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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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Aminu S, Ascandari A, Laamarti M, Safdi NEH, El Allali A, Daoud R. Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities. Crit Rev Microbiol 2023:1-25. [PMID: 38006569 DOI: 10.1080/1040841x.2023.2282447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/06/2023] [Indexed: 11/27/2023]
Abstract
The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments.
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Affiliation(s)
- Suleiman Aminu
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - AbdulAziz Ascandari
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Meriem Laamarti
- Faculty of Medical Sciences, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Nour El Houda Safdi
- AgroBioSciences Program, College for Sustainable Agriculture and Environmental Science, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Achraf El Allali
- Bioinformatics Laboratory, College of Computing, University Mohammed VI Polytechnic, Ben Guerir, Morocco
| | - Rachid Daoud
- Chemical and Biochemical Sciences-Green Process Engineering, University Mohammed VI Polytechnic, Ben Guerir, Morocco
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Khelaifia S, Virginie P, Belkacemi S, Tassery H, Terrer E, Aboudharam G. Culturing the Human Oral Microbiota, Updating Methodologies and Cultivation Techniques. Microorganisms 2023; 11:microorganisms11040836. [PMID: 37110259 PMCID: PMC10143722 DOI: 10.3390/microorganisms11040836] [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: 01/24/2023] [Revised: 03/16/2023] [Accepted: 03/23/2023] [Indexed: 04/29/2023] Open
Abstract
Recent years have been marked by a paradigm shift in the study of the human microbiota, with a re-emergence of culture-dependent approaches. Numerous studies have been devoted to the human microbiota, while studies on the oral microbiota still remain limited. Indeed, various techniques described in the literature may enable an exhaustive study of the microbial composition of a complex ecosystem. In this article, we report different methodologies and culture media described in the literature that can be applied to study the oral microbiota by culture. We report on specific methodologies for targeted culture and specific culture techniques and selection methodologies for cultivating members of the three kingdoms of life commonly found in the human oral cavity, namely, eukaryota, bacteria and archaea. This bibliographic review aims to bring together the various techniques described in the literature, enabling a comprehensive study of the oral microbiota in order to demonstrate its involvement in oral health and diseases.
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Affiliation(s)
- Saber Khelaifia
- Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
- Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Pilliol Virginie
- Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
- Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Souad Belkacemi
- Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Herve Tassery
- Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Elodie Terrer
- Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
- Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
| | - Gérard Aboudharam
- Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Univ, IRD, MEPHI, AP-HM, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
- Ecole de Médecine Dentaire, 27 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France
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Johnstone KF, Herzberg MC. Antimicrobial peptides: Defending the mucosal epithelial barrier. FRONTIERS IN ORAL HEALTH 2022; 3:958480. [PMID: 35979535 PMCID: PMC9376388 DOI: 10.3389/froh.2022.958480] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
The recent epidemic caused by aerosolized SARS-CoV-2 virus illustrates the importance and vulnerability of the mucosal epithelial barrier against infection. Antimicrobial proteins and peptides (AMPs) are key to the epithelial barrier, providing immunity against microbes. In primitive life forms, AMPs protect the integument and the gut against pathogenic microbes. AMPs have also evolved in humans and other mammals to enhance newer, complex innate and adaptive immunity to favor the persistence of commensals over pathogenic microbes. The canonical AMPs are helictical peptides that form lethal pores in microbial membranes. In higher life forms, this type of AMP is exemplified by the defensin family of AMPs. In epithelial tissues, defensins, and calprotectin (complex of S100A8 and S100A9) have evolved to work cooperatively. The mechanisms of action differ. Unlike defensins, calprotectin sequesters essential trace metals from microbes, which inhibits growth. This review focuses on defensins and calprotectin as AMPs that appear to work cooperatively to fortify the epithelial barrier against infection. The antimicrobial spectrum is broad with overlap between the two AMPs. In mice, experimental models highlight the contribution of both AMPs to candidiasis as a fungal infection and periodontitis resulting from bacterial dysbiosis. These AMPs appear to contribute to innate immunity in humans, protecting the commensal microflora and restricting the emergence of pathobionts and pathogens. A striking example in human innate immunity is that elevated serum calprotectin protects against neonatal sepsis. Calprotectin is also remarkable because of functional differences when localized in epithelial and neutrophil cytoplasm or released into the extracellular environment. In the cytoplasm, calprotectin appears to protect against invasive pathogens. Extracellularly, calprotectin can engage pathogen-recognition receptors to activate innate immune and proinflammatory mechanisms. In inflamed epithelial and other tissue spaces, calprotectin, DNA, and histones are released from degranulated neutrophils to form insoluble antimicrobial barriers termed neutrophil extracellular traps. Hence, calprotectin and other AMPs use several strategies to provide microbial control and stimulate innate immunity.
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Affiliation(s)
| | - Mark C. Herzberg
- Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, United States
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