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Gholamzad A, Khakpour N, Hashemi SMA, Goudarzi Y, Ahmadi P, Gholamzad M, Mohammadi M, Hashemi M. Exploring the virome: An integral part of human health and disease. Pathol Res Pract 2024; 260:155466. [PMID: 39053136 DOI: 10.1016/j.prp.2024.155466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/06/2024] [Accepted: 07/12/2024] [Indexed: 07/27/2024]
Abstract
The human microbiome is a complex network of microorganisms that includes viruses, bacteria, and fungi. The gut virome is an essential component of the immune system, which is responsible for regulating the growth and responses of the host's immune system. The virome maintains a crucial role in the development of numerous diseases, including inflammatory bowel disease (IBD), Crohn's disease, and neurodegenerative disorders. The human virome has emerged as a promising biomarker and therapeutic target. This comprehensive review summarizes the present understanding of the virome and its implications in matters of health and disease, with a focus on the Human Microbiome Project.
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Affiliation(s)
- Amir Gholamzad
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Niloofar Khakpour
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Mohammad Ali Hashemi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Yalda Goudarzi
- Department of Biology, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Parisa Ahmadi
- Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehrdad Gholamzad
- Department of Microbiology and Immunology, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mahya Mohammadi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology ,Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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Haas CB, Shiels MS, Pfeiffer RM, D'Arcy M, Luo Q, Yu K, Austin AA, Cohen C, Miller P, Morawski BM, Pawlish K, Robinson WT, Engels EA. Cancers with epidemiologic signatures of viral oncogenicity among immunocompromised populations in the United States. J Natl Cancer Inst 2024:djae159. [PMID: 38954841 DOI: 10.1093/jnci/djae159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Immunosuppressed individuals have elevated risk of virus-related cancers. Identifying cancers with elevated risk in people with HIV (PWH) and solid organ transplant recipients (SOTRs), two immunosuppressed populations, may help identify novel etiologic relationships with infectious agents. METHODS We utilized two linkages of population-based cancer registries with HIV and transplant registries in the United States. Cancer entities were systematically classified based on site and histology codes. Standardized incidence ratios (SIRs) were used to compare risk in PWH and SOTRs with the general population. For selected cancer entities, incidence rate ratios (IRRs) were calculated for indicators of immunosuppression within each population. FINDINGS We identified 38,047 cancer cases in SOTRs and 53,592 in PWH, yielding overall SIRs of 1.66 (95%CI = 1.65-1.68) and 1.49 (95%CI = 1.47-1.50), respectively. Forty-three cancer entities met selection criteria, including conjunctival squamous cell carcinoma (SCC) (PWH SIR = 7.1, 95%CI = 5.5-9.2; SOTRs SIR = 9.4; 95%CI = 6.8-12.6). Sebaceous adenocarcinoma was elevated in SOTRs (SIR = 16.2; 95%CI = 14.0-18.6) and, among SOTRs, associated with greater risk in lung/heart transplant recipients compared to recipients of other organs (IRR = 2.3; 95%CI = 1.7-3.2). Salivary gland tumors, malignant fibrous histiocytoma (MFH), and intrahepatic cholangiocarcinoma showed elevated risk in SOTRs (SIR = 3.9; SIR = 4.7; and SIR = 3.2, respectively) but not in PWH. However, risks for these cancers were elevated following an AIDS diagnosis among PWH (IRR = 2.4; IRR = 4.3; and IRR = 2.0, respectively). INTERPRETATION Elevated SIRs among SOTRs and PWH, and associations with immunosuppression within these populations, suggest novel infectious causes for several cancers including conjunctival SCC, sebaceous adenocarcinoma, salivary gland tumors, MFH, and intrahepatic cholangiocarcinoma.
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Affiliation(s)
- Cameron B Haas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Meredith S Shiels
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Ruth M Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Monica D'Arcy
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Qianlai Luo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kelly Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Colby Cohen
- Florida Department of Health, Tallahassee, Florida, USA
| | - Paige Miller
- Cancer Epidemiology and Surveillance Branch, Texas Department of State Health Services, Austin, Texas, USA
| | | | - Karen Pawlish
- New Jersey Department of Health, Trenton, New Jersey, USA
| | | | - Eric A Engels
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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Conradie T, Caparros-Martin JA, Egan S, Kicic A, Koks S, Stick SM, Agudelo-Romero P. Exploring the Complexity of the Human Respiratory Virome through an In Silico Analysis of Shotgun Metagenomic Data Retrieved from Public Repositories. Viruses 2024; 16:953. [PMID: 38932245 PMCID: PMC11209621 DOI: 10.3390/v16060953] [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: 03/21/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases' pathogenesis. Nevertheless, our understanding of respiratory microbiota is limited by technical constraints, predominantly focusing on bacteria and neglecting crucial populations like viruses. Despite recent efforts to improve our understanding of viral diversity in the human body, our knowledge of viral diversity associated with the human respiratory tract remains limited. METHODS Following a comprehensive search in bibliographic and sequencing data repositories using keyword terms, we retrieved shotgun metagenomic data from public repositories (n = 85). After manual curation, sequencing data files from 43 studies were analyzed using EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Complete and high-quality contigs were further assessed for genomic and taxonomic characterization. RESULTS Viral contigs were obtained from 194 out of the 868 FASTQ files processed through EVEREST. Of the 1842 contigs that were quality assessed, 8% (n = 146) were classified as complete/high-quality genomes. Most of the identified viral contigs were taxonomically classified as bacteriophages, with taxonomic resolution ranging from the superkingdom level down to the species level. Captured contigs were spread across 25 putative families and varied between RNA and DNA viruses, including previously uncharacterized viral genomes. Of note, airway samples also contained virus(es) characteristic of the human gastrointestinal tract, which have not been previously described as part of the lung virome. Additionally, by performing a meta-analysis of the integrated datasets, ecological trends within viral populations linked to human disease states and their biogeographical distribution along the respiratory tract were observed. CONCLUSION By leveraging publicly available repositories of shotgun metagenomic data, the present study provides new insights into viral genomes associated with specimens from the human respiratory tract across different disease spectra. Further studies are required to validate our findings and evaluate the potential impact of these viral communities on respiratory tract physiology.
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Affiliation(s)
- Talya Conradie
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA 6009, Australia
- Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
| | | | - Siobhon Egan
- Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA 6150, Australia
- Centre for Computational and Systems Medicine, Health Future Institute, Murdoch University, Perth, WA 6150, Australia
| | - Anthony Kicic
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA 6009, Australia
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital for Children, Perth, WA 6009, Australia
- Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, Perth, WA 6009, Australia
- School of Population Health, Curtin University, Perth, WA 6102, Australia
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Stephen M. Stick
- Department of Respiratory and Sleep Medicine, Perth Children’s Hospital for Children, Perth, WA 6009, Australia
- Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, Perth, WA 6009, Australia
| | - Patricia Agudelo-Romero
- Wal-Yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA 6009, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
- European Virus Bioinformatics Centre, Friedrich-Schiller-Universitat Jena, 07737 Jena, Germany
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Characterisation of the Upper Respiratory Tract Virome of Feedlot Cattle and Its Association with Bovine Respiratory Disease. Viruses 2023; 15:v15020455. [PMID: 36851669 PMCID: PMC9961997 DOI: 10.3390/v15020455] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 02/10/2023] Open
Abstract
Bovine respiratory disease (BRD) is a major health problem within the global cattle industry. This disease has a complex aetiology, with viruses playing an integral role. In this study, metagenomics was used to sequence viral nucleic acids in the nasal swabs of BRD-affected cattle. The viruses detected included those that are well known for their association with BRD in Australia (bovine viral diarrhoea virus 1), as well as viruses known to be present but not fully characterised (bovine coronavirus) and viruses that have not been reported in BRD-affected cattle in Australia (bovine rhinitis, bovine influenza D, and bovine nidovirus). The nasal swabs from a case-control study were subsequently tested for 10 viruses, and the presence of at least one virus was found to be significantly associated with BRD. Some of the more recently detected viruses had inconsistent associations with BRD. Full genome sequences for bovine coronavirus, a virus increasingly associated with BRD, and bovine nidovirus were completed. Both viruses belong to the Coronaviridae family, which are frequently associated with disease in mammals. This study has provided greater insights into the viral pathogens associated with BRD and highlighted the need for further studies to more precisely elucidate the roles viruses play in BRD.
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Tithi SS, Aylward FO, Jensen RV, Zhang L. FastViromeExplorer-Novel: Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data. JOURNAL OF COMPUTATIONAL BIOLOGY : A JOURNAL OF COMPUTATIONAL MOLECULAR CELL BIOLOGY 2023; 30:391-408. [PMID: 36607772 DOI: 10.1089/cmb.2022.0397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Despite the recent surge of viral metagenomic studies, recovering complete virus/phage genomes from metagenomic data is still extremely difficult and most viral contigs generated from de novo assembly programs are highly fragmented, posing serious challenges to downstream analysis and inference. In this study, we develop FastViromeExplorer (FVE)-novel, a computational pipeline for reconstructing complete or near-complete viral draft genomes from metagenomic data. The FVE-novel deploys FVE to efficiently map metagenomic reads to viral reference genomes, performs de novo assembly of the mapped reads to generate contigs, and extends the contigs through iterative assembly to produce final viral scaffolds. We applied FVE-novel to an ocean metagenomic sample and obtained 268 viral scaffolds that potentially come from novel viruses. Through manual examination and validation of the 10 longest scaffolds, we successfully recovered 4 complete viral genomes, 2 are novel as they cannot be found in the existing databases and the other 2 are related to known phages. This hybrid reference-based and de novo assembly approach used by FVE-novel represents a powerful new approach for uncovering near-complete viral genomes in metagenomic data.
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Affiliation(s)
| | - Frank O Aylward
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Roderick V Jensen
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Liqing Zhang
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA
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Tan JS, Ren JM, Fan L, Wei Y, Hu S, Zhu SS, Yang Y, Cai J. Genetic Predisposition of Anti-Cytomegalovirus Immunoglobulin G Levels and the Risk of 9 Cardiovascular Diseases. Front Cell Infect Microbiol 2022; 12:884298. [PMID: 35832381 PMCID: PMC9272786 DOI: 10.3389/fcimb.2022.884298] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/23/2022] [Indexed: 12/20/2022] Open
Abstract
Background Accumulating evidence has indicated that persistent human cytomegalovirus (HCMV) infection is associated with several cardiovascular diseases including atherosclerosis and coronary artery disease. However, whether there is a causal association between the level of anti-HCMV immune response and the risk of cardiovascular diseases remains unknown. Methods Single-nucleotide polymorphisms associated with anti-cytomegalovirus immunoglobulin (Ig) G levels were used as instrumental variables to estimate the causal effect of anti-cytomegalovirus IgG levels on 9 cardiovascular diseases (including atrial fibrillation, coronary artery disease, hypertension, heart failure, peripheral artery disease, pulmonary embolism, deep vein thrombosis of the lower extremities, rheumatic valve diseases, and non-rheumatic valve diseases). For each cardiovascular disease, Mendelian randomization (MR) analyses were performed. Inverse variance-weighted meta-analysis (IVW) with a random-effects model was used as a principal analysis. In addition to this, the weighted median approach and MR-Egger method were used for further sensitivity analysis. Results In the IVW analysis, genetically predicted anti-cytomegalovirus IgG levels were suggestively associated with coronary artery disease with an odds ratio (OR) of 1.076 [95% CI, 1.009–1.147; p = 0.025], peripheral artery disease (OR 1.709; 95% CI, 1.039–2.812; p = 0.035), and deep vein thrombosis (OR 1.002; 95% CI, 1.000–1.004; p = 0.025). In the further analysis, similar causal associations were obtained from weighted median analysis and MR-Egger analysis with lower precision. No notable heterogeneities and horizontal pleiotropies were observed (p > 0.05). Conclusions/Interpretation Our findings first provide direct evidence that genetic predisposition of anti-cytomegalovirus IgG levels increases the risk of coronary artery disease, peripheral artery disease, and deep vein thrombosis.
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Affiliation(s)
- Jiang-Shan Tan
- Emergency Center, Fuwai Hospital, National Center for Cardiovascular Diseases, National Clinical Research Center of Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jia-Meng Ren
- Department of Cardiology and Institute of Vascular Medicine, Peking University Third Hospital, NHC Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education. Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
| | - Luyun Fan
- Hypertension Center, FuWai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuhao Wei
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Song Hu
- Center for Respiratory and Pulmonary Vascular Diseases, Department of Cardiology, Key Laboratory of Pulmonary Vascular Medicine, National Clinical Research Center of Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Sheng-Song Zhu
- Center for Respiratory and Pulmonary Vascular Diseases, Department of Cardiology, Key Laboratory of Pulmonary Vascular Medicine, National Clinical Research Center of Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanmin Yang
- Emergency Center, Fuwai Hospital, National Center for Cardiovascular Diseases, National Clinical Research Center of Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Yangmin Yang, ; Jun Cai,
| | - Jun Cai
- Hypertension Center, FuWai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Yangmin Yang, ; Jun Cai,
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Kaelin EA, Skidmore PT, Łaniewski P, Holland LA, Chase DM, Herbst-Kralovetz MM, Lim ES. Cervicovaginal DNA Virome Alterations Are Associated with Genital Inflammation and Microbiota Composition. mSystems 2022; 7:e0006422. [PMID: 35343798 PMCID: PMC9040584 DOI: 10.1128/msystems.00064-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/09/2022] [Indexed: 12/11/2022] Open
Abstract
While the link between the cervicovaginal bacterial microbiome, human papillomavirus (HPV) infection, and cervical cancer is recognized (P. Łaniewski, D. Barnes, A. Goulder, H. Cui, et al., Sci. Rep. 8:7593, 2018, http://dx.doi.org/10.1038/s41598-018-25879-7; A. Mitra, D. A. MacIntyre, Y. S. Lee, A. Smith, et al., Sci. Rep. 5:16865, 2015, http://dx.doi.org/10.1038/srep16865; A. Mitra, D. A. MacIntyre, J. R. Marchesi, Y. S. Lee, et al., Microbiome 4:58, 2016, http://dx.doi.org/10.1186/s40168-016-0203-0; J. Norenhag, J. Du, M. Olovsson, H. Verstraelen, et al., BJOG, 127:171-180, 2020, http://dx.doi.org/10.1111/1471-0528.15854; E. O. Dareng, B. Ma, A. O. Famooto, S. N. Adebamowo, et al., Epidemiol. Infect. 144:123-137, 2016, http://dx.doi.org/10.1017/S0950268815000965; A. Audirac-Chalifour, K. Torres-Poveda, M. Bahena-Roman, J. Tellez-Sosa et al., PLoS One 11:e0153274, 2016, http://dx.doi.org/10.1371/journal.pone.0153274; M. Di Paola, C. Sani, A. M. Clemente, A. Iossa, et al., Sci. Rep. 7:10200, 2017, http://dx.doi.org/10.1038/s41598-017-09842-6), the role of the cervicovaginal virome remains poorly understood. In this pilot study, we conducted metagenomic next-generation sequencing of cervicovaginal lavage specimens to investigate the relationship between the cervicovaginal DNA virome, bacterial microbiome, genital inflammation, and HPV infection. Specific virome alterations were associated with features of the local microenvironment related to HPV persistence and progression to cervical cancer. Cervicovaginal viromes clustered distinctly by genital inflammation state. Genital inflammation was associated with decreased virome richness and alpha diversity and an increased abundance of Anelloviridae species from the genus Alphatorquevirus. Lactobacillus bacteriophages were closely associated with increased Lactobacillus abundance, consistent with phage-host relationships. Interestingly, bacteria-bacteriophage transkingdom interactions were linked to genital inflammation and showed specific interactions with bacterial vaginosis-associated bacteria, including Gardnerella, Prevotella, and Sneathia. Taken together, our results reveal prominent virome interactions with features of the cervicovaginal microenvironment that are associated with HPV and cervical cancer. These findings expand our understanding of the cervicovaginal host-microbiome interactions in women's health. IMPORTANCE HPV infection is an established risk factor for cervical cancer. However, more broadly, the role of the cervicovaginal virome in cervical cancer progression is not well understood. Here, we identified cervicovaginal DNA virome alterations associated with local microenvironment factors (vaginal microbiota and genital inflammation) that influence HPV persistence and progression to cervical cancer. These findings indicate that the cervicovaginal virome plays an important role in women's health.
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Affiliation(s)
- Emily A. Kaelin
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Peter T. Skidmore
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Paweł Łaniewski
- Department of Basic Medical Sciences, College of Medicine—Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - LaRinda A. Holland
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Dana M. Chase
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- UA Cancer Center, University of Arizona, Tucson, Arizona, USA
| | - Melissa M. Herbst-Kralovetz
- Department of Basic Medical Sciences, College of Medicine—Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- UA Cancer Center, University of Arizona, Tucson, Arizona, USA
| | - Efrem S. Lim
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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Guo Y, Huang X, Sun X, Yu Y, Wang Y, Zhang B, Cao J, Wen S, Li Y, Wang X, Cai S, Xia W, Wei F, Duan J, Dong H, Guo S, Zhang F, Zheng D, Sun Z. The Underrated Salivary Virome of Men Who Have Sex With Men Infected With HIV. Front Immunol 2021; 12:759253. [PMID: 34925329 PMCID: PMC8674211 DOI: 10.3389/fimmu.2021.759253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Salivary virome is important for oral ecosystem, but there are few reports on people living with HIV. We performed metagenomic sequencing to compare composition and functional genes of salivary virobiota between one HIV-negative and four HIV-positive groups in which participants were all men who have sex with men (MSM) with different immunosuppression statuses (five samples per group) to find the evidence that salivary virobiota plays a role in the pathogenesis of oral disease. Acute-stage subjects achieved a positive result of HIV RNA, but HIV antibody negative or indeterminate, whereas individuals with mild, moderate, and severe immunosuppression exhibited CD4+ T-lymphocyte counts of at least 500, 200–499, and less than 200 cells/μL or opportunistic infection, respectively. The results showed the composition of salivary virus genera in subjects with mild immunosuppression was the most similar to that in healthy people, followed by that in the acute stage; under severe immunosuppression, virus genera were suppressed and more similar to that under moderate immunosuppression. Furthermore, abnormally high abundance of Lymphocryptovirus was particularly obvious in MSM with HIV infection. Analysis of KEGG Pathway revealed that Caulobacter cell cycle, which affects cell duplication, became shorter in HIV-positive subjects. It is worth noting that in acute-stage participants, protein digestion and absorption related to the anti-HIV-1 activity of secretory leukocyte protease inhibitor was increased. Moreover, in the severely immunosuppressed subjects, glutathione metabolism, which is associated with the activation of lymphocytes, was enhanced. Nevertheless, the ecological dysbiosis in HIV-positive salivary virobiota possibly depended on the changes in blood viral load, and salivary dysfunction of MSM infected with HIV may be related to CD4 counts. Ribonucleoside diphosphate reductase subunit M1 in purine metabolism was negatively correlated, though weakly, to CD4 counts, which may be related to the promotion of HIV-1 DNA synthesis in peripheral blood lymphocytes. 7-Cyano-7-deazaguanine synthase in folate biosynthesis was weakly positively correlated with HIV viral load, suggesting that this compound was produced excessively to correct oral dysfunction for maintaining normal cell development. Despite the limited number of samples, the present study provided insight into the potential role of salivary virome in the oral function of HIV infected MSM.
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Affiliation(s)
- Ying Guo
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xiaojie Huang
- Department of Infectious Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xintong Sun
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yixi Yu
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yan Wang
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Baojin Zhang
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jie Cao
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Shuo Wen
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yuchen Li
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xin Wang
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Siyu Cai
- Center for Clinical Epidemiology and Evidence-Based Medicine, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Wei Xia
- Department of Infectious Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Feili Wei
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Junyi Duan
- Department of Infectious Disease, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Haozhi Dong
- Department of Stomatology, Beijing Daxing District Hospital of Integrated Chinese and Western Medicine, Beijing, China
| | - Shan Guo
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Fengqiu Zhang
- Beijing Stomatological Hospital, Capital Medical University, Beijing, China
| | - Dongxiang Zheng
- Department of Stomatology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Zheng Sun
- Beijing Stomatological Hospital, Capital Medical University, Beijing, China
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Brown RB. Sodium Toxicity in the Nutritional Epidemiology and Nutritional Immunology of COVID-19. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:739. [PMID: 34440945 PMCID: PMC8399536 DOI: 10.3390/medicina57080739] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/17/2021] [Accepted: 07/19/2021] [Indexed: 02/06/2023]
Abstract
Dietary factors in the etiology of COVID-19 are understudied. High dietary sodium intake leading to sodium toxicity is associated with comorbid conditions of COVID-19 such as hypertension, kidney disease, stroke, pneumonia, obesity, diabetes, hepatic disease, cardiac arrhythmias, thrombosis, migraine, tinnitus, Bell's palsy, multiple sclerosis, systemic sclerosis, and polycystic ovary syndrome. This article synthesizes evidence from epidemiology, pathophysiology, immunology, and virology literature linking sodium toxicological mechanisms to COVID-19 and SARS-CoV-2 infection. Sodium toxicity is a modifiable disease determinant that impairs the mucociliary clearance of virion aggregates in nasal sinuses of the mucosal immune system, which may lead to SARS-CoV-2 infection and viral sepsis. In addition, sodium toxicity causes pulmonary edema associated with severe acute respiratory syndrome, as well as inflammatory immune responses and other symptoms of COVID-19 such as fever and nasal sinus congestion. Consequently, sodium toxicity potentially mediates the association of COVID-19 pathophysiology with SARS-CoV-2 infection. Sodium dietary intake also increases in the winter, when sodium losses through sweating are reduced, correlating with influenza-like illness outbreaks. Increased SARS-CoV-2 infections in lower socioeconomic classes and among people in government institutions are linked to the consumption of foods highly processed with sodium. Interventions to reduce COVID-19 morbidity and mortality through reduced-sodium diets should be explored further.
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Affiliation(s)
- Ronald B Brown
- School of Public Health Sciences, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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10
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Schwierzeck V, Hülpüsch C, Reiger M. Microbiome of Barrier Organs in Allergy: Who Runs the World? Germs! Handb Exp Pharmacol 2021; 268:53-65. [PMID: 34228203 DOI: 10.1007/164_2021_478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Over the last few decades, allergic diseases have been steadily increasing worldwide, a phenomenon that is not yet completely understood. Recent evidence, however, suggests that alterations in the microbiome may be a contributing factor. The microbiome refers to all microorganisms in a habitat including bacteria, fungi, and viruses. Using modern sequencing technologies, we are now capable of detecting and analyzing the human microbiome in more detail than ever before. Epidemiological and experimental studies have indicated that a complex intestinal microbiome supports the development of the immune system during childhood, thus providing protection from allergic diseases, including food allergy. The microbiome becomes an important part of human physiology and forms dynamic relationships with our various barrier systems. For example, bacterial dysbiosis is a hallmark of atopic eczema and correlates with disease progression. Similarly, the lung and nasopharyngeal microbiome is altered in patients with asthma and allergic rhinitis. While these results are interesting, the underlying mechanisms are still unclear and need to be investigated with functional studies. This review gives a short overview of the terminology and methods used in microbiome research before highlighting results concerning the lung, skin, and intestinal microbiome in allergic diseases.
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Affiliation(s)
- Vera Schwierzeck
- Institute of Hygiene, University Hospital Muenster, Munster, Germany
| | - Claudia Hülpüsch
- Department of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany.,Institute of Environmental Medicine, Helmholtz Zentrum Muenchen, Augsburg, Germany.,CK CARE - Christine Kuehne Center for Allergy Research and Education, Davos, Switzerland
| | - Matthias Reiger
- Department of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany. .,Institute of Environmental Medicine, Helmholtz Zentrum Muenchen, Augsburg, Germany. .,CK CARE - Christine Kuehne Center for Allergy Research and Education, Davos, Switzerland.
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11
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Iorio A, Biazzo M, Gardini S, Muda AO, Perno CF, Dallapiccola B, Putignani L. Cross-correlation of virome-bacteriome-host-metabolome to study respiratory health. