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Yu PS, Tu CC, Wara-Aswapati N, Wang CY, Tu YK, Hou HH, Ueno T, Chen IH, Fu KL, Li HY, Chen YW. Microbiome of periodontitis and peri-implantitis before and after therapy: Long-read 16S rRNA gene amplicon sequencing. J Periodontal Res 2024; 59:657-668. [PMID: 38718089 DOI: 10.1111/jre.13269] [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: 12/15/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 07/16/2024]
Abstract
AIMS The microbial profiles of peri-implantitis and periodontitis (PT) are inconclusive. The controversies mainly arise from the differences in sampling sites, targeted gene fragment, and microbiome analysis techniques. The objective of this study was to explore the microbiomes of peri-implantitis (PI), control implants (CI), PT and control teeth (CT), and the microbial change of PI after nonsurgical treatment (PIAT). METHODS Twenty-two patients diagnosed with both PT and peri-implantitis were recruited. Clinical periodontal parameters and radiographic bone levels were recorded. In each patient, the subgingival and submucosal plaque samples were collected from sites with PI, CI, PT, CT, and PIAT. Microbiome diversity was analyzed by high-throughput amplicon sequencing using full-length of 16S rRNA gene by next generation sequencing. RESULTS The 16S rRNA gene sequencing analysis revealed 512 OTUs in oral microbiome and 377 OTUs reached strain levels. The PI and PT groups possessed their own unique core microbiome. Treponema denticola was predominant in PI with probing depth of 8-10 mm. Interestingly, Thermovirga lienii DSM 17291 and Dialister invisus DSM 15470 were found to associate with PI. Nonsurgical treatment for peri-implantitis did not significantly alter the microbiome, except Rothia aeria. CONCLUSION Our study suggests Treponemas species may play a pivotal role in peri-implantitis. Nonsurgical treatment did not exert a major influence on the peri-implantitis microbiome in short-term follow-up. PT and peri-implantitis possess the unique microbiome profiles, and different therapeutic strategies may be suggested in the future.
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Affiliation(s)
- Pei-Shiuan Yu
- Department of Dentistry, National Taiwan University Hospital and Graduate Institute of Clinical Dentistry, National Taiwan University, Taipei, Taiwan
| | - Che-Chang Tu
- Department of Dentistry, National Taiwan University Hospital and Graduate Institute of Clinical Dentistry, National Taiwan University, Taipei, Taiwan
| | - Nawarat Wara-Aswapati
- Department of Periodontology, Faculty of Dentistry, Khon Kaen University, Khon Kaen, Thailand
| | - Chen-Ying Wang
- Department of Dentistry, National Taiwan University Hospital and Graduate Institute of Clinical Dentistry, National Taiwan University, Taipei, Taiwan
| | - Yu-Kang Tu
- Institute of Health Data Analytics and Statistics, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Hsin-Han Hou
- Graduate Institute of Oral Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Takaaki Ueno
- Department of Dentistry and Oral Surgery, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - I-Hui Chen
- Department of Dentistry, National Taiwan University Hospital and Graduate Institute of Clinical Dentistry, National Taiwan University, Taipei, Taiwan
- Division of Periodontology, Department of Dentistry, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Kuan-Lun Fu
- Department of Dentistry, National Taiwan University Hospital and Graduate Institute of Clinical Dentistry, National Taiwan University, Taipei, Taiwan
| | - Huei-Ying Li
- Medical Microbiota Center of the First Core Laboratory, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Wen Chen
- Department of Dentistry, National Taiwan University Hospital and Graduate Institute of Clinical Dentistry, National Taiwan University, Taipei, Taiwan
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Regueira-Iglesias A, Suárez-Rodríguez B, Blanco-Pintos T, Relvas M, Alonso-Sampedro M, Balsa-Castro C, Tomás I. The salivary microbiome as a diagnostic biomarker of periodontitis: a 16S multi-batch study before and after the removal of batch effects. Front Cell Infect Microbiol 2024; 14:1405699. [PMID: 39071165 PMCID: PMC11272481 DOI: 10.3389/fcimb.2024.1405699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 06/17/2024] [Indexed: 07/30/2024] Open
Abstract
Introduction Microbiome-based clinical applications that improve diagnosis related to oral health are of great interest to precision dentistry. Predictive studies on the salivary microbiome are scarce and of low methodological quality (low sample sizes, lack of biological heterogeneity, and absence of a validation process). None of them evaluates the impact of confounding factors as batch effects (BEs). This is the first 16S multi-batch study to analyze the salivary microbiome at the amplicon sequence variant (ASV) level in terms of differential abundance and machine learning models. This is done in periodontally healthy and periodontitis patients before and after removing BEs. Methods Saliva was collected from 124 patients (50 healthy, 74 periodontitis) in our setting. Sequencing of the V3-V4 16S rRNA gene region was performed in Illumina MiSeq. In parallel, searches were conducted on four databases to identify previous Illumina V3-V4 sequencing studies on the salivary microbiome. Investigations that met predefined criteria were included in the analysis, and the own and external sequences were processed using the same bioinformatics protocol. The statistical analysis was performed in the R-Bioconductor environment. Results The elimination of BEs reduced the number of ASVs with differential abundance between the groups by approximately one-third (Before=265; After=190). Before removing BEs, the model constructed using all study samples (796) comprised 16 ASVs (0.16%) and had an area under the curve (AUC) of 0.944, sensitivity of 90.73%, and specificity of 87.16%. The model built using two-thirds of the specimens (training=531) comprised 35 ASVs (0.36%) and had an AUC of 0.955, sensitivity of 86.54%, and specificity of 90.06% after being validated in the remaining one-third (test=265). After removing BEs, the models required more ASVs (all samples=200-2.03%; training=100-1.01%) to obtain slightly lower AUC (all=0.935; test=0.947), lower sensitivity (all=81.79%; test=78.85%), and similar specificity (all=91.51%; test=90.68%). Conclusions The removal of BEs controls false positive ASVs in the differential abundance analysis. However, their elimination implies a significantly larger number of predictor taxa to achieve optimal performance, creating less robust classifiers. As all the provided models can accurately discriminate health from periodontitis, implying good/excellent sensitivities/specificities, the salivary microbiome demonstrates potential clinical applicability as a precision diagnostic tool for periodontitis.
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Affiliation(s)
- Alba Regueira-Iglesias
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Berta Suárez-Rodríguez
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Triana Blanco-Pintos
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Marta Relvas
- Instituto Universitário de Ciências da Saúde, Cooperativa de Ensino Superior Politécnico e Universitário (IUCS-CESPU), Unidade de Investigação em Patologia e Reabilitação Oral (UNIPRO), Gandra, Portugal
| | - Manuela Alonso-Sampedro
- Department of Internal Medicine and Clinical Epidemiology, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario, Santiago de Compostela, Spain
| | - Carlos Balsa-Castro
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Inmaculada Tomás
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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Lundtorp-Olsen C, Nygaard N, Massarenti L, Constancias F, Damgaard C, Kahraman Gursoy U, van Splunter A, Bikker FJ, Gursoy M, Markvart M, Belstrøm D. Supragingival microbiota, cytokines, and proteins in individuals with different trajectories in experimental gingivitis. J Oral Microbiol 2024; 16:2372861. [PMID: 38979478 PMCID: PMC11229773 DOI: 10.1080/20002297.2024.2372861] [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: 02/01/2024] [Accepted: 05/09/2024] [Indexed: 07/10/2024] Open
Abstract
Background Gingivitis in response to biofilm formation may exhibit different trajectories. The purposes of the present study were to characterize the composition of the supragingival microbiota and salivary cytokine and protein levels in healthy individuals with different gingivitis patterns, to test the hypothesis that manifestations of gingivitis associate with specific profiles in terms of supragingival microbiota, salivary cytokines, and proteins. Methods Forty orally and systemically healthy individuals refrained from all oral hygiene procedures for a period of 14 days, followed by a resolution period of 14 days with regular oral care. Supragingival plaque level and bleeding on probing (BOP) were recorded, and supragingival plaque as well as saliva samples were collected at baseline, day 14, and day 28. Based on change in BOP% from baseline to day 14, rapid (n = 15), moderate (n = 10), and slow (n = 15) responders were identified. Supragingival microbiota composition, salivary cytokine, and protein levels were compared between groups at baseline, day 14, and day 28. Results A significantly higher baseline abundance of Capnocytophaga, Eikenella, and Campylobacter species were recorded in rapid responders, whereas a significantly higher baseline abundance of Streptococcus species were detected in slow responders. Slow responders expressed a high degree of resilience, with minimal difference in microbial composition at baseline and after 14 days of resolution (day 28). On the contrary, significant differences in relative abundance of members of the core microbiota, Streptococcus, Actinomyces, and Rothia species, was noted in baseline samples versus day 28 samples in rapid responders. Comparable baseline cytokine and protein levels were recorded in all groups. Conclusion Supragingival microbiota composition, but not saliva cytokine and protein profiles, seems to influence the extent of the inflammatory response during development of gingivitis in systemically healthy individuals.
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Affiliation(s)
- Christine Lundtorp-Olsen
- Department of Odontology, Section for Clinical Oral Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nikoline Nygaard
- Department of Odontology, Section for Clinical Oral Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laura Massarenti
- Department of Odontology, Section for Oral Biology and Immunopathology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen, Denmark
| | - Florentin Constancias
- Department of Odontology, Section for Clinical Oral Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Damgaard
- Department of Odontology, Section for Oral Biology and Immunopathology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulvi Kahraman Gursoy
- Department of Periodontology, Institute of Dentistry, University of Turku, Turku, Finland
| | - Annina van Splunter
- Department of Oral Biochemistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit, Amsterdam, Netherlands
| | - Floris J. Bikker
- Department of Oral Biochemistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and Vrije Universiteit, Amsterdam, Netherlands
| | - Mervi Gursoy
- Department of Periodontology, Institute of Dentistry, University of Turku, Turku, Finland
| | - Merete Markvart
- Department of Odontology, Section for Clinical Oral Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Daniel Belstrøm
- Department of Odontology, Section for Clinical Oral Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Ryu EP, Gautam Y, Proctor DM, Bhandari D, Tandukar S, Gupta M, Gautam GP, Relman DA, Shibl AA, Sherchand JB, Jha AR, Davenport ER. Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601557. [PMID: 39005279 PMCID: PMC11244963 DOI: 10.1101/2024.07.01.601557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Background Lifestyle plays an important role in shaping the gut microbiome. However, its contributions to the oral microbiome remains less clear, due to the confounding effects of geography and methodology in investigations of populations studied to date. Furthermore, while the oral microbiome seems to differ between foraging and industrialized populations, we lack insight into whether transitions to and away from agrarian lifestyles shape the oral microbiota. Given the growing interest in so-called 'vanishing microbiomes' potentially being a risk factor for increased disease prevalence in industrialized populations, it is important that we distinguish lifestyle from geography in the study of microbiomes across populations. Results Here, we investigate salivary microbiomes of 63 Nepali individuals representing a spectrum of lifestyles: foraging, subsistence farming (individuals that transitioned from foraging to farming within the last 50 years), agriculturalists (individuals that have transitioned to farming for at least 300 years), and industrialists (expatriates that immigrated to the United States within the last 20 years). We characterize the role of lifestyle in microbial diversity, identify microbes that differ between lifestyles, and pinpoint specific lifestyle factors that may be contributing to differences in the microbiomes across populations. Contrary to prevailing views, when geography is controlled for, oral microbiome alpha diversity does not differ significantly across lifestyles. Microbiome composition, however, follows the gradient of lifestyles from foraging through agrarianism to industrialism, supporting the notion that lifestyle indeed plays a role in the oral microbiome. Relative abundances of several individual taxa, including Streptobacillus and an unclassified Porphyromonadaceae genus, also mirror lifestyle. Finally, we identify specific lifestyle factors associated with microbiome composition across the gradient of lifestyles, including smoking and grain source. Conclusion Our findings demonstrate that by controlling for geography, we can isolate an important role for lifestyle in determining oral microbiome composition. In doing so, we highlight the potential contributions of several lifestyle factors, underlining the importance of carefully examining the oral microbiome across lifestyles to improve our understanding of global microbiomes.
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Affiliation(s)
- Erica P. Ryu
- Department of Biology, Pennsylvania State University, University Park, PA
| | - Yoshina Gautam
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Diana M. Proctor
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Dinesh Bhandari
- Public Health Research Laboratory, Institute of Medicine, Maharajgunj, Kathmandu, Nepal
- School of Public Health, University of Adelaide, South Australia, Australia
| | - Sarmila Tandukar
- Public Health Research Laboratory, Institute of Medicine, Maharajgunj, Kathmandu, Nepal
- Organization for Public Health and Environment Management, Lalitpur, Bagmati, Nepal
| | - Meera Gupta
- Department of Biology, Pennsylvania State University, University Park, PA
| | | | - David A. Relman
- Departments of Medicine, and of Microbiology & Immunology, Stanford University, Stanford, CA
- Section of Infectious Diseases, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA
| | - Ahmed A. Shibl
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
- Center for Genomics and Systems Biology, and Public Health Research Center, New York University Abu Dhabi, Abu Dhabi, UAE
| | | | - Aashish R. Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, UAE
- Center for Genomics and Systems Biology, and Public Health Research Center, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Emily R. Davenport
- Department of Biology, Pennsylvania State University, University Park, PA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA
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Bartsch S, Kohnert E, Kreutz C, Woelber JP, Anderson A, Burkhardt AS, Hellwig E, Buchalla W, Hiller KA, Ratka-Krueger P, Cieplik F, Al-Ahmad A. Chlorhexidine digluconate mouthwash alters the oral microbial composition and affects the prevalence of antimicrobial resistance genes. Front Microbiol 2024; 15:1429692. [PMID: 38983634 PMCID: PMC11231401 DOI: 10.3389/fmicb.2024.1429692] [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: 05/08/2024] [Accepted: 06/07/2024] [Indexed: 07/11/2024] Open
Abstract
Introduction Chlorhexidine (CHX) is a commonly used antiseptic in situations of limited oral hygiene ability such as after periodontal surgery. However, CHX is also considered as a possible factor in the emergence of cross-resistance to antibiotics. The aim of this study was to analyze the changes in the oral microbiota and the prevalence of antimicrobial resistance genes (ARGs) due to CHX treatment. Materials and methods We analyzed the oral metagenome of 20 patients who applied a 0.2% CHX mouthwash twice daily for 4 weeks following periodontal surgical procedures. Saliva and supragingival plaque samples were examined before, directly after 4 weeks, and another 4 weeks after discontinuing the CHX treatment. Results Alpha-diversity decreased significantly with CHX use. The Bray-Curtis dissimilarity increased in both sample sites and mainly streptococci showed a higher relative abundance after CHX treatment. Although no significant changes of ARGs could be detected, an increase in prevalence was found for genes that encode for tetracycline efflux pumps. Conclusion CHX treatment appears to promote a caries-associated bacterial community and the emergence of tetracycline resistance genes. Future research should focus on CHX-related changes in the microbial community and whether the discovered tetracycline resistance genes promote resistance to CHX.
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Affiliation(s)
- Sibylle Bartsch
- Center for Dental Medicine, Department of Operative Dentistry and Periodontology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
| | - Eva Kohnert
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
| | - Clemens Kreutz
- Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
| | - Johan P. Woelber
- Policlinic of Operative Dentistry, Periodontology, and Pediatric Dentistry, Medical Faculty Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Annette Anderson
- Center for Dental Medicine, Department of Operative Dentistry and Periodontology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
| | - Ann-Sophie Burkhardt
- Center for Dental Medicine, Department of Operative Dentistry and Periodontology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
| | - Elmar Hellwig
- Center for Dental Medicine, Department of Operative Dentistry and Periodontology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
| | - Wolfgang Buchalla
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - Karl-Anton Hiller
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - Petra Ratka-Krueger
- Center for Dental Medicine, Department of Operative Dentistry and Periodontology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
| | - Fabian Cieplik
- Center for Dental Medicine, Department of Operative Dentistry and Periodontology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - Ali Al-Ahmad
- Center for Dental Medicine, Department of Operative Dentistry and Periodontology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg im Breisgau, Germany
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Lundtorp-Olsen C, Markvart M, Twetman S, Belstrøm D. Effect of Probiotic Supplements on the Oral Microbiota-A Narrative Review. Pathogens 2024; 13:419. [PMID: 38787271 PMCID: PMC11124442 DOI: 10.3390/pathogens13050419] [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: 04/23/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024] Open
Abstract
Data from systematic reviews and meta-analyses show that probiotics positively impact clinical parameters of oral diseases such as gingivitis, dental caries, and periodontitis. However, the working mechanism of probiotics is not fully understood, but is hypothesized to be mediated by direct and indirect interactions with the oral microbiota and the human host. In the present narrative review, we focused on the microbiological effect of probiotic supplements based on data retrieved from randomized clinical trials (RCTs). In addition, we assessed to what extent contemporary molecular methods have been employed in clinical trials in the field of oral probiotics. Multiple RCTs have been performed studying the potential effect of probiotics on gingivitis, dental caries, and periodontitis, as evaluated by microbial endpoints. In general, results are conflicting, with some studies reporting a positive effect, whereas others are not able to record any effect. Major differences in terms of study designs and sample size, as well as delivery route, frequency, and duration of probiotic consumption, hamper comparison across studies. In addition, most RCTs have been performed with a limited sample size using relatively simple methods for microbial identification, such as culturing, qPCR, and DNA-DNA checkerboard, while high-throughput methods such as 16S sequencing have only been employed in a few studies. Currently, state-of-the-art molecular methods such as metagenomics, metatranscriptomics, and metaproteomics have not yet been used in RCTs in the field of probiotics. The present narrative review revealed that the effect of probiotic supplements on the oral microbiota remains largely uncovered. One important reason is that most RCTs are performed without studying the microbiological effect. To facilitate future systematic reviews and meta-analyses, an internationally agreed core outcome set for the reporting of microbial endpoints in clinical trials would be desirable. Such a standardized collection of outcomes would most likely improve the quality of probiotic research in the oral context.
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Affiliation(s)
| | | | | | - Daniel Belstrøm
- Department of Odontology, Section for Clinical Oral Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (C.L.-O.); (M.M.); (S.T.)
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Chattopadhyay S, Malayil L, Chopyk J, Smyth E, Kulkarni P, Raspanti G, Thomas SB, Sapkota A, Mongodin EF, Sapkota AR. Oral microbiome dysbiosis among cigarette smokers and smokeless tobacco users compared to non-users. Sci Rep 2024; 14:10394. [PMID: 38710815 DOI: 10.1038/s41598-024-60730-2] [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: 10/02/2023] [Accepted: 04/26/2024] [Indexed: 05/08/2024] Open
Abstract
Tobacco use significantly influences the oral microbiome. However, less is known about how different tobacco products specifically impact the oral microbiome over time. To address this knowledge gap, we characterized the oral microbiome of cigarette users, smokeless tobacco users, and non-users over 4 months (four time points). Buccal swab and saliva samples (n = 611) were collected from 85 participants. DNA was extracted from all samples and sequencing was carried out on an Illumina MiSeq, targeting the V3-V4 region of the 16S rRNA gene. Cigarette and smokeless tobacco users had more diverse oral bacterial communities, including a higher relative abundance of Firmicutes and a lower relative abundance of Proteobacteria, when compared to non-users. Non-users had a higher relative abundance of Actinomyces, Granulicatella, Haemophilus, Neisseria, Oribacterium, Prevotella, Pseudomonas, Rothia, and Veillonella in buccal swab samples, compared to tobacco users. While the most abundant bacterial genera were relatively constant over time, some species demonstrated significant shifts in relative abundance between the first and last time points. In addition, some opportunistic pathogens were detected among tobacco users including Neisseria subflava, Bulleidia moorei and Porphyromonas endodontalis. Overall, our results provide a more holistic understanding of the structure of oral bacterial communities in tobacco users compared to non-users.
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Affiliation(s)
- Suhana Chattopadhyay
- Department of Global, Environmental, and Occupational Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Leena Malayil
- Department of Global, Environmental, and Occupational Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Jessica Chopyk
- Department of Global, Environmental, and Occupational Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Eoghan Smyth
- Department of Global, Environmental, and Occupational Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Prachi Kulkarni
- Department of Global, Environmental, and Occupational Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Greg Raspanti
- Department of Global, Environmental, and Occupational Health, School of Public Health, University of Maryland, College Park, MD, USA
| | - Stephen B Thomas
- Center for Health Equity, School of Public Health, University of Maryland, College Park, MD, USA
| | - Amir Sapkota
- Department of Epidemiology and Biostatistics, School of Public Health, University of Maryland, College Park, MD, USA
| | - Emmanuel F Mongodin
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Division of Lung Diseases, National Institutes of Health (NIH), National Heart, Lung and Blood Institute (NHLBI), Bethesda, MD, USA
| | - Amy R Sapkota
- Department of Global, Environmental, and Occupational Health, School of Public Health, University of Maryland, College Park, MD, USA.
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Zhang J, Yu D, Wang T, Gao N, Shi L, Wang Y, Huo Y, Ji Z, Li J, Zhang X, Zhang L, Yan J. Body fluids should be identified before estimating the time since deposition (TsD) in microbiome-based stain analyses for forensics. Microbiol Spectr 2024; 12:e0248023. [PMID: 38470485 PMCID: PMC10986545 DOI: 10.1128/spectrum.02480-23] [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: 06/14/2023] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
Identification and the time since deposition (TsD) estimation of body fluid stains from a crime scene could provide valuable information for solving the cases and are always difficult for forensics. Microbial characteristics were considered as a promising biomarker to address the issues. However, changes in the microbiota may damage the specific characteristics of body fluids. Correspondingly, incorrect body fluid identification may result in inaccurate TsD estimation. The mutual influence is not well understood and limited the codetection. In the current study, saliva, semen, vaginal secretion, and menstrual blood samples were exposed to indoor conditions and collected at eight time points (from fresh to 30 days). High-throughput sequencing based on the 16S rRNA gene was performed to characterize the microbial communities. The results showed that a longer TsD could decrease the discrimination of different body fluid stains. However, the accuracies of identification still reached a quite high value even without knowing the TsD. Correspondingly, the mean absolute error (MAE) of TsD estimation significantly increased without distinguishing the types of body fluids. The predictive TsD of menstrual blood reached a quite low MAE (1.54 ± 0.39 d). In comparison, those of saliva (6.57 ± 1.17 d), semen (6.48 ± 1.33 d), and vaginal secretion (5.35 ± 1.11 d) needed to be further improved. The great effect of individual differences on these stains limited the TsD estimation accuracy. Overall, microbial characteristics allow for codetection of body fluid identification and TsD estimation, and body fluids should be identified before estimating TsD in microbiome-based stain analyses.IMPORTANCEEmerged evidences suggest microbial characteristics could be considered a promising tool for identification and time since deposition (TsD) estimation of body fluid stains. However, the two issues should be studied together due to a potential mutual influence. The current study provides the first evidence to understand the mutual influence and determines an optimal process for codetection of identification and TsD estimation for unknown stains for forensics. In addition, we involved aged stains into our study for identification of body fluid stains, rather than only using fresh stains like previous studies. This increased the predictive accuracy. We have preliminary verified that individual differences in microbiotas limited the predictive accuracy of TsD estimation for saliva, semen, and vaginal secretion. Microbial characteristics could provide an accurate TsD estimation for menstrual blood. Our study benefits the comprehensive understanding of microbiome-based stain analyses as an essential addition to previous studies.
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Affiliation(s)
- Jun Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Daijing Yu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Tian Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Niu Gao
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Linyu Shi
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Yaya Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Yumei Huo
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Zhimin Ji
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Junli Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Xiaomeng Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Liwei Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, Shanxi, China
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9
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Pignatelli P, Curia MC, Tenore G, Bondi D, Piattelli A, Romeo U. Oral bacteriome and oral potentially malignant disorders: A systematic review of the associations. Arch Oral Biol 2024; 160:105891. [PMID: 38295615 DOI: 10.1016/j.archoralbio.2024.105891] [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: 11/29/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 02/02/2024]
Abstract
INTRODUCTION Periodontal bacteria can infiltrate the epithelium, activate signaling pathways, induce inflammation, and block natural killer and cytotoxic cells, all of which contribute to the vicious circle of carcinogenesis. It is unknown whether oral dysbiosis has an impact on the etiology or prognosis of OPMD. AIMS Within this paradigm, this work systemically investigated and reported on the composition of oral microbiota in patients with oral potentially malignant disorders (OPMD) versus healthy controls. METHODS Observational studies that reported next generation sequencing analysis of oral tissue or salivary samples and found at least three bacterial species were included. Identification, screening, citation analysis, and graphical synthesis were carried out. RESULTS For oral lichen planus (OLP), the bacteria with the highest abundance were Fusobacterium, Capnocytophaga, Gemella, Granulicatella, Porphyromonas, and Rothia; for oral leukoplakia (OLK), Prevotella. Streptococci levels in OLK and OLP were lower. The usage of alcohol or smoke had no effect on the outcomes. CONCLUSIONS An increase in periodontal pathogenic bacteria could promote the development and exacerbation of lichen. Effective bacteriome-based biomarkers are worthy of further investigation and application, as are bacteriome-based treatments.
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Affiliation(s)
- Pamela Pignatelli
- COMDINAV DUE, Nave Cavour, Italian Navy, Stazione Navale Mar Grande, Viale Ionio, 74122 Taranto, Italy.
| | - Maria Cristina Curia
- Department of Medical, Oral and Biotechnological Sciences, "G. d'Annunzio" University of Chieti-Pescara, Via dei Vestini, 66100 Chieti, Italy
| | - Gianluca Tenore
- Department of Oral Sciences and Maxillofacial Surgery, Sapienza University of Rome, Via Caserta, 00161 Rome, Italy
| | - Danilo Bondi
- Department of Neuroscience, Imaging and Clinical Sciences, "G. d'Annunzio" University of Chieti-Pescara, Via dei Vestini, 66100 Chieti, Italy
| | - Adriano Piattelli
- School of Dentistry, Saint Camillus International University for Health Sciences, 00131 Rome, Italy; Facultad de Medicina, UCAM Universidad Católica San Antonio de Murcia, Guadalupe, 30107 Murcia, Spain
| | - Umberto Romeo
- Department of Oral Sciences and Maxillofacial Surgery, Sapienza University of Rome, Via Caserta, 00161 Rome, Italy
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10
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Wang S, Song F, Song M, Wei X, Zhou Y, Jiang L, Wang Z, Sun C, Yao H, Liang W, Luo H. Explore variation of salivary bacteria across time and geolocations. Int J Legal Med 2024; 138:547-554. [PMID: 37353677 DOI: 10.1007/s00414-023-03045-7] [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: 03/09/2023] [Accepted: 06/13/2023] [Indexed: 06/25/2023]
Abstract
Saliva is an informative body fluid that can be found at various crime scenes, and the salivary bacterial community has been revealed it is a potential auxiliary target for forensic identification. However, the variation of salivary bacterial community composition across time and geolocation needs to be explored. The study was designed to be carried out during the winter vacation that was across about 50 days and eight geographic locations. The high throughput sequencing was performed with the V3-V4 region of the16S rRNA gene to explore salivary bacterial community composition. An overall slight fluctuation of the salivary bacteria was observed, which primarily occurred in the relative abundance of the salivary bacterial taxa. The results of principal coordinate analysis and hierarchical clustering showed samples were clustered by the individuals. All individuals could be correctly identified with the random forest model. In summation, although the relative abundance of salivary bacteria varied across the changes of time and geolocation, the individualized characteristic of salivary bacteria remained steady, which is beneficial for the salivary bacterial application in personal identification.
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Affiliation(s)
- Shuangshuang Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiaowen Wei
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Zefei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Chaoran Sun
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Hewen Yao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
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11
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Bloch S, Hager-Mair FF, Andrukhov O, Schäffer C. Oral streptococci: modulators of health and disease. Front Cell Infect Microbiol 2024; 14:1357631. [PMID: 38456080 PMCID: PMC10917908 DOI: 10.3389/fcimb.2024.1357631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/05/2024] [Indexed: 03/09/2024] Open
Abstract
Streptococci are primary colonizers of the oral cavity where they are ubiquitously present and an integral part of the commensal oral biofilm microflora. The role oral streptococci play in the interaction with the host is ambivalent. On the one hand, they function as gatekeepers of homeostasis and are a prerequisite for the maintenance of oral health - they shape the oral microbiota, modulate the immune system to enable bacterial survival, and antagonize pathogenic species. On the other hand, also recognized pathogens, such as oral Streptococcus mutans and Streptococcus sobrinus, which trigger the onset of dental caries belong to the genus Streptococcus. In the context of periodontitis, oral streptococci as excellent initial biofilm formers have an accessory function, enabling late biofilm colonizers to inhabit gingival pockets and cause disease. The pathogenic potential of oral streptococci fully unfolds when their dissemination into the bloodstream occurs; streptococcal infection can cause extra-oral diseases, such as infective endocarditis and hemorrhagic stroke. In this review, the taxonomic diversity of oral streptococci, their role and prevalence in the oral cavity and their contribution to oral health and disease will be discussed, focusing on the virulence factors these species employ for interactions at the host interface.
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Affiliation(s)
- Susanne Bloch
- Competence Center for Periodontal Research, University Clinic of Dentistry, Medical University of Vienna, Vienna, Austria
- Department of Chemistry, Institute of Biochemistry, NanoGlycobiology Research Group, Universität für Bodenkultur Wien, Vienna, Austria
| | - Fiona F. Hager-Mair
- Department of Chemistry, Institute of Biochemistry, NanoGlycobiology Research Group, Universität für Bodenkultur Wien, Vienna, Austria
| | - Oleh Andrukhov
- Competence Center for Periodontal Research, University Clinic of Dentistry, Medical University of Vienna, Vienna, Austria
| | - Christina Schäffer
- Department of Chemistry, Institute of Biochemistry, NanoGlycobiology Research Group, Universität für Bodenkultur Wien, Vienna, Austria
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12
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Kamel M, Aleya S, Alsubih M, Aleya L. Microbiome Dynamics: A Paradigm Shift in Combatting Infectious Diseases. J Pers Med 2024; 14:217. [PMID: 38392650 PMCID: PMC10890469 DOI: 10.3390/jpm14020217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/24/2024] Open
Abstract
Infectious diseases have long posed a significant threat to global health and require constant innovation in treatment approaches. However, recent groundbreaking research has shed light on a previously overlooked player in the pathogenesis of disease-the human microbiome. This review article addresses the intricate relationship between the microbiome and infectious diseases and unravels its role as a crucial mediator of host-pathogen interactions. We explore the remarkable potential of harnessing this dynamic ecosystem to develop innovative treatment strategies that could revolutionize the management of infectious diseases. By exploring the latest advances and emerging trends, this review aims to provide a new perspective on combating infectious diseases by targeting the microbiome.
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Affiliation(s)
- Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 11221, Egypt
| | - Sami Aleya
- Faculty of Medecine, Université de Bourgogne Franche-Comté, Hauts-du-Chazal, 25030 Besançon, France
| | - Majed Alsubih
- Department of Civil Engineering, King Khalid University, Guraiger, Abha 62529, Saudi Arabia
| | - Lotfi Aleya
- Laboratoire de Chrono-Environnement, Université de Bourgogne Franche-Comté, UMR CNRS 6249, La Bouloie, 25030 Besançon, France
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13
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Kim HY, Jung YS, Park W, Choi YJ, Kim JY. Can medication-related osteonecrosis of the jaw be attributed to specific microorganisms through oral microbiota analyses? A preliminary study. BMC Oral Health 2024; 24:160. [PMID: 38302952 PMCID: PMC10832156 DOI: 10.1186/s12903-024-03945-z] [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: 11/22/2023] [Accepted: 01/27/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Medication-related osteonecrosis of the jaw (MRONJ) can cause significant pain and loss of aesthetics and function if not treated properly. However, diagnosis still relies on detailed intraoral examinations and imaging. Prognosis varies even among patients with similar stages or conditions of MRONJ, emphasizing the need for a deeper understanding of its complex mechanisms. Thus, this study aimed to identify the oral microbiota of patients with MRONJ. METHODS This single-center prospective cohort study included patients with confirmed MRONJ who visited the Department of Oral and Maxillofacial Surgery at Yonsei University Dental Hospital between 2021 and 2022. Oral swab samples were collected from the affected and unaffected sides of each patient. The composition and enumeration of the microbial communities were analyzed, and the diversity was compared to verify ecological changes in the groups using a next-generation sequencing-based 16S metagenomic analysis. A statistical analysis was performed using Wilcoxon signed-rank test with SPSS version 22, and values of P less than 0.05 were considered statistically significant. RESULTS The final study sample included 12 patients. The mean age was 82.67 ± 5.73 (range, 72-90) years. Changes in microbial composition were observed at different taxonomic levels (phylum, genus, and species). The identified microorganisms were commonly associated with periodontitis, gingival disease, and endodontic infection, suggesting a multifactorial etiology of MRONJ. CONCLUSIONS Although this study is based on a small number of cases, it shows that MRONJ is not caused by a specific microorganism but can rather be caused by a variety of factors. By addressing these findings in large-scale studies, the significance of oral microbiome in pathogenesis can be further elucidated and can facilitate the development of effective therapeutic interventions for patients with MRONJ.
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Affiliation(s)
- Heon-Young Kim
- Department of Oral and Maxillofacial Surgery, Ewha Womans University Medical Centre, Seoul, Republic of Korea
| | - Young-Soo Jung
- Department of Oral and Maxillofacial Surgery, Yonsei University College of Dentistry, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Wonse Park
- Department of Advanced General Dentistry, Yonsei University College of Dentistry, Seoul, Republic of Korea
- Institute for Innovation in Digital Healthcare, Yonsei University, Seoul, Republic of Korea
| | - Yoon Jeong Choi
- Institute for Innovation in Digital Healthcare, Yonsei University, Seoul, Republic of Korea
- Department of Orthodontics, The Institute of Craniofacial Deformity, Yonsei University College of Dentistry, Seoul, Republic of Korea
| | - Jun-Young Kim
- Department of Oral and Maxillofacial Surgery, Yonsei University College of Dentistry, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
- Institute for Innovation in Digital Healthcare, Yonsei University, Seoul, Republic of Korea.
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14
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Hoefer KC, Weber LT, Barbe AG, Graf I, Thom S, Nowag A, Scholz CJ, Wisplinghoff H, Noack MJ, Jazmati N. The tongue microbiome of young patients with chronic kidney disease and their healthy mothers. Clin Oral Investig 2024; 28:110. [PMID: 38265670 PMCID: PMC10808353 DOI: 10.1007/s00784-024-05492-x] [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: 06/09/2023] [Accepted: 01/05/2024] [Indexed: 01/25/2024]
Abstract
OBJECTIVES Oral microbiome plays a crucial role in the incidence and development of oral diseases. An altered intestinal microbiome has been reported in adults with chronic kidney disease (CKD). This study aimed to characterize the tongue microbiome of young patients with CKD compared to their healthy mothers to identify the influence of CKD-associated factors on resilient tongue ecosystem. MATERIAL AND METHODS Thirty patients with CKD (mean age, 14.2 years; 16 males and 14 females) and generalized gingivitis were included in the study. Swabs of the posterior tongue were collected from the patients and 21 mothers (mean age 40.8 years). Next-generation sequencing of 16S rDNA genes was employed to quantitatively characterize microbial communities. RESULTS The bacterial communities were similar in terms of richness and diversity between patients and mothers (p > 0.05). In patients with CKD, 5 core phyla, 20 core genera, and 12 core species were identified. CONCLUSIONS The tongue microbiome of the study participants showed no relevant CKD-associated differences compared to their mothers and appears to be a highly preserved niche in the oral cavity. Differences observed in the abundance of individual species in this study could be attributed to the age rather than CKD, even after a mean disease duration of 11 years. CLINICAL RELEVANCE CKD and its associated metabolic changes appear to have no detectable impact on the resilient tongue microbiome observed in young patients.
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Affiliation(s)
- Karolin C Hoefer
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Polyclinic for Operative Dentistry and Periodontology, Cologne, Germany.
| | - Lutz T Weber
- Children´s and Adolescents Hospital, Pediatric Nephrology, University Hospital of Cologne, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Anna Greta Barbe
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Polyclinic for Operative Dentistry and Periodontology, Cologne, Germany
| | - Isabelle Graf
- Department of Orthodontics, Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
| | | | | | | | - Hilmar Wisplinghoff
- Wisplinghoff Laboratories, Cologne, Germany
- Institute for Virology and Microbiology, Witten/Herdecke University, Witten, Germany
| | - Michael J Noack
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Polyclinic for Operative Dentistry and Periodontology, Cologne, Germany
| | - Nathalie Jazmati
- Wisplinghoff Laboratories, Cologne, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
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15
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Gouello A, Henry L, Chadli D, Salipante F, Gibert J, Boutet-Dubois A, Lavigne JP. Evaluation of the Microbiome Identification of Forensically Relevant Biological Fluids: A Pilot Study. Diagnostics (Basel) 2024; 14:187. [PMID: 38248064 PMCID: PMC10814007 DOI: 10.3390/diagnostics14020187] [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: 11/19/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
In forensic sciences, body fluids, or biological traces, are a major source of information, and their identification can play a decisive role in criminal investigations. Currently, the nature of biological fluids is assessed using immunological, physico-chemical, mRNA and epigenetic methods, but these have limits in terms of sensitivity and specificity. The emergence of next-generation sequencing technologies offers new opportunities to identify the nature of body fluids by determining bacterial communities. The aim of this pilot study was to assess whether analysis of the bacterial communities in isolated and mixed biological fluids could reflect the situation observed in real forensics labs. Several samples commonly encountered in forensic sciences were tested from healthy volunteers: saliva, vaginal fluid, blood, semen and skin swabs. These samples were analyzed alone or in combination in a ratio of 1:1. Sequencing was performed on the Ion Gene StudioTM S5 automated sequencer. Fluids tested alone revealed a typical bacterial signature with specific bacterial orders, enabling formal identification of the fluid of interest, despite inter-individual variations. However, in biological fluid mixtures, the predominance of some bacterial microbiomes inhibited interpretation. Oral and vaginal microbiomes were clearly preponderant, and the relative abundance of their bacterial communities and/or the presence of common species between samples made it impossible to detect bacterial orders or genera from other fluids, although they were distinguishable from one another. However, using the beta diversity, salivary fluids were identified and could be distinguished from fluids in combination. While this method of fluid identification is promising, further analyses are required to consolidate the protocol and ensure reliability.
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Affiliation(s)
- Audrey Gouello
- Institut de Recherche Criminelle de la Gendarmerie Nationale, 95000 Cergy-Pontoise, France; (A.G.); (L.H.); (D.C.); (J.G.)
- VBIC, INSERM U1047, Université Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908 Nîmes, France;
| | - Laura Henry
- Institut de Recherche Criminelle de la Gendarmerie Nationale, 95000 Cergy-Pontoise, France; (A.G.); (L.H.); (D.C.); (J.G.)
- Sciences Sorbonne Universtity, 75005 Paris, France
| | - Djamel Chadli
- Institut de Recherche Criminelle de la Gendarmerie Nationale, 95000 Cergy-Pontoise, France; (A.G.); (L.H.); (D.C.); (J.G.)
- Aix-Marseille University, 13005 Marseille, France
| | - Florian Salipante
- Service de Biostatistiques, Epidémiologie, Santé Publique et Innovation en Méthodologie, Université Montpellier, CHU Nîmes, 30029 Nîmes, France;
| | - Joséphine Gibert
- Institut de Recherche Criminelle de la Gendarmerie Nationale, 95000 Cergy-Pontoise, France; (A.G.); (L.H.); (D.C.); (J.G.)
| | - Adeline Boutet-Dubois
- VBIC, INSERM U1047, Université Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908 Nîmes, France;
| | - Jean-Philippe Lavigne
- VBIC, INSERM U1047, Université Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908 Nîmes, France;
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16
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Cruz MS, Tintelnot J, Gagliani N. Roles of microbiota in pancreatic cancer development and treatment. Gut Microbes 2024; 16:2320280. [PMID: 38411395 PMCID: PMC10900280 DOI: 10.1080/19490976.2024.2320280] [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: 11/06/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease with poor prognosis. This is due to the fact that most cases are only diagnosed at an advanced and palliative disease stage, and there is a high incidence of therapy resistance. Despite ongoing efforts, to date, the mechanisms underlying PDAC oncogenesis and its poor responses to treatment are still largely unclear. As the study of the microbiome in cancer progresses, growing evidence suggests that bacteria or fungi might be key players both in PDAC oncogenesis as well as in its resistance to chemo- and immunotherapy, for instance through modulation of the tumor microenvironment and reshaping of the host immune response. Here, we review how the microbiota exerts these effects directly or indirectly via microbial-derived metabolites. Finally, we further discuss the potential of modulating the microbiota composition as a therapy in PDAC.
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Affiliation(s)
- Mariana Santos Cruz
- II. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), Hamburg, Germany
| | - Joseph Tintelnot
- II. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), Hamburg, Germany
| | - Nicola Gagliani
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), Hamburg, Germany
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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17
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L’Heureux JE, van der Giezen M, Winyard PG, Jones AM, Vanhatalo A. Localisation of nitrate-reducing and highly abundant microbial communities in the oral cavity. PLoS One 2023; 18:e0295058. [PMID: 38127919 PMCID: PMC10735016 DOI: 10.1371/journal.pone.0295058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023] Open
Abstract
The nitrate (NO3-) reducing bacteria resident in the oral cavity have been implicated as key mediators of nitric oxide (NO) homeostasis and human health. NO3--reducing oral bacteria reduce inorganic dietary NO3- to nitrite (NO2-) via the NO3--NO2--NO pathway. Studies of oral NO3--reducing bacteria have typically sampled from either the tongue surface or saliva. The aim of this study was to assess whether other areas in the mouth could contain a physiologically relevant abundance of NO3- reducing bacteria, which may be important for sampling in clinical studies. The bacterial composition of seven oral sample types from 300 individuals were compared using a meta-analysis of the Human Microbiome Project data. This analysis revealed significant differences in the proportions of 20 well-established oral bacteria and highly abundant NO3--reducing bacteria across each oral site. The genera included Actinomyces, Brevibacillus, Campylobacter, Capnocytophaga, Corynebacterium, Eikenella, Fusobacterium, Granulicatella, Haemophilus, Leptotrichia, Microbacterium, Neisseria, Porphyromonas, Prevotella, Propionibacterium, Rothia, Selenomonas, Staphylococcus, Streptococcus and Veillonella. The highest proportion of NO3--reducing bacteria was observed in saliva, where eight of the bacterial genera were found in higher proportion than on the tongue dorsum, whilst the lowest proportions were found in the hard oral surfaces. Saliva also demonstrated higher intra-individual variability and bacterial diversity. This study provides new information on where samples should be taken in the oral cavity to assess the abundance of NO3--reducing bacteria. Taking saliva samples may benefit physiological studies, as saliva contained the highest abundance of NO3- reducing bacteria and is less invasive than other sampling methods. These results inform future studies coupling oral NO3--reducing bacteria research with physiological outcomes affecting human health.
