexed: 01/16/2023]
Abstract
INTRODUCTION Microbiome from a "healthy cohort" is used as a reference for comparison to cases and intervention. However, the studies with cohort-based clinical research have not sufficiently accounted for the multistability in oral microbial community. The screening is limited to phenotypic features with marked variations in microbial genomic markers. Herein, we aimed to assess the stability of the oral microbiome across time from an intervention-free "healthy" cohort. METHODS We obtained 33 supragingival samples of 11 healthy participants from the biobank. For each participant, we processed one sample as baseline (T0) and two samples spaced at 1-month (T1) and 3-month (T2) intervals for 16S ribosomal RNA gene sequencing analysis. RESULTS We observed that taxonomic profiling had a similar pattern of dominant genera, namely, Rothia, Prevotella, and Hemophilus, at all time points. Shannon diversity revealed a significant increase from T0 (p < .05). Bray Curtis dissimilarity was significant (R = -.02, p < .01) within the cohort at each time point. Community stability had negative correlation to synchrony (r = -.739; p = .009) and variance (r = -.605; p = .048) of the species. Clustering revealed marked differences in the grouping patterns between the three time points. For all time points, the clusters presented a substantially dissimilar set of differentially abundant taxonomic and functional biomarkers. CONCLUSION Our observations indicate towards the presence of multistable states within the oral microbiome in an intervention-free healthy cohort. For a conclusive and meaningful long-term reference, dental clinical research should account for multistability in the personalized therapy approach to improve the identification and classification of reliable markers.
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Affiliation(s)
- Utkarsh Mangal
- Department of Orthodontics, Yonsei University College of Dentistry, Seoul, Korea.,Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea
| | - Kowoon Noh
- Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea.,Department and Research Institute of Dental Biomaterials and Bioengineering, Yonsei University College of Dentistry, Seoul, Korea.,BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, Korea
| | - Seeyoon Lee
- Department of Orthodontics, Yonsei University College of Dentistry, Seoul, Korea
| | - Jae-Kook Cha
- Department of Periodontology, Research Institute of Periodontal Regeneration, Yonsei University College of Dentistry, Seoul, Korea
| | - Je Seon Song
- Department of Pediatric Dentistry, Yonsei University College of Dentistry, Seoul, Korea.,Oral Science Research Center, College of Dentistry, Yonsei University, Seoul, Korea
| | - Jung-Yul Cha
- Department of Orthodontics, Yonsei University College of Dentistry, Seoul, Korea.,Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea
| | - Kee-Joon Lee
- Department of Orthodontics, Yonsei University College of Dentistry, Seoul, Korea.,Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea
| | - Kwang-Mahn Kim
- Department and Research Institute of Dental Biomaterials and Bioengineering, Yonsei University College of Dentistry, Seoul, Korea
| | - Jae-Sung Kwon
- Department and Research Institute of Dental Biomaterials and Bioengineering, Yonsei University College of Dentistry, Seoul, Korea.,BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, Korea
| | - Sung-Hwan Choi
- Department of Orthodontics, Yonsei University College of Dentistry, Seoul, Korea.,Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Korea
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10
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Keeler EL, Merenstein C, Reddy S, Taylor LJ, Cobián-Güemes AG, Zankharia U, Collman RG, Bushman FD. Widespread, human-associated redondoviruses infect the commensal protozoan Entamoeba gingivalis. Cell Host Microbe 2023; 31:58-68.e5. [PMID: 36459997 PMCID: PMC9969835 DOI: 10.1016/j.chom.2022.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/05/2022] [Accepted: 11/04/2022] [Indexed: 12/03/2022]
Abstract
Redondoviruses are circular Rep-encoding single-stranded DNA (CRESS) viruses of high prevalence in healthy humans. Redondovirus abundance is increased in oro-respiratory samples from individuals with periodontitis, acute illness, and severe COVID-19. We investigated potential host cells supporting redondovirus replication in oro-respiratory samples and uncovered the oral amoeba Entamoeba gingivalis as a likely host. Redondoviruses are closely related to viruses of Entamoeba and contain reduced GC nucleotide content, consistent with Entamoeba hosts. Redondovirus and E. gingivalis co-occur in metagenomic data from oral disease and healthy human cohorts. When grown in xenic cultures with feeder bacteria, E. gingivalis was robustly positive for redondovirus RNA and DNA. A DNA proximity-ligation assay (Hi-C) on xenic culture cells showed enriched cross-linking of redondovirus and Entamoeba DNA, supporting E. gingivalis as the redondovirus host. While bacteria are established hosts for bacteriophages within the human virome, this work shows that eukaryotic commensals also contribute an abundant human-associated virus.
