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Chaturvedi AK, Vogtmann E, Shi J, Yano Y, Blaser MJ, Bokulich NA, Caporaso JG, Gillison ML, Graubard BI, Hua X, Hullings AG, Kahle L, Knight R, Li S, McLean J, Purandare V, Wan Y, Freedman ND, Abnet CC. Oral Microbiome Profile of the US Population. JAMA Netw Open 2025; 8:e258283. [PMID: 40323603 PMCID: PMC12053784 DOI: 10.1001/jamanetworkopen.2025.8283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Accepted: 03/03/2025] [Indexed: 05/08/2025] Open
Abstract
Importance The oral microbiome likely plays key roles in human health. Yet, population-representative characterizations are lacking. Objective To characterize the composition, diversity, and correlates of the oral microbiome in US adults. Design, Setting, and Participants This cross-sectional study analyzed data from the population-representative National Health and Nutrition Examination Survey (NHANES) from 2009 to 2012. Microbiome data were made publicly available in 2024. NHANES participants were aged 18 to 69 years and provided oral rinse samples in 1 of 2 consecutive NHANES cycles (2009-2010 and 2011-2012). Exposures Demographic, socioeconomic, behavioral, anthropometric, metabolic, and clinical characteristics. Main Outcomes and Measures Oral microbiome measures, characterized through 16S ribosomal RNA gene sequencing, included α diversity (observed amplicon sequence variants [ASVs], Faith phylogenetic diversity, Shannon-Weiner Index, and Simpson Index); β diversity (unweighted UniFrac, weighted UniFrac, and Bray-Curtis dissimilarity); and prevalence and relative abundance at phylum level through genus level. Analyses accounted for the NHANES complex sample design. Results This study included 8237 US adults aged 18 to 69 years, representing 202 314 000 individuals (102 813 000 men [50.8%]; mean [SD] age, 42.3 [14.4] years; 9.3% self-reported as Mexican American, 12.1% as non-Hispanic Black, 64.7% as non-Hispanic White, 5.9% as other Hispanic, and 8.1% as other non-Hispanic individuals). The oral microbiome encompassed 37 bacterial phyla, 99 classes, 212 orders, 446 families, and 1219 genera. Five phyla (Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria, and Fusobacteria) and 6 genera (Veillonella, Streptococcus, Prevotella 7, Rothia, Actinomyces, and Gemella) were present in nearly all US adults (weighted prevalence, >99%). These genera were the most abundant, accounting for 65.7% of total abundance. Observed ASVs showed a quadratic pattern with age (peak at 30 years), were similar by sex, significantly lower among non-Hispanic White individuals, and increased with greater body mass index (BMI), alcohol use, and periodontal disease severity. All covariates together accounted for a modest proportion of oral microbiome variability as measured by β diversity: R2 = 8.7% (95% CI, 8.4%-9.1%) for unweighted UniFrac, R2 = 7.2% (95% CI, 6.6%-7.7%) for weighted UniFrac, and R2 = 6.3% (95% CI, 3.1%-6.7%) for Bray-Curtis matrices. By contrast, relative abundance of a few genera explained a high percentage of variability in β diversity for weighted UniFrac: Aggregatibacter (R2 = 22.4%; 95% CI, 22.1%-22.8%), Lactococcus (R2 = 21.6%; 95% CI, 20.9%-22.3%), and Haemophilus (R2 = 18.4%; 95% CI, 18.1%-18.8%). Prevalence and relative abundance of numerous genera were associated with age, race and ethnicity, smoking, BMI categories, alcohol use, and periodontal disease severity. Conclusions and Relevance This cross-sectional study of the oral microbiome in US adults showed that a few genera were universally present and a different set of genera explained a high percentage of oral microbiome diversity across the population. This comprehensive characterization provides a contemporary reference standard for future studies.
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Affiliation(s)
- Anil K. Chaturvedi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Emily Vogtmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Yukiko Yano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Martin J. Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey
| | | | - J. Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff
| | - Maura L. Gillison
- Department of Thoracic and Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, Texas
| | - Barry I. Graubard
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Autumn G. Hullings
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Lisa Kahle
- Information Management Services, Calverton, Maryland
| | - Rob Knight
- Center for Microbiome Innovation, University of California, San Diego, La Jolla
| | - Shilan Li
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Jody McLean
- National Center for Health Statistics, Centers for Disease Control and Prevention, Hyattsville, Maryland
| | - Vaishnavi Purandare
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Yunhu Wan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Neal D. Freedman
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, Maryland
| | - Christian C. Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
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Govender P, Ghai M. Population-specific differences in the human microbiome: Factors defining the diversity. Gene 2025; 933:148923. [PMID: 39244168 DOI: 10.1016/j.gene.2024.148923] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 08/15/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024]
Abstract
Differences in microbial communities at different body habitats define the microbiome composition of the human body. The gut, oral, skin vaginal fluid and tissue microbiome, are pivotal for human development and immune response and cross talk between these microbiomes is evident. Population studies reveal that various factors, such as host genetics, diet, lifestyle, aging, and geographical location are strongly associated with population-specific microbiome differences. The present review discusses the factors that shape microbiome diversity in humans, and microbiome differences in African, Asian and Caucasian populations. Gut microbiome studies show that microbial species Bacteroides is commonly found in individuals living in Western countries (Caucasian populations), while Prevotella is prevalent in non-Western countries (African and Asian populations). This association is mainly due to the high carbohydrate, high fat diet in western countries in contrast to high fibre, low fat diets in African/ Asian regions. Majority of the microbiome studies focus on the bacteriome component; however, interesting findings reveal that increased bacteriophage richness, which makes up the virome component, correlates with decreased bacterial diversity, and causes microbiome dysbiosis. An increase of Caudovirales (bacteriophages) is associated with a decrease in enteric bacteria in inflammatory bowel diseases. Future microbiome studies should evaluate the interrelation between bacteriome and virome to fully understand their significance in the pathogenesis and progression of human diseases. With ethnic health disparities becoming increasingly apparent, studies need to emphasize on the association of population-specific microbiome differences and human diseases, to develop microbiome-based therapeutics. Additionally, targeted phage therapy is emerging as an attractive alternative to antibiotics for bacterial infections. With rapid rise in microbiome research, focus should be on standardizing protocols, advanced bioinformatics tools, and reducing sequencing platform related biases. Ultimately, integration of multi-omics data (genomics, transcriptomics, proteomics and metabolomics) will lead to precision models for personalized microbiome therapeutics advancement.
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Affiliation(s)
- Priyanka Govender
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa
| | - Meenu Ghai
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, South Africa.
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Wang Q, Wang BY, Williams S, Xie H. Diversity and Characteristics of the Oral Microbiome Associated with Self-Reported Ancestral/Ethnic Groups. Int J Mol Sci 2024; 25:13303. [PMID: 39769067 PMCID: PMC11677810 DOI: 10.3390/ijms252413303] [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: 10/14/2024] [Revised: 12/06/2024] [Accepted: 12/07/2024] [Indexed: 01/11/2025] Open
Abstract
Periodontitis disproportionately affects genetic ancestral/ethnic groups. To characterize the oral microbiome from different genetic ancestral/ethnic groups, we collected 161 dental plaque samples from self-identified African Americans (AAs), Caucasian Americans (CAs), and Hispanic Americans (HAs) with clinical gingival health or biofilm-induced gingivitis on an intact periodontium. DNA was extracted from these samples, and then DNA libraries were prepared and sequenced using an Illumina NovaSeq high-throughput sequencer. We found significant differences in the diversity and abundance of microbial taxa among dental plaque samples of the AA, CA, and HA groups. We also identified unique microbial species in a self-reported ancestral/ethnic group. Moreover, we revealed variations in functional potentials of the oral microbiome among the three ancestral/ethnic groups, with greater diversity and abundance of antibiotic-resistant genes in the oral microbiome and significantly more genes involved in the modification of glycoconjugates and oligo- and polysaccharides in AAs than in CAs and HAs. Our observations suggest that the variations in the oral microbiome associated with ancestral/ethnic backgrounds may directly relate to their virulence potential including their abilities to induce host immune responses and to resist antibiotic treatment. These finding can be a steppingstone for developing precision medicine and personalized periodontal prevention/treatment and for reducing oral health disparities.
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Affiliation(s)
- Qingguo Wang
- School of Medicine, Meharry Medical College, Nashville, TN 37208, USA
| | - Bing-Yan Wang
- School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX 77504, USA;
| | - She’Neka Williams
- School of Dentistry, Meharry Medical College, Nashville, TN 37208, USA;
| | - Hua Xie
- School of Dentistry, Meharry Medical College, Nashville, TN 37208, USA;
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Špiljak B, Ozretić P, Andabak Rogulj A, Lončar Brzak B, Brailo V, Škerlj M, Vidović Juras D. Oral Microbiome Research in Biopsy Samples of Oral Potentially Malignant Disorders and Oral Squamous Cell Carcinoma and Its Challenges. APPLIED SCIENCES 2024; 14:11405. [DOI: 10.3390/app142311405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
Abstract
This study aims to evaluate the potential benefits and challenges of integrating oral microbiome research into the clinical management of oral potentially malignant disorders (OPMD) and oral squamous cell carcinoma (OSCC). The oral microbiome has gained significant attention for its role in the pathogenesis and progression of these conditions, with emerging evidence suggesting its value as a diagnostic and prognostic tool. By critically analyzing current evidence and methodological considerations, this manuscript examines whether microbiome analysis in biopsy samples can aid in the early detection, prognosis, and management of OPMD and OSCC. The complexity and dynamic nature of the oral microbiome require a multifaceted approach to fully understand its clinical utility. Based on this review, we conclude that studying the oral microbiome in this context holds significant promise but also faces notable challenges, including methodological variability and the need for standardization. Ultimately, this manuscript addresses the question, “Should such research be undertaken, given the intricate interactions of various factors and the inherent obstacles involved?”, and also emphasizes the importance of further research to optimize clinical applications and improve patient outcomes.
