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Narayanan A, Kieri O, Vesterbacka J, Manoharan L, Chen P, Ghorbani M, Ljunggren HG, Sällberg Chen M, Aleman S, Sönnerborg A, Ray S, Nowak P. Exploring the interplay between antiretroviral therapy and the gut-oral microbiome axis in people living with HIV. Sci Rep 2024; 14:17820. [PMID: 39090139 PMCID: PMC11294597 DOI: 10.1038/s41598-024-68479-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024] Open
Abstract
The gut and oral microbiome is altered in people living with HIV (PLWH). While antiretroviral treatment (ART) is pivotal in restoring immune function in PLWH, several studies have identified an association between specific antiretrovirals, particularly integrase inhibitors (INSTI), and weight gain. In our study, we explored the differences in the oral and gut microbiota of PLWH under different ART regimens, and its correlation to Body Mass Index (BMI). Fecal and salivary samples were collected from PLWH (n = 69) and healthy controls (HC, n = 80). We performed taxonomy analysis to determine the microbial composition and relationship between microbial abundance and ART regimens, BMI, CD4+T-cell count, CD4/CD8 ratio, and ART duration. PLWH showed significantly lower richness compared to HC in both the oral and gut environment. The gut microbiome composition of INSTI-treated individuals was enriched with Faecalibacterium and Bifidobacterium, whereas non-nucleotide reverse transcriptase inhibitor (NNRTI)-treated individuals were enriched with Gordonibacter, Megasphaera, and Staphylococcus. In the oral microenvironment, Veillonella was significantly more abundant in INSTI-treated individuals and Fusobacterium and Alloprevotella in the NNRTI-treated individuals. Furthermore, Bifidobacterium and Dorea were enriched in gut milieu of PLWH with high BMI. Collectively, our findings identify distinct microbial profiles, which are associated with different ART regimens and BMI in PLWH on successful ART, thereby highlighting significant effects of specific antiretrovirals on the microbiome.
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Affiliation(s)
- Aswathy Narayanan
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden.
| | - Oscar Kieri
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Jan Vesterbacka
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Lokeshwaran Manoharan
- Department of Laboratory Medicine, National Bioinformatics Infrastructure Sweden (NBIS), SciLife, Lund University, Lund, Sweden
| | - Puran Chen
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mahin Ghorbani
- Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Pathology, ANA Futura, Karolinska Institutet, 141 52, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Margaret Sällberg Chen
- Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Pathology, ANA Futura, Karolinska Institutet, 141 52, Stockholm, Sweden
| | - Soo Aleman
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anders Sönnerborg
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, 141 52, Stockholm, Sweden
| | - Shilpa Ray
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden.
| | - Piotr Nowak
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
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Regueira-Iglesias A, Suárez-Rodríguez B, Blanco-Pintos T, Relvas M, Alonso-Sampedro M, Balsa-Castro C, Tomás I. The salivary microbiome as a diagnostic biomarker of periodontitis: a 16S multi-batch study before and after the removal of batch effects. Front Cell Infect Microbiol 2024; 14:1405699. [PMID: 39071165 PMCID: PMC11272481 DOI: 10.3389/fcimb.2024.1405699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 06/17/2024] [Indexed: 07/30/2024] Open
Abstract
Introduction Microbiome-based clinical applications that improve diagnosis related to oral health are of great interest to precision dentistry. Predictive studies on the salivary microbiome are scarce and of low methodological quality (low sample sizes, lack of biological heterogeneity, and absence of a validation process). None of them evaluates the impact of confounding factors as batch effects (BEs). This is the first 16S multi-batch study to analyze the salivary microbiome at the amplicon sequence variant (ASV) level in terms of differential abundance and machine learning models. This is done in periodontally healthy and periodontitis patients before and after removing BEs. Methods Saliva was collected from 124 patients (50 healthy, 74 periodontitis) in our setting. Sequencing of the V3-V4 16S rRNA gene region was performed in Illumina MiSeq. In parallel, searches were conducted on four databases to identify previous Illumina V3-V4 sequencing studies on the salivary microbiome. Investigations that met predefined criteria were included in the analysis, and the own and external sequences were processed using the same bioinformatics protocol. The statistical analysis was performed in the R-Bioconductor environment. Results The elimination of BEs reduced the number of ASVs with differential abundance between the groups by approximately one-third (Before=265; After=190). Before removing BEs, the model constructed using all study samples (796) comprised 16 ASVs (0.16%) and had an area under the curve (AUC) of 0.944, sensitivity of 90.73%, and specificity of 87.16%. The model built using two-thirds of the specimens (training=531) comprised 35 ASVs (0.36%) and had an AUC of 0.955, sensitivity of 86.54%, and specificity of 90.06% after being validated in the remaining one-third (test=265). After removing BEs, the models required more ASVs (all samples=200-2.03%; training=100-1.01%) to obtain slightly lower AUC (all=0.935; test=0.947), lower sensitivity (all=81.79%; test=78.85%), and similar specificity (all=91.51%; test=90.68%). Conclusions The removal of BEs controls false positive ASVs in the differential abundance analysis. However, their elimination implies a significantly larger number of predictor taxa to achieve optimal performance, creating less robust classifiers. As all the provided models can accurately discriminate health from periodontitis, implying good/excellent sensitivities/specificities, the salivary microbiome demonstrates potential clinical applicability as a precision diagnostic tool for periodontitis.
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Affiliation(s)
- Alba Regueira-Iglesias
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Berta Suárez-Rodríguez
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Triana Blanco-Pintos
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Marta Relvas
- Instituto Universitário de Ciências da Saúde, Cooperativa de Ensino Superior Politécnico e Universitário (IUCS-CESPU), Unidade de Investigação em Patologia e Reabilitação Oral (UNIPRO), Gandra, Portugal
| | - Manuela Alonso-Sampedro
- Department of Internal Medicine and Clinical Epidemiology, Instituto de Investigación Sanitaria de Santiago (IDIS), Complejo Hospitalario Universitario, Santiago de Compostela, Spain
| | - Carlos Balsa-Castro
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Inmaculada Tomás
- Oral Sciences Research Group, Special Needs Unit, Department of Surgery and Medical-Surgical Specialties, School of Medicine and Dentistry, Instituto de Investigación Sanitaria de Santiago (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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Ramos Peña DE, Pillet S, Grupioni Lourenço A, Pozzetto B, Bourlet T, Motta ACF. Human immunodeficiency virus and oral microbiota: mutual influence on the establishment of a viral gingival reservoir in individuals under antiretroviral therapy. Front Cell Infect Microbiol 2024; 14:1364002. [PMID: 38660490 PMCID: PMC11039817 DOI: 10.3389/fcimb.2024.1364002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/26/2024] [Indexed: 04/26/2024] Open
Abstract
The role of the oral microbiota in the overall health and in systemic diseases has gained more importance in the recent years, mainly due to the systemic effects that are mediated by the chronic inflammation caused by oral diseases, such as periodontitis, through the microbial communities of the mouth. The chronic infection by the human immunodeficiency virus (HIV) interacts at the tissue level (e.g. gut, genital tract, brain) to create reservoirs; the modulation of the gut microbiota by HIV infection is a good example of these interactions. The purpose of the present review is to assess the state of knowledge on the oral microbiota (microbiome, mycobiome and virome) of HIV-infected patients in comparison to that of HIV-negative individuals and to discuss the reciprocal influence of HIV infection and oral microbiota in patients with periodontitis on the potential establishment of a viral gingival reservoir. The influence of different clinical and biological parameters are reviewed including age, immune and viral status, potent antiretroviral therapies, smoking, infection of the airway and viral coinfections, all factors that can modulate the oral microbiota during HIV infection. The analysis of the literature proposed in this review indicates that the comparisons of the available studies are difficult due to their great heterogeneity. However, some important findings emerge: (i) the oral microbiota is less influenced than that of the gut during HIV infection, although some recurrent changes in the microbiome are identified in many studies; (ii) severe immunosuppression is correlated with altered microbiota and potent antiretroviral therapies correct partially these modifications; (iii) periodontitis constitutes a major factor of dysbiosis, which is exacerbated in HIV-infected patients; its pathogenesis can be described as a reciprocal reinforcement of the two conditions, where the local dysbiosis present in the periodontal pocket leads to inflammation, bacterial translocation and destruction of the supporting tissues, which in turn enhances an inflammatory environment that perpetuates the periodontitis cycle. With the objective of curing viral reservoirs of HIV-infected patients in the future years, it appears important to develop further researches aimed at defining whether the inflamed gingiva can serve of viral reservoir in HIV-infected patients with periodontitis.
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Affiliation(s)
- Diana Estefania Ramos Peña
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
- Team Mucosal Immunity and Pathogen Agents (GIMAP), Centre International de Recherche en Infectiologie (CIRI), Institut national de la santé et de la recherche médicale (INSERM) U1111, Ecole Nationale Supérieure de Lyon, Université de Lyon, Université de Saint-Etienne, Saint-Etienne, France
| | - Sylvie Pillet
- Team Mucosal Immunity and Pathogen Agents (GIMAP), Centre International de Recherche en Infectiologie (CIRI), Institut national de la santé et de la recherche médicale (INSERM) U1111, Ecole Nationale Supérieure de Lyon, Université de Lyon, Université de Saint-Etienne, Saint-Etienne, France
- Department of Infectious Agents and Hygiene, University-Hospital of Saint-Etienne, Saint-Etienne, France
| | - Alan Grupioni Lourenço
- Department of Basic and Oral Biology, Ribeirão Preto School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Bruno Pozzetto
- Team Mucosal Immunity and Pathogen Agents (GIMAP), Centre International de Recherche en Infectiologie (CIRI), Institut national de la santé et de la recherche médicale (INSERM) U1111, Ecole Nationale Supérieure de Lyon, Université de Lyon, Université de Saint-Etienne, Saint-Etienne, France
- Department of Infectious Agents and Hygiene, University-Hospital of Saint-Etienne, Saint-Etienne, France
| | - Thomas Bourlet
- Team Mucosal Immunity and Pathogen Agents (GIMAP), Centre International de Recherche en Infectiologie (CIRI), Institut national de la santé et de la recherche médicale (INSERM) U1111, Ecole Nationale Supérieure de Lyon, Université de Lyon, Université de Saint-Etienne, Saint-Etienne, France
- Department of Infectious Agents and Hygiene, University-Hospital of Saint-Etienne, Saint-Etienne, France
| | - Ana Carolina Fragoso Motta
- Department of Stomatology, Public Health and Forensic Dentistry, Ribeirão Preto School of Dentistry, University of São Paulo, São Paulo, Brazil
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Wadhwa S, Finn TR, Kister K, Matsumura S, Levit M, Cantos A, Shah J, Bohn B, Lalla E, Grbic JT, Demmer RT, Yin MT. Postmenopausal women with HIV have increased tooth loss. BMC Oral Health 2024; 24:52. [PMID: 38191383 PMCID: PMC10775528 DOI: 10.1186/s12903-023-03744-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND With effective antiretroviral therapy, people with HIV (PWH) are living longer and aging; the majority of PWH in the United States are now over the age of 50 and in women have gone through the menopause transition. Menopause potentiates skeletal bone loss at the spine, hip, and radius in PWH. The alveolar bone which surronds the teeth is different than long bones because it is derived from the neural crest. However, few studies have assessed the oral health and alveolar bone in middle aged and older women with HIV. Therefore, the objective of this study was to evaluate periodontal disease and alveolar bone microarchitecture in postmenopausal women with HIV. METHODS 135 self-reported postmenopausal women were recruited (59 HIV-, 76 HIV + on combination antiretroviral therapy with virological suppression) from a single academic center. The following parameters were measured: cytokine levels (IFN-γ, TNF-α, IL-1β, IL-2, IL-5, IL-6, IL-7, IL-8, IL-10, IL-12p70, IL-13, IL-17 A, OPG, and RANKL) in gingival crevicular fluid, bleeding on probing, probing depth, clinical attachment loss, number of teeth present, alveolar crestal height, and alveolar bone microarchitecture. RESULTS The mean age of participants was 57.04+/-6.25 years and a greater proportion of women with HIV were black/African American (HIV + 68.42%, HIV- 23.73%; p < 0.001). There was no significant difference in bleeding on probing (p = 0.17) and attachment loss (p = 0.39) between women who were HIV infected vs. HIV uninfected. Women with HIV had significantly higher RANKL expression in Gingival Crevicular Fluid (HIV + 3.80+/-3.19 pg/ul, HIV- 1.29+/-2.14 pg/ul ; p < 0.001), fewer teeth present (HIV + 17.75+/-7.62, HIV- 22.79+/-5.70; p < 0.001), ), lower trabecular number (HIV + 0.08+/-0.01, HIV- 0.09+/-0.02; p = 0.004) and greater trabecular separation (HIV + 9.23+/-3.11, HIV- 7.99+/-3.23; p = 0.04) compared to women without HIV that remained significant in multivariate logistic regression analysis in a sub-cohort after adjusting for age, race/ethnicity, smoking status, and diabetes. CONCLUSION Postmenopausal women with HIV have deterioration of the alveolar trabecular bone microarchitecture that may contribute to greater tooth loss.