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Affiliation(s)
- Emma L Keeler
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Carter Merenstein
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shantan Reddy
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Louis J Taylor
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ana G Cobián-Güemes
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Urvi Zankharia
- Department of Medicine, Pulmonary, Allergy and Critical Care Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ronald G Collman
- Department of Medicine, Pulmonary, Allergy and Critical Care Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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11
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Klimenko ES, Belkova NL, Romanitsa AI, Pogodina AV, Rychkova LV, Darenskaya MA. Differences in Gut Microbiota Composition and Predicted Metabolic Functions: a Pilot Study of Adolescents with Normal Weight and Obesity. Bull Exp Biol Med 2022; 173:628-632. [DOI: 10.1007/s10517-022-05601-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Indexed: 11/06/2022]
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12
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Ezhilarasan D, Varghese SS. Porphyromonas gingivalis and dental stem cells crosstalk amplify inflammation and bone loss in the periodontitis niche. J Cell Physiol 2022; 237:3768-3777. [PMID: 35926111 DOI: 10.1002/jcp.30848] [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: 05/06/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 11/09/2022]
Abstract
Periodontitis is the sixth most prevalent disease, and almost 3.5 billion people are affected globally by dental caries and periodontal diseases. The microbial shift from a symbiotic microbiota to a dysbiotic microbiota in the oral cavity generally initiates periodontal disease. Pathogens in the periodontal microenvironment interact with stem cells to modulate their regenerative potential. Therefore, this review focuses on the interaction between microbes and stem cells in periodontitis conditions. Microbes direct dental stem cells to secrete a variety of pro-inflammatory cytokines and chemokines, which increase the inflammatory burden in the damaged periodontal tissue, which further aggravates periodontitis. Microbial interaction also decreases the osteogenic differentiation potential of dental stem cells by downregulating alkaline phosphatase, runt-related transcription factor 2, type 1 collagen, osteocalcin, osteopontin, and so on. Microbe and stem cell interaction amplifies pro-inflammatory cytokine signaling in the periodontitis niche, decreasing the osteogenic commitment of dental stem cells. A clear understanding of microbial stem cell interactions is crucial in designing regenerative therapies using stem cells in the management of periodontitis.
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Affiliation(s)
- Devaraj Ezhilarasan
- Department of Pharmacology, Molecular Medicine and Toxicology Lab, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
| | - Sheeja S Varghese
- Department of Periodontology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
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13
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Li S, Guo R, Zhang Y, Li P, Chen F, Wang X, Li J, Jie Z, Lv Q, Jin H, Wang G, Yan Q. A catalog of 48,425 nonredundant viruses from oral metagenomes expands the horizon of the human oral virome. iScience 2022; 25:104418. [PMID: 35663034 PMCID: PMC9160773 DOI: 10.1016/j.isci.2022.104418] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/26/2022] [Accepted: 05/12/2022] [Indexed: 12/18/2022] Open
Abstract
The human oral cavity is a hotspot of numerous, mostly unexplored, viruses that are important for maintaining oral health and microbiome homeostasis. Here, we analyzed 2,792 publicly available oral metagenomes and proposed the Oral Virus Database (OVD) comprising 48,425 nonredundant viral genomes (≥5 kbp). The OVD catalog substantially expanded the known phylogenetic diversity and host specificity of oral viruses, allowing for enhanced delineation of some underrepresented groups such as the predicted Saccharibacteria phages and jumbo viruses. Comparisons of the viral diversity and abundance of different oral cavity habitats suggested strong niche specialization of viromes within individuals. The virome variations in relation to host geography and properties were further uncovered, especially the age-dependent viral compositional signatures in saliva. Overall, the viral genome catalog describes the architecture and variability of the human oral virome, while offering new resources and insights for current and future studies.
