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Moreno E, Ciordia S, Fátima SM, Jiménez D, Martínez-Sanz J, Vizcarra P, Ron R, Sánchez-Conde M, Bargiela R, Sanchez-Carrillo S, Moreno S, Corrales F, Ferrer M, Serrano-Villar S. Proteomic snapshot of saliva samples predicts new pathways implicated in SARS-CoV-2 pathogenesis. Clin Proteomics 2024; 21:37. [PMID: 38778280 PMCID: PMC11112864 DOI: 10.1186/s12014-024-09482-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Information on the microbiome's human pathways and active members that can affect SARS-CoV-2 susceptibility and pathogenesis in the salivary proteome is very scarce. Here, we studied a unique collection of samples harvested from April to June 2020 from unvaccinated patients. METHODS We compared 10 infected and hospitalized patients with severe (n = 5) and moderate (n = 5) coronavirus disease (COVID-19) with 10 uninfected individuals, including non-COVID-19 but susceptible individuals (n = 5) and non-COVID-19 and nonsusceptible healthcare workers with repeated high-risk exposures (n = 5). RESULTS By performing high-throughput proteomic profiling in saliva samples, we detected 226 unique differentially expressed (DE) human proteins between groups (q-value ≤ 0.05) out of 3376 unambiguously identified proteins (false discovery rate ≤ 1%). Major differences were observed between the non-COVID-19 and nonsusceptible groups. Bioinformatics analysis of DE proteins revealed human proteomic signatures related to inflammatory responses, central cellular processes, and antiviral activity associated with the saliva of SARS-CoV-2-infected patients (p-value ≤ 0.0004). Discriminatory biomarker signatures from human saliva include cystatins, protective molecules present in the oral cavity, calprotectins, involved in cell cycle progression, and histones, related to nucleosome functions. The expression levels of two human proteins related to protein transport in the cytoplasm, DYNC1 (p-value, 0.0021) and MAPRE1 (p-value, 0.047), correlated with angiotensin-converting enzyme 2 (ACE2) plasma activity. Finally, the proteomes of microorganisms present in the saliva samples showed 4 main microbial functional features related to ribosome functioning that were overrepresented in the infected group. CONCLUSION Our study explores potential candidates involved in pathways implicated in SARS-CoV-2 susceptibility, although further studies in larger cohorts will be necessary.
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Affiliation(s)
- Elena Moreno
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain.
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - Sergio Ciordia
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Santos Milhano Fátima
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Daniel Jiménez
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
| | - Javier Martínez-Sanz
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Pilar Vizcarra
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Raquel Ron
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Matilde Sánchez-Conde
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Rafael Bargiela
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Sergio Sanchez-Carrillo
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049, Madrid, Spain
- Centro de Biologia Molecular Severo Ochoa (CBM), CSIC-UAM, 28049, Madrid, Spain
| | - Santiago Moreno
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Facultad de Medicina, Universidad de Alcalá de Henares, 28801, Alcalá de Henares, Madrid, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049, Madrid, Spain
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
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Zhou S, Zhu W, Guo H, Nie Y, Sun J, Liu P, Zeng Y. Microbes for lung cancer detection: feasibility and limitations. Front Oncol 2024; 14:1361879. [PMID: 38779090 PMCID: PMC11109454 DOI: 10.3389/fonc.2024.1361879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
As the second most common cancer in the world, the development of lung cancer is closely related to factors such as heredity, environmental exposure, and lung microenvironment, etc. Early screening and diagnosis of lung cancer can be helpful for the treatment of patients. Currently, CT screening and histopathologic biopsy are widely used in the clinical detection of lung cancer, but they have many disadvantages such as false positives and invasive operations. Microbes are another genome of the human body, which has recently been shown to be closely related to chronic inflammatory, metabolic processes in the host. At the same time, they are important players in cancer development, progression, treatment, and prognosis. The use of microbes for cancer therapy has been extensively studied, however, the diagnostic role of microbes is still unclear. This review aims to summarize recent research on using microbes for lung cancer detection and present the current shortcomings of microbes in collection and detection. Finally, it also looks ahead to the clinical benefits that may accrue to patients in the future about screening and early detection.
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Affiliation(s)
- Sirui Zhou
- Department of Respiration, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weijian Zhu
- Department of Orthopedics, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hehua Guo
- Department of Respiration, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yalan Nie
- Department of Respiration, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiazheng Sun
- Department of Respiration, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ping Liu
- Department of Orthopedics, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yulan Zeng
- Department of Respiration, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Park J, Jung SY, Kim HY, Lee KE, Go YJ, Kim HS, Yoon SY, Kwon CO, Park YS. Microbiomic association between the saliva and salivary stone in patients with sialolithiasis. Sci Rep 2024; 14:9184. [PMID: 38649387 PMCID: PMC11035639 DOI: 10.1038/s41598-024-59546-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
Salivary stones, known as sialoliths, form within the salivary ducts due to abnormal salivary composition and cause painful symptoms, for which surgical removal is the primary treatment. This study explored the role of the salivary microbial communities in the formation of sialoliths. We conducted a comparative analysis of microbial communities present in the saliva and salivary stones, and sequenced the 16S rRNA gene in samples obtained from patients with sialoliths and from healthy individuals. Although the diversity in the saliva was high, the essential features of the microbial environment in sialoliths were low diversity and evenness. The association of microbial abundance between stones and saliva revealed a positive correlation between Peptostreptococcus and Porphyromonas, and a negative correlation for Pseudomonas in saliva. The functional potential differences between saliva and stones Bacterial chemotaxis and the citrate cycle were negatively correlated with most genera found in salivary stone samples. However, the functions required for organic compound degradation did not differ between the saliva samples. Although some microbes were shared between the sialoliths and saliva, their compositions differed significantly. Our study presents a novel comparison between salivary stones and salivary microbiomes, suggesting potential preventive strategies against sialolithiasis.
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Affiliation(s)
- Jiwon Park
- Department of Biological Sciences and Biotechnology, School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Soo Yeon Jung
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Ewha Womans University, Seoul, 07865, Republic of Korea.
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Ewha Womans University, 1071 Anyangcheon-ro, Yangcheon-gu, Seoul, 07985, Republic of Korea.
| | - Ha Yeong Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Ewha Womans University, Seoul, 07865, Republic of Korea
| | - Kyeong Eun Lee
- Department of Biological Sciences and Biotechnology, School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Yu Jin Go
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Ewha Womans University, Seoul, 07865, Republic of Korea
| | - Han Su Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Ewha Womans University, Seoul, 07865, Republic of Korea
| | | | - Cheol-O Kwon
- MD Healthcare Inc., Seoul, 03923, Republic of Korea
| | - Yoon Shin Park
- Department of Biological Sciences and Biotechnology, School of Biological Sciences, College of Natural Sciences, Chungbuk National University, Cheongju, 28644, Republic of Korea.
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Buendia P, Fernandez K, Raley C, Rahnavard A, Crandall KA, Castro JG. Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics. Front Microbiol 2024; 15:1346762. [PMID: 38476940 PMCID: PMC10927822 DOI: 10.3389/fmicb.2024.1346762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/22/2024] [Indexed: 03/14/2024] Open
Abstract
Introduction During the COVID-19 Delta variant surge, the CLAIRE cross-sectional study sampled saliva from 120 hospitalized patients, 116 of whom had a positive COVID-19 PCR test. Patients received antibiotics upon admission due to possible secondary bacterial infections, with patients at risk of sepsis receiving broad-spectrum antibiotics (BSA). Methods The saliva samples were analyzed with shotgun DNA metagenomics and respiratory RNA virome sequencing. Medical records for the period of hospitalization were obtained for all patients. Once hospitalization outcomes were known, patients were classified based on their COVID-19 disease severity and the antibiotics they received. Results Our study reveals that BSA regimens differentially impacted the human salivary microbiome and disease progression. 12 patients died and all of them received BSA. Significant associations were found between the composition of the COVID-19 saliva microbiome and BSA use, between SARS-CoV-2 genome coverage and severity of disease. We also found significant associations between the non-bacterial microbiome and severity of disease, with Candida albicans detected most frequently in critical patients. For patients who did not receive BSA before saliva sampling, our study suggests Staphylococcus aureus as a potential risk factor for sepsis. Discussion Our results indicate that the course of the infection may be explained by both monitoring antibiotic treatment and profiling a patient's salivary microbiome, establishing a compelling link between microbiome and the specific antibiotic type and timing of treatment. This approach can aid with emergency room triage and inpatient management but also requires a better understanding of and access to narrow-spectrum agents that target pathogenic bacteria.