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Affiliation(s)
- Joanna E. L’Heureux
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Mark van der Giezen
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
- Biosciences, University of Exeter, Exeter, United Kingdom
- Research Department, Stavanger University Hospital, Stavanger, Norway
| | - Paul G. Winyard
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Andrew M. Jones
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Anni Vanhatalo
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
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18
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Ling Z, Cheng Y, Liu X, Yan X, Wu L, Shao L, Gao J, Lei W, Song Q, Zhao L, Jin G. Altered oral microbiota and immune dysfunction in Chinese elderly patients with schizophrenia: a cross-sectional study. Transl Psychiatry 2023; 13:383. [PMID: 38071192 PMCID: PMC10710460 DOI: 10.1038/s41398-023-02682-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Schizophrenia (SZ) is a complex psychiatric neurodevelopmental disorder with uncertain etiology and pathogenesis. Increasing evidence has recognized the key role of the gut microbiota in SZ. However, few studies have investigated the potential link between oral microbiota and SZ. We studied the tongue coating microbiota and inflammatory profiles of 118 elderly SZ patients and 97 age-matched healthy controls using Illumina MiSeq sequencing and multiplex immunoassays, respectively. Reduced α-diversity, along with a significant difference in β-diversity, were observed in patients with SZ. We have identified SZ-associated oral dysbiosis, characterized by increased Streptococcus and Fusobacterium, as well as decreased Prevotella and Veillonella. These differential genera could potentially serve as biomarkers for SZ, either alone or in combination. Additionally, an elevated Streptococcus/Prevotella ratio could indicate oral dysbiosis. These differential genera formed two distinct clusters: Streptococcus-dominated and Prevotella-dominated, which exhibited different correlations with the altered immunological profiles. Furthermore, we also observed disruptions in the inferred microbiota functions in SZ-associated microbiota, particularly in lipid and amino acid metabolism. Our study provides novel insights into the characteristics of tongue coating microbiota and its associations with immunological disturbances in elderly SZ patients, which offer new targets for the diagnosis and treatment of SZ in the elderly.
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Affiliation(s)
- Zongxin Ling
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 310003, Hangzhou, Zhejiang, China.
- Jinan Microecological Biomedicine Shandong Laboratory, 250000, Jinan, Shandong, China.
| | - Yiwen Cheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 310003, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, 250000, Jinan, Shandong, China
| | - Xia Liu
- Department of Intensive Care Unit, the First Affiliated Hospital, School of Medicine, Zhejiang University, 310003, Hangzhou, Zhejiang, China
| | - Xiumei Yan
- Department of Laboratory Medicine, Lishui Second People's Hospital, 323000, Lishui, Zhejiang, China
| | - Lingbin Wu
- Department of Laboratory Medicine, Lishui Second People's Hospital, 323000, Lishui, Zhejiang, China
| | - Li Shao
- School of Clinical Medicine, Institute of Hepatology and Metabolic Diseases, Hangzhou Normal University, The Affiliated Hospital of Hangzhou Normal University, 310015, Hangzhou, Zhejiang, China
| | - Jie Gao
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, 310003, Hangzhou, Zhejiang, China
| | - Wenhui Lei
- Jinan Microecological Biomedicine Shandong Laboratory, 250000, Jinan, Shandong, China
- School of Basic Medicine, Shandong First Medical University, 250000, Jinan, Shandong, China
| | - Qinghai Song
- Department of Psychiatry, Lishui Second People's Hospital, 323000, Lishui, Zhejiang, China
| | - Longyou Zhao
- Department of Laboratory Medicine, Lishui Second People's Hospital, 323000, Lishui, Zhejiang, China.
| | - Guolin Jin
- Department of Psychiatry, Lishui Second People's Hospital, 323000, Lishui, Zhejiang, China.
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Lin WZ, Chen BY, Qiu P, Zhou LJ, Li YL, Du LJ, Liu Y, Wang YL, Zhu H, Wu XY, Liu X, Duan SZ, Zhu YQ. Altered salivary microbiota profile in patients with abdominal aortic aneurysm. Heliyon 2023; 9:e23040. [PMID: 38144289 PMCID: PMC10746442 DOI: 10.1016/j.heliyon.2023.e23040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/19/2023] [Accepted: 11/24/2023] [Indexed: 12/26/2023] Open
Abstract
Evidence suggests that the DNA of oral pathogens is detectable in the dilated aortic tissue of abdominal aortic aneurysm (AAA), one of the most fatal cardiovascular diseases. However, the association between oral microbial homeostasis and aneurysm formation remains largely unknown. In this study, a cohort of individuals, including 53 AAA patients and 30 control participants (CTL), was recruited for salivary microbiota investigation by 16S rRNA gene sequencing and bioinformatics analysis. Salivary microbial diversity was decreased in AAA compared with CTL, and the microbial structures were significantly separated between the two groups. Additionally, significant taxonomic and functional changes in the salivary microbiota of AAA participants were observed. The genera Streptococcus and Gemella were remarkably enriched, while Selenomonas, Leptotrichia, Lautropia and Corynebacterium were significantly depleted in AAA. Co-occurrence network analysis showed decreased potential interactions among the differentially abundant microbial genera in AAA. A machine-learning model predicted AAA using the combination of 5 genera and 14 differentially enriched functional pathways, which could distinguish AAA from CTL with an area under the receiver-operating curve of 90.3 %. Finally, 16 genera were found to be significantly positively correlated with the morphological parameters of AAA. Our study is the first to show that AAA patients exhibit oral microbial dysbiosis, which has high predictive power for AAA, and the over-representation of specific salivary bacteria may be associated with AAA disease progression. Further studies are needed to better understand the function of putative oral bacteria in the etiopathogenesis of AAA. Importance Host microbial dysbiosis has recently been linked to AAA as a possible etiology. To our knowledge, studies of the oral microbiota and aneurysms remain scarce, although previous studies have indicated that the DNA of some oral pathogens is detectable in aneurysms by PCR method. We take this field one step further by investigating the oral microbiota composition of AAA patients against control participants via high-throughput sequencing technologies and unveiling the potential microbial biomarker associated with AAA formation. Our study will provide new insights into AAA etiology, treatment and prevention from a microecological perspective and highlight the effects of oral microbiota on vascular health.
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Affiliation(s)
- Wen-Zhen Lin
- Department of General Dentistry, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology; Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai, China
| | - Bo-Yan Chen
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology; Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai, China
| | - Peng Qiu
- Department of Vascular Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lu-Jun Zhou
- Department of General Dentistry, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology; Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yu-Lin Li
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology; Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai, China
| | - Lin-Juan Du
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology; Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yuan Liu
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology; Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yong-Li Wang
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology; Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai, China
| | - Hong Zhu
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology; Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai, China
| | - Xiao-Yu Wu
- Department of Vascular Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaobing Liu
- Department of Vascular Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sheng-Zhong Duan
- Laboratory of Oral Microbiota and Systemic Diseases, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology; Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai, China
| | - Ya-Qin Zhu
- Department of General Dentistry, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology; Research Unit of Oral and Maxillofacial Regenerative Medicine, Chinese Academy of Medical Sciences, Shanghai, China
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20
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Fluitman KS, van den Broek T, Reinders I, Wijnhoven HAH, Nieuwdorp M, Visser M, IJzerman RG, Keijser BJF. The Effect of Dietary Advice Aimed at Increasing Protein Intake on Oral Health and Oral Microbiota in Older Adults: A Randomized Controlled Trial. Nutrients 2023; 15:4567. [PMID: 37960220 PMCID: PMC10647493 DOI: 10.3390/nu15214567] [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: 09/08/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Nutrition and oral health are closely related, especially in older adults in whom poor nutrition may lead to oral microbial perturbations, exacerbating poor oral health. In a 6-month randomized controlled trial, we evaluated the effects on oral microbiota and on oral health of dietary advice aimed at increasing protein intake to ≥1.2 g/kg adjusted body weight/day (g/kg aBW/d) in community-dwelling older adults with low habitual protein intake (<1.0 g/kg aBW/d). Food intake was measured via 24 h dietary recalls, oral health was measured via questionnaires, and oral microbial composition was assessed via the 16S rRNA sequencing of tongue swabs. Mean baseline protein intake was 0.8 g/kg aBW/day in both groups. In the high protein group (n = 47), participants increased their protein intake to mean 1.2 g/kg aBW/day at the 6-month follow-up. Protein intake in the control group (n = 43) remained at 0.9 g/kg a BW/day. The intervention did not affect self-reported oral health. While it caused moderate shifts in oral microbiota alpha- and beta-diversity measures, abundances of individual bacterial taxa were not affected. In conclusion, our intervention did not affect self-reported oral health within a period of 6 months, nor did it substantially affect the tongue microbiota composition.
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Affiliation(s)
- Kristina S. Fluitman
- Department of Internal Medicine, Amsterdam University Medical Centers, Location VUmc, 1081 HV Amsterdam, The Netherlands
- Amsterdam Public Health Research Institute, 1081 HV Amsterdam, The Netherlands
| | - Tim van den Broek
- Department of Microbiology and Systems Biology, TNO Earth, Life and Social Sciences, 3704 HE Zeist, The Netherlands
| | - Ilse Reinders
- Amsterdam Public Health Research Institute, 1081 HV Amsterdam, The Netherlands
- Department of Health Sciences, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Hanneke A. H. Wijnhoven
- Amsterdam Public Health Research Institute, 1081 HV Amsterdam, The Netherlands
- Department of Health Sciences, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Max Nieuwdorp
- Department of Internal Medicine, Amsterdam University Medical Centers, Location VUmc, 1081 HV Amsterdam, The Netherlands
- Department of Vascular Medicine, Amsterdam University Medical Centers, Location AMC, 1105 AZ Amsterdam, The Netherlands
| | - Marjolein Visser
- Amsterdam Public Health Research Institute, 1081 HV Amsterdam, The Netherlands
- Department of Health Sciences, Faculty of Science, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Richard G. IJzerman
- Department of Internal Medicine, Amsterdam University Medical Centers, Location VUmc, 1081 HV Amsterdam, The Netherlands
| | - Bart J. F. Keijser
- Department of Microbiology and Systems Biology, TNO Earth, Life and Social Sciences, 3704 HE Zeist, The Netherlands
- Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and VU University, 1081 LA Amsterdam, The Netherlands
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21
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Lee YH, Hong JY. Oral microbiome as a co-mediator of halitosis and periodontitis: a narrative review. FRONTIERS IN ORAL HEALTH 2023; 4:1229145. [PMID: 37719278 PMCID: PMC10500072 DOI: 10.3389/froh.2023.1229145] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023] Open
Abstract
Objective Halitosis or oral malodor is an unpleasant odor from the oral cavity. However, although patients with periodontitis often complain of halitosis, their relationship has not been fully elucidated. We reviewed previous literature based on the hypothesis that the relationship between halitosis and periodontitis is mediated by the oral microbiome. Materials and methods This narrative review sought to provide insight into the causative role of the oral microbiome in influencing halitosis and periodontitis. In addition, we tried to deepen knowledge related to the relationship between halitosis and periodontitis generated by the oral microbiome accumulated over the past 40 years. Results From 1984 to 2023, a total of 106 papers that carefully and scientifically dealt with halitosis and periodontitis were included in this narrative review. Based on previous results, halitosis and periodontitis were closely related. For decades, researchers have taken an intriguing approach to the question of whether there is a relationship between halitosis and periodontitis. Central factors in the relationship between halitosis and periodontitis include volatile sulfur compounds (VSCs), the oral microbiota that produce VSCs, and the inflammatory response. Conclusions Taken together, the more severe periodontitis, the higher the level of VSC in halitosis, which may be mediated by oral microbiome. However, the relationship between the occurrence, maintenance, and exacerbation of periodontitis and halitosis is not a necessary and sufficient condition for each other because they are complex interplay even in one individual.
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Affiliation(s)
- Yeon-Hee Lee
- Department of Orofacial Pain and Oral Medicine, Kyung Hee University School of Dentistry, Kyung Hee University Medical Center, Seoul, Republic of Korea
| | - Ji-Youn Hong
- Department of Periodontology, Periodontal-Implant Clinical Research Institute, School of Dentistry, Kyung Hee University, Seoul, Republic of Korea
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22
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Zhang L, Feng Z, Li Y, Lv C, Li C, Hu Y, Fu M, Song L. Salivary and fecal microbiota: potential new biomarkers for early screening of colorectal polyps. Front Microbiol 2023; 14:1182346. [PMID: 37655344 PMCID: PMC10467446 DOI: 10.3389/fmicb.2023.1182346] [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: 03/08/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
Objective Gut microbiota plays an important role in colorectal cancer (CRC) pathogenesis through microbes and their metabolites, while oral pathogens are the major components of CRC-associated microbes. Multiple studies have identified gut and fecal microbiome-derived biomarkers for precursors lesions of CRC detection. However, few studies have used salivary samples to predict colorectal polyps. Therefore, in order to find new noninvasive colorectal polyp biomarkers, we searched into the differences in fecal and salivary microbiota between patients with colorectal polyps and healthy controls. Methods In this case-control study, we collected salivary and fecal samples from 33 patients with colorectal polyps (CP) and 22 healthy controls (HC) between May 2021 and November 2022. All samples were sequenced using full-length 16S rRNA sequencing and compared with the Nucleotide Sequence Database. The salivary and fecal microbiota signature of colorectal polyps was established by alpha and beta diversity, Linear discriminant analysis Effect Size (LEfSe) and random forest model analysis. In addition, the possibility of microbiota in identifying colorectal polyps was assessed by Receiver Operating Characteristic Curve (ROC). Results In comparison to the HC group, the CP group's microbial diversity increased in saliva and decreased in feces (p < 0.05), but there was no significantly difference in microbiota richness (p > 0.05). The principal coordinate analysis revealed significant differences in β-diversity of salivary and fecal microbiota between the CP and HC groups. Moreover, LEfSe analysis at the species level identified Porphyromonas gingivalis, Fusobacterium nucleatum, Leptotrichia wadei, Prevotella intermedia, and Megasphaera micronuciformis as the major contributors to the salivary microbiota, and Ruminococcus gnavus, Bacteroides ovatus, Parabacteroides distasonis, Citrobacter freundii, and Clostridium symbiosum to the fecal microbiota of patients with polyps. Salivary and fecal bacterial biomarkers showed Area Under ROC Curve of 0.8167 and 0.8051, respectively, which determined the potential of diagnostic markers in distinguishing patients with colorectal polyps from controls, and it increased to 0.8217 when salivary and fecal biomarkers were combined. Conclusion The composition and diversity of the salivary and fecal microbiota were significantly different in colorectal polyp patients compared to healthy controls, with an increased abundance of harmful bacteria and a decreased abundance of beneficial bacteria. A promising non-invasive tool for the detection of colorectal polyps can be provided by potential biomarkers based on the microbiota of the saliva and feces.