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Affiliation(s)
- Shenghui Li
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
- Puensum Genetech Institute, Wuhan 430076, China
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan 430076, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Peng Li
- Puensum Genetech Institute, Wuhan 430076, China
| | - Fang Chen
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xifan Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Jing Li
- Department of Rheumatology and Immunology, Peking University People’s Hospital, Beijing 100044, China
| | - Zhuye Jie
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan 430076, China
| | - Hao Jin
- Puensum Genetech Institute, Wuhan 430076, China
- College of Food Science and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Guangyang Wang
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Qiulong Yan
- Department of Microbiology, College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
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14
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Qin H, Li G, Xu X, Zhang C, Zhong W, Xu S, Yin Y, Song J. The role of oral microbiome in periodontitis under diabetes mellitus. J Oral Microbiol 2022; 14:2078031. [PMID: 35694215 PMCID: PMC9176325 DOI: 10.1080/20002297.2022.2078031] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Periodontitis is among most common human inflammatory diseases and characterized by destruction of tooth-supporting tissues that will eventually lead to tooth loss. Diabetes mellitus (DM) is a group of metabolic disorders characterized by chronic hyperglycemia which results from defects in insulin secretion and/or insulin resistance. Numerous studies have provided evidence for the inter-relationship between DM and periodontitis that has been considered as the sixth most frequent complication of DM. However, the mechanisms are not fully understood yet. The impact of DM on periodontitis through hyperglycemia and inflammatory pathways is well described, but the effects of DM on oral microbiota remain controversial according to previous studies. Recent studies using next-generation sequencing technology indicate that DM can alter the biodiversity and composition of oral microbiome especially subgingival microbiome. This may be another mechanism by which DM risks or aggravates periodontitis. Thus, to understand the role of oral microbiome in periodontitis of diabetics and the mechanism of shifts of oral microbiome under DM would be valuable for making specific therapeutic regimens for treating periodontitis patients with DM or preventing diabetic patients from periodontitis. This article reviews the role of oral microbiome in periodontal health (symbiosis) and disease (dysbiosis), highlights the oral microbial shifts under DM and summarizes the mechanism of the shifts.
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Affiliation(s)
- Han Qin
- College of Stomatology, Chongqing Medical University, Chongqing, Unknown, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, Unknown, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, Unknown, China
| | - Guangyue Li
- College of Stomatology, Chongqing Medical University, Chongqing, Unknown, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, Unknown, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, Unknown, China
| | - Xiaohui Xu
- College of Stomatology, Chongqing Medical University, Chongqing, Unknown, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, Unknown, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, Unknown, China
| | - Chuangwei Zhang
- College of Stomatology, Chongqing Medical University, Chongqing, Unknown, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, Unknown, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, Unknown, China
| | - Wenjie Zhong
- College of Stomatology, Chongqing Medical University, Chongqing, Unknown, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, Unknown, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, Unknown, China
| | - Shihan Xu
- College of Stomatology, Chongqing Medical University, Chongqing, Unknown, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, Unknown, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, Unknown, China
| | - Yuanyuan Yin
- College of Stomatology, Chongqing Medical University, Chongqing, Unknown, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, Unknown, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, Unknown, China
| | - Jinlin Song
- College of Stomatology, Chongqing Medical University, Chongqing, Unknown, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, Unknown, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, Unknown, China
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15