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Affiliation(s)
| | | | - Castle Raley
- The George Washington University Genomics Core, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Ali Rahnavard
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Keith A. Crandall
- The George Washington University Genomics Core, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Jose Guillermo Castro
- Division of Infectious Diseases, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, United States
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Meslier V, Menozzi E, David A, Morabito C, Lucas Del Pozo S, Famechon A, North J, Quinquis B, Koletsi S, Macnaughtan J, Mezabrovschi R, Ehrlich SD, Schapira AHV, Almeida M. Evaluation of an Adapted Semi-Automated DNA Extraction for Human Salivary Shotgun Metagenomics. Biomolecules 2023; 13:1505. [PMID: 37892187 PMCID: PMC10604855 DOI: 10.3390/biom13101505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/29/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Recent attention has highlighted the importance of oral microbiota in human health and disease, e.g., in Parkinson's disease, notably using shotgun metagenomics. One key aspect for efficient shotgun metagenomic analysis relies on optimal microbial sampling and DNA extraction, generally implementing commercial solutions developed to improve sample collection and preservation, and provide high DNA quality and quantity for downstream analysis. As metagenomic studies are today performed on a large number of samples, the next evolution to increase study throughput is with DNA extraction automation. In this study, we proposed a semi-automated DNA extraction protocol for human salivary samples collected with a commercial kit, and compared the outcomes with the DNA extraction recommended by the manufacturer. While similar DNA yields were observed between the protocols, our semi-automated DNA protocol generated significantly higher DNA fragment sizes. Moreover, we showed that the oral microbiome composition was equivalent between DNA extraction methods, even at the species level. This study demonstrates that our semi-automated protocol is suitable for shotgun metagenomic analysis, while allowing for improved sample treatment logistics with reduced technical variability and without compromising the structure of the oral microbiome.
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Affiliation(s)
- Victoria Meslier
- MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France (C.M.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
| | - Elisa Menozzi
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London (UCL), London WC1E 6BT, UK
| | - Aymeric David
- MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France (C.M.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
| | - Christian Morabito
- MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France (C.M.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
| | - Sara Lucas Del Pozo
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London (UCL), London WC1E 6BT, UK
| | - Alexandre Famechon
- MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France (C.M.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
| | - Janet North
- Research Department of Hematology, Cancer Institute, University College London (UCL), London WC1E 6BT, UK
| | - Benoit Quinquis
- MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France (C.M.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
| | - Sofia Koletsi
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London (UCL), London WC1E 6BT, UK
| | - Jane Macnaughtan
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
- Liver Failure Group, Institute for Liver and Digestive Health, University College London, London WC1E 6BT, UK
| | - Roxana Mezabrovschi
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London (UCL), London WC1E 6BT, UK
| | - S. Dusko Ehrlich
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London (UCL), London WC1E 6BT, UK
| | - Anthony H. V. Schapira
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London (UCL), London WC1E 6BT, UK
| | - Mathieu Almeida
- MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France (C.M.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA (S.K.); (R.M.); (S.D.E.)
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Armstrong AJS, Horton DB, Andrews T, Greenberg P, Roy J, Gennaro ML, Carson JL, Panettieri RA, Barrett ES, Blaser MJ. Saliva microbiome in relation to SARS-CoV-2 infection in a prospective cohort of healthy US adults. EBioMedicine 2023; 94:104731. [PMID: 37487417 PMCID: PMC10382861 DOI: 10.1016/j.ebiom.2023.104731] [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: 03/16/2023] [Revised: 06/08/2023] [Accepted: 07/13/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND The clinical outcomes of SARS-CoV-2 infection vary in severity, potentially influenced by the resident human microbiota. There is limited consensus on conserved microbiome changes in response to SARS-CoV-2 infection, with many studies focusing on severely ill individuals. This study aimed to assess the variation in the upper respiratory tract microbiome using saliva specimens in a cohort of individuals with primarily mild to moderate disease. METHODS In early 2020, a cohort of 831 adults without known SARS-CoV-2 infection was followed over a six-month period to assess the occurrence and natural history of SARS-CoV-2 infection. From this cohort, 81 participants with a SARS-CoV-2 infection, along with 57 unexposed counterparts were selected with a total of 748 serial saliva samples were collected for analysis. Total bacterial abundance, composition, population structure, and gene function of the salivary microbiome were measured using 16S rRNA gene and shotgun metagenomic sequencing. FINDINGS The salivary microbiome remained stable in unexposed individuals over the six-month study period, as evidenced by all measured metrics. Similarly, participants with mild to moderate SARS-CoV-2 infection showed microbiome stability throughout and after their infection. However, there were significant reductions in microbiome diversity among SARS-CoV-2-positive participants with severe symptoms early after infection. Over time, the microbiome diversity in these participants showed signs of recovery. INTERPRETATION These findings demonstrate the resilience of the salivary microbiome in relation to SARS-CoV-2 infection. Mild to moderate infections did not significantly disrupt the stability of the salivary microbiome, suggesting its ability to maintain its composition and function. However, severe SARS-CoV-2 infection was associated with temporary reductions in microbiome diversity, indicating the limits of microbiome resilience in the face of severe infection. FUNDING This project was supported in part by Danone North America and grants from the National Institutes of Health, United States.
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Affiliation(s)
- Abigail J S Armstrong
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - Daniel B Horton
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA; Rutgers Center for Pharmacoepidemiology and Treatment Science, Institute for Health, Health Care Policy, and Aging Research, New Brunswick, New Jersey, USA; Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey, USA
| | - Tracy Andrews
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey, USA
| | - Patricia Greenberg
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey, USA
| | - Jason Roy
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey, USA
| | - Maria Laura Gennaro
- Department of Medicine, Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Jeffrey L Carson
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Reynold A Panettieri
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Emily S Barrett
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey, USA; Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, New Jersey, USA
| | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA.
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Bang E, Oh S, Ju U, Chang HE, Hong JS, Baek HJ, Kim KS, Lee HJ, Park KU. Factors influencing oral microbiome analysis: from saliva sampling methods to next-generation sequencing platforms. Sci Rep 2023; 13:10086. [PMID: 37344534 DOI: 10.1038/s41598-023-37246-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/19/2023] [Indexed: 06/23/2023] Open
Abstract
The exploration of oral microbiome has been increasing due to its relatedness with various systemic diseases, but standardization of saliva sampling for microbiome analysis has not been established, contributing to the lack of data comparability. Here, we evaluated the factors that influence the microbiome data. Saliva samples were collected by the two collection methods (passive drooling and mouthwash) using three saliva-preservation methods (OMNIgene, DNA/RNA shield, and simple collection). A total of 18 samples were sequenced by both Illumina short-read and Nanopore long-read next-generation sequencing (NGS). The component of the oral microbiome in each sample was compared with alpha and beta diversity and the taxonomic abundances, to find out the effects of factors on oral microbiome data. The alpha diversity indices of the mouthwash sample were significantly higher than that of the drooling group with both short-read and long-read NGS, while no significant differences in microbial diversities were found between the three saliva-preservation methods. Our study shows mouthwash and simple collection are not inferior to other sample collection and saliva-preservation methods, respectively. This result is promising since the convenience and cost-effectiveness of mouthwash and simple collection can simplify the saliva sample preparation, which would greatly help clinical operators and lab workers.
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Affiliation(s)
- Eunsik Bang
- Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sujin Oh
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Uijin Ju
- Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | - Jin-Sil Hong
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Hyeong-Jin Baek
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Keun-Suh Kim
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Hyo-Jung Lee
- Department of Periodontology, Section of Dentistry, Seoul National University Bundang Hospital, Seongnam, Republic of Korea.
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea.
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Noh JW, Jang JH, Yoon HS, Kim KB, Heo MH, Jang HE, Kim YJ, Lee Y. Evaluation of Salivary Biomarkers of Periodontal Disease Based on Smoking Status: A Systematic Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:14619. [PMID: 36361498 PMCID: PMC9657317 DOI: 10.3390/ijerph192114619] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
Saliva is a useful biomarker for diagnosing oral health conditions, including periodontal disease (PD). Smoking is a risk factor for PD. The aim of this systematic review was to summarize the salivary biomarkers associated with PD based on smoking status. A comprehensive search of the MEDLINE (via PubMed), EMBASE, Cochrane, SCOPUS, and Web of Sciences databases was conducted up to 1 January 2021 using key terms relevant to the topic of our research and Cochrane methodology and improved with searching a gray literature resource. The methodological quality of all included studies was assessed with the revised Quality Assessment of Diagnostic Accuracy Studies-2. Seven studies were included. Smokers had increased levels of malondialdehyde, sialic acid, salivary cortisol, salivary interleukin 1β, albumin, tissue inhibitor of matrix metalloproteinase (TIMP), and the pyridinoline cross-linked carboxyterminal telopeptide of type I collagen (ICTP), as well as decreased levels of superoxide dismutase, activity of lactate dehydrogenase, activity of enzyme activity of β-glucuronidase, uric acid, matrix metalloproteinase-8 (MMP-8)/TIMP-1 ratio, and combinations of MMP-8 and ICTP. However, mixed results were observed some studies in detecting glutathione peroxidase, MMP-8, and MMP-14. The results were interpreted with caution because of limitations in the number of included studies and the study design. Some salivary biomarkers are potentially useful in combination or alone for diagnosing PD. Methodological and systematic studies are needed to develop more effective biomarkers.
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Affiliation(s)
- Jin-won Noh
- Division of Health Administration, College of Software and Digital Healthcare Convergence, Yonsei University, Gangwon-do, Wonju 26493, Korea
| | - Jong-Hwa Jang
- Department of Dental Hygiene, College of Health Science, Dankook University, Chungcheongnam-do, Cheonan 31116, Korea
- Department of Public Health Science, Dankook University Graduate School, Chungcheongnam-do, Cheonan 31116, Korea
| | - Hae-Soo Yoon
- Department of Public Health Science, Dankook University Graduate School, Chungcheongnam-do, Cheonan 31116, Korea
| | - Kyoung-Beom Kim
- Department of Health Administration, Dankook University, Chungcheongnam-do, Cheonan 31116, Korea
- Industry-Academic Cooperation Foundation, Yonsei University, Gangwon-do, Wonju 26493, Korea
| | - Min-Hee Heo
- Department of Health Administration, Yonsei University Graduate School, Gangwon-do, Wonju 26493, Korea
| | - Ha-eun Jang
- Department of Healthcare Management, College of Bio Convergence, Eulji University, Gyeonggi-do, Seongnam 13135, Korea
| | - Young-Jin Kim
- Department of Health Administration, Yonsei University Graduate School, Gangwon-do, Wonju 26493, Korea
| | - Yejin Lee
- Department of Public Health Graduate School, Korea University, Seoul 02841, Korea
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9
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Nagata N, Nishijima S, Kojima Y, Hisada Y, Imbe K, Miyoshi-Akiyama T, Suda W, Kimura M, Aoki R, Sekine K, Ohsugi M, Miki K, Osawa T, Ueki K, Oka S, Mizokami M, Kartal E, Schmidt TSB, Molina-Montes E, Estudillo L, Malats N, Trebicka J, Kersting S, Langheinrich M, Bork P, Uemura N, Itoi T, Kawai T. Metagenomic Identification of Microbial Signatures Predicting Pancreatic Cancer From a Multinational Study. Gastroenterology 2022; 163:222-238. [PMID: 35398347 DOI: 10.1053/j.gastro.2022.03.054] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/23/2022] [Accepted: 03/29/2022] [Indexed: 12/26/2022]
Abstract
BACKGROUND & AIMS To identify gut and oral metagenomic signatures that accurately predict pancreatic ductal carcinoma (PDAC) and to validate these signatures in independent cohorts. METHODS We conducted a multinational study and performed shotgun metagenomic analysis of fecal and salivary samples collected from patients with treatment-naïve PDAC and non-PDAC controls in Japan, Spain, and Germany. Taxonomic and functional profiles of the microbiomes were characterized, and metagenomic classifiers to predict PDAC were constructed and validated in external datasets. RESULTS Comparative metagenomics revealed dysbiosis of both the gut and oral microbiomes and identified 30 gut and 18 oral species significantly associated with PDAC in the Japanese cohort. These microbial signatures achieved high area under the curve values of 0.78 to 0.82. The prediction model trained on the Japanese gut microbiome also had high predictive ability in Spanish and German cohorts, with respective area under the curve values of 0.74 and 0.83, validating its high confidence and versatility for PDAC prediction. Significant enrichments of Streptococcus and Veillonella spp and a depletion of Faecalibacterium prausnitzii were common gut signatures for PDAC in all the 3 cohorts. Prospective follow-up data revealed that patients with certain gut and oral microbial species were at higher risk of PDAC-related mortality. Finally, 58 bacteriophages that could infect microbial species consistently enriched in patients with PDAC across the 3 countries were identified. CONCLUSIONS Metagenomics targeting the gut and oral microbiomes can provide a powerful source of biomarkers for identifying individuals with PDAC and their prognoses. The identification of shared gut microbial signatures for PDAC in Asian and European cohorts indicates the presence of robust and global gut microbial biomarkers.
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Affiliation(s)
- Naoyoshi Nagata
- Department of Gastroenterological Endoscopy, Tokyo Medical University, Tokyo, Japan; Department of Gastroenterology and Hepatology, National Center for Global Health and Medicine, Tokyo, Japan.
| | - Suguru Nishijima
- Computational Bio-Big Data Open Innovation Lab, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan; Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Yasushi Kojima
- Department of Gastroenterology and Hepatology, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yuya Hisada
- Department of Gastroenterology and Hepatology, National Center for Global Health and Medicine, Tokyo, Japan
| | - Koh Imbe
- Department of Gastroenterology and Hepatology, National Center for Global Health and Medicine, Tokyo, Japan
| | - Tohru Miyoshi-Akiyama
- Pathogenic Microbe Laboratory, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Moto Kimura
- Department of Clinical Research Strategic Planning Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo, Japan
| | - Ryo Aoki
- Institute of Health Sciences, Ezaki Glico Co., Ltd., Osaka, Japan
| | - Katsunori Sekine
- Department of Gastroenterology and Hepatology, National Center for Global Health and Medicine, Kohnodai Hospital, Tokyo, Japan
| | - Mitsuru Ohsugi
- Department of Diabetes, Endocrinology, and Metabolism, Center Hospital, National Center for Global Health and Medicine, Tokyo, Japan; Diabetes and Metabolism Information Center, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kuniko Miki
- Department of Gastroenterological Endoscopy, Tokyo Medical University, Tokyo, Japan; Department of Gastroenterology and Hepatology, National Center for Global Health and Medicine, Tokyo, Japan
| | - Tsuyoshi Osawa
- Division of Nutriomics and Oncology, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Kohjiro Ueki
- Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masashi Mizokami
- Genome Medical Sciences Project, Research Institute, National Center for Global Health and Medicine, Chiba, Japan
| | - Ece Kartal
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Thomas S B Schmidt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Esther Molina-Montes
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center (CNIO), Madrid, and CIBERONC, Spain
| | - Lidia Estudillo
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center (CNIO), Madrid, and CIBERONC, Spain
| | - Nuria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center (CNIO), Madrid, and CIBERONC, Spain
| | - Jonel Trebicka
- Section for Translational Hepatology, Department of Internal Medicine I, Goehte University Frankfurt, Frankfurt, Germany; European Foundation for the Study of Chronic Liver Failure, Barcelona, Spain
| | - Stephan Kersting
- Department of Surgery, University Hospital of Erlangen, Erlangen, Germany; Department of Surgery, University Clinic Greifswald, Greifswald, Germany
| | - Melanie Langheinrich
- Department of Surgery, University Hospital of Erlangen, Erlangen, Germany; Department of Surgery, University Clinic Greifswald, Greifswald, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany; Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Naomi Uemura
- Department of Gastroenterological Endoscopy, Tokyo Medical University, Tokyo, Japan; Department of Gastroenterology and Hepatology, National Center for Global Health and Medicine, Kohnodai Hospital, Tokyo, Japan
| | - Takao Itoi
- Department of Gastroenterology and Hepatology, Tokyo Medical University, Tokyo, Japan
| | - Takashi Kawai
- Department of Gastroenterological Endoscopy, Tokyo Medical University, Tokyo, Japan
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