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Affiliation(s)
- Sunil Wadhwa
- Division of Orthodontics, Columbia University College of Dental Medicine, New York, NY, USA.
| | - Taylor R Finn
- Division of Orthodontics, Columbia University College of Dental Medicine, New York, NY, USA
| | - Karolina Kister
- Division of Orthodontics, Columbia University College of Dental Medicine, New York, NY, USA
| | - Satoko Matsumura
- Division of Oral and Maxillofacial Radiology, Columbia University College of Dental Medicine, New York, NY, USA
| | - Michael Levit
- Division of Orthodontics, Columbia University College of Dental Medicine, New York, NY, USA
| | - Anyelina Cantos
- Division of Infectious Diseases, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Jayesh Shah
- Division of Infectious Diseases, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Bruno Bohn
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Evanthia Lalla
- Division of Periodontics, Columbia University College of Dental Medicine, New York, NY, USA
| | - John T Grbic
- Division of Foundational Sciences, Columbia University College of Dental Medicine, New York, NY, USA
| | - Ryan T Demmer
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Michael T Yin
- Division of Infectious Diseases, Columbia University College of Physicians and Surgeons, New York, NY, USA
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O'Connell LM, Mann AE, Osagie E, Akhigbe P, Blouin T, Soule A, Obuekwe O, Omoigberale A, Burne RA, Coker MO, Richards VP. Supragingival mycobiome of HIV-exposed-but-uninfected children reflects a stronger correlation with caries-free-associated taxa compared to HIV-infected or uninfected children. Microbiol Spectr 2023; 11:e0149123. [PMID: 37874172 PMCID: PMC10715047 DOI: 10.1128/spectrum.01491-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/15/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE Globally, caries is among the most frequent chronic childhood disease, and the fungal component of the microbial community responsible is poorly studied despite evidence that fungi contribute to increased acid production exacerbating enamel demineralization. HIV infection is another global health crisis. Perinatal HIV exposure with infection are caries risk factors; however, the caries experience in the context of perinatal HIV exposure without infection is less clear. Using high-throughput amplicon sequencing, we find taxonomic differences that become pronounced during late-stage caries. Notably, we show a stronger correlation with health-associated taxa for HIV-exposed-but-uninfected children when compared to unexposed and uninfected children. This aligns with a lower incidence of caries in primary teeth at age 6 or less for exposed yet uninfected children. Ultimately, these findings could contribute to improved risk assessment, intervention, and prevention strategies such as biofilm disruption and the informed design of pro-, pre-, and synbiotic oral therapies.
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Affiliation(s)
- Lauren M. O'Connell
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Allison E. Mann
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Esosa Osagie
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Paul Akhigbe
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Thomas Blouin
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Ashlyn Soule
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Ozoemene Obuekwe
- Department of Oral and Maxillofacial Surgery, University of Benin Teaching Hospital, Benin, Edo State, Nigeria
| | - Augustine Omoigberale
- Department of Child Health, University of Benin Teaching Hospital, Benin, Edo State, Nigeria
| | - Robert A. Burne
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Modupe O. Coker
- Institute of Human Virology Nigeria, Abuja, Nigeria
- Department of Oral Biology, School of Dental Medicine, Rutgers University, Newark, New Jersey, USA
| | - Vincent P. Richards
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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Li S, Su B, Wu H, He Q, Zhang T. Integrated analysis of gut and oral microbiome in men who have sex with men with HIV Infection. Microbiol Spectr 2023; 11:e0106423. [PMID: 37850756 PMCID: PMC10714972 DOI: 10.1128/spectrum.01064-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 09/11/2023] [Indexed: 10/19/2023] Open
Abstract
IMPORTANCE Our longitudinal integrated study has shown the marked alterations in the gut and oral microbiome resulting from acute and chronic HIV infection and from antiretroviral therapy. Importantly, the relationship between oral and gut microbiomes in people living with acute and chronic HIV infection and "healthy" controls has also been explored. These findings might contribute to a better understanding of the interactions between the oral and gut microbiomes and its potential role in HIV disease progression.
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Affiliation(s)
- Shuang Li
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Hao Wu
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Qiushui He
- Institute of Biomedicine, Research Center for Infections and Immunity, University of Turku, Turku, Finland
- Department of Medical Microbiology, Capital Medical University, Beijing, China
| | - Tong Zhang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
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Austin GI, Park H, Meydan Y, Seeram D, Sezin T, Lou YC, Firek BA, Morowitz MJ, Banfield JF, Christiano AM, Pe'er I, Uhlemann AC, Shenhav L, Korem T. Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data. Nat Biotechnol 2023; 41:1820-1828. [PMID: 36928429 PMCID: PMC10504420 DOI: 10.1038/s41587-023-01696-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 01/23/2023] [Indexed: 03/18/2023]
Abstract
Sequencing-based approaches for the analysis of microbial communities are susceptible to contamination, which could mask biological signals or generate artifactual ones. Methods for in silico decontamination using controls are routinely used, but do not make optimal use of information shared across samples and cannot handle taxa that only partially originate in contamination or leakage of biological material into controls. Here we present Source tracking for Contamination Removal in microBiomes (SCRuB), a probabilistic in silico decontamination method that incorporates shared information across multiple samples and controls to precisely identify and remove contamination. We validate the accuracy of SCRuB in multiple data-driven simulations and experiments, including induced contamination, and demonstrate that it outperforms state-of-the-art methods by an average of 15-20 times. We showcase the robustness of SCRuB across multiple ecosystems, data types and sequencing depths. Demonstrating its applicability to microbiome research, SCRuB facilitates improved predictions of host phenotypes, most notably the prediction of treatment response in melanoma patients using decontaminated tumor microbiome data.
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Affiliation(s)
- George I Austin
- Department of Computer Science, Columbia University, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Heekuk Park
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY, USA
| | - Yoli Meydan
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Dwayne Seeram
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY, USA
| | - Tanya Sezin
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY, USA
| | - Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Brian A Firek
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Michael J Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Angela M Christiano
- Department of Dermatology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Itsik Pe'er
- Department of Computer Science, Columbia University, New York, NY, USA
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Data Science Institute, Columbia University, New York, NY, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY, USA
| | - Liat Shenhav
- Center for Studies in Physics and Biology, Rockefeller University, New York, NY, USA.
| | - Tal Korem
- Program for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA.
- CIFAR Azrieli Global Scholars program, CIFAR, Toronto, Canada.
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8
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Pan Z, Wu N, Jin C. Intestinal Microbiota Dysbiosis Promotes Mucosal Barrier Damage and Immune Injury in HIV-Infected Patients. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:3080969. [PMID: 37927531 PMCID: PMC10625490 DOI: 10.1155/2023/3080969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/08/2023] [Accepted: 10/12/2023] [Indexed: 11/07/2023]
Abstract
The intestinal microbiota is an "invisible organ" in the human body, with diverse components and complex interactions. Homeostasis of the intestinal microbiota plays a pivotal role in maintaining the normal physiological process and regulating immune homeostasis. By reviewing more than one hundred related studies concerning HIV infection and intestinal microbiota from 2011 to 2023, we found that human immunodeficiency virus (HIV) infection can induce intestinal microbiota dysbiosis, which not only worsens clinical symptoms but also promotes the occurrence of post-sequelae symptoms and comorbidities. In the early stage of HIV infection, the intestinal mucosal barrier is damaged and a persistent inflammatory response is induced. Mucosal barrier damage and immune injury play a pivotal role in promoting the post-sequelae symptoms caused by HIV infection. This review summarizes the relationship between dysbiosis of the intestinal microbiota and mucosal barrier damage during HIV infection and discusses the potential mechanisms of intestinal barrier damage induced by intestinal microbiota dysbiosis and inflammation. Exploring these molecular mechanisms might provide new ideas to improve the efficacy of HIV treatment and reduce the incidence of post-sequelae symptoms.
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Affiliation(s)
- Zhaoyi Pan
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Nanping Wu
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Changzhong Jin
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Kuhn L, Wang T, Li F, Strehlau R, Tobin NH, Violari A, Brooker S, Patel F, Liberty A, Shiau S, Arpadi SM, Wadhwa S, Yin MT, Wang S, Tiemessen CT, Aldrovandi GM. Microbiota in the oral cavity of school-age children with HIV who started antiretroviral therapy at young ages in South Africa. AIDS 2023; 37:1583-1591. [PMID: 37199568 PMCID: PMC10524539 DOI: 10.1097/qad.0000000000003599] [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] [Indexed: 05/19/2023]
Abstract
BACKGROUND Infancy is an important developmental period when the microbiome is shaped. We hypothesized that earlier antiretroviral therapy (ART) initiation would attenuate HIV effects on microbiota in the mouth. METHODS Oral swabs were collected from 477 children with HIV (CWH) and 123 children without (controls) at two sites in Johannesburg, South Africa. CWH had started ART less than 3 years of age; 63% less than 6 months of age. Most were well controlled on ART at median age 11 years when the swab was collected. Controls were age-matched and recruited from the same communities. Sequencing of V4 amplicon of 16S rRNA was done. Differences in microbial diversity and relative abundances of taxa were compared between the groups. RESULTS CWH had lower alpha diversity than controls. Genus-level abundances of Granulicatella, Streptococcus, and Gemella were greater and Neisseria and Haemophilus less abundant among CWH than controls. Associations were stronger among boys. Associations were not attenuated with earlier ART initiation. Shifts in genus-level taxa abundances in CWH relative to controls were most marked in children on lopinavir/ritonavir regimens, with fewer shifts seen if on efavirenz ART regimens. CONCLUSION A distinct profile of less diverse oral bacterial taxa was observed in school-aged CWH on ART compared with uninfected controls suggesting modulation of microbiota in the mouth by HIV and/or its treatments. Earlier ART initiation was not associated with microbiota profile. Proximal factors, including current ART regimen, were associated with contemporaneous profile of oral microbiota and may have masked associations with distal factors such as age at ART initiation.