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Wu F, Fang B, Wuri G, Zhao L, Liu F, Zhang M. Metagenomic Analysis Reveals a Mitigating Role for Lactobacillus paracasei and Bifidobacterium animalis in Experimental Periodontitis. Nutrients 2022; 14:2125. [PMID: 35631266 PMCID: PMC9146436 DOI: 10.3390/nu14102125 10.3390/nu14102125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Probiotics have aroused increasing concern as an intervention strategy for periodontitis (PD), but their underlying mechanism of action remains poorly characterized. Regarding the significance of oral microbiota dysbiosis related to PD, we predicted that the preventive activity of probiotics may be influenced by suppressing the bacterial pathogenicity. Herein, we investigated the effects of Lactobacillus paracasei L9 (L9) and Bifidobacterium animalis A6 (A6) on PD using a rat model, and demonstrated a regulatory effect of probiotics on oral flora from a metagenomics perspective. Oral administration of A6 or L9 effectively relieved gingival bleeding, periodontal inflammatory infiltration, and alveolar bone resorption. In addition, A6 or L9 treatment reduced the inflammatory response and increased the expression of anti-inflammatory cytokines, which we expected to ameliorate alveolar bone resorption as mediated by the receptor activator of the nuclear factor-κB ligand/OPG signaling pathway. More importantly, using metagenomic sequencing, we showed that probiotics significantly altered the taxonomic composition of the subgingival microbiome, and reduced the relative proportions of pathogenic bacterial genera such as Streptococcus, Fusobacterium, Veillonella, and Escherichia. Both probiotics significantly inhibited levels of bacterial virulence factors related to adherence, invasion, exoenzyme, and complement protease functions that are strongly correlated with the pathogenesis of PD. Our overall results suggest that A6 and L9 may constitute promising prophylactic agents for PD, and should thus be further explored in the future.
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Affiliation(s)
- Fang Wu
- School of Food and Health, Beijing Technology and Business University, Beijing 100084, China; (F.W.); (G.W.)
| | - Bing Fang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China;
| | - Guna Wuri
- School of Food and Health, Beijing Technology and Business University, Beijing 100084, China; (F.W.); (G.W.)
| | - Liang Zhao
- Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China;
- Beijing Laboratory of Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Fudong Liu
- Inner Mongolia Dairy Technology Research Institute Co., Ltd., Hohhot 010110, China;
- Inner Mongolia Yili Industrial Group Co., Ltd., Hohhot 010110, China
| | - Ming Zhang
- School of Food and Health, Beijing Technology and Business University, Beijing 100084, China; (F.W.); (G.W.)
- Correspondence:
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16
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Wu F, Fang B, Wuri G, Zhao L, Liu F, Zhang M. Metagenomic Analysis Reveals a Mitigating Role for Lactobacillus paracasei and Bifidobacterium animalis in Experimental Periodontitis. Nutrients 2022; 14:2125. [PMID: 35631266 PMCID: PMC9146436 DOI: 10.3390/nu14102125+10.3390/nu14102125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
Probiotics have aroused increasing concern as an intervention strategy for periodontitis (PD), but their underlying mechanism of action remains poorly characterized. Regarding the significance of oral microbiota dysbiosis related to PD, we predicted that the preventive activity of probiotics may be influenced by suppressing the bacterial pathogenicity. Herein, we investigated the effects of Lactobacillus paracasei L9 (L9) and Bifidobacterium animalis A6 (A6) on PD using a rat model, and demonstrated a regulatory effect of probiotics on oral flora from a metagenomics perspective. Oral administration of A6 or L9 effectively relieved gingival bleeding, periodontal inflammatory infiltration, and alveolar bone resorption. In addition, A6 or L9 treatment reduced the inflammatory response and increased the expression of anti-inflammatory cytokines, which we expected to ameliorate alveolar bone resorption as mediated by the receptor activator of the nuclear factor-κB ligand/OPG signaling pathway. More importantly, using metagenomic sequencing, we showed that probiotics significantly altered the taxonomic composition of the subgingival microbiome, and reduced the relative proportions of pathogenic bacterial genera such as Streptococcus, Fusobacterium, Veillonella, and Escherichia. Both probiotics significantly inhibited levels of bacterial virulence factors related to adherence, invasion, exoenzyme, and complement protease functions that are strongly correlated with the pathogenesis of PD. Our overall results suggest that A6 and L9 may constitute promising prophylactic agents for PD, and should thus be further explored in the future.