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Affiliation(s)
- Bruno Špiljak
- Department of Oral Medicine, University of Zagreb School of Dental Medicine, 10000 Zagreb, Croatia
| | - Petar Ozretić
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Ana Andabak Rogulj
- Department of Oral Medicine, University of Zagreb School of Dental Medicine, 10000 Zagreb, Croatia
- Clinical Department of Oral Diseases, Dental Clinic, University Hospital Centre (UHC) Zagreb, 10000 Zagreb, Croatia
| | - Božana Lončar Brzak
- Department of Oral Medicine, University of Zagreb School of Dental Medicine, 10000 Zagreb, Croatia
| | - Vlaho Brailo
- Department of Oral Medicine, University of Zagreb School of Dental Medicine, 10000 Zagreb, Croatia
- Clinical Department of Oral Diseases, Dental Clinic, University Hospital Centre (UHC) Zagreb, 10000 Zagreb, Croatia
| | - Marija Škerlj
- Oncological Cytology Department, Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre Milosrdnice University Hospital Center Zagreb, 10000 Zagreb, Croatia
| | - Danica Vidović Juras
- Department of Oral Medicine, University of Zagreb School of Dental Medicine, 10000 Zagreb, Croatia
- Clinical Department of Oral Diseases, Dental Clinic, University Hospital Centre (UHC) Zagreb, 10000 Zagreb, Croatia
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Chaturvedi AK, Vogtmann E, Shi J, Yano Y, Blaser MJ, Bokulich NA, Caporaso JG, Gillison ML, Graubard BI, Hua X, Hullings AG, Kahle L, Knight R, Li S, McLean J, Purandare V, Wan Y, Freedman ND, Abnet CC. The mouth of America: the oral microbiome profile of the US population. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.12.03.24318415. [PMID: 39677463 PMCID: PMC11643230 DOI: 10.1101/2024.12.03.24318415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2024]
Abstract
Importance The oral microbiome is increasingly recognized to play key roles in human health and disease; yet, population-representative characterizations are lacking. Objective Characterize the composition, diversity, and correlates of the oral microbiome among US adults. Design Cross-sectional population-representative survey. Setting The National Health and Nutrition Examination Survey (NHANES, 2009-2012), a stratified multistage probability sample of the US population. Participants NHANES participants aged 18-69 years (n=8,237, representing 202,314,000 individuals). Exposures Demographic, socioeconomic, behavioral, anthropometric, metabolic, and clinical characteristics. Main outcomes Oral microbiome, characterized through 16S rRNA sequencing. Microbiome metrics were alpha diversity (number of observed Amplicon Sequence Variants [ASV], Faith's Phylogenetic diversity, Shannon-Weiner Index, and Simpson Index); beta diversity (unweighted UniFrac, weighted UniFrac, and Bray-Curtis dissimilarity); and prevalence and relative abundance at taxonomic levels (phylum through genus). Analyses accounted for the NHANES complex sample design. Results Among US adults aged 18-69 years, the oral microbiome encompassed 37 bacterial phyla, 99 classes, 212 orders, 446 families, and 1,219 genera. Five phyla-Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria, and Fusobacteria and six genera-Veillonella, Streptococcus, Prevotella7, Rothia, Actinomyces, and Gemella, were present in nearly all US adults (weighted-prevalence >99%). These genera also were the most abundant, accounting for 65.7% of abundance. Observed ASVs showed a quadratic pattern with age (peak at 30 years), was similar by sex, significantly lower among non-Hispanic White individuals, and increased with higher body mass index (BMI) categories, alcohol use, and periodontal disease severity. All covariates together accounted for a modest proportion of oral microbiome variability, as measured by beta diversity (unweighted UniFrac=8.7%, weighted UniFrac=7.2%, and Bray-Curtis=6.3%). By contrast, relative abundance of a few genera explained a high percentage of variability in beta diversity (weighted UniFrac: Aggregatibacter=22.4%, Lactococcus=21.6%, Haemophilus=18.4%). Prevalence and relative abundance of numerous genera were significantly associated (Bonferroni-corrected Wald-p<0.0002) with age, race and ethnicity, smoking, BMI categories, alcohol use, and periodontal disease severity. Conclusions We provide a contemporary reference standard for the oral microbiome of the US adult population. Our results indicate that a few genera were universally present in US adults and a different set of genera explained a high percentage of oral microbiome diversity across the population.
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Affiliation(s)
- Anil K. Chaturvedi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD., USA
| | - Emily Vogtmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD., USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD., USA
| | - Yukiko Yano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD., USA
| | - Martin J. Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers, Piscataway, NJ, USA
| | | | - J. Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Maura L. Gillison
- Department of Thoracic and Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Barry I. Graubard
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD., USA
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD., USA
| | - Autumn G. Hullings
- Department of Nutrition, University of North Carolina, Chapel Hill, NC, USA
| | - Lisa Kahle
- Information Management Services, Calverton, MD, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Shilan Li
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jody McLean
- National Center for Health Statistics, Centers for Disease Control and Prevention, Hyattsville, MD. USA
| | - Vaishnavi Purandare
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD., USA
| | - Yunhu Wan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD., USA
| | - Neal D. Freedman
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD., USA
| | - Christian C. Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD., USA
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Tan R, Merrill C, Riley CF, Hammer MA, Kenney RT, Riley AA, Li J, Zink AC, Karl ST, Price KM, Sharabidze LK, Rowland SN, Bailey SJ, Stiemsma LT, Pennell A. Acute inorganic nitrate ingestion does not impact oral microbial composition, cognitive function, or high-intensity exercise performance in female team-sport athletes. Eur J Appl Physiol 2024; 124:3511-3525. [PMID: 39017740 PMCID: PMC11568988 DOI: 10.1007/s00421-024-05552-w] [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: 06/10/2024] [Accepted: 06/25/2024] [Indexed: 07/18/2024]
Abstract
The purpose of this study was to investigate the effects of acute nitrate (NO3-)-rich beetroot juice ingestion on explosive and high-intensity exercise performance, oral microbiota composition, and cognitive flexibility (i.e., function), before and after maximal intermittent running exercise. Fifteen women team-sport athletes were assigned in a randomized, double-blind, crossover design to consume concentrated NO3--depleted beetroot juice (PL; 0.1 mmol NO3-) and NO3--rich beetroot juice (BR; 12.0 mmol NO3-) 2.5 h prior to performing a battery of exercise performance tasks and cognitive testing before and after the Yo-Yo intermittent recovery level 1 (YYIR1) running test. Resting plasma [NO3-] and plasma nitrite ([NO2-]) were elevated following BR (P < 0.001). BR did not impact global composition or relative abundance of taxa in the oral microbiome (P > 0.05) or cognitive flexibility before or after exercise (P > 0.05). There was no significant difference in performance during 20-m (PRE, PL: 4.38 ± 0.27 vs. BR: 4.38 ± 0.32 s; POST, PL: 4.45 ± 0.29 vs. BR: 4.43 ± 0.35 s) and 10-m sprints (PRE, PL 2.78 ± 0.15 vs. BR 2.79 ± 0.18 s; POST, PL: 2.82 ± 0.16 vs. BR: 2.81 ± 0.19 s), isokinetic handgrip dynamometry, medicine ball throw, horizontal countermovement jump, or YYIR1 (PL: 355 ± 163 m vs. BR: 368 ± 184 m) between BR and PL (P > 0.05). These findings indicate that acute dietary NO3- may not influence the oral microbiome, explosive and high-intensity exercise performance, or cognitive function in women team-sport athletes.
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Affiliation(s)
- Rachel Tan
- Natural Science Division, Pepperdine University, Malibu, CA, 90263, USA.
| | - Courtney Merrill
- Natural Science Division, Pepperdine University, Malibu, CA, 90263, USA
| | - Chandler F Riley
- Natural Science Division, Pepperdine University, Malibu, CA, 90263, USA
| | - Maya A Hammer
- Natural Science Division, Pepperdine University, Malibu, CA, 90263, USA
| | - Ryan T Kenney
- Natural Science Division, Pepperdine University, Malibu, CA, 90263, USA
| | - Alyssa A Riley
- Natural Science Division, Pepperdine University, Malibu, CA, 90263, USA
| | - Jeffrey Li
- Natural Science Division, Pepperdine University, Malibu, CA, 90263, USA
| | - Alexandra C Zink
- Natural Science Division, Pepperdine University, Malibu, CA, 90263, USA
| | - Sean T Karl
- Natural Science Division, Pepperdine University, Malibu, CA, 90263, USA
| | - Katherine M Price
- Natural Science Division, Pepperdine University, Malibu, CA, 90263, USA
| | - Luka K Sharabidze
- Natural Science Division, Pepperdine University, Malibu, CA, 90263, USA
| | - Samantha N Rowland
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Stephen J Bailey
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Leah T Stiemsma
- Natural Science Division, Pepperdine University, Malibu, CA, 90263, USA
| | - Adam Pennell
- Natural Science Division, Pepperdine University, Malibu, CA, 90263, USA
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Nath S, Zilm P, Jamieson L, Ketagoda DHK, Kapellas K, Weyrich L. Characterising healthy Australian oral microbiomes for 'super donor' selection. J Dent 2024; 151:105435. [PMID: 39461582 DOI: 10.1016/j.jdent.2024.105435] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 10/21/2024] [Accepted: 10/23/2024] [Indexed: 10/29/2024] Open
Abstract
OBJECTIVES Among healthy people, we understand very little about the sociodemographic, lifestyle, and dental hygiene behaviours that shape their oral microbiota. This study investigates how sociodemographic, lifestyle and dental hygiene behaviours shape oral microbiota diversity and composition in an Australian population to better inform healthy oral microbiota donors for Oral Microbiota Transplantation (OMT). METHODS The study comprised 93 healthy adults who underwent comprehensive oral examinations and questionnaires to assess their health status. Participants were excluded if they had any active systemic or oral disease. All completed a questionnaire containing information on socio-economic, lifestyle, behavioural, and oral health factors. Supragingival plaque was collected, and 16S ribosomal RNA (rRNA) amplicon sequencing was used to analyse microbial composition. Associations between the core microbiome, alpha- (within-sample), beta-diversity (between-sample) and an individual's co-variates were tested for statistical significance. A redundancy analysis (RDA), multivariate adonis, differential abundance and correlation analysis were performed to characterise which factors drive the variation in the healthy oral microbiome. RESULTS Streptococcus and Corynebacterium were the most prevalent and abundant genera among healthy Australians. The alpha and beta diversity were higher among unemployed non-Australian-born students who consumed low carbohydrates, fat, and sugar and had not visited the dentist for over 12 months. Additionally, beta diversity was significantly higher among daily flossers who abstained from fluoride treatment and had high salivary pH, although no single factor explained >4 % of the total variation (R2= 0.042). Alloprevotella, Lachnosporacea, and Parvimonas were significantly abundant among non-Australians who did not visit the dentist within a year. The RDA analysis revealed associations between microbiome composition and factors such as high carbohydrate, sugar, and fat consumption, low fibre intake, and regular dental checks among Australian-born individuals. CONCLUSION These findings indicate that alpha and beta diversity of the oral microbiome varied significantly with sociodemographic, lifestyle, and dietary factors, including non-Australian birthplaces, unemployment, diet, and infrequent dental visits. CLINICAL SIGNIFICANCE These findings underscore the importance of considering diverse sociodemographic, lifestyle, and dietary factors in oral health management. Before microbiome transplantations, clinicians should account for individual characteristics that may be beneficial for shaping and maintaining optimal oral microbiome diversity and health.
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Affiliation(s)
- Sonia Nath
- Adelaide Dental School, The University of Adelaide, Adelaide, SA, Australia.
| | - Peter Zilm
- Adelaide Dental School, The University of Adelaide, Adelaide, SA, Australia
| | - Lisa Jamieson
- Adelaide Dental School, The University of Adelaide, Adelaide, SA, Australia
| | | | - Kostas Kapellas
- Adelaide Dental School, The University of Adelaide, Adelaide, SA, Australia
| | - Laura Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia; Department of Anthropology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
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Ruan X, Chen Y, Chauhan A, Howell KS. Stimulation of Saliva Affects the Release of Aroma in Wine: A Study of Microbiota, Biochemistry, and Participant Origin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:25847-25859. [PMID: 39526633 PMCID: PMC11583974 DOI: 10.1021/acs.jafc.4c05116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
Abstract
Saliva influences the release of aroma in the oral cavity. The composition of human saliva varies depending on stimulation and host's origin; however, the compositional differences of saliva and their influences on aroma release have not been fully evaluated. In this study, we recruited 30 healthy adults (15 Australians and 15 Chinese) and collected saliva samples at three stages: before, during, and after stimulation. Salivary samples were characterized by the flow rate, total protein concentration, esterase activity, microbiome composition by full-length 16S rRNA gene sequencing, and the ability to release aroma from wine by headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS). Differences in salivary composition and specific wine volatiles were found between Australian and Chinese participants and among the three stimulation stages. Significant correlations between the relative abundance of 3 bacterial species and 10 wine volatiles were observed. Our results confirm the influence of participant's geographic origin and stimulation on the salivary composition, highlighting the role of salivary components, especially salivary bacteria, on the release of aroma from wine.