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Affiliation(s)
- Limin Zhang
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Ziying Feng
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Yinghua Li
- Central Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Cuiting Lv
- Central Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Chunchun Li
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Yue Hu
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Mingsheng Fu
- Department of Gastroenterology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Liang Song
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
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23
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Irie K, Azuma T, Tomofuji T, Yamamoto T. Exploring the Role of IL-17A in Oral Dysbiosis-Associated Periodontitis and Its Correlation with Systemic Inflammatory Disease. Dent J (Basel) 2023; 11:194. [PMID: 37623290 PMCID: PMC10453731 DOI: 10.3390/dj11080194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023] Open
Abstract
Oral microbiota play a pivotal role in maintaining homeostasis, safeguarding the oral cavity, and preventing the onset of disease. Oral dysbiosis has the potential to trigger pro-inflammatory effects and immune dysregulation, which can have a negative impact on systemic health. It is regarded as a key etiological factor for periodontitis. The emergence and persistence of oral dysbiosis have been demonstrated to mediate inflammatory pathology locally and at distant sites. The heightened inflammation observed in oral dysbiosis is dependent upon the secretion of interleukin-17A (IL-17A) by various innate and adaptive immune cells. IL-17A has been found to play a significant role in host defense mechanisms by inducing antibacterial peptides, recruiting neutrophils, and promoting local inflammation via cytokines and chemokines. This review seeks to present the current knowledge on oral dysbiosis and its prevention, as well as the underlying role of IL-17A in periodontitis induced by oral dysbiosis and its impact on systemic inflammatory disease.
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Affiliation(s)
- Koichiro Irie
- Department of Preventive Dentistry and Dental Public Health, Kanagawa Dental University, Yokosuka 238-8580, Japan;
| | - Tetsuji Azuma
- Department of Community Oral Health, School of Dentistry, Asahi University, Mizuho 501-0296, Japan; (T.A.); (T.T.)
| | - Takaaki Tomofuji
- Department of Community Oral Health, School of Dentistry, Asahi University, Mizuho 501-0296, Japan; (T.A.); (T.T.)
| | - Tatsuo Yamamoto
- Department of Preventive Dentistry and Dental Public Health, Kanagawa Dental University, Yokosuka 238-8580, Japan;
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24
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You Y, Yin M, Zheng X, Liang Q, Zhang H, Wu BL, Xu W. Saccharibacteria (TM7), but not other bacterial taxa, are associated with childhood caries regardless of age in a South China population. PeerJ 2023; 11:e15605. [PMID: 37397017 PMCID: PMC10309052 DOI: 10.7717/peerj.15605] [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: 04/07/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023] Open
Abstract
Background Human microbiome dysbiosis is related to various human diseases, and identifying robust and consistent biomarkers that apply in different populations is a key challenge. This challenge arises when identifying key microbial markers of childhood caries. Methods We analyzed unstimulated saliva and supragingival plaque samples from children of different ages and sexes, performed 16S rRNA gene sequencing, and sought to identify whether consistent markers exist among subpopulations by using a multivariate linear regression model. Results We found that Acinetobacter and Clostridiales bacterial taxa were associated with caries in plaque and saliva, respectively, while Firmicutes and Clostridia were found in plaque isolated from children of different ages in preschool and school. These identified bacterial markers largely differ between different populations, leaving only Saccharibacteria as a significant caries-associated phylum in children. Saccharibacteria is a newly identified phylum, and our taxonomic assignment database could not be used to identify its specific genus. Conclusion Our data indicated that, in a South China population, oral microbial signatures for dental caries show age and sex differences, but Saccharibacteria might be a consistent signal and worth further investigation, considering the lack of research on this microbe.
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Affiliation(s)
- Yang You
- Department of Pediatric Dentistry, Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, ShenZhen, GuangDong, China
| | - Meixiang Yin
- Department of Pediatric Dentistry, Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, ShenZhen, GuangDong, China
- Department of Stomatology, Shenzhen Samii Medical Center, ShenZhen, GuangDong, China
| | - Xiao Zheng
- Department of Pediatric Dentistry, Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, ShenZhen, GuangDong, China
| | - Qiuying Liang
- Department of Pediatric Dentistry, Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, ShenZhen, GuangDong, China
| | - Hui Zhang
- Department of Pediatric Dentistry, Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, ShenZhen, GuangDong, China
| | - Bu-Ling Wu
- Department of Endodontics, Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, ShenZhen, GuangDong, China
| | - Wenan Xu
- Department of Pediatric Dentistry, Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, ShenZhen, GuangDong, China
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25
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Schamarek I, Anders L, Chakaroun RM, Kovacs P, Rohde-Zimmermann K. The role of the oral microbiome in obesity and metabolic disease: potential systemic implications and effects on taste perception. Nutr J 2023; 22:28. [PMID: 37237407 DOI: 10.1186/s12937-023-00856-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Obesity and its metabolic sequelae still comprise a challenge when it comes to understanding mechanisms, which drive these pandemic diseases. The human microbiome as a potential key player has attracted the attention of broader research for the past decade. Most of it focused on the gut microbiome while the oral microbiome has received less attention. As the second largest niche, the oral microbiome is associated with a multitude of mechanisms, which are potentially involved in the complex etiology of obesity and associated metabolic diseases. These mechanisms include local effects of oral bacteria on taste perception and subsequent food preference as well as systemic effects on adipose tissue function, the gut microbiome and systemic inflammation. This review summarizes a growing body of research, pointing towards a more prominent role of the oral microbiome in obesity and associated metabolic diseases than expected. Ultimately, our knowledge on the oral microbiome may support the development of new patient oriented therapeutic approaches inevitable to relieve the health burden of metabolic diseases and to reach long-term benefits in patients´ lives.
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Affiliation(s)
- Imke Schamarek
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG), Helmholtz Center Munich at the University Leipzig and the University Clinic Leipzig, AöR, Liebigstraße 20, 04103, Leipzig, Germany.
- Department of Medicine III, Division of Endocrinology, Nephrology and Rheumatology, University of Leipzig, Liebigstraße 20, 04103, Leipzig, Germany.
| | - Lars Anders
- Department of Medicine III, Division of Endocrinology, Nephrology and Rheumatology, University of Leipzig, Liebigstraße 20, 04103, Leipzig, Germany
| | - Rima M Chakaroun
- Department of Medicine III, Division of Endocrinology, Nephrology and Rheumatology, University of Leipzig, Liebigstraße 20, 04103, Leipzig, Germany
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 41345, Gothenburg, Sweden
| | - Peter Kovacs
- Department of Medicine III, Division of Endocrinology, Nephrology and Rheumatology, University of Leipzig, Liebigstraße 20, 04103, Leipzig, Germany
- Deutsches Zentrum Für Diabetesforschung, 85764, Neuherberg, Germany
| | - Kerstin Rohde-Zimmermann
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG), Helmholtz Center Munich at the University Leipzig and the University Clinic Leipzig, AöR, Liebigstraße 20, 04103, Leipzig, Germany
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Bruno JS, Al-Qadami GH, Laheij AMGA, Bossi P, Fregnani ER, Wardill HR. From Pathogenesis to Intervention: The Importance of the Microbiome in Oral Mucositis. Int J Mol Sci 2023; 24:ijms24098274. [PMID: 37175980 PMCID: PMC10179181 DOI: 10.3390/ijms24098274] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/11/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Oral mucositis (OM) is a common and impactful toxicity of standard cancer therapy, affecting up to 80% of patients. Its aetiology centres on the initial destruction of epithelial cells and the increase in inflammatory signals. These changes in the oral mucosa create a hostile environment for resident microbes, with oral infections co-occurring with OM, especially at sites of ulceration. Increasing evidence suggests that oral microbiome changes occur beyond opportunistic infection, with a growing appreciation for the potential role of the microbiome in OM development and severity. This review collects the latest articles indexed in the PubMed electronic database which analyse the bacterial shift through 16S rRNA gene sequencing methodology in cancer patients under treatment with oral mucositis. The aims are to assess whether changes in the oral and gut microbiome causally contribute to oral mucositis or if they are simply a consequence of the mucosal injury. Further, we explore the emerging role of a patient's microbial fingerprint in OM development and prediction. The maintenance of resident bacteria via microbial target therapy is under constant improvement and should be considered in the OM treatment.
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Affiliation(s)
- Julia S Bruno
- Instituto de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo 01308-060, Brazil
| | - Ghanyah H Al-Qadami
- School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Alexa M G A Laheij
- Department of Oral Medicine, Academic Centre for Dentistry (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, 1081 LA Amsterdam, The Netherlands
- Department of Preventive Dentistry, Academic Centre for Dentistry (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, 1081 LA Amsterdam, The Netherlands
- Department of Oral Maxillofacial Surgery, Amsterdam UMC, University of Amsterdam, 1081 LA Amsterdam, The Netherlands
| | - Paolo Bossi
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, University of Brescia, 25121 Brescia, Italy
| | - Eduardo R Fregnani
- Instituto de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo 01308-060, Brazil
| | - Hannah R Wardill
- School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide 5005, Australia
- The Supportive Oncology Research Group, Precision Cancer Medicine Theme, The South Australian Health and Medical Research Institute, Adelaide 5000, Australia
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27
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Gregorczyk-Maga I, Fiema M, Kania M, Jachowicz-Matczak E, Romaniszyn D, Gerreth K, Klupa T, Wójkowska-Mach J. Oral Microbiota-One Habitat or Diverse Niches? A Pilot Study of Sampling and Identification of Oral Bacterial and Fungal Biota in Patients with Type I Diabetes Mellitus Treated with Insulin Pump. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2252. [PMID: 36767617 PMCID: PMC9914992 DOI: 10.3390/ijerph20032252] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
OBJECTIVE The oral microbiota is a very complex and dynamic microbial ecosystem. Alterations of its balance can result in oral and systemic diseases. We aimed to characterize the microbiota in particular niches of the oral cavity in adult type 1 diabetes patients treated with continuous infusion of insulin with insulin pump (IP). In addition, we aimed to determine optimal sites of oral microbiota sampling in studies of large research groups of patients with DM I. DESIGN In this pilot study, we sampled the buccal and soft palate mucosa, tongue, palatal and buccal dental surfaces and gingival pockets of adult DM I patients treated with IP. RESULTS In total, 23 patients were recruited. The oral microbiota was dominated by Streptococus and Neisseria, with a low incidence of cariogenic S. mutans and Lactobacillus, as well as periodontal pathogens such as Prevotella. There were significant differences in overall CFU counts of all strains, Gram-positive, Staphylococci, Streptococci and S. oralis strains between mucosal and dental surface sites. The overall CFU counts of all strains and Gram-positive strains were higher in dental sites vs. mucosal sites (both p < 0.001). CFU counts of S. oralis were significantly higher in dental sites vs. gingival pocket sites (p = 0.013). Candida species were rare. The mucosal sites on the buccae presented lower diversity and bacterial counts. CONCLUSIONS In the study group of adult DM I patients treated with IP, the microbiota in particular niches of the oral cavity was significantly different. Three distinct and optimally appropriate sampling sites for oral microflora were identified: buccal and palatal mucosa, dental surface and gingival pockets. The results of this study may be the basis for further studies of large groups of patients with DM I.
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Affiliation(s)
- Iwona Gregorczyk-Maga
- Institute of Dentistry, Faculty of Medicine, Jagiellonian University Medical College, 31-155 Krakow, Poland
| | - Mateusz Fiema
- Department of Endocrinology, University Hospital, 30-688 Krakow, Poland
| | - Michal Kania
- Doctoral School of Medicine and Health Sciences, Jagiellonian University Medical College, 31-008 Krakow, Poland
- Department of Metabolic Diseases, Center of Advanced Technologies in Diabetes, Faculty of Medicine, Jagiellonian University Medical College, 30-688 Krakow, Poland
| | - Estera Jachowicz-Matczak
- Department of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, 31-121 Krakow, Poland
| | - Dorota Romaniszyn
- Department of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, 31-121 Krakow, Poland
| | - Karolina Gerreth
- Department of Risk Group Dentistry, Chair of Pediatric Dentistry, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Tomasz Klupa
- Department of Metabolic Diseases, Center of Advanced Technologies in Diabetes, Faculty of Medicine, Jagiellonian University Medical College, 30-688 Krakow, Poland
| | - Jadwiga Wójkowska-Mach
- Department of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, 31-121 Krakow, Poland
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qPCR Detection and Quantification of Aggregatibacter actinomycetemcomitans and Other Periodontal Pathogens in Saliva and Gingival Crevicular Fluid among Periodontitis Patients. Pathogens 2023; 12:pathogens12010076. [PMID: 36678429 PMCID: PMC9861831 DOI: 10.3390/pathogens12010076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/14/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVE The detection of special bacterial species in patients with periodontitis is considered useful for clinical diagnosis and treatment. The aim of this study was to investigate the presence of specific periopathogens and investigate whether there is a correlation between the results of different bacterial species in whole saliva and pooled subgingival plaque samples (healthy and diseased sites) from individuals with periodontitis and periodontally healthy subjects. MATERIALS AND METHODS In total, 52 patients were recruited and divided into two groups: non-periodontitis and periodontitis patients. For each group, the following periodontal pathogens were detected using real-time polymerase chain reaction: A. actinomycetemcomitans JP2 clone, A. actinomycetemcomitans non JP2 clone, Porphyromonasgingivalis, and total eubacteria. RESULTS Higher levels of the various studied bacteria were present in both saliva and plaque samples from the periodontitis group in comparison to non-periodontitis subjects. There were significant differences in P. gingivalis and A. actinomycetemcomitans JP2 clones in the saliva of periodontitis patient compared to the control group. Subgingival plaque of diseased sites presented a significant and strong positive correlation between A. actinomycetemcomitans and P. gingivalis. In saliva samples, there was a significant positive correlation between A. actinomycetemcomitans JP2 clone and P. gingivalis (p ≤ 0.002). CONCLUSION Quantifying and differentiating these periodontal species from subgingival plaque and saliva samples showed a good potential as diagnostic markers for periodontal disease. Regarding the prevalence of the studied bacteria, specifically A. actinomycetemcomitans JP2 clone, found in this work, and the high rate of susceptibility to periodontal species in Africa, future larger studies are recommended.