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Affiliation(s)
- Louise Kuhn
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons; and Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - Tian Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - Fan Li
- Department of Pediatrics, University of California Los Angeles, Los Angeles, CA
| | - Renate Strehlau
- VIDA Nkanyezi Research Unit, Rahima Moosa Mother and Child Hospital, Department of Paediatrics and Child Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole H. Tobin
- Department of Pediatrics, University of California Los Angeles, Los Angeles, CA
| | - Avy Violari
- Perinatal HIV Research Unit, Chris Hani Baragwanath Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sarah Brooker
- Department of Pediatrics, University of California Los Angeles, Los Angeles, CA
| | - Faeezah Patel
- Wits RHI, Shandukani Research Centre, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Afaaf Liberty
- Perinatal HIV Research Unit, Chris Hani Baragwanath Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephanie Shiau
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ
| | - Stephen M. Arpadi
- Gertrude H. Sergievsky Center, Vagelos College of Physicians and Surgeons; and Department of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - Sunil Wadhwa
- College of Dental Medicine, Columbia University Irving Medical Center, New York, NY
| | - Michael T. Yin
- Division of Infectious Diseases, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - Caroline T. Tiemessen
- National Institutes for Communicable Diseases, and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Grace M. Aldrovandi
- Department of Pediatrics, University of California Los Angeles, Los Angeles, CA
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Ghahari N, Telittchenko R, Loucif H, Isnard S, Routy JP, Olagnier D, van Grevenynghe J. Harnessing Autophagy to Overcome Antigen-Specific T-Cell Dysfunction: Implication for People Living with HIV-1. Int J Mol Sci 2023; 24:11018. [PMID: 37446195 DOI: 10.3390/ijms241311018] [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: 06/09/2023] [Revised: 06/29/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023] Open
Abstract
Like other chronic viral infections, HIV-1 persistence inhibits the development of antigen-specific memory T-cells, resulting in the exhaustion of the immune response and chronic inflammation. Autophagy is a major lysosome-dependent mechanism of intracellular large-target degradation such as lipid and protein aggregates, damaged organelles, and intracellular pathogens. Although it is known that autophagy may target HIV-1 for elimination, knowledge of its function as a metabolic contributor in such viral infection is only in its infancy. Recent data show that elite controllers (EC), who are HIV-1-infected subjects with natural and long-term antigen (Ag)-specific T-cell protection against the virus, are characterized by distinct metabolic autophagy-dependent features in their T-cells compared to other people living with HIV-1 (PLWH). Despite durable viral control with antiretroviral therapy (ART), HIV-1-specific immune dysfunction does not normalize in non-controller PLWH. Therefore, the hypothesis of inducing autophagy to strengthen their Ag-specific T-cell immunity against HIV-1 starts to be an enticing concept. The aim of this review is to critically analyze promises and potential limitations of pharmacological and dietary interventions to activate autophagy in an attempt to rescue Ag-specific T-cell protection among PLWH.
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Affiliation(s)
- Nazanin Ghahari
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, QC H7V 1M7, Canada
| | - Roman Telittchenko
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, QC H7V 1M7, Canada
| | - Hamza Loucif
- EVAH Corp., 500 Boulevard Cartier Ouest, Laval, QC H7V 5B7, Canada
| | - Stephane Isnard
- Chronic Viral Illness Service and Division of Hematology, McGill University Health Centre, Glen Site, Montreal, QC H4A 3J1, Canada
| | - Jean-Pierre Routy
- Chronic Viral Illness Service and Division of Hematology, McGill University Health Centre, Glen Site, Montreal, QC H4A 3J1, Canada
| | - David Olagnier
- Department of Biomedicine, Research Center for Innate Immunology, Aarhus University, 8000 Aarhus, Denmark
| | - Julien van Grevenynghe
- Institut National de la Recherche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, QC H7V 1M7, Canada
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11
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Beall CJ, Lilly EA, Granada C, Treas K, Dubois KR, Hashmi SB, Vazquez JA, Hagensee ME, Griffen AL, Leys EJ, Fidel PL. Independent Effects of HIV and Antiretroviral Therapy on the Oral Microbiome Identified by Multivariate Analyses. mBio 2023; 14:e0040923. [PMID: 37071004 PMCID: PMC10294613 DOI: 10.1128/mbio.00409-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/29/2023] [Indexed: 04/19/2023] Open
Abstract
The oral microbiome is an important predictor of health and disease. We recently reported significant yet modest effects of HIV under highly active antiretroviral therapy (ART) on the oral microbiome (bacterial and fungal) in a large cohort of HIV-positive (HIV+) and matched HIV-negative (HIV-) individuals. As it was unclear whether ART added to or masked further effects of HIV on the oral microbiome, the present study aimed to analyze the effects of HIV and ART independently, which also included HIV- subjects on preexposure prophylaxis (PrEP) therapy. Cross-sectional analyses of the effect of HIV devoid of ART (HIV+ ART- versus matched HIV- subjects) showed a significant effect on both the bacteriome and mycobiome (P < 0.024) after controlling for other clinical variables (permutational multivariate analysis of variance [PERMANOVA] of Bray-Curtis dissimilarity). Cross-sectional analyses evaluating the effects of ART (HIV+ ART+ versus HIV+ ART- subjects) revealed a significant effect on the mycobiome (P < 0.007) but not the bacteriome. In parallel longitudinal analyses, ART (before versus after the initiation of ART) had a significant effect on the bacteriome, but not the mycobiome, of HIV+ and HIV- PrEP subjects (P < 0.005 and P < 0.016, respectively). These analyses also revealed significant differences in the oral microbiome and several clinical variables between HIV- PrEP subjects (pre-PrEP) and the HIV-matched HIV- group (P < 0.001). At the species level, a small number of differences in both bacterial and fungal taxa were identified within the effects of HIV and/or ART. We conclude that the effects of HIV and ART on the oral microbiome are similar to those of the clinical variables but collectively are modest overall. IMPORTANCE The oral microbiome can be an important predictor of health and disease. For persons living with HIV (PLWH), HIV and highly active antiretroviral therapy (ART) may have a significant influence on their oral microbiome. We previously reported a significant effect of HIV with ART on both the bacteriome and mycobiome. It was unclear whether ART added to or masked further effects of HIV on the oral microbiome. Hence, it was important to evaluate the effects of HIV and ART independently. For this, multivariate cross-sectional and longitudinal oral microbiome analyses (bacteriome and mycobiome) were conducted within the cohort, including HIV+ ART+ subjects and HIV+ and HIV- (preexposure prophylaxis [PrEP]) subjects before and after the initiation of ART. While we report independent significant effects of HIV and ART on the oral microbiome, we conclude that their influence is similar to that of the clinical variables but collectively modest overall.
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Affiliation(s)
- Clifford J. Beall
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Elizabeth A. Lilly
- Center of Excellence in Oral and Craniofacial Biology, Louisiana State University Health Center School of Dentistry, New Orleans, Louisiana, USA
| | - Carolina Granada
- Division of Infectious Diseases, Department of Medicine, Augusta University, Medical College of Georgia, Augusta, Georgia, USA
| | - Kelly Treas
- Center of Excellence in Oral and Craniofacial Biology, Louisiana State University Health Center School of Dentistry, New Orleans, Louisiana, USA
| | - Kenneth R. Dubois
- Center of Excellence in Oral and Craniofacial Biology, Louisiana State University Health Center School of Dentistry, New Orleans, Louisiana, USA
| | - Shahr B. Hashmi
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Jose A. Vazquez
- Division of Infectious Diseases, Department of Medicine, Augusta University, Medical College of Georgia, Augusta, Georgia, USA
| | - Michael E. Hagensee
- Section of Infectious Diseases, Department of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Ann L. Griffen
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
- Division of Pediatric Dentistry, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Eugene J. Leys
- Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio, USA
| | - Paul L. Fidel
- Center of Excellence in Oral and Craniofacial Biology, Louisiana State University Health Center School of Dentistry, New Orleans, Louisiana, USA
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12
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Meng J, Tao J, Abu Y, Sussman DA, Girotra M, Franceschi D, Roy S. HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome. Microbiol Spectr 2023; 11:e0247222. [PMID: 36511710 PMCID: PMC9927552 DOI: 10.1128/spectrum.02472-22] [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: 06/29/2022] [Accepted: 11/27/2022] [Indexed: 12/15/2022] Open
Abstract
This study characterized compositional and functional shifts in the intestinal and oral microbiome in HIV-positive patients on antiretroviral therapy compared to HIV-negative individuals. Seventy-nine specimens were collected from 5 HIV-positive and 12 control subjects from five locations (colon brush, colon wash, terminal ileum [TI] brush, TI wash, and saliva) during colonoscopy and at patient visits. Microbiome composition was characterized using 16S rRNA sequencing, and microbiome function was predicted using bioinformatics tools (PICRUSt and BugBase). Our analysis indicated that the β-diversity of all intestinal samples (colon brush, colon wash, TI brush, and TI wash) from patients with HIV was significantly different from patients without HIV. Specifically, bacteria from genera Prevotella, Fusobacterium, and Megasphaera were more abundant in samples from HIV-positive patients. On the other hand, bacteria from genera Ruminococcus, Blautia, and Clostridium were more abundant in samples from HIV-negative patients. Additionally, HIV-positive patients had higher abundances of biofilm-forming and pathogenic bacteria. Furthermore, pathways related to translation and nucleotide metabolism were elevated in HIV-positive patients, whereas pathways related to lipid and carbohydrate metabolism were positively correlated with samples from HIV-negative patients. Our analyses further showed variations in microbiome composition in HIV-positive and negative patients by sampling site. Samples from colon wash, colon brush, and TI wash were significant between groups, while samples from TI brush and saliva were not significant. Taken together, here, we report altered intestinal microbiome composition and predicted function in patients with HIV compared to uninfected patients, though we found no changes in the oral microbiome. IMPORTANCE Over 37 million people worldwide are living with HIV. Although the availability of antiretroviral therapy has significantly reduced the number of AIDS-related deaths, individuals living with HIV are at increased risk for opportunistic infections. We now know that HIV interacts with the trillions of bacteria, fungi, and viruses in the human body termed the microbiome. Only a limited number of previous studies have compared variations in the oral and gastrointestinal microbiome with HIV infection. Here, we detail how the oral and gastrointestinal microbiome changes with HIV infection, having used 5 different sampling sites to gain a more comprehensive view of these changes by location. Our results show site-specific changes in the intestinal microbiome associated with HIV infection. Additionally, we show that while there were significant changes in the intestinal microbiome, there were no significant changes in the oral microbiome.
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Affiliation(s)
- Jingjing Meng
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Junyi Tao
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Yaa Abu
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Daniel Andrew Sussman
- Department of Gastroenterology, University of Miami Medical Group, Miami, Florida, USA
| | - Mohit Girotra
- Department of Gastroenterology, University of Miami Medical Group, Miami, Florida, USA
| | - Dido Franceschi
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
| | - Sabita Roy
- Department of Surgery, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida, USA
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13
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Pereira LL, Veiga Siqueira Amorim D, Brito Sampaio W, Almeida Cruz Azevêdo T, Bispo Pereira Cardoso V, Barreto Lemos F, Silva Chang A, Machado F, Pereira Lima F, Sampaio Neves F, Leal Figueiredo AC. Factors Associated with Periodontitis in Patients with and without HIV. Int J Dent 2023; 2023:9929835. [PMID: 37159593 PMCID: PMC10163962 DOI: 10.1155/2023/9929835] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/27/2023] [Accepted: 04/05/2023] [Indexed: 05/11/2023] Open
Abstract
Purpose The aim of this study was to compare clinical periodontal conditions in HIV-positive people on HAART with an HIV-negative group, in addition to investigating factors associated with periodontitis in the entire sample. Methods This was a cross-sectional study. Data were collected by oral clinical examination for the diagnosis of periodontitis, review of medical records, and application of a questionnaire containing personal data, deleterious habits, and oral hygiene habits for the other variables. The results were analyzed by Pearson's χ 2 test and Student's t-test. A logistic regression model was constructed for the multivariate analysis and periodontitis was defined as a dependent variable. The analysis was performed on the entire sample (HIV+ and HIV-) and also on the group consisting of only people living with HIV. Results Individuals older than 43 years old and with HIV were more likely to develop moderate and severe periodontitis (47.80 and 4.84 times, respectively). When analyzing only HIV+, in addition to age (OR = 2.795; CI = 1.080-7.233), the use of nonnucleoside reverse transcriptase inhibitors (NNRTIs) (OR = 2.841; CI = 1.135-7.112) was also associated with moderate and severe periodontitis. Conclusion It was possible to observe a higher prevalence of periodontitis among individuals with HIV, showing an association between the virus, advanced age, and moderate or severe periodontitis.
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Affiliation(s)
- Luanderson Lopes Pereira
- Postgraduate Program in Dentistry and Health, Federal University of Bahia (UFBA), Salvador, Brazil
| | | | - Willian Brito Sampaio
- Postgraduate Program in Dentistry and Health, Federal University of Bahia (UFBA), Salvador, Brazil
| | | | | | - Felipe Barreto Lemos
- Postgraduate Program in Dentistry and Health, Federal University of Bahia (UFBA), Salvador, Brazil
| | - Andressa Silva Chang
- Postgraduate Program in Dentistry and Health, Federal University of Bahia (UFBA), Salvador, Brazil
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14
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Huang W, Tang X, Bao J. Commentary: The oral microbiome in young women at different stages of periodontitis: Prevotella dominant in stage III periodontitis. Front Cell Infect Microbiol 2023; 13:1141285. [PMID: 36816593 PMCID: PMC9936083 DOI: 10.3389/fcimb.2023.1141285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Affiliation(s)
- Weiqiang Huang
- The Fourth Affiliated College Of Zhejiang Chinese Medical University, Hangzhou, China
| | - Xinyu Tang
- The Fourth Affiliated College Of Zhejiang Chinese Medical University, Hangzhou, China
| | - Jianfeng Bao
- Department of Hepatology, Affiliated Hangzhou Xixi Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- *Correspondence: Jianfeng Bao,
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15
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Branton WG, Fernandes JP, Mohammadzadeh N, Doan MAL, Laman JD, Gelman BB, Fagrouch Z, Kondova I, Mooij P, Koopman G, Power C. Microbial molecule ingress promotes neuroinflammation and brain CCR5 expression in persons with HIV-associated neurocognitive disorders. Brain Behav Immun 2023; 107:110-123. [PMID: 36202168 DOI: 10.1016/j.bbi.2022.09.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Systemic inflammation accompanies HIV-1 infection, resulting in microbial translocation from different tissues. We investigated interactions between lentivirus infections, neuroinflammation and microbial molecule presence in the brain. METHODS Brain tissues from adult humans with (n = 22) and without HIV-1 (n = 11) infection as well as adult nonhuman primates (NHPs) with (n = 11) and without (n = 4) SIVmac251 infection were investigated by RT-PCR/ddPCR, immunofluorescence and western blotting. Studies of viral infectivity, host immune gene expression and viability were performed in primary human neural cells. FINDINGS Among NHPs, SIV DNA quantitation in brain showed increased levels among animals with SIV encephalitis (n = 5) that was associated with bacterial genomic copy number as well as CCR5 and CASP1 expression in brain. Microbial DnaK and peptidoglycan were immunodetected in brains from uninfected and SIV-infected animals, chiefly in glial cells. Human microglia infected by HIV-1 showed increased p24 production after exposure to peptidoglycan that was associated CCR5 induction. HIV-1 Vpr application to human neurons followed by peptidoglycan exposure resulted in reduced mitochondrial function and diminished beta-III tubulin expression. In human brains, bacterial genome copies (250-550 copies/gm of tissue), were correlated with increased bacterial rRNA and GroEL transcript levels in patients with HIV-associated neurocognitive disorders (HAND). Glial cells displayed microbial GroEL and peptidoglycan immunoreactivity accompanied by CCR5 induction in brains from patients with HAND. INTERPRETATION Increased microbial genomes and proteins were evident in brain tissues from lentivirus-infected humans and animals and associated with neurological disease. Microbial molecule translocation into the brain might exacerbate neuroinflammatory disease severity and represent a driver of lentivirus-associated brain disease.
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Affiliation(s)
- William G Branton
- Departments of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Jason P Fernandes
- Medical Microbiology & Immunology, University of Alberta, Edmonton, AB, Canada
| | | | - Mathew A L Doan
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
| | - Jon D Laman
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, Netherlands
| | - Benjamin B Gelman
- Departments of Pathology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Zahra Fagrouch
- Department of Virology and Animal Science Department, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Ivanela Kondova
- Department of Virology and Animal Science Department, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Petra Mooij
- Department of Virology and Animal Science Department, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Gerrit Koopman
- Department of Virology and Animal Science Department, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Christopher Power
- Departments of Medicine, University of Alberta, Edmonton, AB, Canada; Medical Microbiology & Immunology, University of Alberta, Edmonton, AB, Canada; Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada.
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Girija AS, Ganesh PS. Functional biomes beyond the bacteriome in the oral ecosystem. JAPANESE DENTAL SCIENCE REVIEW 2022; 58:217-226. [PMID: 35814739 PMCID: PMC9260289 DOI: 10.1016/j.jdsr.2022.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/28/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022] Open
Abstract
Selective constraint and pressures upon the host tissues often signifies a beneficial microbiome in any species. In the context of oral microbiome this displays a healthy microbial cosmos resisting the colonization and helps in rendering protection. This review highlights the endeavors of the oral microbiome beyond the bacteriome encompassing virome, mycobiome, protozoa and archaeomes in maintaining the oral homeostasis in health and disease. Scientific data based on the peer-reviewed publications on the microbial communities of the oral microbiome were selected and collated from the scientific database collection sites of web of science (WOS), pubmed central, Inspec etc., from 2010 to 2021 using the search key words like oral microbiome, oral microbiota, oral virome, oral bacteriome, oral mycobiome and oral archaeome. Data excluded were from conference proceedings, abstracts and book chapters. The oral homeostasis in both the health and disease conditions, mostly is balanced by the unrevealed virome, mycobiome, oral protozoa and archaeome. The review documents the need to comprehend the diversity that prevails among the kingdoms in order to determine the specific role played by each domain. Oral microbiome is also a novel research arena to develop drug and targeted therapies to treat various oro-dental infections.
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Briceño O, Gónzalez-Navarro M, Montufar N, Chávez-Torres M, Abato I, Espinosa-Sosa A, Ablanedo-Terrazas Y, Luna-Villalobos Y, Ávila-Ríos S, Reyes-Terán G, Pinto-Cardoso S. Mucosal immune cell populations and the bacteriome of adenoids and tonsils from people living with HIV on suppressive antiretroviral therapy. Front Microbiol 2022; 13:958739. [PMID: 36033845 PMCID: PMC9404693 DOI: 10.3389/fmicb.2022.958739] [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: 06/01/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
Ear, nose, and throat (ENT) conditions are prevalent in people living with HIV (PLWH) and occur at all strata of CD4 counts and despite antiretroviral therapy (ART). ENT conditions are underreported in PLWH. Also, little is known about the adenotonsillar microbiota and its relation to resident adaptive and innate immune cells. To bridge this gap, we characterized immune cell populations and the bacterial microbiota of two anatomical sites (adenoids, tonsils) and the oral cavity. Adenoids and tonsils were obtained from PLWH (n = 23) and HIV-seronegative individuals (SN, n = 16) after nasal surgery and tonsillectomy and processed for flow cytometry. Nasopharyngeal, oropharyngeal swabs, and oral rinses were collected prior to surgery for 16S sequencing. Wilcoxon rank sum test, principal coordinate analysis, permutational multivariate analysis of variance, and linear discriminant analysis (LEfSe) were used to assess differences between PLWH and SN. Spearman’s correlations were performed to explore interactions between the bacteriome and mucosal immune cells. Of the 39 individuals included, 30 (77%) were men; the median age was 32 years. All PLWH were on ART, with a median CD4 of 723 cells. ENT conditions were classified as inflammatory or obstructive, with no differences observed between PLWH and SN. PLWH had higher frequencies of activated CD4+ and CD8+ T cells, increased T helper (Th)1 and decreased Th2 cells; no differences were observed for B cells and innate immune cells. Alpha diversity was comparable between PLWH and SN at all 3 anatomical sites (adenoids, tonsils, and oral cavity). The impact of HIV infection on the bacterial community structure at each site, as determined by Permutational multivariate analysis of variance, was minor and not significant. Two discriminant genera were identified in adenoids using LEfSe: Staphylococcus for PLWH and Corynebacterium for SN. No discriminant genera were identified in the oropharynx and oral cavity. Niche-specific differences in microbial diversity and communities were observed. PLWH shared less of a core microbiota than SN. In the oropharynx, correlation analysis revealed that Th17 cells were inversely correlated with bacterial richness and diversity, Filifactor, Actinomyces and Treponema; and positively correlated with Streptococcus. Our study contributes toward understanding the role of the adenotonsillar microbiota in the pathophysiology of ENT conditions.
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Affiliation(s)
- Olivia Briceño
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas”, Ciudad de México, Mexico
| | - Mauricio Gónzalez-Navarro
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas”, Ciudad de México, Mexico
| | - Nadia Montufar
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas”, Ciudad de México, Mexico
| | - Monserrat Chávez-Torres
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas”, Ciudad de México, Mexico
| | - Indira Abato
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas”, Ciudad de México, Mexico
| | - Ariana Espinosa-Sosa
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas”, Ciudad de México, Mexico
| | - Yuria Ablanedo-Terrazas
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas”, Ciudad de México, Mexico
| | - Yara Luna-Villalobos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas”, Ciudad de México, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas”, Ciudad de México, Mexico
| | - Gustavo Reyes-Terán
- Comisión Coordinadora de Institutos Nacional de Salud y Hospitales de Alta Especialidad, Secretaría de Salud, Ciudad de México, Mexico
| | - Sandra Pinto-Cardoso
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias “Ismael Cosío Villegas”, Ciudad de México, Mexico
- *Correspondence: Sandra Pinto-Cardoso,
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Xu X, Xiao J, Niu Y. Editorial: The Pivotal Role of Oral Microbiota Dysbiosis and Microbiota-Host Interactions in Diseases. Front Cell Infect Microbiol 2022; 12:947638. [PMID: 35811683 PMCID: PMC9267765 DOI: 10.3389/fcimb.2022.947638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- Xin Xu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jin Xiao
- Eastman Institute for Oral Health, University of Rochester Medical Center, Rochester, NY, United States
| | - Yulong Niu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Evaluation of Association of Oral Bacterial Profile with HBV and HCV Infection and T Lymphocyte Level in HIV-Positive Patients. Int J Dent 2022; 2022:8622181. [PMID: 35783688 PMCID: PMC9246570 DOI: 10.1155/2022/8622181] [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: 03/02/2022] [Revised: 04/04/2022] [Accepted: 04/28/2022] [Indexed: 11/26/2022] Open
Abstract
Background This study was aimed to determine the oral bacterial profile of HIV-positive patients and their correlation with T lymphocyte and CD4 count and hepatitis B and C incidence. Methods In this study, 73 patients who were diagnosed HIV-positive and were referred to Shiraz HIV research center for routine dental treatment were enrolled. Demographic data including sex, ethnicity, CD4+ T cell, and T lymphocyte counts were collected from their medical records. Supragingival dental plaque and samples from the dorsal of the tongue were collected by sterile swabs. These samples were transferred to the microbiology laboratory of Jahrom University of Medical Sciences. After primary biochemical test of cultured samples, assessment of bacterial biofilms was done by DNA extraction. Real-time PCR with specific primer of each bacterial species was done, and assessment of the results of real time PCR led to determination of the species of the evaluated bacteria. The correlation of bacterial prevalence with hepatitis B and C was evaluated by chi-square test. Furthermore, Mann–Whitney test was used to evaluate the association of bacterial species prevalence with CD4 and T lymphocyte level. Results The prevalence of none of the detected bacteria had statistically significant relationship with hepatitis C, except for Peptostreptococcaceae (p value = 0.016) in the tongue plaque and Leptotrichia (p value = 0.022) in dental plaque. None of the evaluated bacteria showed any significant association with CD4 and T lymphocytes level, except for Kingella (p value = 0.025, 0.019, respectively), and also no significant correlation was reported with CD4, except for Gemella (p value = 0.021) and Campylobacter gracilis (p value = 0.029). Conclusions The diversity of the detected bacteria was more in dental plaque, while their density was more noticeable in the tongue plaque. No significant correlation was found between the prevalence of most of the detected bacteria and CD4 level and T lymphocyte level and incidence of hepatitis B and C.
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Peña DER, Santos EDS, Bezerra RDS, Nobre ÁVV, Pólvora TLS, da Fonseca BAL, Pozzetto B, Lourenço AG, do Nascimento C, Motta ACF. Nonsurgical periodontal debridement affects subgingival bacterial diversity in human immunodeficiency virus (HIV)-1 infected patients with periodontitis. J Periodontol 2022; 93:1455-1467. [PMID: 34986272 DOI: 10.1002/jper.21-0466] [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: 08/06/2021] [Revised: 10/18/2021] [Accepted: 11/03/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Following HIV-1 infection and antiretroviral therapy, the development of periodontal disease was shown to be favored. However, the influence of HIV-1 infection on the periodontal microbiota after nonsurgical periodontal debridement (NSPD) needs a broad comprehension. This work aimed to compare the subgingival microbiological content of HIV-infected and control patients with periodontitis undergoing NSPD. METHODS The bacterial profile of subgingival biofilm samples of HIV-1-infected (n = 18) and control (n = 14) patients with periodontitis was assessed using 16S rRNA gene sequencing. The samples were collected at baseline, 30 and 90 days after NSPD. The taxonomic analysis of gingival microbiota was performed using a ribosomal RNA database. The microbiota content was evaluated in the light of CD4 cell count and viral load. RESULTS Both HIV and control groups showed similar stages and grades of periodontitis. At baseline, the HIV group showed higher alpha diversity for both healthy (HS) and periodontal sites (PS). Streptococcus, Fusobacterium, Veillonella and Prevotella were the predominant bacterial genera. A low abundance of periodontopathogenic bacteria was observed, and the NSPD induced shifts in the subgingival biofilm of HIV-infected patients, leading to a microbiota similar to that of control patients. CONCLUSION Different subgingival microbiota profiles were identified - a less diverse microbiota was found in HIV-1-infected patients, in contrast to a more diverse microbiota in control patients. NSPD caused changes in the microbiota of both groups, with a greater impact on the HIV group, leading to a decrease in alpha diversity, and produced a positive impact on the serological immune markers in HIV-1-infected patients. Control of periodontitis should be included as part of an oral primary care, providing the oral health benefits and better control of HIV-1 infection. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Diana Estefania Ramos Peña
- Department of Oral & Maxillofacial Surgery, and Periodontology, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Emerson de Souza Santos
- Department of Clinical Analyses, Toxicology and Food Science of the School of Pharmaceutical Sciences of Ribeirão Preto
| | - Rafael Dos Santos Bezerra
- Blood Center of Ribeirao Preto, Faculty of Medicine of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Átila V V Nobre
- Department of Oral & Maxillofacial Surgery, and Periodontology, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Tábata L S Pólvora
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, SP, Brazil
| | - Benedito A L da Fonseca
- Department of Medical Clinic of Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Bruno Pozzetto
- Team Mucosal Immunity and Pathogen Agents, University of Lyon, University of Saint-Etienne, Saint-Etienne, France
| | - Alan G Lourenço
- Department of Basic and Oral Biology, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Cássio do Nascimento
- Department of Dental Materials and Prosthodontics, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Ana Carolina F Motta
- Department of Stomatology, Public Health and Forensic Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
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21
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Xie Y, Sun J, Hu C, Ruan B, Zhu B. Oral Microbiota Is Associated With Immune Recovery in Human Immunodeficiency Virus-Infected Individuals. Front Microbiol 2021; 12:794746. [PMID: 34956162 PMCID: PMC8696184 DOI: 10.3389/fmicb.2021.794746] [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: 10/14/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
The role of the oral microbiota in HIV-infected individuals deserves attention as either HIV infection or antiretroviral therapy (ART) may have effect on the diversity and the composition of the oral microbiome. However, few studies have addressed the oral microbiota and its interplay with different immune responses to ART in HIV-infected individuals. Salivary microbiota and immune activation were studied in 30 HIV-infected immunological responders (IR) and 34 immunological non-responders (INR) (≥500 and < 200 CD4 + T-cell counts/μl after 2 years of HIV-1 viral suppression, respectively) with no comorbidities. Metagenome sequencing revealed that the IR and the INR group presented similar salivary bacterial richness and diversity. The INR group presented a significantly higher abundance of genus Selenomonas_4, while the IR group manifested higher abundances of Candidatus_Saccharimonas and norank_p_Saccharimonas. Candidatus_Saccharimonas and norank_p_Saccharimonas were positively correlated with the current CD4 + T-cells. Candidatus_Saccharimonas was positively correlated with the markers of adaptive immunity CD4 + CD57 + T-cells, while negative correlation was found between norank _p_Saccharimonas and the CD8 + CD38 + T-cells as well as the CD4/CD8 + HLADR + CD38 + T-cells. The conclusions are that the overall salivary microbiota structure was similar in the immunological responders and immunological non-responders, while there were some taxonomic differences in the salivary bacterial composition. Selenomona_4, Candidatus_Saccharimonas, and norank _p_Saccharimonas might act as important factors of the immune recovery in the immunodeficiency patients, and Candidatus_Saccharimonas could be considered in the future as screening biomarkers for the immune responses in the HIV-infected individuals.
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Affiliation(s)
- Yirui Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Jia Sun
- Ningbo Medical Center Lihuili Hospital, Ningbo, China
| | - Caiqin Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Bing Ruan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Biao Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Department of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
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22
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Lopera TJ, Lujan JA, Zurek E, Zapata W, Hernandez JC, Toro MA, Alzate JF, Taborda NA, Rugeles MT, Aguilar-Jimenez W. A specific structure and high richness characterize intestinal microbiota of HIV-exposed seronegative individuals. PLoS One 2021; 16:e0260729. [PMID: 34855852 PMCID: PMC8638974 DOI: 10.1371/journal.pone.0260729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/15/2021] [Indexed: 02/05/2023] Open
Abstract
Intestinal microbiota facilitates food breakdown for energy metabolism and influences the immune response, maintaining mucosal homeostasis. Overall, HIV infection is associated with intestinal dysbiosis and immune activation, which has been related to seroconversion in HIV-exposed individuals. However, it is unclear whether microbiota dysbiosis is the cause or the effect of immune alterations and disease progression or if it could modulate the risk of acquiring the HIV infection. We characterize the intestinal microbiota and determine its association with immune regulation in HIV-exposed seronegative individuals (HESN), HIV-infected progressors (HIV+), and healthy control (HC) subjects. For this, feces and blood were collected. The microbiota composition of HESN showed a significantly higher alpha (p = 0.040) and beta diversity (p = 0.006) compared to HC, but no differences were found compared to HIV+. A lower Treg percentage was observed in HESN (1.77%) than HC (2.98%) and HIV+ (4.02%), with enrichment of the genus Butyrivibrio (p = 0.029) being characteristic of this profile. Moreover, we found that Megasphaera (p = 0.017) and Victivallis (p = 0.0029) also are enriched in the microbiota composition in HESN compared to HC and HIV+ subjects. Interestingly, an increase in Succinivibrio and Prevotella, and a reduction in Bacteroides genus, which is typical of HIV-infected individuals, were observed in both HESN and HIV+, compared to HC. Thus, HESNs have a microbiota profile, similar to that observed in HIV+, most likely because HESN are cohabiting with their HIV+ partners.
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Affiliation(s)
- Tulio J. Lopera
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Jorge A. Lujan
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Eduardo Zurek
- Department of System Engineering, Universidad del Norte, Barranquilla, Colombia
| | - Wildeman Zapata
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
- Facultad de Medicina, Grupo Infettare, Universidad Cooperativa de Colombia, Medellín, Colombia
| | - Juan C. Hernandez
- Facultad de Medicina, Grupo Infettare, Universidad Cooperativa de Colombia, Medellín, Colombia
| | - Miguel A. Toro
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica -CNSG, Sede de Investigación Universitaria -SIU, Universidad de Antioquia UdeA, Medellin, Colombia
- Facultad de Medicina, Grupo de Parasitología, Universidad de Antioquia, Medellín, Colombia
| | - Juan F. Alzate
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica -CNSG, Sede de Investigación Universitaria -SIU, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Natalia A. Taborda
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
- Facultad de Ciencias de la Salud, Grupo de Investigaciones Biomédicas Uniremington, Programa de Medicina, Corporación Universitaria Remington, Medellín, Colombia
| | - Maria T. Rugeles
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Wbeimar Aguilar-Jimenez
- Facultad de Medicina, Grupo Inmunovirología, Universidad de Antioquia UdeA, Medellín, Colombia
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23
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Li S, Su B, He QS, Wu H, Zhang T. Alterations in the oral microbiome in HIV infection: causes, effects and potential interventions. Chin Med J (Engl) 2021; 134:2788-2798. [PMID: 34670249 PMCID: PMC8667981 DOI: 10.1097/cm9.0000000000001825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Indexed: 12/02/2022] Open
Abstract
ABSTRACT A massive depletion of CD4+ T lymphocytes has been described in early and acute human immunodeficiency virus (HIV) infection, leading to an imbalance between the human microbiome and immune responses. In recent years, a growing interest in the alterations in gut microbiota in HIV infection has led to many studies; however, only few studies have been conducted to explore the importance of oral microbiome in HIV-infected individuals. Evidence has indicated the dysbiosis of oral microbiota in people living with HIV (PLWH). Potential mechanisms might be related to the immunodeficiency in the oral cavity of HIV-infected individuals, including changes in secretory components such as reduced levels of enzymes and proteins in saliva and altered cellular components involved in the reduction and dysfunction of innate and adaptive immune cells. As a result, disrupted oral immunity in HIV-infected individuals leads to an imbalance between the oral microbiome and local immune responses, which may contribute to the development of HIV-related diseases and HIV-associated non-acquired immunodeficiency syndrome comorbidities. Although the introduction of antiretroviral therapy (ART) has led to a significant decrease in occurrence of the opportunistic oral infections in HIV-infected individuals, the dysbiosis in oral microbiome persists. Furthermore, several studies with the aim to investigate the ability of probiotics to regulate the dysbiosis of oral microbiota in HIV-infected individuals are ongoing. However, the effects of ART and probiotics on oral microbiome in HIV-infected individuals remain unclear. In this article, we review the composition of the oral microbiome in healthy and HIV-infected individuals and the possible effect of oral microbiome on HIV-associated oral diseases. We also discuss how ART and probiotics influence the oral microbiome in HIV infection. We believe that a deeper understanding of composition and function of the oral microbiome is critical for the development of effective preventive and therapeutic strategies for HIV infection.
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Affiliation(s)
- Shuang Li
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Qiu-Shui He
- Institute of Biomedicine, Research Center for Infections and Immunity, University of Turku, Turku 20520, Finland
| | - Hao Wu
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Tong Zhang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
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24
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Coker MO, Cairo C, Garzino-Demo A. HIV-Associated Interactions Between Oral Microbiota and Mucosal Immune Cells: Knowledge Gaps and Future Directions. Front Immunol 2021; 12:676669. [PMID: 34616391 PMCID: PMC8488204 DOI: 10.3389/fimmu.2021.676669] [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: 03/05/2021] [Accepted: 08/06/2021] [Indexed: 02/02/2023] Open
Abstract
Even with sustained use of antiretroviral therapy (ART), HIV-infected individuals have an increased risk of systemic comorbid conditions and oral pathologies, including opportunistic infections, oral mucosal inflammation, and gingival and periodontal diseases. The immune-mediated mechanisms that drive this increased risk, in the context of sustained viral suppression, are unclear. HIV infection, even when controlled, alters microbial communities contributing to a chronic low-grade inflammatory state that underlies these non-HIV co-morbidities. The higher prevalence of dental caries, and mucosal and periodontal inflammation reported in HIV-infected individuals on ART is often associated with differentially abundant oral microbial communities, possibly leading to a heightened susceptibility to inflammation. This mini-review highlights current gaps in knowledge regarding the microbe-mediated oral mucosal immunity with HIV infection while discussing opportunities for future research investigations and implementation of novel approaches to elucidate these gaps. Interventions targeting both inflammation and microbial diversity are needed to mitigate oral inflammation-related comorbidities, particularly in HIV-infected individuals. More broadly, additional research is needed to bolster general models of microbiome-mediated chronic immune activation and aid the development of precise microbiota-targeted interventions to reverse or mitigate adverse outcomes.
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Affiliation(s)
- Modupe O Coker
- Department of Oral Biology, School of Dental Medicine at Rutgers, Newark, NJ, United States.,Department of Epidemiology, School of Public Health at Rutgers, Newark, NJ, United States
| | - Cristiana Cairo
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, MD, United States.,Department of Medicine, School of Medicine, University of Maryland, Baltimore, MD, United States
| | - Alfredo Garzino-Demo
- Institute of Human Virology, School of Medicine, University of Maryland, Baltimore, MD, United States.,Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, MD, United States.,Department of Molecular Medicine, University of Padova, Padova, Italy
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25
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Stage II and stage III periodontitis clinical burdens of HIV-1 undergoing antiretroviral therapy. Clin Oral Investig 2021; 26:2187-2195. [PMID: 34601633 PMCID: PMC8487450 DOI: 10.1007/s00784-021-04201-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/22/2021] [Indexed: 12/01/2022]
Abstract
Objectives The aim of this retrospective cross-sectional study was to estimate the association of HIV-1 infection under highly active antiretroviral treatment (HAART) on the clinical parameters of periodontitis. Materials and methods A total of 205 patients were divided in two groups: 74 HIV + and 131 HIV − . Periodontal probing depth (PPD), clinical attachment loss (CAL), bleeding on probing (BOP), and visible supragingival biofilm (VSB) were recorded. The association of HIV-1 infection with the presence of at least 3 sites with PPD ≥ 5 mm and/or CAL ≥ 4 mm in non-adjacent teeth was estimated using binary logistic regression models. Results The variables HIV-1 infection (OR = 5.53, p < 0.0001, 95% CI: 2.45–13.64), age [range 35–50 years old (OR = 5.73, p < 0.0001, 95% CI: 2.49–13.20); > 50 years old (OR = 6.29, p = 0.002, 95% CI: 1.94–20.42)], and VSB (OR = 23.68, p < 0.0001, 95% CI: 8.07–69.53) showed a significant direct association with BOP outcome. Conclusions HIV-1 infection under HAART did not have association with the presence of at least 3 sites with PPD ≥ 5 mm and/or CAL ≥ 4 mm. However, HIV patients on HAART had direct association of HIV-1 infection with BOP and an inverse association with PPD. Clinical relevance These results support that monitoring gingival bleeding associated with oral prophylaxis would be beneficial in the prevention and management of periodontitis in HIV-1 patients on HAART.
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26
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Zhang L, Zhan H, Xu W, Yan S, Ng SC. The role of gut mycobiome in health and diseases. Therap Adv Gastroenterol 2021; 14:17562848211047130. [PMID: 34589139 PMCID: PMC8474302 DOI: 10.1177/17562848211047130] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 08/31/2021] [Indexed: 02/04/2023] Open
Abstract
The gut microbiome comprised of microbes from multiple kingdoms, including bacteria, fungi, and viruses. Emerging evidence suggests that the intestinal fungi (the gut "mycobiome") play an important role in host immunity and inflammation. Advances in next generation sequencing methods to study the fungi in fecal samples and mucosa tissues have expanded our understanding of gut fungi in intestinal homeostasis and systemic immunity in health and their contribution to different human diseases. In this review, the current status of gut mycobiome in health, early life, and different diseases including inflammatory bowel disease, colorectal cancer, and metabolic diseases were summarized.
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Affiliation(s)
| | | | - Wenye Xu
- Center for Gut Microbiota Research, Faculty of
Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong,
China,Li Ka Shing Institute of Health Science, The
Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive disease,
Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin,
Hong Kong, China,Department of Medicine and Therapeutics,
Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong,
China
| | - Shuai Yan
- Center for Gut Microbiota Research, Faculty of
Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong,
China,Li Ka Shing Institute of Health Science, The
Chinese University of Hong Kong, Shatin, Hong Kong, China,State Key Laboratory for Digestive disease,
Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin,
Hong Kong, China,Department of Anaesthesia and Intensive Care
and Peter Hung Pain Research Institute, The Chinese University of Hong Kong,
Shatin, Hong Kong, China
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27
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Villar CC, Dongari-Bagtzoglou A. Fungal diseases: Oral dysbiosis in susceptible hosts. Periodontol 2000 2021; 87:166-180. [PMID: 34463992 DOI: 10.1111/prd.12378] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The oral cavity is colonized by a large number of microorganisms that are referred to collectively as the oral microbiota. These indigenous microorganisms have evolved in symbiotic relationships with the oral mucosal immune system and are involved in maintaining homeostasis in the oral cavity. Although Candida species are commonly found in the healthy oral cavity without causing infection, these fungi can become pathogenic. Recents advances indicate that the development of oral candidiasis is driven both by Candida albicans overgrowth in a dysbiotic microbiome and by disturbances in the host's immune system. Perturbation of the oral microbiota triggered by host-extrinsic (ie, medications), host-intrinsic (ie, host genetics), and microbiome-intrinsic (ie, microbial interactions) factors may increase the risk of oral candidiasis. In this review, we provide an overview of the oral mycobiome, with a particular focus on the interactions of Candida albicans with some of the most common oral bacteria and the oral mucosal immune system. Also, we present a summary of our current knowledge of the host-intrinsic and host-extrinsic factors that can predispose to oral candidiasis.
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Affiliation(s)
- Cristina Cunha Villar
- Division of Periodontics, Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Anna Dongari-Bagtzoglou
- Department of Oral Health and Diagnostic Sciences, University of Connecticut School of Dental Medicine, Farmington, CT, USA
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28
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Barabona G, Mahiti M, Toyoda M, Kamori D, Masoud S, Judicate GP, Sunguya B, Lyamuya E, Ueno T. Advanced baseline immunosuppression is associated with elevated levels of plasma markers of fungal translocation and inflammation in long-term treated HIV-infected Tanzanians. AIDS Res Ther 2021; 18:55. [PMID: 34446039 PMCID: PMC8394626 DOI: 10.1186/s12981-021-00381-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/17/2021] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND For over a decade, antiretroviral therapy (ART) in resource-limited countries was only recommended for patients with advanced HIV disease. We investigated this group of patients in order to determine any relationship between degree of immunosuppression during treatment initiation and the subsequent levels of inflammatory biomarkers, reservoir size and plasma marker of fungal translocation after achieving long-term virological control. METHODS We analyzed 115 virally suppressed (female 83.5%) and 40 untreated (female 70%) subjects from Dar es Salaam, Tanzania. The size of HIV latent reservoir (proviral DNA copy) was determined using quantitative PCR. Inflammatory biomarkers; IL-6, IL-10, and soluble CD14 (sCD14), were measured using multiplex cytometric beads array. Antibody titers for Cytomegalovirus (CMV) and Epstein Barr virus (EBV), plasma level of 1-3-beta-D-Glucan (BDG) was measured using ELISA. High-sensitivity C-reactive protein (hsCRP) was measured using nephelometric method. RESULTS The median age was 36 (IQR 32-44) and 47 (IQR 43-54) years in untreated and virally suppressed patients respectively. Median duration of treatment for virally suppressed patients was 9 years (IQR 7-12) and median baseline CD4 count was 147 cells/mm3 (IQR 65-217). Virally suppressed patients were associated with significantly lower plasma levels of IL-10, sCD14 and BDG (P < 0.05) when compared to untreated patients. However, plasma level of IL-6 was similar between the groups. Baseline advanced level of immunosuppression (CD4 < 100cells/cm3) was associated with significantly higher plasma level of IL-6 (P = 0.02), hsCRP (P = 0.036) and BDG (P = 0.0107). This relationship was not seen in plasma levels of other tested markers. Degree of baseline immunosuppression was not associated with the subsequent proviral DNA copy. In addition, plasma levels of inflammatory marker were not associated with sex, CMV or EBV antibody titers, treatment duration or regimen. CONCLUSIONS Our data suggest that advanced immunosuppression at ART initiation is associated with severity of inflammation and elevated fungal translocation marker despite long term virological control. Further studies are needed to evaluate the potential increased burden of non-AIDS comorbidities that are linked to elevated inflammatory and fungal translocation markers as a result of the policy of HIV treatment at CD4 count < 200 cells/cm3 implemented for over a decade in Tanzania.
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Affiliation(s)
- Godfrey Barabona
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, 2-2-1 Chuo-ku, Honjo, Kumamoto, 860-0811, Japan
| | - Macdonald Mahiti
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Mako Toyoda
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, 2-2-1 Chuo-ku, Honjo, Kumamoto, 860-0811, Japan
| | - Doreen Kamori
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Salim Masoud
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - George P Judicate
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, 2-2-1 Chuo-ku, Honjo, Kumamoto, 860-0811, Japan
| | - Bruno Sunguya
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, 2-2-1 Chuo-ku, Honjo, Kumamoto, 860-0811, Japan
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Eligius Lyamuya
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, 2-2-1 Chuo-ku, Honjo, Kumamoto, 860-0811, Japan
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Takamasa Ueno
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, 2-2-1 Chuo-ku, Honjo, Kumamoto, 860-0811, Japan.
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.
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Markazi A, Meng W, Bracci PM, McGrath MS, Gao SJ. The Role of Bacteria in KSHV Infection and KSHV-Induced Cancers. Cancers (Basel) 2021; 13:cancers13174269. [PMID: 34503079 PMCID: PMC8428360 DOI: 10.3390/cancers13174269] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/05/2021] [Accepted: 08/19/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The aim of this article is to review the complex interactions of bacteria with Kaposi’s sarcoma-associated herpesvirus (KSHV) infection and KSHV-induced cancers. KSHV is causally associated with multiple cancers including Kaposi’s sarcoma (KS) and primary effusion lymphoma. Among patients coinfected by HIV and KSHV, patients with KS have a distinct oral microbiome compared to patients without KS. Moreover, KSHV patients have increased levels of salivary bacterial pathogen-associated molecular patterns compared to KSHV-negative patients. KSHV-associated bacterial species can increase KSHV replication and dissemination, and enhance cell proliferation of KSHV-transformed cells. The analysis of bacterial biomarkers associated with KSHV may help improve our understanding of the mechanisms driving KSHV-induced oncogenesis and identify novel targets for improving therapies of KSHV-related cancers. Abstract The objective of this article is to review the current status of the bacteria-virus interplay in Kaposi’s sarcoma-associated herpesvirus (KSHV) infection and KSHV-driven cancers. KSHV is the etiological agent of several cancers, including Kaposi’s sarcoma (KS) and primary effusion lymphoma. Due to immunosuppression, patients with KSHV are at an increased risk for bacterial infections. Moreover, among patients coinfected by HIV and KSHV, patients with KS have distinct oral microbiota compared to non-KS patients. Bacterial biomarkers associated with KSHV-driven cancers can provide insights in discerning the mechanisms of KSHV-induced oncogenesis. For example, pathogen-associated molecular patterns and bacterial products of certain bacterial species can regulate the expression of KSHV lytic and latent genes, thereby affecting viral replication and dissemination. In addition, infection with distinct opportunistic bacterial species have been associated with increased cell proliferation and tumorigenesis in KSHV-induced cancers through activation of pro-survival and -mitogenic cell signaling pathways. By elucidating the various mechanisms in which bacteria affect KSHV-associated pathogenesis, we will be able to pinpoint therapeutic targets for KSHV infection and KSHV-related cancers.
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Affiliation(s)
- Ashley Markazi
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA; (A.M.); (W.M.)
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Wen Meng
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA; (A.M.); (W.M.)
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Paige M. Bracci
- Department of Epidemiology and Biostatistics, University of California at San Francisco, San Francisco, CA 94158, USA;
| | - Michael S. McGrath
- Department of Laboratory Medicine, Pathology and Medicine, University of California at San Francisco, San Francisco, CA 94143, USA;
| | - Shou-Jiang Gao
- Cancer Virology Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA; (A.M.); (W.M.)
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
- Correspondence:
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30
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Brookes ZLS, Belfield LA, Ashworth A, Casas-Agustench P, Raja M, Pollard AJ, Bescos R. Effects of chlorhexidine mouthwash on the oral microbiome. J Dent 2021; 113:103768. [PMID: 34418463 DOI: 10.1016/j.jdent.2021.103768] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/11/2021] [Accepted: 07/29/2021] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION/OBJECTIVES Chlorhexidine (CHX) is a commonly used mouthwash with potent anti-microbial effects useful for the management of oral disease. However, we are moving away from the view of simply 'killing' bacteria, towards managing oral microbial ecosystems (oral microbiome), as an integrated system, to promote oral and systemic health. Here, we aimed to review the effects of CHX mouthwash on the balance of microbial communities in the mouth in vivo in oral health and disease. SOURCES AND STUDY SECTION The hierarchy of evidence was applied, with systematic reviews and randomised controlled trials consulted where available and case controlled studies being described thereafter. Search terms for each subject category were entered into MEDLINE, PubMed, Google Scholar and the Cochrane database. Focussing on metagenomics studies provides unique overview of the oral microbiome as an integrated system. DATA Evidence was limited, but several next generation sequencing case-controlled studies suggested that in an integrated system, CHX may cause a shift towards lower bacterial diversity and abundance, in particular nitrate-reducing bacteria in vivo. CHX also appeared to alter salivary pH, lactate, nitrate and nitrite concentrations in saliva. Evidence regarding the effects of CHX on the oral microbiome during oral disease is still emerging. CONCLUSIONS CHX alters the composition the oral microbiome. However, as CHX use remains widespread in dentistry to manage oral disease, urgent research using metagenomics studies of microbial communities in vivo are still needed to determine CHX mouthwash is 'good', 'bad' or otherwise for bacteria, in the context of oral and systemic health.
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Affiliation(s)
- Zoë L S Brookes
- Peninsula Dental School, Faculty of Health, University of Plymouth, Plymouth, PL4 8AA, United Kingdom.
| | - Louise A Belfield
- Peninsula Dental School, Faculty of Health, University of Plymouth, Plymouth, PL4 8AA, United Kingdom
| | - Ann Ashworth
- Institute of Health & Community, University of Plymouth, Plymouth, PL4 8AA, United Kingdom
| | - Patricia Casas-Agustench
- School of Health Professions, Faculty of Health, University of Plymouth, Plymouth, PL4 8AA, United Kingdom; Department of Health Sciences, Open University of Catalonia, Barcelona, Spain
| | | | - Alexander J Pollard
- Peninsula Dental School, Faculty of Health, University of Plymouth, Plymouth, PL4 8AA, United Kingdom; Bristol Dental School, University of Bristol, Bristol BS1 2LY, United Kingdom
| | - Raul Bescos
- School of Health Professions, Faculty of Health, University of Plymouth, Plymouth, PL4 8AA, United Kingdom.
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31
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Srinivasan M. Taste Dysfunction and Long COVID-19. Front Cell Infect Microbiol 2021; 11:716563. [PMID: 34336725 PMCID: PMC8317431 DOI: 10.3389/fcimb.2021.716563] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 06/28/2021] [Indexed: 12/15/2022] Open
Affiliation(s)
- Mythily Srinivasan
- Department of Oral Pathology, Medicine and Radiology, Indiana University School of Dentistry, Indiana University Purdue University at Indianapolis, Indianapolis, IN, United States
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32
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Li S, Zhu J, Su B, Wei H, Chen F, Liu H, Wei J, Yang X, Zhang Q, Xia W, Wu H, He Q, Zhang T. Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy. Front Cell Infect Microbiol 2021; 11:695515. [PMID: 34336719 PMCID: PMC8317457 DOI: 10.3389/fcimb.2021.695515] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022] Open
Abstract
Despite the antiretroviral therapy (ART), human immunodeficiency virus (HIV)-related oral disease remains a common problem for people living with HIV (PLWH). Evidence suggests that impairment of immune function in HIV infection might lead to the conversion of commensal bacteria to microorganisms with increased pathogenicity. However, limited information is available about alteration in oral microbiome in PLWH on ART. We performed a longitudinal comparative study on men who have sex with men (MSM) with acute HIV infection (n=15), MSM with chronic HIV infection (n=15), and HIV-uninfected MSM controls (n=15). Throat swabs were collected when these subjects were recruited (W0) and 12 weeks after ART treatment (W12) from the patients. Genomic DNAs were extracted and 16S rRNA gene sequencing was performed. Microbiome diversity was significantly decreased in patients with acute and chronic HIV infections compared with those in controls at the sampling time of W0 and the significant difference remained at W12. An increased abundance of unidentified Prevotellaceae was found in patients with acute and chronic HIV infections. Moreover, increased abundances of Prevotella in subjects with acute HIV infection and Streptococcus in subjects with chronic HIV infection were observed. In contrast, greater abundance in Lactobacillus, Rothia, Lautropia, and Bacteroides was found in controls. After effective ART, Bradyrhizobium was enriched in both acute and chronic HIV infections, whereas in controls, Lactobacillus, Rothia, Clostridia, Actinobacteria, and Ruminococcaceae were enriched. In addition, we found that lower CD4+ T-cell counts (<200 cells/mm3) were associated with lower relative abundances of Haemophilus, Actinomyces, unidentified Ruminococcaceae, and Rothia. This study has shown alteration in oral microbiome resulting from HIV infection and ART. The results obtained warrant further studies in a large number of subjects with different ethnics. It might contribute to improved oral health in HIV-infected individuals.
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Affiliation(s)
- Shuang Li
- Beijing Key Laboratory for HIV/AIDS Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Junping Zhu
- Department of Medical Microbiology, Capital Medical University, Beijing, China
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Huanhuan Wei
- Department of Medical Microbiology, Capital Medical University, Beijing, China
| | - Fei Chen
- Department of Medical Microbiology, Capital Medical University, Beijing, China
| | - Hongshan Liu
- Department of Medical Microbiology, Capital Medical University, Beijing, China
| | - Jiaqi Wei
- Beijing Key Laboratory for HIV/AIDS Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xiaodong Yang
- Beijing Key Laboratory for HIV/AIDS Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Qiuyue Zhang
- Beijing Key Laboratory for HIV/AIDS Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Wei Xia
- Beijing Key Laboratory for HIV/AIDS Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Hao Wu
- Beijing Key Laboratory for HIV/AIDS Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Qiushui He
- Department of Medical Microbiology, Capital Medical University, Beijing, China.,Institute of Biomedicine, Research Center for Infections and Immunity, University of Turku, Turku, Finland
| | - Tong Zhang
- Beijing Key Laboratory for HIV/AIDS Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
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Abstract
The oral microbiome is likely a key element of homeostasis in the oral cavity. With >600 bacterial species and >160 fungal species comprising the oral microbiome, influences on its composition can have an impact on both local and systemic health. The oral microbiome is considered an important factor in health and disease. We recently reported significant effects of HIV and several other clinical variables on the oral bacterial communities in a large cohort of HIV-positive and -negative individuals. The purpose of the present study was to similarly analyze the oral mycobiome in the same cohort. To identify fungi, the internal transcribed spacer 2 (ITS2) of the fungal rRNA genes was sequenced using oral rinse samples from 149 HIV-positive and 88 HIV-negative subjects that had previously undergone bacterial amplicon sequencing. Quantitative PCR was performed for total fungal content and total bacterial content. Interestingly, samples often showed predominance of a single fungal species with four major clusters predominated by Candida albicans, Candida dubliniensis, Malassezia restricta, or Saccharomyces cerevisiae. Quantitative PCR analysis showed the Candida-dominated sample clusters had significantly higher total fungal abundance than the Malassezia or Saccharomyces species. Of the 25 clinical variables evaluated for potential influences on the oral mycobiome, significant effects were associated with caries status, geographical site of sampling, sex, HIV under highly active antiretroviral therapy (HAART), and missing teeth, in rank order of statistical significance. Investigating specific interactions between fungi and bacteria in the samples often showed Candida species positively correlated with Firmicutes or Actinobacteria and negatively correlated with Fusobacteria, Proteobacteria, and Bacteroidetes. Our data suggest that the oral mycobiome, while diverse, is often dominated by a limited number of species per individual; is affected by several clinical variables, including HIV positivity and HAART; and shows genera-specific associations with bacterial groups.
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Gut dysbiosis and mortality in hemodialysis patients. NPJ Biofilms Microbiomes 2021; 7:20. [PMID: 33658514 PMCID: PMC7930281 DOI: 10.1038/s41522-021-00191-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 01/27/2021] [Indexed: 02/08/2023] Open
Abstract
Little is known about the relationship between gut dysbiosis, inflammation, and adverse outcomes in patients with chronic kidney disease. We examined the association of microbial diversity with all-cause mortality in hemodialysis patients. The gut microbiota was assessed by 16S ribosomal RNA gene sequencing. During a median follow-up of 2.1 years, the adjusted risk of death among patients with higher diversity (above median) was 74% lower than that among patients with lower diversity (below median). We then compared the microbial composition between nonsurvivors and survivors in a matched case-control study. We observed significantly lower microbial diversity and higher proinflammatory cytokines among nonsurvivors than survivors. Specifically, the relative abundance of Succinivibrio and Anaerostipes, two short-chain fatty acid-producing bacteria, was markedly reduced in nonsurvivors. Thus, a unique gut microbial composition is associated with an increased risk of mortality among hemodialysis patients and may be used to identify subjects with a poor prognosis.
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35
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Geng ST, Zhang ZY, Wang YX, Lu D, Yu J, Zhang JB, Kuang YQ, Wang KH. Regulation of Gut Microbiota on Immune Reconstitution in Patients With Acquired Immunodeficiency Syndrome. Front Microbiol 2020; 11:594820. [PMID: 33193273 PMCID: PMC7652894 DOI: 10.3389/fmicb.2020.594820] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/28/2020] [Indexed: 12/12/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) infection of CD4+ T cells in the gut plays an insidious role in acquired immunodeficiency syndrome (AIDS) pathogenesis. Host immune function is closely related to gut microbiota. Changes in the gut microbiota cause a different immune response. Previous studies revealed that HIV-1 infection caused changes in gut microbiota, which induced immune deficiency. HIV-1 infection results in an abnormal composition and function of the gut microbiota, which may disrupt the intestinal epithelial barrier and microbial translocation, leading to long-term immune activation, including inflammation and metabolic disorders. At the same time, an abnormal gut microbiota also hinders the effect of antiviral therapy and affects the immune reconstruction of patients. However, studies on the impact of the gut microbiota on immune reconstitution in patients with HIV/AIDS are still limited. In this review, we focus on changes in the gut microbiota caused by HIV infection, as well as the impact and regulation of the gut microbiota on immune function and immune reconstitution, while we also discuss the potential impact of probiotics/prebiotics and fecal microbiota transplantation (FMT) on immune reconstitution.
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Affiliation(s)
- Shi-Tao Geng
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.,Department of Gastrointestinal and Hernia Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Zun-Yue Zhang
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yue-Xin Wang
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.,Department of Gastrointestinal and Hernia Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Danfeng Lu
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Juehua Yu
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jian-Bo Zhang
- Department of Dermatology, Second People's Hospital of Dali City, Dali, China
| | - Yi-Qun Kuang
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Kun-Hua Wang
- NHC Key Laboratory of Drug Addiction Medicine, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China.,Department of Gastrointestinal and Hernia Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China.,Scientific Research Laboratory Center, First Affiliated Hospital of Kunming Medical University, Kunming, China
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36
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Diaz PI, Dongari-Bagtzoglou A. Critically Appraising the Significance of the Oral Mycobiome. J Dent Res 2020; 100:133-140. [PMID: 32924741 DOI: 10.1177/0022034520956975] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Recent efforts to understand the oral microbiome have focused on its fungal component. Since fungi occupy a low proportion of the oral microbiome biomass, mycobiome studies rely on sequencing of internal transcribed spacer (ITS) amplicons. ITS-based studies usually detect hundreds of fungi in oral samples. Here, we review the oral mycobiome, critically appraising the significance of such large fungal diversity. When harsh lysis methods are used to extract DNA, 2 oral mycobiome community types (mycotypes) are evident, each dominated by only 1 genus, either Candida or Malassezia. The rest of the diversity in ITS surveys represents low-abundance fungi possibly acquired from the environment and ingested food. So far, Candida is the only genus demonstrated to reach a significant biomass in the oral cavity and clearly shown to be associated with a distinct oral ecology. Candida thrives in the presence of lower oral pH and is enriched in caries, with mechanistic studies in animal models suggesting it participates in the disease process by synergistically interacting with acidogenic bacteria. Candida serves as the main etiological agent of oral mucosal candidiasis, in which a Candida-bacteriome partnership plays a key role. The function of other potential oral colonizers, such as lipid-dependent Malassezia, is still unclear, with further studies needed to establish whether Malassezia are metabolically active oral commensals. Low-abundance oral mycobiome members acquired from the environment may be viable in the oral cavity, and although they may not play a significant role in microbiome communities, they could serve as opportunistic pathogens in immunocompromised hosts. We suggest that further work is needed to ascertain the significance of oral mycobiome members beyond Candida. ITS-based surveys should be complemented with other methods to determine the in situ biomass and metabolic state of fungi thought to play a role in the oral environment.
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Affiliation(s)
- P I Diaz
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, State University of New York, Buffalo, NY, USA.,UB Microbiome Center, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - A Dongari-Bagtzoglou
- Division of Periodontology, Department of Oral Health and Diagnostic Sciences, School of Dental Medicine, UConn Health, Farmington, CT, USA
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37
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Sodré CS, Rodrigues PMG, Vieira MS, Marques Paes da Silva A, Gonçalves LS, Ribeiro MG, de Carvalho Ferreira D. Oral mycobiome identification in atopic dermatitis, leukemia, and HIV patients - a systematic review. J Oral Microbiol 2020; 12:1807179. [PMID: 32944157 PMCID: PMC7482892 DOI: 10.1080/20002297.2020.1807179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/27/2020] [Accepted: 08/03/2020] [Indexed: 01/04/2023] Open
Abstract
INTRODUCTION Oral mycobiome profiling is important to understand host-pathogen interactions that occur in various diseases. Invasive fungal infections are particularly relevant for patients who have received chemotherapy and for those who have HIV infection. In addition, changes in fungal microbiota are associated with the worsening of chronic conditions like atopic dermatitis (AD). This work aims, through a systematic review, to analyze the methods used in previous studies to identify oral fungi and their most frequent species in patients with the following conditions: HIV infection, leukemia, and atopic dermatitis. METHODS A literature search was performed on several different databases. Inclusion criteria were: written in English or Portuguese; published between September 2009 and September 2019; analyzed oral fungi of HIV-infected, leukemia, or AD patients. RESULTS 21 studies were included and the most identified species was Candida. The predominant methods of identification were morphological (13/21) and sugar fermentation and assimilation tests (11/21). Polymerase chain reaction (PCR) was the most used molecular method (8/21) followed by sequencing techniques (3/21). CONCLUSIONS Although morphological and biochemical tests are still used, they are associated with high-throughput sequencing techniques, due to their accuracy and time saving for profiling the predominant species in oral mycobiome.
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Affiliation(s)
- Camila Stofella Sodré
- Faculty of Medicine, Department of Clinical Medicine, Universidade Federal do Rio de Janeiro - UFRJ, Rio de Janeiro, Brazil
| | - Paulo Matheus Guerra Rodrigues
- Laboratory of Oral and Systemic Infections, Faculty of Dentistry, Estácio de Sá University- UNESA, Rio de Janeiro, Brazil
| | | | | | - Lucio Souza Gonçalves
- Laboratory of Oral and Systemic Infections, Faculty of Dentistry, Estácio de Sá University- UNESA, Rio de Janeiro, Brazil
| | - Marcia Gonçalves Ribeiro
- Medical Genetics Service, Martagão Gesteira Pediatric Institute (IPPMG- UFRJ), Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, Brazil
| | - Dennis de Carvalho Ferreira
- Laboratory of Oral and Systemic Infections, Faculty of Dentistry, Estácio de Sá University- UNESA, Rio de Janeiro, Brazil
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38
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Alvarez X, Sestak K, Byrareddy SN, Mohan M. Long Term Delta-9-tetrahydrocannabinol Administration Inhibits Proinflammatory Responses in Minor Salivary Glands of Chronically Simian Immunodeficieny Virus Infected Rhesus Macaques. Viruses 2020; 12:v12070713. [PMID: 32630206 PMCID: PMC7412369 DOI: 10.3390/v12070713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
HIV/SIV-associated oral mucosal disease/dysfunction (HAOMD) (gingivitis/periodontitis/salivary adenitis) represents a major comorbidity affecting HIV patients on anti-retroviral therapy. Using a systems biology approach, we investigated molecular changes (mRNA/microRNA) underlying HAOMD and its modulation by phytocannabinoids (delta-9-tetrahydrocannabinol (∆9-THC)) in uninfected (n = 5) and SIV-infected rhesus macaques untreated (VEH-untreated/SIV; n = 7) or treated with vehicle (VEH/SIV; n = 3) or ∆9-THC (THC/SIV; n = 3). Relative to controls, fewer mRNAs were upregulated in THC/SIV compared to VEH-untreated/SIV macaques. Gene enrichment analysis showed differential enrichment of biological functions involved in anti-viral defense, Type-I interferon, Toll-like receptor, RIG-1 and IL1R signaling in VEH-untreated/SIV macaques. We focused on the anti-ER-stress anterior gradient-2 (AGR2), epithelial barrier protecting and anti-dysbiotic WAP Four-Disulfide Core Domain-2 (WFDC2) and glucocorticoid-induced anti-inflammatory TSC22D3 (TSC22-domain family member-3) that were significantly downregulated in oropharyngeal mucosa (OPM) of VEH-untreated/SIV macaques. All three proteins localized to minor salivary gland acini and secretory ducts and showed enhanced and reduced expression in OPM of THC/SIV and VEH/SIV macaques, respectively. Additionally, inflammation associated miR-21, miR-142-3p and miR-29b showed significantly higher expression in OPM of VEH-untreated/SIV macaques. TSC22D3 was validated as a target of miR-29b. These preliminary translational findings suggest that phytocannabinoids may safely and effectively reduce oral inflammatory responses in HIV/SIV and other (autoimmune) diseases.
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Affiliation(s)
- Xavier Alvarez
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
| | - Karol Sestak
- PreCliniTria, LLC., Mandeville, LA 70471, USA;
- Tulane National Primate Research Center, Covington, LA 70433, USA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Correspondence: (S.N.B.); (M.M.)
| | - Mahesh Mohan
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
- Correspondence: (S.N.B.); (M.M.)
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Abstract
Alterations in the gut microbiome during HIV infection have been implicated in chronic inflammation, but the role of the oral microbiome in this process is less clear. The article by M. K. Annavajhala, S. D. Khan, S. B. Sullivan, J. Alterations in the gut microbiome during HIV infection have been implicated in chronic inflammation, but the role of the oral microbiome in this process is less clear. The article by M. K. Annavajhala, S. D. Khan, S. B. Sullivan, J. Shah, et al. (mSphere 5:e00798-19, 2020, https://doi.org/10.1128/mSphere.00798-19) investigated the relationship between oral and gut microbiome diversity and immune activation in patients with HIV on antiretroviral therapy. In this study, oral microbiome diversity was inversely associated with inflammatory markers such as soluble CD14 (sCD14), but surprisingly similar associations were not seen with gut microbiome diversity. Oral microbiome diversity was also associated with periodontitis in these patients. This study highlights the importance of continuing multisite examinations in studying the gastrointestinal tract microbiome and also stimulates important directions for future research defining the role of the oral-gut axis in HIV-associated inflammation.
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