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Affiliation(s)
- Xinwei Ruan
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, University of Melbourne, Parkville 3010, Australia
| | - Yipeng Chen
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, University of Melbourne, Parkville 3010, Australia
| | - Aafreen Chauhan
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, University of Melbourne, Parkville 3010, Australia
| | - Kate S Howell
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, University of Melbourne, Parkville 3010, Australia
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Vinerbi E, Morini G, Picozzi C, Tofanelli S. Human Salivary Microbiota Diversity According to Ethnicity, Sex, TRPV1 Variants and Sensitivity to Capsaicin. Int J Mol Sci 2024; 25:11585. [PMID: 39519137 PMCID: PMC11546822 DOI: 10.3390/ijms252111585] [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: 09/30/2024] [Revised: 10/21/2024] [Accepted: 10/25/2024] [Indexed: 11/16/2024] Open
Abstract
The salivary microbiota of Italian and sub-Saharan African individuals was investigated using Nanopore sequencing technology (ONT: Oxford Nanopore Technologies). We detected variations in community composition in relation to endogenous (ethnicity, sex, and diplotypic variants of the TRPV1 gene) and exogenous (sensitivity to capsaicin) factors. The results showed that Prevotella, Haemophilus, Neisseria, Streptococcus, Veillonella, and Rothia are the most abundant genera, in accordance with the literature. However, alpha diversity and frequency spectra differed significantly between DNA pools. The microbiota in African, male TRPV1 bb/ab diplotype and capsaicin low-sensitive DNA pools was more diverse than Italian, female TRPV1 aa diplotype and capsaicin high-sensitive DNA pools. Relative abundance differed at the phylum, genus, and species level.
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Affiliation(s)
- Elena Vinerbi
- Dipartimento di Biologia, Università di Pisa, 56126 Pisa, Italy
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), 09042 Monserrato, Italy
| | | | - Claudia Picozzi
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università Degli Studi di Milano, 20133 Milano, Italy
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10
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Wang Q, Wang BY, Williams S, Xie H. Diversity and characteristics of the oral microbiome influenced by race and ethnicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.07.617037. [PMID: 39416080 PMCID: PMC11482769 DOI: 10.1101/2024.10.07.617037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Periodontitis disproportionately affects racial/ethnic populations. Besides social determinants contributing to disparities in periodontal health, variations of oral microbial communities may also be a key factor influencing oral immune responses. To characterize the oral microbiome from different racial/ethnic populations, we collected 161 dental plaque samples from African Americans (AAs), Caucasian Americans (CAs), and Hispanic Americans (HAs) with clinical gingival health or biofilm-induced gingivitis on an intact periodontium. Using metagenomic sequencing, we found significant difference in diversity and abundance of microbial taxa in the dental plaque samples from AA, CA, and HA groups and unique microbial species that can only be detected in a particular racial/ethnic group. Moreover, we revealed racial/ethnic associated variations in functional potential of the oral microbiome, showing that diversity and abundance of antibiotic resistant genes were greater in the oral microbiome of the AAs than those in CAs or HAs, and that the AAs exhibited higher levels of genes involving in modification of glycoconjugates, oligo- and polysaccharides. These findings indicate more complex and higher virulence potential oral microbiome in AA and HA populations, which likely contributes to higher prevalence of periodontitis in AAs and HAs.
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Affiliation(s)
- Qingguo Wang
- School of Medicine, Meharry Medical College, Nashville, TN, USA
| | - Bing-Yan Wang
- School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Hua Xie
- School of Dentistry, Meharry Medical College, Nashville, TN, USA
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11
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Naumova OY, Dobrynin PV, Khafizova GV, Grigorenko EL. The Association of the Oral Microbiota with Cognitive Functioning in Adolescence. Genes (Basel) 2024; 15:1263. [PMID: 39457387 PMCID: PMC11507344 DOI: 10.3390/genes15101263] [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: 08/30/2024] [Revised: 09/24/2024] [Accepted: 09/25/2024] [Indexed: 10/28/2024] Open
Abstract
Background: A growing body of research supports the role of the microbial communities residing in the digestive system in the host's cognitive functioning. Most of these studies have been focused on the gut microbiome and its association with clinical phenotypes in middle-aged and older adults. There is an insufficiency of population-based research exploring the association of normative cognitive functioning with the microbiome particularly with the oral microbiota. Methods: In this study, using metagenomics and metabolomics, we characterized the salivary microbiome diversity in a sample of 51 males of Hispanic and African American origin aged 12-18 years and explored the associations between the microbiome and the youths' cognitive performance captured with the Kaufman Assessment Battery for Children II (KABC-II). Results: Several bacterial species of the oral microbiota and related metabolic pathways were associated with cognitive function. In particular, we found negative associations between indicators of general intelligence and the relative abundance of Bacteroidetes and Lachnospiraceae and positive associations with Bifidobacteriaceae and Prevotella histicola sp. Among metabolic pathways, the super pathways related to bacterial cell division and GABA metabolism were linked to cognitive function. Conclusions: The results of our work are consistent with the literature reporting on the association between microbiota and cognitive function and support further population work to elucidate the potential for a healthy oral microbiome to improve cognitive health.
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Affiliation(s)
- Oxana Y. Naumova
- Department of Psychology, University of Houston, Houston, TX 77204, USA; (O.Y.N.); (P.V.D.); (G.V.K.)
- Vavilov Institute of General Genetics RAS, Moscow 119991, Russia
| | - Pavel V. Dobrynin
- Department of Psychology, University of Houston, Houston, TX 77204, USA; (O.Y.N.); (P.V.D.); (G.V.K.)
| | - Galina V. Khafizova
- Department of Psychology, University of Houston, Houston, TX 77204, USA; (O.Y.N.); (P.V.D.); (G.V.K.)
| | - Elena L. Grigorenko
- Department of Psychology, University of Houston, Houston, TX 77204, USA; (O.Y.N.); (P.V.D.); (G.V.K.)
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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12
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Demehri S, Vardar S, Godoy C, Lopez JV, Samuel P, Kawai T, Ozga AT. Supragingival Plaque Microbiomes in a Diverse South Florida Population. Microorganisms 2024; 12:1921. [PMID: 39338595 PMCID: PMC11434252 DOI: 10.3390/microorganisms12091921] [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: 07/26/2024] [Revised: 08/31/2024] [Accepted: 09/05/2024] [Indexed: 09/30/2024] Open
Abstract
Trillions of microbes comprise the human oral cavity, collectively acting as another bodily organ. Although research is several decades into the field, there is no consensus on how oral microbiomes differ in underrepresented groups such as Hispanic, Black, and Asian populations living in the United States. Here, using 16S ribosomal RNA sequencing, we examine the bacterial ecology of supragingival plaque from four quadrants of the mouth along with a tongue swab from 26 healthy volunteers from South Florida (131 total sequences after filtering). As an area known to be a unique amalgamation of diverse cultures from across the globe, South Florida allows us to address the question of how supragingival plaque microbes differ across ethnic groups, thus potentially impacting treatment regiments related to oral issues. We assess overall phylogenetic abundance, alpha and beta diversity, and linear discriminate analysis of participants based on sex, ethnicity, sampling location in the mouth, and gingival health. Within this cohort, we find the presence of common phyla such as Firmicutes and common genera such as Streptococcus. Additionally, we find significant differences across sampling locations, sex, and gingival health. This research stresses the need for the continued incorporation of diverse populations within human oral microbiome studies.
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Affiliation(s)
- Sharlene Demehri
- Department of Periodontology, College of Dental Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA; (S.D.); (S.V.)
| | - Saynur Vardar
- Department of Periodontology, College of Dental Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA; (S.D.); (S.V.)
| | - Cristina Godoy
- Department of Oral Science and Translational Research, College of Dental Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
- Department of Public Health, Dr. Kiran C. Patel College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Jose V. Lopez
- Department of Biological Sciences, Halmos College of Arts and Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL 33328, USA (P.S.)
| | - Paisley Samuel
- Department of Biological Sciences, Halmos College of Arts and Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL 33328, USA (P.S.)
| | - Toshihisa Kawai
- Department of Oral Science and Translational Research, College of Dental Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328, USA
| | - Andrew T. Ozga
- Department of Biological Sciences, Halmos College of Arts and Sciences, Guy Harvey Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL 33328, USA (P.S.)
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13
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Fan KD, Ogunrinde E, Wan Z, Li C, Jiang W. Racial Disparities in Plasma Cytokine and Microbiome Profiles. Microorganisms 2024; 12:1453. [PMID: 39065221 PMCID: PMC11279229 DOI: 10.3390/microorganisms12071453] [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: 05/01/2024] [Revised: 07/05/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Many health issues prevalent in African American (AA) populations are associated with chronic inflammation and related health conditions, including autoimmune diseases, infectious diseases, neurologic disorders, metabolic syndromes, and others. The current study aims to understand plasma microbiome translocation as a potential trigger for chronic inflammation. METHODS In this study, 16 Caucasian American (CA) and 22 African American (AA) healthy individuals were recruited. Microbial DNA was isolated from the plasma samples and sequenced via microbial 16S rRNA V3-4 sequencing. The plasma levels of 33 cytokines and chemokines were evaluated. The proinflammatory microbiomes were verified using human THP-1 cells in vitro. RESULTS The plasma levels of IL-6, IL-15, MIP-1α, MIP-1β, and MIP-3α were higher in the AA people, whereas IL-1α and IL-27 were elevated in the CA people. The plasma microbiomes exhibited eight bacterial genera/phyla differentially enriched in the CA and AA people. Given the critical role of IL-6 in chronic inflammation and associated diseases, we identified five bacteria genera significantly associated with IL-6. The abundance of Actinomyces was positively correlated with the plasma IL-6 level (r = 0.41, p = 0.01), while the abundance of Kurthia (r = -0.34, p = 0.04), Noviherbaspirillum (r = -0.34, p = 0.04), Candidatus Protochlamydia (r = -0.36, p = 0.03), and Reyranella (r = -0.39, p = 0.02) was negatively correlated with this. Finally, the THP-1 cells treated with heat-killed bacteria produced higher levels of IL-6 in vitro in response to the Actinomyces species compared to the species in the genus either uncorrelated or negatively correlated with IL-6. CONCLUSIONS This is the first study to report potential blood microbiome translocation as a driver for persistently elevated IL-6 levels in the periphery in healthy AA versus CA people. Understanding the plasma microbiome linked to the IL-6 levels in people with different racial backgrounds is essential to unraveling the therapeutic approaches to improve precision medicine.
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Affiliation(s)
- Kevin D. Fan
- Department of Microbiology & Immunology, Medical University of South Carolina, 173 Ashley Ave. Basic Science Building BS208F, Charleston, SC 29425, USA; (K.D.F.); (Z.W.)
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Zhuang Wan
- Department of Microbiology & Immunology, Medical University of South Carolina, 173 Ashley Ave. Basic Science Building BS208F, Charleston, SC 29425, USA; (K.D.F.); (Z.W.)
| | - Chao Li
- Oklahoma State University Center for Health Sciences, Tulsa, OK 74106, USA;
| | - Wei Jiang
- Department of Microbiology & Immunology, Medical University of South Carolina, 173 Ashley Ave. Basic Science Building BS208F, Charleston, SC 29425, USA; (K.D.F.); (Z.W.)
- Ralph H. Johnson VA Medical Center, Charleston, SC 29401, USA
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14
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Hernández-Cabanyero C, Vonaesch P. Ectopic colonization by oral bacteria as an emerging theme in health and disease. FEMS Microbiol Rev 2024; 48:fuae012. [PMID: 38650052 PMCID: PMC11065354 DOI: 10.1093/femsre/fuae012] [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: 11/10/2023] [Revised: 03/23/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024] Open
Abstract
The number of research papers published on the involvement of the oral microbiota in systemic diseases has grown exponentially over the last 4 years clearly demonstrating the growing interest in this field. Indeed, accumulating evidence highlights the central role of ectopic colonization by oral bacteria in numerous noncommunicable diseases including inflammatory bowel diseases (IBDs), undernutrition, preterm birth, neurological diseases, liver diseases, lung diseases, heart diseases, or colonic cancer. There is thus much interest in understanding the molecular mechanisms that lead to the colonization and maintenance of ectopic oral bacteria. The aim of this review is to summarize and conceptualize the current knowledge about ectopic colonization by oral bacteria, highlight wherever possible the underlying molecular mechanisms and describe its implication in health and disease. The focus lies on the newly discovered molecular mechanisms, showcasing shared pathophysiological mechanisms across different body sites and syndromes and highlighting open questions in the field regarding the pathway from oral microbiota dysbiosis to noncommunicable diseases.