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Duarte-Coimbra S, Forcina G, Pérez-Pardal L, Beja-Pereira A. Characterization of tongue dorsum microbiome in wine tasters. Food Res Int 2023; 163:112259. [PMID: 36596171 DOI: 10.1016/j.foodres.2022.112259] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 12/05/2022]
Abstract
Taste plays a paramount role in food and beverage choice, with recent studies pointing to a potential influence of the microorganisms from the tongue dorsum - particularly bacteria - on flavor perception. Thus, the association between tongue dorsum biofilm and taste is a fundamental prerequisite for a better understanding of the role played by these bacteria in wine tasting. To study this impact, we have analyzed the microbiomes from 58 samples of the tongue dorsum surface from professional wine tasters and 30 samples from non professional wine tasters. The microbiome of each sample was characterized through metagenome sequencing of the 16S rRNA gene for taxonomic discrimination of bacteria. A total of 497 taxa were identified in the tongue dorsum, and significant differences in diversity were observed between the wine taster and the control group. The comparison of bacterial diversity between samples collected before and after wine tasting along with the presence of new bacterial taxa indicates a direct effect of wine on the microbiome of frequent wine tasters, particularly in those tasting sparkling wines.
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Affiliation(s)
- Sofia Duarte-Coimbra
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Giovanni Forcina
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Universidad de Alcalá (UAH), Global Change Ecology and Evolution Research Group (GloCEE), Departamento de Ciencias de la Vida, 28805 Alcalá de Henares, Madrid, Spain
| | - Lucía Pérez-Pardal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal.
| | - Albano Beja-Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; DGAOT, Faculty of Sciences, Universidade do Porto, Rua Campo Alegre 687, 4169-007 Porto, Portugal; Sustainable Agrifood Production Research Centre (GreenUPorto), Universidade do Porto, Rua da Agrária 747, 4485-646 Vairão, Portugal.
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30
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Fungal composition in saliva and plaque in children with caries: Differences and influencing factors. MEDICINE IN MICROECOLOGY 2023. [DOI: 10.1016/j.medmic.2023.100076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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31
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Tansirichaiya S, Hutton W, Roberts AP. Functional and Sequence-Specific Screening Protocols for the Detection of Novel Antimicrobial Resistance Genes in Metagenomic DNA. Methods Mol Biol 2023; 2555:51-72. [PMID: 36306078 DOI: 10.1007/978-1-0716-2795-2_4] [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] [Indexed: 03/23/2023]
Abstract
Antimicrobial resistance (AMR) is an increasingly important global challenge for healthcare systems as well as agricultural food production systems. Our ability to prepare for, and respond to, emerging AMR threats is dependent on our knowledge of genes able to confer AMR that are circulating within various environmental, animal, and human microbiomes. Targeted, sequence-specific, detection of AMR genes and functional resistance assays, described here, carried out on metagenomic DNA gives us unique insights into the presence of AMR genes and how these are associated with mobile genetic elements that may be responsible for their dissemination and can also provide important information about the mechanisms of resistance underpinning the phenotype.
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Affiliation(s)
- Supathep Tansirichaiya
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - William Hutton
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Adam P Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK.
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Jeong J, Ahn K, Mun S, Yun K, Kim YT, Jung W, Lee KE, Kim MY, Ahn Y, Han K. Understanding the bacterial compositional network associations between oral and gut microbiome within healthy Koreans. J Oral Microbiol 2023; 15:2186591. [PMID: 36891192 PMCID: PMC9987756 DOI: 10.1080/20002297.2023.2186591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Oral microbial ecosystem could influence intestinal diseases, but there have been insufficient studies demonstrating the association of microbial composition between the oral cavity and the intestinal system. Thus, we aimed to investigate the compositional network within the oral microbiome related to gut enterotype from saliva and stool samples collected from 112 healthy Korean subjects. Here, we performed bacterial 16S amplicon sequencing from clinical samples. Then, we determined oral microbiome type related to individual's gut enterotype for healthy Korean. The co-occurrence analysis was performed to interactivity prediction of microbiome within saliva samples. As a result, it could be classified into two Korean oral microbiome types (KO) and four oral-gut-associated microbiome types (KOGA) according to distribution and significant differences of oral microflora. The co-occurrence analysis showed various bacterial compositional networks linked around Streptococcus and Haemophilus within healthy subjects. The present study was first approach in healthy Koreans to identify the oral microbiome types related to the gut microbiome and investigate their characteristics. Hence, we suggest that our results could be potential healthy control data for identifying differences in microbial composition between healthy people and oral disease patients and studying microbial association with the gut microbial environment (oral-gut microbiome axis).
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Affiliation(s)
- Jinuk Jeong
- Department of Bioconvergence Engineering, Dankook University, Yongin, Republic of Korea
| | - Kung Ahn
- Department of Human microbiome research HuNbiome Co. Ltd, R&D Center, Seoul, Republic of Korea
| | - Seyoung Mun
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan, Republic of Korea.,Center for Bio‑Medical Engineering Core Facility, Dankook University, Cheonan, Republic of Korea
| | - Kyeongeui Yun
- Department of Human microbiome research HuNbiome Co. Ltd, R&D Center, Seoul, Republic of Korea.,Department of Microbiology, College of Science & Technology, Dankook University, Cheonan, Republic of Korea
| | - Yeon-Tae Kim
- Department of Periodontology, Daejeon Dental Hospital, Institute of Wonkwang Dental Research, Wonkwang University College of Dentistry, Daejeon, Republic of Korea
| | - Won Jung
- Department of Oral Medicine, School of Dentistry, Jeonbuk National University, Jeonju, Republic of Korea
| | - Kyung Eun Lee
- Department of Oral Medicine, School of Dentistry, Jeonbuk National University, Jeonju, Republic of Korea
| | - Moon-Young Kim
- Department of Oral and Maxillofacial Surgery, College of Dentistry, Dankook University, Cheonan, Republic of Korea
| | - Yongju Ahn
- Department of Human microbiome research HuNbiome Co. Ltd, R&D Center, Seoul, Republic of Korea
| | - Kyudong Han
- Department of Bioconvergence Engineering, Dankook University, Yongin, Republic of Korea.,Department of Human microbiome research HuNbiome Co. Ltd, R&D Center, Seoul, Republic of Korea.,Department of Microbiology, College of Science & Technology, Dankook University, Cheonan, Republic of Korea.,Center for Bio‑Medical Engineering Core Facility, Dankook University, Cheonan, Republic of Korea
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Genome-Centric Dynamics Shape the Diversity of Oral Bacterial Populations. mBio 2022; 13:e0241422. [PMID: 36214570 PMCID: PMC9765137 DOI: 10.1128/mbio.02414-22] [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] [Indexed: 11/20/2022] Open
Abstract
Two major viewpoints have been put forward for how microbial populations change, differing in whether adaptation is driven principally by gene-centric or genome-centric processes. Longitudinal sampling at microbially relevant timescales, i.e., days to weeks, is critical for distinguishing these mechanisms. Because of its significance for both microbial ecology and human health and its accessibility and high level of curation, we used the oral microbiota to study bacterial intrapopulation genome dynamics. Metagenomes were generated by shotgun sequencing of total community DNA from the healthy tongues of 17 volunteers at four to seven time points obtained over intervals of days to weeks. We obtained 390 high-quality metagenome-assembled genomes (MAGs) defining population genomes from 55 genera. The vast majority of genes in each MAG were tightly linked over the 2-week sampling window, indicating that the majority of the population's genomes were temporally stable at the MAG level. MAG-defined populations were composed of up to 5 strains, as determined by single-nucleotide-variant frequencies. Although most were stable over time, individual strains carrying over 100 distinct genes that rose from low abundance to dominance in a population over a period of days were detected. These results indicate a genome-wide as opposed to a gene-level process of population change. We infer that genome-wide selection of ecotypes is the dominant mode of adaptation in the oral populations over short timescales. IMPORTANCE The oral microbiome represents a microbial community of critical relevance to human health. Recent studies have documented the diversity and dynamics of different bacteria to reveal a rich, stable ecosystem characterized by strain-level dynamics. However, bacterial populations and their genomes are neither monolithic nor static; their genomes are constantly evolving to lose, gain, or alter their functional potential. To better understand how microbial genomes change in complex communities, we used culture-independent approaches to reconstruct the genomes (MAGs) for bacterial populations that approximated different species, in 17 healthy donors' mouths over a 2-week window. Our results underscored the importance of strain-level dynamics, which agrees with and expands on the conclusions of previous research. Altogether, these observations reveal patterns of genomic dynamics among strains of oral bacteria occurring over a matter of days.
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McLean AR, Torres-Morales J, Dewhirst FE, Borisy GG, Welch JLM. Site-tropism of streptococci in the oral microbiome. Mol Oral Microbiol 2022; 37:229-243. [PMID: 36073311 PMCID: PMC9691528 DOI: 10.1111/omi.12387] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/08/2022] [Accepted: 08/28/2022] [Indexed: 11/29/2022]
Abstract
A detailed understanding of where bacteria localize is necessary to advance microbial ecology and microbiome-based therapeutics. The site-specialist hypothesis predicts that most microbes in the human oral cavity have a primary habitat type within the mouth where they are most abundant. We asked whether this hypothesis accurately describes the distribution of the members of the genus Streptococcus, a clinically relevant taxon that dominates most oral sites. Prior analysis of 16S rRNA gene sequencing data indicated that some oral Streptococcus clades are site-specialists while others may be generalists. However, within complex microbial populations composed of numerous closely related species and strains, such as the oral streptococci, genome-scale analysis is necessary to provide the resolution to discriminate closely related taxa with distinct functional roles. Here, we assess whether individual species within this genus are specialists using publicly available genomic sequence data that provide species-level resolution. We chose a set of high-quality representative genomes for human oral Streptococcus species. Onto these genomes, we mapped shotgun metagenomic sequencing reads from supragingival plaque, tongue dorsum, and other sites in the oral cavity. We found that every abundant Streptococcus species in the healthy human oral cavity showed strong site-tropism and that even closely related species such as S. mitis, S. oralis, and S. infantis specialized in different sites. These findings indicate that closely related bacteria can have distinct habitat distributions in the absence of dispersal limitation and under similar environmental conditions and immune regimes. Substantial overlap between the core genes of these three species suggests that site-specialization is determined by subtle differences in genomic content.
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Affiliation(s)
- Anthony R. McLean
- The Forsyth Institute, Cambridge, MA 02142
- Marine Biological Laboratory, Woods Hole, MA 02543
| | | | - Floyd E. Dewhirst
- The Forsyth Institute, Cambridge, MA 02142
- Harvard School of Dental Medicine, Boston, MA 02115
| | | | - Jessica L. Mark Welch
- The Forsyth Institute, Cambridge, MA 02142
- Marine Biological Laboratory, Woods Hole, MA 02543
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Evaluation of the correlation between oral infections and systemic complications in kidney transplant patients: a retrospective pilot study. BMC Oral Health 2022; 22:530. [PMID: 36424574 PMCID: PMC9685840 DOI: 10.1186/s12903-022-02590-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/14/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Data regarding the efficacy of the dental clearance required prior to kidney transplantation (KT) for preventing post-transplant complications is controversial. The aim of this retrospective study was to investigate a possible correlation between any untreated oral infectious foci and the onset of systemic complications in KT patients. METHODS Patients scheduled for regular check-ups during the post-transplant period were visited at the C.I.R. Dental School in Turin, Italy. Patients were asked to bring orthopantomography (OPT) acquired prior to transplantation to compare the possible presence of untreated infectious foci at the time of transplantation with the time of their post-transplant visit. Patients were then divided, according to the evaluation of the OPT obtained prior to the transplantation, into two groups according to their dental status prior to the transplant. "Group Infected" was comprised of patients with no dental clearance, and "Group Clear" included patients with dental clearance. The medical records were then retrospectively reviewed for the evaluation of any systemic complications that occurred after transplantation. The following medical complications were considered: fever, pneumonia, urinary tract infections, systemic infections, kidney rejection, and death. Complications were divided in two groups: early complications, which occurred within 100 days of transplantation, and late complications, which occurred more than 100 days after transplantation. RESULTS A total of 77 patients were enrolled in the study. Group Infected was composed of 19 subjects (25%), while Group Clear was composed of 58 patients (75%). In Group Infected, 13 (68%) patients developed complications within 100 days of transplantation, and 11 (58%) did so after 100 days. In Group Clear, 31 (53%) patients had complications within 100 days of the transplant, and 23 (40%) did after 100 days. Patients in Group Infected had a statistically significant increase in episodes of fever (p = 0.03), compared to Group Clear, with a higher relative risk (RR) of 3.66 in the first 100 days after transplantation. CONCLUSION Within the limitations of the present retrospective pilot study, and based on the results, a correlation between the absence of dental clearance prior to KT and a higher RR of developing a fever within the first 100 days post transplantation was highlighted. The present results encourage doctors to continue research on the topic, which remains controversial. Further prospective studies are required to confirm the results of the present study.
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Abstract
Oral commensal streptococci are primary colonizers of the oral cavity. These streptococci produce many adhesins, metabolites, and antimicrobials that modulate microbial succession and diversity within the oral cavity. Often, oral commensal streptococci antagonize cariogenic and periodontal pathogens such as Streptococcus mutans and Porphyromonas gingivalis, respectively. Mechanisms of antagonism are varied and range from the generation of hydrogen peroxide, competitive metabolite scavenging, the generation of reactive nitrogen intermediates, and bacteriocin production. Furthermore, several oral commensal streptococci have been shown to alter the host immune response at steady state and in response to oral pathogens. Collectively, these features highlight the remarkable ability of oral commensal streptococci to regulate the structure and function of the oral microbiome. In this review, we discuss mechanisms used by oral commensal streptococci to interact with diverse oral pathogens, both physically and through the production of antimicrobials. Finally, we conclude by exploring the critical roles of oral commensal streptococci in modulating the host immune response and maintaining health and homeostasis.
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Noh JW, Jang JH, Yoon HS, Kim KB, Heo MH, Jang HE, Kim YJ, Lee Y. Evaluation of Salivary Biomarkers of Periodontal Disease Based on Smoking Status: A Systematic Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:14619. [PMID: 36361498 PMCID: PMC9657317 DOI: 10.3390/ijerph192114619] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Saliva is a useful biomarker for diagnosing oral health conditions, including periodontal disease (PD). Smoking is a risk factor for PD. The aim of this systematic review was to summarize the salivary biomarkers associated with PD based on smoking status. A comprehensive search of the MEDLINE (via PubMed), EMBASE, Cochrane, SCOPUS, and Web of Sciences databases was conducted up to 1 January 2021 using key terms relevant to the topic of our research and Cochrane methodology and improved with searching a gray literature resource. The methodological quality of all included studies was assessed with the revised Quality Assessment of Diagnostic Accuracy Studies-2. Seven studies were included. Smokers had increased levels of malondialdehyde, sialic acid, salivary cortisol, salivary interleukin 1β, albumin, tissue inhibitor of matrix metalloproteinase (TIMP), and the pyridinoline cross-linked carboxyterminal telopeptide of type I collagen (ICTP), as well as decreased levels of superoxide dismutase, activity of lactate dehydrogenase, activity of enzyme activity of β-glucuronidase, uric acid, matrix metalloproteinase-8 (MMP-8)/TIMP-1 ratio, and combinations of MMP-8 and ICTP. However, mixed results were observed some studies in detecting glutathione peroxidase, MMP-8, and MMP-14. The results were interpreted with caution because of limitations in the number of included studies and the study design. Some salivary biomarkers are potentially useful in combination or alone for diagnosing PD. Methodological and systematic studies are needed to develop more effective biomarkers.
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Affiliation(s)
- Jin-won Noh
- Division of Health Administration, College of Software and Digital Healthcare Convergence, Yonsei University, Gangwon-do, Wonju 26493, Korea
| | - Jong-Hwa Jang
- Department of Dental Hygiene, College of Health Science, Dankook University, Chungcheongnam-do, Cheonan 31116, Korea
- Department of Public Health Science, Dankook University Graduate School, Chungcheongnam-do, Cheonan 31116, Korea
| | - Hae-Soo Yoon
- Department of Public Health Science, Dankook University Graduate School, Chungcheongnam-do, Cheonan 31116, Korea
| | - Kyoung-Beom Kim
- Department of Health Administration, Dankook University, Chungcheongnam-do, Cheonan 31116, Korea
- Industry-Academic Cooperation Foundation, Yonsei University, Gangwon-do, Wonju 26493, Korea
| | - Min-Hee Heo
- Department of Health Administration, Yonsei University Graduate School, Gangwon-do, Wonju 26493, Korea
| | - Ha-eun Jang
- Department of Healthcare Management, College of Bio Convergence, Eulji University, Gyeonggi-do, Seongnam 13135, Korea
| | - Young-Jin Kim
- Department of Health Administration, Yonsei University Graduate School, Gangwon-do, Wonju 26493, Korea
| | - Yejin Lee
- Department of Public Health Graduate School, Korea University, Seoul 02841, Korea
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Jitvaropas R, Mayuramart O, Sawaswong V, Kaewsapsak P, Payungporn S. Classification of salivary bacteriome in asymptomatic COVID-19 cases based on long-read nanopore sequencing. Exp Biol Med (Maywood) 2022; 247:1937-1946. [PMID: 36082397 PMCID: PMC9742750 DOI: 10.1177/15353702221118091] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The coronavirus (COVID-19) global pandemic has impacted the health of almost everyone, including changes in their salivary microbiota. Since 2019, there has been an increase in the number of new COVID-19 cases in Thailand. Therefore, COVID-19 active case finding is important for early detection and epidemic control. Moreover, the dynamic changes of salivary bacteriome in asymptomatic COVID-19 cases are largely unknown. This research aimed to investigate and compare the salivary bacteriome and the co-infectious bacterial pathogens in the asymptomatic COVID-19 positive group to the negative group, based on novel nanopore sequencing. This cohort was a cross-sectional study including saliva samples collected from 82 asymptomatic participants (39 COVID-19 positive and 43 COVID-19 negative cases). All samples were sequenced for the full-length bacterial 16S rDNA. The alpha and beta diversity analyses were not significantly different between groups. The three major species in salivary bacteriome including Veillonella parvula, Streptococcus mitis, and Prevotella melaninogenica were observed in both groups. Interestingly, Lautropia mirabilis was a significantly enriched species in the saliva of the asymptomatic COVID-19-positive cases based on linear discriminant analysis effect size (LEfSe) analysis. The results suggested that L. mirabilis was a co-infectious agent in the asymptomatic COVID-19 group. However, the potential role of L. mirabilis should be validated in further experimental studies.
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Affiliation(s)
- Rungrat Jitvaropas
- Division of Biochemistry, Department of Preclinical Science, Faculty of Medicine, Thammasat University, Pathum Thani 10120, Thailand
| | - Oraphan Mayuramart
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Vorthon Sawaswong
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pornchai Kaewsapsak
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand,Sunchai Payungporn.
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The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations. NPJ Biofilms Microbiomes 2022; 8:85. [PMID: 36266278 PMCID: PMC9584946 DOI: 10.1038/s41522-022-00343-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
Human saliva contains diverse bacterial communities, reflecting health status, dietary patterns and contributing to variability in the sensory perception of food. Many descriptions of the diversity of the salivary microbiome have focused on the changes induced by certain diseased states, but the commonalities and differences within healthy saliva have not been fully described. Here, we define and explore the core membership of the human salivary microbial community by collecting and re-analysing raw 16S rRNA amplicon sequencing data from 47 studies with 2206 saliva samples. We found 68 core bacterial taxa that were consistently detected. Differences induced by various host intrinsic and behaviour factors, including gender, age, geographic location, tobacco usage and alcohol consumption were evident. The core of the salivary microbiome was verified by collecting and analysing saliva in an independent study. These results suggest that the methods used can effectively define a core microbial community in human saliva. The core salivary microbiome demonstrated both stability and variability among populations. Geographic location was identified as the host factor that is most associated with the structure of salivary microbiota. The independent analysis confirmed the prevalence of the 68 core OTUs we defined from the global data and provides information about how bacterial taxa in saliva varies across human populations.
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Treerat P, McGuire B, Palmer E, Dahl EM, Karstens L, Merritt J, Kreth J. Oral microbiome diversity: The curious case of Corynebacterium sp. isolation. Mol Oral Microbiol 2022; 37:167-179. [PMID: 35859343 PMCID: PMC9578355 DOI: 10.1111/omi.12381] [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: 05/06/2022] [Revised: 06/29/2022] [Accepted: 07/14/2022] [Indexed: 01/28/2023]
Abstract
Oral microbiome sequencing efforts revealed the presence of hundreds of different microbes. Interindividual differences at strain and species resolution suggest that microbiome diversity could lead to mechanistically distinct gene regulation as well as species-related differences in phenotypes. Commonly, gene regulation and related phenotypes are studied in a few selected strains of a particular species with conclusions that are mostly generalized. The aim of this study was to isolate several species of Corynebacterium using an established protocol that led to the previous isolation of C. durum. Characterization of C. durum interspecies interactions revealed a specific mechanism for chain elongation in Streptococcus sanguinis that was the result of corynebacterial fatty acid production and secretion. While the protocol was successfully applied to isolate what we presumed to be additional Corynebacterium based on several phenotypic traits that seem to be identical to C. durum, genome sequencing of the newly isolated strains placed them closer to Actinomyces. Both Corynebacterium and Actinomyces are suborders of the Actinobacteridae and related species. Our study suggests to take several comprehensive strategies into consideration when taxonomically identifying closely related microorganisms. Furthermore, it seems to be important to test common core phenotypes in bacterial ecology to understand the behavior of specific groups of microbes, rather than simply relying upon genome sequence homology to establish relationships in the microbiome.
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Affiliation(s)
- Puthayalai Treerat
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, Oregon, USA
| | - Brian McGuire
- Department of Pediatric Dentistry, Oregon Health & Science University, Portland, Oregon, USA
- Portsmouth Pediatric Dentistry and Orthodontics, 150 Griffin Rd #1, Portsmouth, NH 03801, USA
| | - Elizabeth Palmer
- Department of Pediatric Dentistry, Oregon Health & Science University, Portland, Oregon, USA
| | - Erin M. Dahl
- Department of Medical Informatics and Clinical Epidemiology, Division of Bioinformatics and Computational Biomedicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Lisa Karstens
- Department of Medical Informatics and Clinical Epidemiology, Division of Bioinformatics and Computational Biomedicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health & Science University, Portland, Oregon, USA
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Pignatelli P, Romei FM, Bondi D, Giuliani M, Piattelli A, Curia MC. Microbiota and Oral Cancer as A Complex and Dynamic Microenvironment: A Narrative Review from Etiology to Prognosis. Int J Mol Sci 2022; 23:ijms23158323. [PMID: 35955456 PMCID: PMC9368704 DOI: 10.3390/ijms23158323] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/23/2022] Open
Abstract
A complex balanced equilibrium of the bacterial ecosystems exists in the oral cavity that can be altered by tobacco smoking, psychological stressors, bad dietary habit, and chronic periodontitis. Oral dysbiosis can promote the onset and progression of oral squamous cell carcinoma (OSCC) through the release of toxins and bacterial metabolites, stimulating local and systemic inflammation, and altering the host immune response. During the process of carcinogenesis, the composition of the bacterial community changes qualitatively and quantitatively. Bacterial profiles are characterized by targeted sequencing of the 16S rRNA gene in tissue and saliva samples in patients with OSCC. Capnocytophaga gingivalis, Prevotella melaninogenica, Streptococcus mitis, Fusobacterium periodonticum, Prevotella tannerae, and Prevotella intermedia are the significantly increased bacteria in salivary samples. These have a potential diagnostic application to predict oral cancer through noninvasive salivary screenings. Oral lactic acid bacteria, which are commonly used as probiotic therapy against various disorders, are valuable adjuvants to improve the response to OSCC therapy.
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Affiliation(s)
- Pamela Pignatelli
- Department of Oral and Maxillofacial Sciences, Sapienza University of Rome, Via Caserta 6, 00161 Rome, Italy
- Correspondence:
| | - Federica Maria Romei
- Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University of Chieti-Pescara, Via dei Vestini, 66100 Chieti, Italy; (F.M.R.); (M.C.C.)
| | - Danilo Bondi
- Department of Neuroscience, Imaging and Clinical Sciences, “G. d’Annunzio” University of Chieti-Pescara, Via dei Vestini, 66100 Chieti, Italy;
| | - Michele Giuliani
- Department of Clinical and Experimental Medicine, University of Foggia, Via Rovelli 50, 71122 Foggia, Italy;
| | - Adriano Piattelli
- School of Dentistry, Saint Camillus International University for Health Sciences (Unicamillus), 00131 Rome, Italy;
- Fondazione Villa Serena per la Ricerca, 65013 Città Sant’Angelo, Italy
- Casa di Cura Villa Serena, 65013 Città Saint’Angelo, Italy
| | - Maria Cristina Curia
- Department of Medical, Oral and Biotechnological Sciences, “G. d’Annunzio” University of Chieti-Pescara, Via dei Vestini, 66100 Chieti, Italy; (F.M.R.); (M.C.C.)
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Comparison of microbial composition and diversity in the upper respiratory tract between SARS-CoV-2 and influenza virus infections. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1469-1472. [PMID: 35349047 PMCID: PMC8962226 DOI: 10.1007/s11427-021-2092-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 03/12/2022] [Indexed: 10/26/2022]
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Hu Y, Amir A, Huang X, Li Y, Huang S, Wolfe E, Weiss S, Knight R, Xu ZZ. Diurnal and eating-associated microbial patterns revealed via high-frequency saliva sampling. Genome Res 2022; 32:1112-1123. [PMID: 35688483 DOI: 10.1101/gr.276482.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 05/18/2022] [Indexed: 11/24/2022]
Abstract
The oral microbiome is linked to oral and systemic health, but its fluctuation under frequent daily activities remains elusive. Here, we sampled saliva at 10- to 60-min intervals to track the high-resolution microbiome dynamics during the course of human activities. This dense time series data showed that eating activity markedly perturbed the salivary microbiota, with tongue-specific Campylobacter concisus and Oribacterium sinus and dental plaque-specific Lautropia mirabilis, Rothia aeria, and Neisseria oralis increased after every meal in a temporal order. The observation was reproducible in multiple subjects and across an 11-mo period. The microbiome composition showed significant diurnal oscillation patterns at different taxonomy levels with Prevotella/Alloprevotella increased at night and Bergeyella HMT 206/Haemophilus slowly increased during the daytime. We also identified microbial co-occurring patterns in saliva that are associated with the intricate biogeography of the oral microbiome. Microbial source tracking analysis showed that the contributions of distinct oral niches to the salivary microbiome were dynamically affected by daily activities, reflecting the role of saliva in exchanging microbes with other oral sites. Collectively, our study provides insights into the temporal microbiome variation in saliva and highlights the need to consider daily activities and diurnal factors in design of oral microbiome studies.
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Affiliation(s)
- Yichen Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, PR China
| | - Amnon Amir
- Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA.,Sheba Medical Center, Ramat Gan 52621, Israel
| | - Xiaochang Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, PR China
| | - Yan Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, PR China
| | - Shi Huang
- Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA
| | - Elaine Wolfe
- Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA
| | - Sophie Weiss
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California 92093, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, California 92093, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California 92093, USA.,Department of Bioengineering, University of California San Diego, La Jolla, California 92093, USA
| | - Zhenjiang Zech Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, PR China.,Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen 518001, China.,Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510280, China
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Bryan NS, Burleigh MC, Easton C. The oral microbiome, nitric oxide and exercise performance. Nitric Oxide 2022; 125-126:23-30. [PMID: 35636654 DOI: 10.1016/j.niox.2022.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 05/12/2022] [Accepted: 05/22/2022] [Indexed: 12/15/2022]
Abstract
The human microbiome comprises ∼1013-1014 microbial cells which form a symbiotic relationship with the host and play a critical role in the regulation of human metabolism. In the oral cavity, several species of bacteria are capable of reducing nitrate to nitrite; a key precursor of the signaling molecule nitric oxide. Nitric oxide has myriad physiological functions, which include the maintenance of cardiovascular homeostasis and the regulation of acute and chronic responses to exercise. This article provides a brief narrative review of the research that has explored how diversity and plasticity of the oral microbiome influences nitric oxide bioavailability and related physiological outcomes. There is unequivocal evidence that dysbiosis (e.g. through disease) or disruption (e.g. by use of antiseptic mouthwash or antibiotics) of the oral microbiota will suppress nitric oxide production via the nitrate-nitrite-nitric oxide pathway and negatively impact blood pressure. Conversely, there is preliminary evidence to suggest that proliferation of nitrate-reducing bacteria via the diet or targeted probiotics can augment nitric oxide production and improve markers of oral health. Despite this, it is yet to be established whether purposefully altering the oral microbiome can have a meaningful impact on exercise performance. Future research should determine whether alterations to the composition and metabolic activity of bacteria in the mouth influence the acute responses to exercise and the physiological adaptations to exercise training.
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Affiliation(s)
- Nathan S Bryan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mia C Burleigh
- Institute for Clinical Exercise and Health Science, University of the West of Scotland, Blantyre, UK
| | - Chris Easton
- Institute for Clinical Exercise and Health Science, University of the West of Scotland, Blantyre, UK.
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La X, Jiang H, Chen A, Zheng H, Shen L, Chen W, Yang F, Zhang L, Cai X, Mao H, Cheng L. Profile of the oral microbiota from preconception to the third trimester of pregnancy and its association with oral hygiene practices. J Oral Microbiol 2022; 14:2053389. [PMID: 35341210 PMCID: PMC8942530 DOI: 10.1080/20002297.2022.2053389] [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] [Indexed: 12/13/2022] Open
Abstract
Background The oral microbiota plays vital roles in both oral and systemic health, but limited studies have explored the transition of the female oral microbiota from preconception to pregnancy along with pronounced hormonal fluctuations. Aim To characterize the oral microbiota among women in preconception and pregnancy through a prospective study and to explore the associations between the oral microbiota and oral hygiene practices. Methods A total of 202 unstimulated saliva samples were collected from 101 women in both preconception and late pregnancy. The oral microbiota was analyzed using 16S rRNA gene sequencing. Results The Ace and phylogenetic diversity (PD) index were significantly lower in the third trimester than preconception. The pathogenic taxa Prevotella and Atopobium parvulum were significantly higher during late pregnancy than preconception. Women with overall better oral hygiene practice showed lower richness and diversity in preconception compared to women with poorer oral hygiene practice. The abundance of pathogens such as Dialister during both preconception and pregnancy decreased among women with better oral hygiene practice. Conclusions The composition of the oral microbiota changed slightly from preconception to late pregnancy, with more pathogens in saliva samples during pregnancy. Improving oral hygiene practices has the potential to maintain oral micro-ecological balance.
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Affiliation(s)
- Xuena La
- School of Public Health, Key Laboratory of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, Xuhui District, Shanghai,China.,Department of Non-communicable Diseases Surveillance, Shanghai Municipal Center for Disease Control and Prevention (SCDC), Changning District, Shanghai,China
| | - Hong Jiang
- School of Public Health, Key Laboratory of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, Xuhui District, Shanghai,China
| | - An Chen
- Institute of Healthcare Engineering, Management and Architecture (HEMA), Department of Industrial Engineering and Management, Aalto University, Espoo, Finland
| | - Huajun Zheng
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Fudan University, Xuhui District, Shanghai,China
| | - Liandi Shen
- Department of Administrative Office, Jiading Maternal and Child Health Care Hospital, Jiading District, Shanghai,China
| | - Weiyi Chen
- School of Public Health, Key Laboratory of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, Xuhui District, Shanghai,China
| | - Fengyun Yang
- Department of Administrative Office, Jiading Maternal and Child Health Care Hospital, Jiading District, Shanghai,China
| | - Lifeng Zhang
- Department of Administrative Office, Jiading Maternal and Child Health Care Hospital, Jiading District, Shanghai,China
| | - Xushan Cai
- Department of Woman Health care, Jiading Maternal and Child Health Care Hospital, Jiading District, Shanghai, China
| | - Hongfang Mao
- Department of Woman Health care, Jiading Maternal and Child Health Care Hospital, Jiading District, Shanghai, China
| | - Lu Cheng
- Department of Computer Science, Aalto University, Espoo, Finland
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Klimenko ES, Igumnov IA, Markova DP, Belkova NL, Suturina LV. Does Salivary Microbiome Reflect The Functional Activity Profile Of Oral Microbiota? RUSSIAN OPEN MEDICAL JOURNAL 2022. [DOI: 10.15275/rusomj.2022.0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Human oral cavity is a diverse habitat, consisting of many locations with its microbiotas. It was proven that bacteria detected in saliva could be the indicators of disease and be useful for diagnosis, monitoring, and overall assessment of the patient health. As pilot research of microbial communities associated with polycystic ovary syndrome (PCOS), biomaterials were collected from two patients (saliva, the contents of gingival pockets) for sequencing the amplicon libraries V4-V6 of variable regions of the 16S rRNA gene. Our study aimed at comparing the taxonomic and functional profiles of different locations in the oral cavity. Material and Methods — DNA samples were sequenced using Illumina MiSeq; the qiime2-2020.2 and PICRUSt2 v2.4.1 software packages were used to process the sequencing results of the amplicon libraries. Results — We demonstrated that the salivary microbiome had a greater taxonomic diversity, compared with the microbiome of the periodontal pockets. Regarding the ratios of different taxonomic group abundances, the species ratio in the saliva community significantly differed from the ratio in periodontal pockets. The microbiota of the oral cavity was classified as a producing community, since many different biosynthetic pathways were predicted. Similar functional features were identified for microbial communities in other locations. Conclusions — Different locations in the biotope of the oral cavity have varying species richness of their communities and specific taxonomic composition. However, the microbiotas of different microniches perform similar metabolic functions. This finding allows considering the analysis of saliva microbiota sufficiently representative tool for characterization of the entire oral microbiome.
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Affiliation(s)
- Elizaveta S. Klimenko
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Ilya A. Igumnov
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Daria P. Markova
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Natalia L. Belkova
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Larisa V. Suturina
- Scientific Center for Family Health and Human Reproduction Problems, Irkutsk, Russia
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Bergamo AZN, Casarin RCV, do Nascimento C, Matsumoto MAN, de Carvalho FK, da Silva RAB, da Silva LAB, Nelson-Filho P. Self-ligating brackets exhibit accumulation of high levels of periodontopathogens in gingival crevicular fluid. Odontology 2022; 110:460-466. [PMID: 35037112 DOI: 10.1007/s10266-021-00677-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/29/2021] [Indexed: 10/19/2022]
Abstract
Different types of brackets seem to influence the disruption of the oral microbial environment. Therefore, the aim of this study was to evaluate the influence of self-ligating brackets on the gingival crevicular fluid levels of the putative periodontal pathogens Aggregatibacter actinomycetemcomitans sorotype a (Aaa), Tannerella forsythia, Fusobacterium nucleatum, and Porphyromonas gingivalis. Sixty samples of crevicular fluid of twenty patients (11 boys and 9 girls) were analysed at baseline (T0) and after 30 (T1) and 60 (T2) days of bonding of the self-ligating (In-Ovation®R, Dentsply, GAC or SmartClip™, 3 M Unitek, Monrovia, CA, USA) and of one conventional bracket (Gemini™, 3 M Unitek, Monrovia, CA, USA) used with elastomeric ligatures. Total DNA from samples was extracted using CTAB-DNA precipitation method and Real-time PCR was performed to analyse bacterial level. Non-parametric Friedman and Wilcoxon tests were used for data analysis (p value of < 0.05). F. nucleatum presented a different level among the different brackets at T1 (p = 0.025), the highest level in the Gemini™ bracket when compared to the SmartClip™ bracket (p = 0.043). P. ginigvalis levels increased in the In-Ovation®R (p = 0.028) at T1. The subgingival levels of bacterial species associated with periodontal disease P. ginigvalis increased in the self-ligating brackets In-Ovation®R.Clinical Relevance: Some kinds of brackets could provide more retentive sites than others, and it seems to modulate the subgingival microbiota, since, in this study, we could observe the increase of the species associated with periodontal disease. Preventive protocols should be adopted in the use of self-ligating brackets.
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Affiliation(s)
- Ana Zilda Nazar Bergamo
- Department of Pediatric Clinics, School of Dentistry of Ribeirão Preto, University of São Paulo, Avenida Do Café, S/N, Monte Alegre, Ribeirão Preto, SP, CEP: 14040-904, Brazil.
| | - Renato Corrêa Viana Casarin
- Department of Prosthodontics and Periodontology, School of Dentistry of Piracicaba, University of Campinas, Campinas, SP, Brazil
| | - Cássio do Nascimento
- Department of Dental Materials and Prosthodontics, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Mírian Aiko Nakane Matsumoto
- Department of Pediatric Clinics, School of Dentistry of Ribeirão Preto, University of São Paulo, Avenida Do Café, S/N, Monte Alegre, Ribeirão Preto, SP, CEP: 14040-904, Brazil
| | - Fabrício Kitazono de Carvalho
- Department of Pediatric Clinics, School of Dentistry of Ribeirão Preto, University of São Paulo, Avenida Do Café, S/N, Monte Alegre, Ribeirão Preto, SP, CEP: 14040-904, Brazil
| | - Raquel Assed Bezerra da Silva
- Department of Pediatric Clinics, School of Dentistry of Ribeirão Preto, University of São Paulo, Avenida Do Café, S/N, Monte Alegre, Ribeirão Preto, SP, CEP: 14040-904, Brazil
| | - Léa Assed Bezerra da Silva
- Department of Pediatric Clinics, School of Dentistry of Ribeirão Preto, University of São Paulo, Avenida Do Café, S/N, Monte Alegre, Ribeirão Preto, SP, CEP: 14040-904, Brazil
| | - Paulo Nelson-Filho
- Department of Pediatric Clinics, School of Dentistry of Ribeirão Preto, University of São Paulo, Avenida Do Café, S/N, Monte Alegre, Ribeirão Preto, SP, CEP: 14040-904, Brazil
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Gouello A, Dunyach-Remy C, Siatka C, Lavigne JP. Analysis of Microbial Communities: An Emerging Tool in Forensic Sciences. Diagnostics (Basel) 2021; 12:diagnostics12010001. [PMID: 35054168 PMCID: PMC8774847 DOI: 10.3390/diagnostics12010001] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 01/16/2023] Open
Abstract
The objective of forensic sciences is to find clues in a crime scene in order to reconstruct the scenario. Classical samples include DNA or fingerprints, but both have inherent limitations and can be uninformative. Another type of sample has emerged recently in the form of the microbiome. Supported by the Human Microbiome Project, the characteristics of the microbial communities provide real potential in forensics. They are highly specific and can be used to differentiate and classify the originating body site of a human biological trace. Skin microbiota is also highly specific and different between individuals, leading to its possibility as an identification tool. By extension, the possibilities of the microbial communities to be deposited on everyday objects has also been explored. Other uses include the determination of the post-mortem interval or the analysis of soil communities. One challenge is that the microbiome changes over time and can be influenced by many environmental and lifestyle factors. This review offers an overview of the main methods and applications to demonstrate the benefit of the microbiome to provide forensically relevant information.
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Affiliation(s)
- Audrey Gouello
- Institut de Recherche Criminelle de la Gendarmerie Nationale, 95037 Cergy-Pontoise, France;
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
| | - Catherine Dunyach-Remy
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
| | | | - Jean-Philippe Lavigne
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
- Correspondence: ; Tel.: +33-466683202
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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.
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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;
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Stability of healthy subgingival microbiome across space and time. Sci Rep 2021; 11:23987. [PMID: 34907334 PMCID: PMC8671439 DOI: 10.1038/s41598-021-03479-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 11/19/2021] [Indexed: 12/12/2022] Open
Abstract
The subgingival microbiome is one of the most stable microbial ecosystems in the human body. Alterations in the subgingival microbiome have been associated with periodontal disease, but their variations over time and between different subgingival sites in periodontally healthy individuals have not been well described. We performed extensive, longitudinal sampling of the subgingival microbiome from five periodontally healthy individuals to define baseline spatial and temporal variations. A total of 251 subgingival samples from 5 subjects were collected over 6–12 months and deep sequenced. The overall microbial diversity and composition differed significantly between individuals. Within each individual, we observed considerable differences in microbiome composition between different subgingival sites. However, for a given site, the microbiome was remarkably stable over time, and this stability was associated with increased microbial diversity but was inversely correlated with the enrichment of putative periodontal pathogens. In contrast to microbiome composition, the predicted functional metagenome was similar across space and time, suggesting that periodontal health is associated with shared gene functions encoded by different microbiome consortia that are individualized. To our knowledge, this is one of the most detailed longitudinal analysis of the healthy subgingival microbiome to date that examined the longitudinal variability of different subgingival sites within individuals. These results suggest that a single measurement of the healthy subgingival microbiome at a given site can provide long term information of the microbial composition and functional potential, but sampling of each site is necessary to define the composition and community structure at individual subgingival sites.
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