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Affiliation(s)
- Fang Wu
- School of Food and Health, Beijing Technology and Business University, Beijing 100084, China; (F.W.); (G.W.)
| | - Bing Fang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China;
| | - Guna Wuri
- School of Food and Health, Beijing Technology and Business University, Beijing 100084, China; (F.W.); (G.W.)
| | - Liang Zhao
- Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China;
- Beijing Laboratory of Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Fudong Liu
- Inner Mongolia Dairy Technology Research Institute Co., Ltd., Hohhot 010110, China;
- Inner Mongolia Yili Industrial Group Co., Ltd., Hohhot 010110, China
| | - Ming Zhang
- School of Food and Health, Beijing Technology and Business University, Beijing 100084, China; (F.W.); (G.W.)
- Correspondence:
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17
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Metagenomic Analysis Reveals a Mitigating Role for Lactobacillus paracasei and Bifidobacterium animalis in Experimental Periodontitis. Nutrients 2022; 14:nu14102125. [PMID: 35631266 PMCID: PMC9146436 DOI: 10.3390/nu14102125] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/14/2022] [Accepted: 05/17/2022] [Indexed: 12/15/2022] Open
Abstract
Probiotics have aroused increasing concern as an intervention strategy for periodontitis (PD), but their underlying mechanism of action remains poorly characterized. Regarding the significance of oral microbiota dysbiosis related to PD, we predicted that the preventive activity of probiotics may be influenced by suppressing the bacterial pathogenicity. Herein, we investigated the effects of Lactobacillus paracasei L9 (L9) and Bifidobacterium animalis A6 (A6) on PD using a rat model, and demonstrated a regulatory effect of probiotics on oral flora from a metagenomics perspective. Oral administration of A6 or L9 effectively relieved gingival bleeding, periodontal inflammatory infiltration, and alveolar bone resorption. In addition, A6 or L9 treatment reduced the inflammatory response and increased the expression of anti-inflammatory cytokines, which we expected to ameliorate alveolar bone resorption as mediated by the receptor activator of the nuclear factor-κB ligand/OPG signaling pathway. More importantly, using metagenomic sequencing, we showed that probiotics significantly altered the taxonomic composition of the subgingival microbiome, and reduced the relative proportions of pathogenic bacterial genera such as Streptococcus, Fusobacterium, Veillonella, and Escherichia. Both probiotics significantly inhibited levels of bacterial virulence factors related to adherence, invasion, exoenzyme, and complement protease functions that are strongly correlated with the pathogenesis of PD. Our overall results suggest that A6 and L9 may constitute promising prophylactic agents for PD, and should thus be further explored in the future.
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18
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Leclaire S, Pineaux M, Blanchard P, White J, Hatch SA. Microbiota composition and diversity of multiple body sites vary according to reproductive performance in a seabird. Mol Ecol 2022; 32:2115-2133. [PMID: 35152516 DOI: 10.1111/mec.16398] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/03/2022] [Accepted: 02/07/2022] [Indexed: 11/30/2022]
Abstract
The microbiota is suggested to be a fundamental contributor to host reproduction and survival, but associations between microbiota and fitness are rare, especially for wild animals. Here, we tested the association between microbiota and two proxies of breeding performance in multiple body sites of the black-legged kittiwake, a seabird species. First we found that, in females, nonbreeders (i.e., birds that did not lay eggs) hosted different microbiota composition to that of breeders in neck and flank feathers, in the choanae, in the outer-bill and in the cloacae, but not in preen feathers and tracheae. These differences in microbiota might reflect variations in age or individual quality between breeders and nonbreeders. Second, we found that better female breeders (i.e., with higher body condition, earlier laying date, heavier eggs, larger clutch, and higher hatching success) had lower abundance of several Corynebacteriaceae in cloaca than poorer female breeders, suggesting that these bacteria might be pathogenic. Third, in females, better breeders had different microbiota composition and lower microbiota diversity in feathers, especially in preen feathers. They had also reduced dispersion in microbiota composition across body sites. These results might suggest that good breeding females are able to control their feather microbiota-potentially through preen secretions-more tightly than poor breeding females. We did not find strong evidence for an association between reproductive outcome and microbiota in males. Our results are consistent with the hypothesis that natural variation in the microbiota is associated with differences in host fitness in wild animals, but the causal relationships remain to be investigated.
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Affiliation(s)
- Sarah Leclaire
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
| | - Maxime Pineaux
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
| | - Pierrick Blanchard
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
| | - Joël White
- Laboratoire Evolution et Diversité Biologique (EDB) UMR5174 Université Toulouse 3 Paul Sabatier CNRS, IRD Toulouse France
- ENSFEA Castanet‐Tolosan France
| | - Scott A Hatch
- Institute for Seabird Research and Conservation Anchorage AK 99516 USA
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19
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Veith PD, Glew MD, Gorasia DG, Cascales E, Reynolds EC. The Type IX Secretion System and Its Role in Bacterial Function and Pathogenesis. J Dent Res 2021; 101:374-383. [PMID: 34889148 DOI: 10.1177/00220345211051599] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Porphyromonas, Tannerella, and Prevotella species found in severe periodontitis use the Type IX Secretion System (T9SS) to load their outer membrane surface with an array of virulence factors. These virulence factors are then released on outer membrane vesicles (OMVs), which penetrate the host to dysregulate the immune response to establish a positive feedback loop of chronic, inflammatory destruction of the tooth's supporting tissues. In this review, we present the latest information on the molecular architecture of the T9SS and provide mechanistic insight into its role in secretion and attachment of cargo proteins to produce a virulence coat on cells and OMVs. The recent molecular structures of the T9SS motor comprising PorL and PorM as well as the secretion pore Sov, together with advances in the overall interactome, have provided insight into the possible mechanisms of secretion. We propose the presence of PorL/M motors arranged in a circle at the inner membrane with bent periplasmic rotors interacting with the PorN protein. At the outer membrane, we envisage a slide carousel model where the PorN protein is driven around a circular track composed of PorK. Cargo proteins are transported by PorN to PorW and the Sov translocon just as slides are rotated to the projection window. Secreted proteins are proposed to then be shuttled along highways consisting of the PorV shuttle protein to an array of attachment complexes distributed around the cell. The cell surface attachment of cargo is a hallmark of the T9SS, and in Porphyromonas gingivalis and Tannerella forsythia, this attachment is achieved via covalent bonding to a linking sugar synthesized by the Wbp/Vim pathway. The cell-surface attached cargo are enriched on OMVs, which are then released from the cell.
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Affiliation(s)
- P D Veith
- Oral Health CRC, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - M D Glew
- Oral Health CRC, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - D G Gorasia
- Oral Health CRC, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - E Cascales
- Laboratoire d'Ingénierie des Syst èmes Macromol éculaires (LISM), Institut de Microbiologie, Bioénergies and Biotechnologie (IM2B), Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS), UMR7255, Marseille Cedex, France
| | - E C Reynolds
- Oral Health CRC, Melbourne Dental School, Bio21 Institute, The University of Melbourne, Victoria, Australia
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20
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Paz HES, Monteiro MF, Stolf CS, Altabtbaei K, Casati MZ, Casarin RCV, Kumar PS. Predicted functional and taxonomic analysis of subgingival biofilm of grade C periodontitis in young patients under maintenance therapy. J Periodontol 2021; 93:1119-1130. [PMID: 34727386 DOI: 10.1002/jper.21-0411] [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: 07/14/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 11/09/2022]
Abstract
BACKGROUND In Grade C periodontitis in young patients (PerioC-Y), the functional roles of the subgingival community after years of periodontal treatment are still underexplored. This study evaluated the taxonomic and predicted functional content of the subgingival microbiome of PerioC-Y patients under supportive periodontal therapy (SPT). METHODS Clinical and microbiological data from subgingival biofilm were assessed from 10 PerioC-Y patients at two time points: at baseline and after 5.7±1.3 years of SPT. This was compared to 15 patients without a history of periodontitis. The V1-V3 and V4-V5 regions of the 16S rRNA were sequenced using the Illumina Miseq. Microbial composition was evaluated by the core microbiome, and alpha- and beta-diversity. The microbiome functional content was predicted using Picrust2, and the gene differential abundance was analyzed with DESeq2. RESULTS Clinical improvements were seen in PerioC-Y-SPT. Differences in β-diversity between PerioC-Y and Health were observed (Health x PerioC-Y-baseline, p = 0.02; Health x PerioC-Y-SPT, p = 0.05). Moreover, although β-diversity did not statistically change between baseline and SPT in PerioC-Y, the microbial correlation evidenced increased Streptococcus and decreased Treponema network contributions during SPT. Based on predicted functional data, treatment induced a reduction in genes related to flagellar protein and signal transduction in PerioC-Y. However, compared to healthy individuals, some genes remained more highly abundant in PerioC-Y-SPT, such as quorum sensing and efflux pump transporters. CONCLUSION Despite clinical improvements and a shift in taxonomic composition, the PerioC-Y patients' periodontal treatment was not enough to reach a similar microbiome to patients without disease experience. Some functional content in this biofilm remained altered in PerioC-Y regardless of disease control. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hélvis E S Paz
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Mabelle F Monteiro
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Camila S Stolf
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Khaled Altabtbaei
- Department of Periodontology, School of Dentistry, University of Alberta, Edmonton, Canada
| | - Márcio Z Casati
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Renato C V Casarin
- Periodontics Division, Department of Prosthodontics and Periodontics, Piracicaba Dental School, University of Campinas, Piracicaba, SP, Brazil
| | - Purnima S Kumar
- Department of Periodontology, College of Dentistry, The Ohio State University, Columbus, OH, USA
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21
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Huang Y, Zhao X, Cui L, Huang S. Metagenomic and Metatranscriptomic Insight Into Oral Biofilms in Periodontitis and Related Systemic Diseases. Front Microbiol 2021; 12:728585. [PMID: 34721325 PMCID: PMC8548771 DOI: 10.3389/fmicb.2021.728585] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 09/21/2021] [Indexed: 01/03/2023] Open
Abstract
The oral microbiome is one of the most complex microbial communities in the human body and is closely related to oral and systemic health. Dental plaque biofilms are the primary etiologic factor of periodontitis, which is a common chronic oral infectious disease. The interdependencies that exist among the resident microbiota constituents in dental biofilms and the interaction between pathogenic microorganisms and the host lead to the occurrence and progression of periodontitis. Therefore, accurately and comprehensively detecting periodontal organisms and dissecting their corresponding functional activity characteristics are crucial for revealing periodontitis pathogenesis. With the development of metagenomics and metatranscriptomics, the composition and structure of microbial communities as well as the overall functional characteristics of the flora can be fully profiled and revealed. In this review, we will critically examine the currently available metagenomic and metatranscriptomic evidence to bridge the gap between microbial dysbiosis and periodontitis and related systemic diseases.
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Affiliation(s)
- Yi Huang
- Stomatological Hospital, Southern Medical University and Guangdong Provincial Stomatological Hospital, Guangzhou, China
| | - Xinyuan Zhao
- Stomatological Hospital, Southern Medical University and Guangdong Provincial Stomatological Hospital, Guangzhou, China
| | - Li Cui
- Stomatological Hospital, Southern Medical University and Guangdong Provincial Stomatological Hospital, Guangzhou, China
- School of Dentistry and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, United States
| | - Shaohong Huang
- Stomatological Hospital, Southern Medical University and Guangdong Provincial Stomatological Hospital, Guangzhou, China
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