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Affiliation(s)
- Carla Hernández-Cabanyero
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, UNIL-Sorge, 1015 Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, UNIL-Sorge, 1015 Lausanne, Switzerland
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15
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Albandar JM. Disparities and social determinants of periodontal diseases. Periodontol 2000 2024. [PMID: 38217495 DOI: 10.1111/prd.12547] [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: 10/19/2023] [Accepted: 12/08/2023] [Indexed: 01/15/2024]
Abstract
Periodontal diseases are highly prevalent in populations worldwide and are a major global public health problem, with major negative impacts on individuals and communities. This study investigates evidence of disparities in periodontal diseases by age groups, gender, and socioeconomic factors. There is ample evidence that these diseases disproportionally affect poorer and marginalized groups and are closely associated with certain demographics and socioeconomic status. Disparities in periodontal health are associated with social inequalities, which in turn are caused by old age, gender inequality, income and education gaps, access to health care, social class, and other factors. In health care, these factors may result in some individuals receiving better and more professional care compared to others. This study also reviews the potential causes of these disparities and the means to bridge the gap in disease prevalence. Identifying and implementing effective strategies to eliminate inequities among minorities and marginalized groups in oral health status and dental care should be prioritized in populations globally.
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Affiliation(s)
- Jasim M Albandar
- Department of Periodontology and Oral Implantology, Temple University School of Dentistry, Philadelphia, Pennsylvania, USA
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16
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Kim EJ, Kim JS, Park SE, Seo SH, Cho KM, Kwon SJ, Lee MH, Kim JH, Son HS. Association between Mild Cognitive Impairment and Gut Microbiota in Elderly Korean Patients. J Microbiol Biotechnol 2023; 33:1376-1383. [PMID: 37463853 PMCID: PMC10619554 DOI: 10.4014/jmb.2305.05009] [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: 05/10/2023] [Revised: 06/02/2023] [Accepted: 06/11/2023] [Indexed: 07/20/2023]
Abstract
Recent studies have confirmed that gut microbiota differs according to race or country in many diseases, including mild cognitive impairment (MCI) and Alzheimer's disease. However, no study has analyzed the characteristics of Korean MCI patients. This study was performed to observe the association between gut microbiota and MCI in the Korean elderly and to identify potential markers for Korean MCI patients. For this purpose, we collected fecal samples from Korean subjects who were divided into an MCI group (n = 40) and control group (n = 40) for 16S rRNA gene amplicon sequencing. Although no significant difference was observed in the overall microbial community profile, the relative abundance of several genera, including Bacteroides, Prevotella, and Akkermansia, showed significant differences between the two groups. In addition, the relative abundance of Prevotella was negatively correlated with that of Bacteroides (r = 0.733). This study may provide Korean-specific basic data for comparing the characteristics of the gut microbiota between Korean and non-Korean MCI patients.
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Affiliation(s)
- Eun-Ju Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jae-Seong Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Seong-Eun Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | | | | | | | - Mee-Hyun Lee
- College of Korean Medicine, Dongshin University, Naju 58245, Republic of Korea
| | - Jae-Hong Kim
- Department of Acupuncture and Moxibustion Medicine, College of Korean Medicine, Dongshin University, Naju 58245, Republic of Korea
| | - Hong-Seok Son
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
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17
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German R, Marino N, Hemmerich C, Podicheti R, Rusch DB, Stiemsma LT, Gao H, Xuei X, Rockey P, Storniolo AM. Exploring breast tissue microbial composition and the association with breast cancer risk factors. Breast Cancer Res 2023; 25:82. [PMID: 37430354 DOI: 10.1186/s13058-023-01677-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 06/20/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND Microbial dysbiosis has emerged as an important element in the development and progression of various cancers, including breast cancer. However, the microbial composition of the breast from healthy individuals, even relative to risk of developing breast cancer, remains unclear. Here, we performed a comprehensive analysis of the microbiota of the normal breast tissue, which was analyzed in relation to the microbial composition of the tumor and adjacent normal tissue. METHODS The study cohorts included 403 cancer-free women (who donated normal breast tissue cores) and 76 breast cancer patients (who donated tumor and/or adjacent normal tissue samples). Microbiome profiling was obtained by sequencing the nine hypervariable regions of the 16S rRNA gene (V1V2, V2V3, V3V4, V4V5, V5V7, and V7V9). Transcriptome analysis was also performed on 190 normal breast tissue samples. Breast cancer risk score was assessed using the Tyrer-Cuzick risk model. RESULTS The V1V2 amplicon sequencing resulted more suitable for the analysis of the normal breast microbiome and identified Lactobacillaceae (Firmicutes phylum), Acetobacterraceae, and Xanthomonadaceae (both Proteobacteria phylum) as the most abundant families in the normal breast. However, Ralstonia (Proteobacteria phylum) was more abundant in both breast tumors and histologically normal tissues adjacent to malignant tumors. We also conducted a correlation analysis between the microbiome and known breast cancer risk factors. Abundances of the bacterial taxa Acetotobacter aceti, Lactobacillus vini, Lactobacillus paracasei, and Xanthonomas sp. were associated with age (p < 0.0001), racial background (p < 0.0001), and parity (p < 0.0001). Finally, transcriptome analysis of normal breast tissues showed an enrichment in metabolism- and immune-related genes in the tissues with abundant Acetotobacter aceti, Lactobacillus vini, Lactobacillus paracasei, and Xanthonomas sp., whereas the presence of Ralstonia in the normal tissue was linked to dysregulation of genes involved in the carbohydrate metabolic pathway. CONCLUSIONS This study defines the microbial features of normal breast tissue, thus providing a basis to understand cancer-related dysbiosis. Moreover, the findings reveal that lifestyle factors can significantly affect the normal breast microbial composition.
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Affiliation(s)
- Rana German
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, 450 University Blvd, Indianapolis, IN, 46202, USA.
| | - Natascia Marino
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, 450 University Blvd, Indianapolis, IN, 46202, USA.
- Hematology/Oncology Division, Department of Medicine, Indiana University School of Medicine, 980 W. Walnut St, R3-C238, Indianapolis, IN, 46202, USA.
| | - Chris Hemmerich
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Ram Podicheti
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Leah T Stiemsma
- Natural Science Division, Pepperdine University, Malibu, CA, 90263, USA
| | - Hongyu Gao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Xiaoling Xuei
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Pam Rockey
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, 450 University Blvd, Indianapolis, IN, 46202, USA
| | - Anna Maria Storniolo
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, 450 University Blvd, Indianapolis, IN, 46202, USA
- Hematology/Oncology Division, Department of Medicine, Indiana University School of Medicine, 980 W. Walnut St, R3-C238, Indianapolis, IN, 46202, USA
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18
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Yano Y, Vogtmann E, Shreves AH, Weinstein SJ, Black A, Diaz-Mayoral N, Wan Y, Zhou W, Hua X, Dagnall CL, Hutchinson A, Jones K, Hicks BD, Wyatt K, Brotzman M, Gerlanc N, Huang WY, Albert PS, Wentzensen N, Abnet CC. Evaluation of alcohol-free mouthwash for studies of the oral microbiome. PLoS One 2023; 18:e0284956. [PMID: 37104300 PMCID: PMC10138257 DOI: 10.1371/journal.pone.0284956] [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: 01/24/2023] [Accepted: 04/12/2023] [Indexed: 04/28/2023] Open
Abstract
Oral bacteria play important roles in human health and disease. Oral samples collected using ethanol-containing mouthwash are widely used for oral microbiome studies. However, ethanol is flammable and not ideal for transportation/storage in large quantities, and some individuals may avoid ethanol due to the burning sensation or due to various personal, medical, religious, and/or cultural factors. Here, we compared ethanol-free and ethanol-containing mouthwashes using multiple microbiome metrics and assessed the stability of the mouthwash samples stored up to 10 days before processing. Forty volunteers provided oral wash samples collected using ethanol-free and ethanol-containing mouthwashes. From each sample, one aliquot was immediately frozen, one was stored at 4°C for 5 days and frozen, while the third aliquot was stored for 5 days at 4°C and 5 days at ambient temperature to mimic shipping delays and then frozen. DNA was extracted, the 16S rRNA gene V4 region was amplified and sequenced, and bioinformatic processing was performed using QIIME 2. Microbiome metrics measured in the two mouthwash types were very similar, with intraclass correlation coefficients (ICCs) for alpha and beta diversity metrics greater than 0.85. Relative abundances of some taxa were significantly different, but ICCs of the top four most abundant phyla and genera were high (> 0.75) for the comparability of the mouthwashes. Stability during delayed processing was also high for both mouthwashes based on alpha and beta diversity measures and relative abundances of the top four phyla and genera (ICCs ≥ 0.90). These results demonstrate ethanol-free mouthwash performs similarly to ethanol-containing mouthwash for microbial analyses, and both mouthwashes are stable for at least 10 days without freezing prior to laboratory processing. Ethanol-free mouthwash is suitable for collecting and shipping oral wash samples, and these results have important implications for planning future epidemiologic studies of the oral microbiome.
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Affiliation(s)
- Yukiko Yano
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Emily Vogtmann
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Alaina H. Shreves
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Stephanie J. Weinstein
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Amanda Black
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Norma Diaz-Mayoral
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Yunhu Wan
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Weiyin Zhou
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Xing Hua
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle Washington, United States of America
| | - Casey L. Dagnall
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Amy Hutchinson
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Kristine Jones
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Belynda D. Hicks
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Kathleen Wyatt
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Michelle Brotzman
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Nicole Gerlanc
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Wen-Yi Huang
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Paul S. Albert
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Christian C. Abnet
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
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19
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Sami A, Elimairi I, Ryan CA, Stanton C, Patangia D, Ross RP. Altered oral microbiome in Sudanese Toombak smokeless tobacco users carries a newly emerging risk of squamous cell carcinoma development and progression. Sci Rep 2023; 13:6645. [PMID: 37095112 PMCID: PMC10125980 DOI: 10.1038/s41598-023-32892-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/04/2023] [Indexed: 04/26/2023] Open
Abstract
There are an estimated 6-10 million smokeless tobacco (Toombak) users in Sudan, the majority being males. Toombak is known to be a carcinogenic product that is likely to modify the oral microbiome spatiality into a high-risk potential for the development and progression of oral cancer, but previous studies are lacking in this field. Here, we endeavour for the first time the exploration of the oral microbiome in key mucosal areas of the oral cavity and assess the microbiome variations in premalignant and oral squamous cell carcinoma (OSCC) samples from both users and non-users of Toombak. 16S rRNA sequencing was performed on DNA obtained from pooled saliva, oral mucosa and supragingival plaque from 78 Sudanese users and non-users of Toombak, aged between 20 and 70 years. In 32 of the pooled saliva samples, the mycobiome (fungal) environment was analysed through ITS sequencing. Then, 46 formalin-fixed paraffin-embedded samples of premalignant and OSCC samples were collected, and their associated microbiomes sequenced. The oral Sudanese microbiome was found to be enriched in Streptococcaceae, but Staphylococcaceae were significantly more abundant amongst Toombak users. Genera enriched in the oral cavity of Toombak users included Corynebacterium_1 and Cardiobacterium while in non-users, Prevotella, Lactobacillus and Bifidobacterium were prominent. Aspergillus was the most abundant fungus in the mouths of Toombak users with a marked loss of Candida. The genus Corynebacterium_1 was abundant in the buccal, floor of the mouth and saliva microbiomes as well as in oral cancer samples from Toombak users indicating a possible role for this genus in the early stages of oral cancer development. An oral cancer microbiome that favours poor survival and metastasis in those who use Toombak also emerged that includes the genera Stenotrophomonas and Schlegelella. Those utilising Toombak carry an altered oral microbiome that may be an additional risk factor for this products carcinogenicity to the oral structures. These significant microbiome modulations are a newly emerging key driving factor in oral cancer development and progression in Toombak users while it is also shown that Toombak users carry an oral cancer microbiome that may increase the potential for a poorer prognosis.
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Affiliation(s)
- Amel Sami
- APC Microbiome Ireland, School of Microbiology, University College Cork, Cork, T12 YN60, Ireland
- Department of Oral and Maxillofacial Surgery and Oral Medicine, Faculty of Dentistry, National Ribat University, Nile street, 1111, Khartoum, Sudan
| | - Imad Elimairi
- Department of Oral and Maxillofacial Surgery and Oral Medicine, Faculty of Dentistry, National Ribat University, Nile street, 1111, Khartoum, Sudan
| | - C Anthony Ryan
- Department of Paediatrics and Child Health, University College Cork, Cork, T12 DFK4, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, School of Microbiology, University College Cork, Cork, T12 YN60, Ireland.
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, P61 C996, Ireland.
| | - Dhrati Patangia
- APC Microbiome Ireland, School of Microbiology, University College Cork, Cork, T12 YN60, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, School of Microbiology, University College Cork, Cork, T12 YN60, Ireland
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20
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Szalai E, Tajti P, Szabó B, Hegyi P, Czumbel LM, Shojazadeh S, Varga G, Németh O, Keremi B. Daily use of chlorine dioxide effectively treats halitosis: A meta-analysis of randomised controlled trials. PLoS One 2023; 18:e0280377. [PMID: 36634129 PMCID: PMC9836286 DOI: 10.1371/journal.pone.0280377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023] Open
Abstract
OBJECTIVES We aimed to conduct a systematic review on published data in order to investigate the efficacy of mouthwash products containing chlorine dioxide in halitosis. STUDY DESIGN Systematic review and meta-analysis. METHODS Our search was conducted on 14th October 2021. We searched the following electronic databases: MEDLINE, Embase, Scopus, Web of Science, and CENTRAL. We analysed data on adults with halitosis, included only randomised controlled trials and excluded in vitro and animal studies. The interventional groups used chlorine dioxide, and the comparator groups used a placebo or other mouthwash. Our primary outcomes were changes in organoleptic test scores (OLS) and Volatile Sulfur Compound (VSC) levels from baseline to the last available follow-up. RESULTS We found 325 articles in databases. After the selection process, ten articles were eligible for qualitative synthesis, and 7 RCTs with 234 patients were involved in the meta-analysis. Our findings showed a significant improvement in the parameters of the chlorine dioxide group compared to the placebo group in OLS one-day data (mean difference (MD): -0.82; 95% confidence intervals (95% CIs): [-1.04 --0.6]; heterogeneity: I2 = 0%, p = 0.67); and one-week OLS data (MD: -0.24; 95% CIs: [-0.41 --0.07]; I2 = 0%, p = 0.52); and also changes in H2S one-day data (standardised mean difference (SMD): -1.81; 95% CIs: [-2.52 --1.10]); I2 = 73.4%, p = 0.02). CONCLUSION Our data indicate that chlorine dioxide mouthwash may be a good supportive therapy in oral halitosis without known side effects.
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Affiliation(s)
- Eszter Szalai
- Department of Restorative Dentistry and Endodontics, Semmelweis University, Budapest, Hungary
- Centre for Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Péter Tajti
- Centre for Translational Medicine, Semmelweis University, Budapest, Hungary
- Department of Prosthodontics, Semmelweis University, Budapest, Hungary
| | - Bence Szabó
- Centre for Translational Medicine, Semmelweis University, Budapest, Hungary
| | - Péter Hegyi
- Centre for Translational Medicine, Semmelweis University, Budapest, Hungary
- Institute for Translational Medicine, Szentágothai Research Centre, Medical School, University of Pécs, Pécs, Hungary
- Institute of Pancreatic Diseases, Semmelweis University, Budapest, Hungary
| | - László Márk Czumbel
- Centre for Translational Medicine, Semmelweis University, Budapest, Hungary
- Department of Periodontology, Semmelweis University, Budapest, Hungary
| | | | - Gábor Varga
- Centre for Translational Medicine, Semmelweis University, Budapest, Hungary
- Department of Oral Biology, Semmelweis University, Budapest, Hungary
| | - Orsolya Németh
- Centre for Translational Medicine, Semmelweis University, Budapest, Hungary
- Department of Community Dentistry, Semmelweis University, Budapest, Hungary
| | - Beata Keremi
- Department of Restorative Dentistry and Endodontics, Semmelweis University, Budapest, Hungary
- Centre for Translational Medicine, Semmelweis University, Budapest, Hungary
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21
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Wang BY, Cao A, Ho MH, Wilus D, Sheng S, Meng HW, Guerra E, Hong J, Xie H. Identification of microbiological factors associated with periodontal health disparities. Front Cell Infect Microbiol 2023; 13:1137067. [PMID: 36875522 PMCID: PMC9978005 DOI: 10.3389/fcimb.2023.1137067] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/07/2023] [Indexed: 02/18/2023] Open
Abstract
The present study aimed at identifying risk factors associated with periodontitis development and periodontal health disparities with emphasis on differential oral microbiota. The prevalence of periodontitis is recently rising dentate adults in the US, which presents a challenge to oral health and overall health. The risk of developing periodontitis is higher in African Americans (AAs), and Hispanic Americans (HAs) than in Caucasian Americans (CAs). To identify potentially microbiological determinations of periodontal health disparities, we examined the distribution of several potentially beneficial and pathogenic bacteria in the oral cavities of AA, CA, and HA study participants. Dental plaque samples from 340 individuals with intact periodontium were collected prior to any dental treatment, and levels of some key oral bacteria were quantitated using qPCR, and the medical and dental histories of participants were obtained retrospectively from axiUm. Data were analyzed statistically using SAS 9.4, IBM SPSS version 28, and R/RStudio version 4.1.2. Amongst racial/ethnic groups: 1) neighborhood medium incomes were significantly higher in the CA participants than the AA and the HA participants; 2) levels of bleeding on probing (BOP) were higher in the AAs than in the CAs and HAs; 3) Porphyromonas gingivalis levels were higher in the HAs compared to that in the CAs; 4) most P. gingivalis detected in the AAs were the fimA genotype II strain that was significantly associated with higher BOP indexes along with the fimA type IV strain. Our results suggest that socioeconomic disadvantages, higher level of P. gingivalis, and specific types of P. gingivalis fimbriae, particularly type II FimA, contribute to risks for development of periodontitis and periodontal health disparities.
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Affiliation(s)
- Bing-Yan Wang
- School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, United States
- *Correspondence: Bing-Yan Wang, ; Hua Xie,
| | - Aize Cao
- School of Applied Computational Sciences, Meharry Medical College, Nashville, TN, United States
| | - Meng-Hsuan Ho
- School of Dentistry, Meharry Medical College, Nashville, TN, United States
| | - Derek Wilus
- School of Graduate Studies, Meharry Medical College, Nashville, TN, United States
| | - Sally Sheng
- School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Hsiu-Wan Meng
- School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Elissa Guerra
- School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Jianming Hong
- School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Hua Xie
- School of Dentistry, Meharry Medical College, Nashville, TN, United States
- *Correspondence: Bing-Yan Wang, ; Hua Xie,
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22
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Host circadian behaviors exert only weak selective pressure on the gut microbiome under stable conditions but are critical for recovery from antibiotic treatment. PLoS Biol 2022; 20:e3001865. [PMID: 36350921 PMCID: PMC9645659 DOI: 10.1371/journal.pbio.3001865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/03/2022] [Indexed: 11/11/2022] Open
Abstract
The circadian rhythms of hosts dictate an approximately 24 h transformation in the environment experienced by their gut microbiome. The consequences of this cyclic environment on the intestinal microbiota are barely understood and are likely to have medical ramifications. Can daily rhythmicity in the gut act as a selective pressure that shapes the microbial community? Moreover, given that several bacterial species have been reported to exhibit circadian rhythms themselves, we test here whether a rhythmic environment is a selective pressure that favors clock-harboring bacteria that can anticipate and prepare for consistent daily changes in the environment. We observed that the daily rhythmicity of the mouse gut environment is a stabilizing influence that facilitates microbiotal recovery from antibiotic perturbation. The composition of the microbiome recovers to pretreatment conditions when exposed to consistent daily rhythmicity, whereas in hosts whose feeding and activity patterns are temporally disrupted, microbiotal recovery is incomplete and allows potentially unhealthy opportunists to exploit the temporal disarray. Unexpectedly, we found that in the absence of antibiotic perturbation, the gut microbiome is stable to rhythmic versus disrupted feeding and activity patterns. Comparison of our results with those of other studies reveals an intriguing correlation that a stable microbiome may be resilient to one perturbation alone (e.g., disruption of the daily timing of host behavior and feeding), but not to multiple perturbations in combination. However, after a perturbation of the stable microbiome, a regular daily pattern of host behavior/feeding appears to be essential for the microbiome to recover to the original steady state. Given the inconsistency of daily rhythms in modern human life (e.g., shiftwork, social jet-lag, irregular eating habits), these results emphasize the importance of consistent daily rhythmicity to optimal health not only directly to the host, but also indirectly by preserving the host's microbiome in the face of perturbations.
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23
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Chen R, Duan ZY, Duan XH, Chen QH, Zheng J. Progress in research on gut microbiota in ethnic minorities in China and consideration of intervention strategies based on ethnic medicine: A review. Front Cell Infect Microbiol 2022; 12:1027541. [DOI: 10.3389/fcimb.2022.1027541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
One of the variables affecting gut microbiota is ethnicity. There are 56 ethnic subgroups in China, and their intestinal flora differs. A wealth of medical resources has also been produced by the presence of numerous ethnic minorities. In this study, we reviewed the pertinent literature on the intestinal flora of ethnic minorities in China and abroad using the CiteSpace visualization software, and we used bibliometric techniques to find the most widely prescribed medications for preventing and treating endemic diseases in ethnic minorities. Based on the gut microbiology of minority populations, we suggest that by comprehensive development involving literature, experimental, and clinical research, the pharmacological action mechanisms for interventions in endemic diseases can be drawn from ethnic medicine. This point of view has not been discussed before and will offer a fresh perspective on the creation and application of ethnic medications as well as a fresh method for the management of prevalent diseases in ethnic communities.
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24
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Syromyatnikov M, Nesterova E, Gladkikh M, Smirnova Y, Gryaznova M, Popov V. Characteristics of the Gut Bacterial Composition in People of Different Nationalities and Religions. Microorganisms 2022; 10:microorganisms10091866. [PMID: 36144468 PMCID: PMC9501501 DOI: 10.3390/microorganisms10091866] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/25/2022] Open
Abstract
High-throughput sequencing has made it possible to extensively study the human gut microbiota. The links between the human gut microbiome and ethnicity, religion, and race remain rather poorly understood. In this review, data on the relationship between gut microbiota composition and the nationality of people and their religion were generalized. The unique gut microbiome of a healthy European (including Slavic nationality) is characterized by the dominance of the phyla Firmicutes, Bacteroidota, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia. Among the African population, the typical members of the microbiota are Bacteroides and Prevotella. The gut microbiome of Asians is very diverse and rich in members of the genera Prevotella, Bacteroides Lactobacillus, Faecalibacterium, Ruminococcus, Subdoligranulum, Coprococcus, Collinsella, Megasphaera, Bifidobacterium, and Phascolarctobacterium. Among Buddhists and Muslims, the Prevotella enterotype is characteristic of the gut microbiome, while other representatives of religions, including Christians, have the Bacteroides enterotype. Most likely, the gut microbiota of people of different nationalities and religions are influenced by food preferences. The review also considers the influences of pathologies such as obesity, Crohn’s disease, cancer, diabetes, etc., on the bacterial composition of the guts of people of different nationalities.
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Affiliation(s)
- Mikhail Syromyatnikov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
- Correspondence:
| | - Ekaterina Nesterova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Maria Gladkikh
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - Yuliya Smirnova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Mariya Gryaznova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Vasily Popov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
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25
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Li J, George Markowitz RH, Brooks AW, Mallott EK, Leigh BA, Olszewski T, Zare H, Bagheri M, Smith HM, Friese KA, Habibi I, Lawrence WM, Rost CL, Lédeczi Á, Eeds AM, Ferguson JF, Silver HJ, Bordenstein SR. Individuality and ethnicity eclipse a short-term dietary intervention in shaping microbiomes and viromes. PLoS Biol 2022; 20:e3001758. [PMID: 35998206 PMCID: PMC9397868 DOI: 10.1371/journal.pbio.3001758] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 07/14/2022] [Indexed: 11/28/2022] Open
Abstract
Many diseases linked with ethnic health disparities associate with changes in microbial communities in the United States, but the causes and persistence of ethnicity-associated microbiome variation are not understood. For instance, microbiome studies that strictly control for diet across ethnically diverse populations are lacking. Here, we performed multiomic profiling over a 9-day period that included a 4-day controlled vegetarian diet intervention in a defined geographic location across 36 healthy Black and White females of similar age, weight, habitual diets, and health status. We demonstrate that individuality and ethnicity account for roughly 70% to 88% and 2% to 10% of taxonomic variation, respectively, eclipsing the effects a short-term diet intervention in shaping gut and oral microbiomes and gut viromes. Persistent variation between ethnicities occurs for microbial and viral taxa and various metagenomic functions, including several gut KEGG orthologs, oral carbohydrate active enzyme categories, cluster of orthologous groups of proteins, and antibiotic-resistant gene categories. In contrast to the gut and oral microbiome data, the urine and plasma metabolites tend to decouple from ethnicity and more strongly associate with diet. These longitudinal, multiomic profiles paired with a dietary intervention illuminate previously unrecognized associations of ethnicity with metagenomic and viromic features across body sites and cohorts within a single geographic location, highlighting the importance of accounting for human microbiome variation in research, health determinants, and eventual therapies. Trial Registration: ClinicalTrials.gov ClinicalTrials.gov Identifier: NCT03314194.
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Affiliation(s)
- Junhui Li
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Robert H George Markowitz
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Andrew W Brooks
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Stanford University Genetics Department, Stanford University, Palo Alto, California, United States of America
| | - Elizabeth K Mallott
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Brittany A Leigh
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Timothy Olszewski
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Medicine, Vanderbilt University Medical Center, School of Medicine, Nashville, Tennessee, United States of America
| | - Hamid Zare
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Software Integrated Systems, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Minoo Bagheri
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Holly M Smith
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Katie A Friese
- Department of Medicine, Vanderbilt University Medical Center, School of Medicine, Nashville, Tennessee, United States of America
| | - Ismail Habibi
- School for Science and Math at Vanderbilt, Collaborative for STEM Education and Outreach, Department of Teaching and Learning, Vanderbilt University, Nashville, Tennessee, United States of America
| | - William M Lawrence
- School for Science and Math at Vanderbilt, Collaborative for STEM Education and Outreach, Department of Teaching and Learning, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Charlie L Rost
- School for Science and Math at Vanderbilt, Collaborative for STEM Education and Outreach, Department of Teaching and Learning, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Ákos Lédeczi
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Software Integrated Systems, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Angela M Eeds
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- School for Science and Math at Vanderbilt, Collaborative for STEM Education and Outreach, Department of Teaching and Learning, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jane F Ferguson
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Medicine, Vanderbilt University Medical Center, School of Medicine, Nashville, Tennessee, United States of America
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Heidi J Silver
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Medicine, Vanderbilt University Medical Center, School of Medicine, Nashville, Tennessee, United States of America
- Tennessee Valley Healthcare System, Department of Veterans Affairs, Nashville, Tennessee, United States of America
| | - Seth R Bordenstein
- Vanderbilt Microbiome Innovation Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, School of Medicine, Nashville, Tennessee, United States of America
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26
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Díez López C, Montiel González D, Vidaki A, Kayser M. Prediction of Smoking Habits From Class-Imbalanced Saliva Microbiome Data Using Data Augmentation and Machine Learning. Front Microbiol 2022; 13:886201. [PMID: 35928158 PMCID: PMC9343866 DOI: 10.3389/fmicb.2022.886201] [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: 02/28/2022] [Accepted: 06/21/2022] [Indexed: 11/24/2022] Open
Abstract
Human microbiome research is moving from characterization and association studies to translational applications in medical research, clinical diagnostics, and others. One of these applications is the prediction of human traits, where machine learning (ML) methods are often employed, but face practical challenges. Class imbalance in available microbiome data is one of the major problems, which, if unaccounted for, leads to spurious prediction accuracies and limits the classifier's generalization. Here, we investigated the predictability of smoking habits from class-imbalanced saliva microbiome data by combining data augmentation techniques to account for class imbalance with ML methods for prediction. We collected publicly available saliva 16S rRNA gene sequencing data and smoking habit metadata demonstrating a serious class imbalance problem, i.e., 175 current vs. 1,070 non-current smokers. Three data augmentation techniques (synthetic minority over-sampling technique, adaptive synthetic, and tree-based associative data augmentation) were applied together with seven ML methods: logistic regression, k-nearest neighbors, support vector machine with linear and radial kernels, decision trees, random forest, and extreme gradient boosting. K-fold nested cross-validation was used with the different augmented data types and baseline non-augmented data to validate the prediction outcome. Combining data augmentation with ML generally outperformed baseline methods in our dataset. The final prediction model combined tree-based associative data augmentation and support vector machine with linear kernel, and achieved a classification performance expressed as Matthews correlation coefficient of 0.36 and AUC of 0.81. Our method successfully addresses the problem of class imbalance in microbiome data for reliable prediction of smoking habits.
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Affiliation(s)
| | | | | | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
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27
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Herremans KM, Riner AN, Cameron ME, McKinley KL, Triplett EW, Hughes SJ, Trevino JG. The oral microbiome, pancreatic cancer and human diversity in the age of precision medicine. MICROBIOME 2022; 10:93. [PMID: 35701831 PMCID: PMC9199224 DOI: 10.1186/s40168-022-01262-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 03/23/2022] [Indexed: 05/09/2023]
Abstract
Pancreatic cancer is a deadly disease with limited diagnostic and treatment options. Not all populations are affected equally, as disparities exist in pancreatic cancer prevalence, treatment and outcomes. Recently, next-generation sequencing has facilitated a more comprehensive analysis of the human oral microbiome creating opportunity for its application in precision medicine. Oral microbial shifts occur in patients with pancreatic cancer, which may be appreciated years prior to their diagnosis. In addition, pathogenic bacteria common in the oral cavity have been found within pancreatic tumors. Despite these findings, much remains unknown about how or why the oral microbiome differs in patients with pancreatic cancer. As individuals develop, their oral microbiome reflects both their genotype and environmental influences. Genetics, race/ethnicity, smoking, socioeconomics and age affect the composition of the oral microbiota, which may ultimately play a role in pancreatic carcinogenesis. Multiple mechanisms have been proposed to explain the oral dysbiosis found in patients with pancreatic cancer though they have yet to be confirmed. With a better understanding of the interplay between the oral microbiome and pancreatic cancer, improved diagnostic and therapeutic approaches may be implemented to reduce healthcare disparities. Video Abstract.
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Affiliation(s)
- Kelly M. Herremans
- Department of Surgery, University of Florida College of Medicine, P.O. Box 100286, Gainesville, FL 32610 USA
| | - Andrea N. Riner
- Department of Surgery, University of Florida College of Medicine, P.O. Box 100286, Gainesville, FL 32610 USA
| | - Miles E. Cameron
- Department of Surgery, University of Florida College of Medicine, P.O. Box 100286, Gainesville, FL 32610 USA
| | - Kelley L. McKinley
- Department of Microbiology and Cell Science, University of Florida, P.O. Box 110700, Gainesville, FL 32611-0700 USA
| | - Eric W. Triplett
- Department of Microbiology and Cell Science, University of Florida, P.O. Box 110700, Gainesville, FL 32611-0700 USA
| | - Steven J. Hughes
- Department of Surgery, University of Florida College of Medicine, P.O. Box 100286, Gainesville, FL 32610 USA
| | - Jose G. Trevino
- Division of Surgical Oncology, Virginia Commonwealth University, 1200 E Broad St, Richmond, VA 23298-0645 USA
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28
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Tortora SC, Bodiwala VM, Quinn A, Martello LA, Vignesh S. Microbiome and colorectal carcinogenesis: Linked mechanisms and racial differences. World J Gastrointest Oncol 2022; 14:375-395. [PMID: 35317317 PMCID: PMC8918999 DOI: 10.4251/wjgo.v14.i2.375] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/26/2021] [Accepted: 01/14/2022] [Indexed: 02/06/2023] Open
Abstract
Various studies have shown the interplay between the intestinal microbiome, environmental factors, and genetic changes in colorectal cancer (CRC) development. In this review, we highlight the various gut and oral microbiota associated with CRC and colorectal adenomas, and their proposed molecular mechanisms in relation to the processes of “the hallmarks of cancer”, and differences in microbial diversity and abundance between race/ethnicity. Patients with CRC showed increased levels of Bacteroides, Prevotella, Escherichia coli, enterotoxigenic Bacteroides fragilis, Streptococcus gallolyticus, Enterococcus faecalis, Fusobacterium nucleatum (F. nucleatum) and Clostridium difficile. Higher levels of Bacteroides have been found in African American (AA) compared to Caucasian American (CA) patients. Pro-inflammatory bacteria such as F. nucleatum and Enterobacter species were significantly higher in AAs. Also, AA patients have been shown to have decreased microbial diversity compared to CA patients. Some studies have shown that using microbiome profiles in conjunction with certain risk factors such as age, race and body mass index may help predict healthy colon vs one with adenomas or carcinomas. Periodontitis is one of the most common bacterial infections in humans and is more prevalent in Non-Hispanic-Blacks as compared to Non-Hispanic Whites. This condition causes increased systemic inflammation, immune dysregulation, gut microbiota dysbiosis and thereby possibly influencing colorectal carcinogenesis. Periodontal-associated bacteria such as Fusobacterium, Prevotella, Bacteroides and Porphyromonas have been found in CRC tissues and in feces of CRC patients. Therefore, a deeper understanding of the association between oral and gastrointestinal bacterial profile, in addition to identifying prevalent bacteria in patients with CRC and the differences observed in ethnicity/race, may play a pivotal role in predicting incidence, prognosis, and lead to the development of new treatments.
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Affiliation(s)
- Sofia C Tortora
- Department of Medicine and Division of Gastroenterology & Hepatology, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, United States
| | - Vimal M Bodiwala
- Department of Medicine and Division of Gastroenterology & Hepatology, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, United States
| | - Andrew Quinn
- Department of Medicine and Division of Gastroenterology & Hepatology, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, United States
| | - Laura A Martello
- Department of Medicine and Division of Gastroenterology & Hepatology, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, United States
| | - Shivakumar Vignesh
- Department of Medicine and Division of Gastroenterology & Hepatology, SUNY Downstate Health Sciences University, Brooklyn, NY 11203, United States
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29
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Petrick JL, Wilkinson JE, Michaud DS, Cai Q, Gerlovin H, Signorello LB, Wolpin BM, Ruiz-Narváez EA, Long J, Yang Y, Johnson WE, Shu XO, Huttenhower C, Palmer JR. The oral microbiome in relation to pancreatic cancer risk in African Americans. Br J Cancer 2022; 126:287-296. [PMID: 34718358 PMCID: PMC8770575 DOI: 10.1038/s41416-021-01578-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 09/14/2021] [Accepted: 10/01/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND African Americans have the highest pancreatic cancer incidence of any racial/ethnic group in the United States. The oral microbiome was associated with pancreatic cancer risk in a recent study, but no such studies have been conducted in African Americans. Poor oral health, which can be a cause or effect of microbial populations, was associated with an increased risk of pancreatic cancer in a single study of African Americans. METHODS We prospectively investigated the oral microbiome in relation to pancreatic cancer risk among 122 African-American pancreatic cancer cases and 354 controls. DNA was extracted from oral wash samples for metagenomic shotgun sequencing. Alpha and beta diversity of the microbial profiles were calculated. Multivariable conditional logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for associations between microbes and pancreatic cancer risk. RESULTS No associations were observed with alpha or beta diversity, and no individual microbial taxa were differentially abundant between cases and control, after accounting for multiple comparisons. Among never smokers, there were elevated ORs for known oral pathogens: Porphyromonas gingivalis (OR = 1.69, 95% CI: 0.80-3.56), Prevotella intermedia (OR = 1.40, 95% CI: 0.69-2.85), and Tannerella forsythia (OR = 1.36, 95% CI: 0.66-2.77). CONCLUSIONS Previously reported associations between oral taxa and pancreatic cancer were not present in this African-American population overall.
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Affiliation(s)
| | - Jeremy E Wilkinson
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Dominique S Michaud
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Hanna Gerlovin
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Lisa B Signorello
- Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Edward A Ruiz-Narváez
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yaohua Yang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - W Evan Johnson
- Department of Medicine, Division of Computational Biomedicine, Boston University, Boston, MA, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA.
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Balakrishnan B, Selvaraju V, Chen J, Ayine P, Yang L, Ramesh Babu J, Geetha T, Taneja V. Ethnic variability associating gut and oral microbiome with obesity in children. Gut Microbes 2022; 13:1-15. [PMID: 33596768 PMCID: PMC7894456 DOI: 10.1080/19490976.2021.1882926] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Obesity is a growing worldwide problem that generally starts in the early years of life and affects minorities more often than Whites. Thus, there is an urgency to determine factors that can be used as targets as indicators of obesity. In this study, we attempt to generate a profile of gut and oral microbial clades predictive of disease status in African American (AA) and European American (EA) children. 16S rDNA sequencing of the gut and saliva microbial profiles were correlated with salivary amylase, socioeconomic factors (e.g., education and family income), and obesity in both ethnic populations. Gut and oral microbial diversity between AA and EA children showed significant differences in alpha-, beta-, and taxa-level diversity. While gut microbial diversity between obese and non-obese was not evident in EA children, the abundance of gut Klebsiella and Magasphaera was associated with obesity in AA children. In contrast, an abundance of oral Aggregatibacter and Eikenella in obese EA children was observed. These observations suggest an ethnicity-specific association with gut and oral microbial profiles. Socioeconomic factors influenced microbiota in obesity, which were ethnicity dependent, suggesting that specific approaches to confront obesity are required for both populations.
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Affiliation(s)
| | - Vaithinathan Selvaraju
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL, USA
| | - Jun Chen
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Priscilla Ayine
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL, USA
| | - Lu Yang
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Jeganathan Ramesh Babu
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL, USA,Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL, USA
| | - Thangiah Geetha
- Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL, USA,Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL, USA,Thangiah Geetha Department of Nutrition, Dietetics, and Hospitality Management, Auburn University, Auburn, AL, USA
| | - Veena Taneja
- Department of Immunology, Mayo Clinic, Rochester, MN, USA,CONTACT Veena Taneja Department of Immunology, Mayo Clinic, 200 First St SWRochester, MN55905, USA
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31
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Price CA, Jospin G, Brownell K, Eisen JA, Laraia B, Epel ES. Differences in gut microbiome by insulin sensitivity status in Black and White women of the National Growth and Health Study (NGHS): A pilot study. PLoS One 2022; 17:e0259889. [PMID: 35045086 PMCID: PMC8769296 DOI: 10.1371/journal.pone.0259889] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 10/28/2021] [Indexed: 12/22/2022] Open
Abstract
The prevalence of overweight and obesity is greatest amongst Black women in the U.S., contributing to disproportionately higher type 2 diabetes prevalence compared to White women. Insulin resistance, independent of body mass index, tends to be greater in Black compared to White women, yet the mechanisms to explain these differences are not completely understood. The gut microbiome is implicated in the pathophysiology of obesity, insulin resistance and cardiometabolic disease. Only two studies have examined race differences in Black and White women, however none characterizing the gut microbiome based on insulin sensitivity by race and sex. Our objective was to determine if gut microbiome profiles differ between Black and White women and if so, determine if these race differences persisted when accounting for insulin sensitivity status. In a pilot cross-sectional analysis, we measured the relative abundance of bacteria in fecal samples collected from a subset of 168 Black (n = 94) and White (n = 74) women of the National Growth and Health Study (NGHS). We conducted analyses by self-identified race and by race plus insulin sensitivity status (e.g. insulin sensitive versus insulin resistant as determined by HOMA-IR). A greater proportion of Black women were classified as IR (50%) compared to White women (30%). Alpha diversity did not differ by race nor by race and insulin sensitivity status. Beta diversity at the family level was significantly different by race (p = 0.033) and by the combination of race plus insulin sensitivity (p = 0.038). Black women, regardless of insulin sensitivity, had a greater relative abundance of the phylum Actinobacteria (p = 0.003), compared to White women. There was an interaction between race and insulin sensitivity for Verrucomicrobia (p = 0.008), where among those with insulin resistance, Black women had four fold higher abundance than White women. At the family level, we observed significant interactions between race and insulin sensitivity for Lachnospiraceae (p = 0.007) and Clostridiales Family XIII (p = 0.01). Our findings suggest that the gut microbiome, particularly lower beta diversity and greater Actinobacteria, one of the most abundant species, may play an important role in driving cardiometabolic health disparities of Black women, indicating an influence of social and environmental factors on the gut microbiome.
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Affiliation(s)
- Candice A. Price
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Guillaume Jospin
- Genome Center, University of California Davis, Davis, CA, United States of America
| | - Kristy Brownell
- Center for Obesity Assessment, Study and Treatment, University of California, San Francisco, California, United States of America
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Jonathan A. Eisen
- Genome Center, University of California Davis, Davis, CA, United States of America
- Department of Evolution and Ecology, University of California, Davis, CA, United States of America
- Department of Medical Microbiology and Immunology, University of California, Davis, CA, United States of America
| | - Barbara Laraia
- Center for Obesity Assessment, Study and Treatment, University of California, San Francisco, California, United States of America
- School of Public Health, University of California, Berkeley, California, United States of America
| | - Elissa S. Epel
- Department of Psychiatry, University of California, San Francisco, CA, United States of America
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Ahrodia T, Das S, Bakshi S, Das B. Structure, functions, and diversity of the healthy human microbiome. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 191:53-82. [DOI: 10.1016/bs.pmbts.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Chi L, Cheng X, Lin L, Yang T, Sun J, Feng Y, Liang F, Pei Z, Teng W. Porphyromonas gingivalis-Induced Cognitive Impairment Is Associated With Gut Dysbiosis, Neuroinflammation, and Glymphatic Dysfunction. Front Cell Infect Microbiol 2021; 11:755925. [PMID: 34926316 PMCID: PMC8672439 DOI: 10.3389/fcimb.2021.755925] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/22/2021] [Indexed: 12/20/2022] Open
Abstract
Background Periodontal pathogen and gut microbiota are closely associated with the pathogenesis of Alzheimer's disease (AD). Porphyromonas gingivalis (Pg), the keystone periodontal pathogen, can induce cognitive impairment. The gut has a connection and communication with the brain, which is an important aspect of the gut-brain axis (GBA). In the present study, we investigate whether Pg induces cognitive impairment through disturbing the GBA. Methods In this study, Pg was orally administered to mice, three times a week for 1 month. The effects of Pg administration on the gut and brain were evaluated through behaviors, gut microbiota, immune cells, glymphatic pathway clearance, and neuroinflammation. Results Pg induced cognitive impairment and dysbiosis of gut microbiota. The α-diversity parameters did not show significant change after Pg administration. The β-diversity demonstrated that the gut microbiota compositions were different between the Pg-administered and control groups. At the species level, the Pg group displayed a lower abundance of Parabacteroides gordonii and Ruminococcus callidus than the control group, but a higher abundance of Mucispirillum schaedleri. The proportions of lymphocytes in the periphery and myeloid cells infiltrating the brain were increased in Pg-treated animals. In addition, the solute clearance efficiency of the glymphatic system decreased. Neurons in the hippocampus and cortex regions were reduced in mice treated with Pg. Microglia, astrocytes, and apoptotic cells were increased. Furthermore, amyloid plaque appeared in the hippocampus and cortex regions in Pg-treated mice. Conclusions These findings indicate that Pg may play an important role in gut dysbiosis, neuroinflammation, and glymphatic system impairment, which may in turn lead to cognitive impairment.
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Affiliation(s)
- Li Chi
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Xiao Cheng
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Lishan Lin
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou, China
| | - Tao Yang
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Jianbo Sun
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Yiwei Feng
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Fengyin Liang
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou, China
| | - Zhong Pei
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou, China
| | - Wei Teng
- Hospital of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Institute of Stomatological Research, Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
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Chen JW, Wu JH, Chiang WF, Chen YL, Wu WS, Wu LW. Taxonomic and Functional Dysregulation in Salivary Microbiomes During Oral Carcinogenesis. Front Cell Infect Microbiol 2021; 11:663068. [PMID: 34604102 PMCID: PMC8482814 DOI: 10.3389/fcimb.2021.663068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/23/2021] [Indexed: 01/04/2023] Open
Abstract
Exploring microbial community compositions in humans with healthy versus diseased states is crucial to understand the microbe-host interplay associated with the disease progression. Although the relationship between oral cancer and microbiome was previously established, it remained controversial, and yet the ecological characteristics and their responses to oral carcinogenesis have not been well studied. Here, using the bacterial 16S rRNA gene amplicon sequencing along with the in silico function analysis by PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2), we systematically characterized the compositions and the ecological drivers of saliva microbiome in the cohorts of orally healthy, non-recurrent oral verrucous hyperplasia (a pre-cancer lesion), and oral verrucous hyperplasia–associated oral cancer at taxonomic and function levels, and compared them with the re-analysis of publicly available datasets. Diversity analyses showed that microbiome dysbiosis in saliva was significantly linked to oral health status. As oral health deteriorated, the number of core species declined, and metabolic pathways predicted by PICRUSt2 were dysregulated. Partitioned beta-diversity revealed an extremely high species turnover but low function turnover. Functional beta-diversity in saliva microbiome shifted from turnover to nestedness during oral carcinogenesis, which was not observed at taxonomic levels. Correspondingly, the quantitative analysis of stochasticity ratios showed that drivers of microbial composition and functional gene content of saliva microbiomes were primarily governed by the stochastic processes, yet the driver of functional gene content shifted toward deterministic processes as oral cancer developed. Re-analysis of publicly accessible datasets supported not only the distinctive family taxa of Veillonellaceae and Actinomycetaceae present in normal cohorts but also that Flavobacteriaceae and Peptostreptococcaceae as well as the dysregulated metabolic pathways of nucleotides, amino acids, fatty acids, and cell structure were related to oral cancer. Using predicted functional profiles to elucidate the correlations to the oral health status shows superior performance than using taxonomic data among different studies. These findings advance our understanding of the oral ecosystem in relation to oral carcinogenesis and provide a new direction to the development of microbiome-based tools to study the interplay of the oral microbiome, metabolites, and host health.
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Affiliation(s)
- Jiung-Wen Chen
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Fan Chiang
- Department of Oral & Maxillofacial Surgery, Chi-Mei Medical Center, Liouying, Taiwan.,School of Dentistry, National Yang-Ming University, Taipei, Taiwan
| | - Yuh-Ling Chen
- Institute of Oral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Li-Wha Wu
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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35
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Yano Y, Etemadi A, Abnet CC. Microbiome and Cancers of the Esophagus: A Review. Microorganisms 2021; 9:1764. [PMID: 34442842 PMCID: PMC8398938 DOI: 10.3390/microorganisms9081764] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/11/2021] [Accepted: 08/14/2021] [Indexed: 01/04/2023] Open
Abstract
Esophageal cancer (EC) is an aggressive malignant disease ranking amongst the leading causes of cancer deaths in the world. The two main histologic subtypes, esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC), have distinct geographic and temporal patterns and risk factor profiles. Despite decades of research, the factors underlying these geo-temporal patterns are still not fully understood. The human microbiome has recently been implicated in various health conditions and disease, and it is possible that the microbiome may play an important role in the etiology of EC. Although studies of the microbiome and EC are still in their early stages, we review our current understanding of the potential links between ESCC, EAC, and bacterial communities in the oral cavity and esophagus. We also provide a summary of the epidemiology of EC and highlight some key challenges and future directions.
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Affiliation(s)
- Yukiko Yano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (A.E.); (C.C.A.)
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36
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Nasopharyngeal Microbiome Community Composition and Structure Is Associated with Severity of COVID-19 Disease and Breathing Treatment. Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1020014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Viral infections are known to modulate the upper respiratory tract microbiome, but few studies have addressed differences in the nasopharyngeal microbiome following SARS-CoV-2 infection. Using nasopharyngeal swab medical waste samples from 79 confirmed SARS-CoV-2 positive and 20 SARS-CoV-2 negative patients, we assessed microbiome composition with metagenomic sequencing. COVID-19 status and breathing assistive device use was associated with differences in beta diversity, principal component analyses, community composition and abundance of several species. Serratia more frequently appeared in COVID-19 patient samples compared to negative patient samples, and Serratia, Streptococcus, Enterobacter, Veillonella, Prevotella, and Rothia appeared more frequently in samples of those who used breathing assistive devices. Smoking and age were associated with differences in alpha diversity. Cross-sectional differences in the microbiome were apparent with SARS-CoV-2 infection, but longitudinal studies are needed to understand the dynamics of viral and breathing treatment modulation of microbes.
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Minas TZ, Kiely M, Ajao A, Ambs S. An overview of cancer health disparities: new approaches and insights and why they matter. Carcinogenesis 2021; 42:2-13. [PMID: 33185680 PMCID: PMC7717137 DOI: 10.1093/carcin/bgaa121] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/01/2020] [Accepted: 11/06/2020] [Indexed: 12/13/2022] Open
Abstract
Cancer health disparities remain stubbornly entrenched in the US health care system. The Affordable Care Act was legislation to target these disparities in health outcomes. Expanded access to health care, reduction in tobacco use, uptake of other preventive measures and cancer screening, and improved cancer therapies greatly reduced cancer mortality among women and men and underserved communities in this country. Yet, disparities in cancer outcomes remain. Underserved populations continue to experience an excessive cancer burden. This burden is largely explained by health care disparities, lifestyle factors, cultural barriers, and disparate exposures to carcinogens and pathogens, as exemplified by the COVID-19 epidemic. However, research also shows that comorbidities, social stress, ancestral and immunobiological factors, and the microbiome, may contribute to health disparities in cancer risk and survival. Recent studies revealed that comorbid conditions can induce an adverse tumor biology, leading to a more aggressive disease and decreased patient survival. In this review, we will discuss unanswered questions and new opportunities in cancer health disparity research related to comorbid chronic diseases, stress signaling, the immune response, and the microbiome, and what contribution these factors may have as causes of cancer health disparities.
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Affiliation(s)
- Tsion Zewdu Minas
- Laboratory of Human Carcinogenesis, Center of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maeve Kiely
- Laboratory of Human Carcinogenesis, Center of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Anuoluwapo Ajao
- Laboratory of Human Carcinogenesis, Center of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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38
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Zhang X, Hoffman KL, Wei P, Elhor Gbito KY, Joseph R, Li F, Scheet P, Chang S, Petrosino JF, Daniel CR. Baseline Oral Microbiome and All-cancer Incidence in a Cohort of Nonsmoking Mexican American Women. Cancer Prev Res (Phila) 2020; 14:383-392. [PMID: 33277317 DOI: 10.1158/1940-6207.capr-20-0405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/12/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022]
Abstract
Given the increasing evidence that the oral microbiome is involved in obesity, diabetes, and cancer risk, we investigated baseline oral microbiota profiles in relation to all-cancer incidence among nonsmoking women enrolled in a Texas cohort of first- and second-generation immigrants of Mexican origin. We characterized the 16Sv4 rDNA microbiome in oral mouthwash samples collected at baseline from a representative subset of 305 nonsmoking women, ages 20-75 years. We evaluated within- (alpha) and between-sample (beta) diversity by incident cancer status and applied linear discriminant analysis (LDA) effect size analysis to assess differentially abundant taxa. Diversity and candidate taxa in relation to all-cancer incidence were evaluated in multivariable-adjusted Cox regression models. Over 8.8 median years of follow-up, 31 incident cancer cases were identified and verified. Advanced age, greater acculturation, and cardiometabolic risk factors were associated with all-cancer incidence. Higher alpha diversity (age-adjusted P difference < 0.01) and distinct biological communities (P difference = 0.002) were observed by incident cancer status. Each unit increase in the Shannon diversity index yielded >8-fold increase in all-cancer and obesity-related cancer risk [multivariable-adjusted HR (95% confidence interval), 8.11 (3.14-20.94) and 10.72 (3.30-34.84), respectively] with similar findings for the inverse Simpson index. Streptococcus was enriched among women who did not develop cancer, while Fusobacterium, Prevotella, Mogibacterium, Campylobacter, Lachnoanaerobaculum, Dialister, and Atopobium were higher among women who developed cancer (LDA score ≥ 3; q-value < 0.01). This initial study of oral microbiota and overall cancer risk in nonsmoking Mexican American women suggests the readily accessible oral microbiota as a promising biomarker. PREVENTION RELEVANCE: Mexican American women suffer a disproportionate burden of chronic health conditions that increase cancer risk. Few investigations of the microbiome, a key determinant of host health, have been conducted among this group. Oral microbiota profiles may provide early and accessible cancer biomarker data on invasive bacteria or community disruptions.
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Affiliation(s)
- Xiaotao Zhang
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Dan L Duncan Comprehensive Cancer Center, Epidemiology & Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Kristi L Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Peng Wei
- Division of Cancer Prevention and Population Sciences, Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kplola Y Elhor Gbito
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Reji Joseph
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Fangyu Li
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paul Scheet
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shine Chang
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Carrie R Daniel
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Hao Y, Tang C, Du Q, Zhou X, Peng X, Cheng L. Comparative analysis of oral microbiome from Zang and Han populations living at different altitudes. Arch Oral Biol 2020; 121:104986. [PMID: 33246246 DOI: 10.1016/j.archoralbio.2020.104986] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVES The aim of this study was to obtain greater insight into the environmental and genetic factors affecting the oral microbiome. DESIGN To this end, we investigated the oral microbiome composition in Han and Zang populations living at different altitudes. The saliva microbiome in 115 individuals from Zang and Han populations living at different altitudes was analyzed using the 16 s rRNA gene sequencing method on the Illumina MiSeq platform. The dominant species in the oral microbiome were verified by quantitative real-time polymerase chain reaction (qPCR) analysis. RESULTS The Han population, living at an altitude of 500 m, had higher microbiome diversity than the Zang population living at altitudes of 3000-4000 m. People living at 3000 m had a higher relative abundance of Leptothrix genus, but people living at 500 m had a higher relative abundance of Capnocytophaga genus according to Lefse difference analysis (P < 0.05). Compared to the Zang population, the Han population had higher relative abundances of Porphyromonas and Treponema genus organisms, especially Porphyromonas (P < 0.001). qPCR analysis confirmed that people living at high altitudes had the highest relative abundance of Porphyromonas gingivalis (P < 0.01). CONCLUSIONS This study showed that both genetics and the environment had significant influences on the oral microbiome composition. The study proposed a meaningful research direction to explore the relationship between different ethnic and altitude groups and oral diseases, such as periodontal diseases.
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Affiliation(s)
- Yu Hao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cariology and Endodontics West China School of Stomatology, Sichuan University, Chengdu 610041, China.
| | - Can Tang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cariology and Endodontics West China School of Stomatology, Sichuan University, Chengdu 610041, China; Department of Stomatology, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu 610041, China.
| | - Qilian Du
- Department of Stomatology, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region, Chengdu 610041, China.
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cariology and Endodontics West China School of Stomatology, Sichuan University, Chengdu 610041, China.
| | - Xian Peng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cariology and Endodontics West China School of Stomatology, Sichuan University, Chengdu 610041, China.
| | - Lei Cheng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Dept. of Cariology and Endodontics West China School of Stomatology, Sichuan University, Chengdu 610041, China.
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Abstract
Despite widely used preventive measures such as sealant programs to control caries prevalence, disparities are seen among ethnic groups. Supragingival plaque harbors hundreds of bacterial species, playing a significant role in oral health and disease. It is unknown whether the ethnic variation influences the supragingival microbiota in children. In our study, variations in microbiota of the supragingival plaque was investigated from 96 children between 6 and 11 years old in four ethnic groups (African American, Burmese, Caucasian, and Hispanic) from the same geographic location by 16S rRNA gene sequencing. We found that the microbial alpha and beta diversity of supragingival microbiota significantly differed between ethnic groups. The supragingival plaque microbiota had the most complex microbial community in Burmese children. Within-group microbiota similarity in Burmese or Caucasian children was significantly higher than between-groups similarity. We identified seven ethnic group-specific bacterial taxa after adjusting for dental plaque index, decayed missing filled teeth (DMFT) and the frequency of brushing. Children with high plaque index and high DMFT values were more similar to each other in the overall microbial community, compared to low plaque index or low DMFT groups in which inter-subject variation is high. Several bacterial taxa associated with high plaque index or high DMFT were ethnic group-specific. These results demonstrated that supragingival microbiota differed among ethnicity groups in children.
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Byrd DA, Carson TL, Williams F, Vogtmann E. Elucidating the role of the gastrointestinal microbiota in racial and ethnic health disparities. Genome Biol 2020; 21:192. [PMID: 32746938 PMCID: PMC7397581 DOI: 10.1186/s13059-020-02117-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Doratha A Byrd
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tiffany L Carson
- Division of Preventive Medicine, Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.,O'Neal Comprehensive Cancer Center at UAB, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Faustine Williams
- Division of Intramural Research, National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Emily Vogtmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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Reply to Kenyon, "Are Differences in the Oral Microbiome Due to Ancestry or Socioeconomics?". mSystems 2020; 5:5/2/e00891-19. [PMID: 32156801 PMCID: PMC7065519 DOI: 10.1128/msystems.00891-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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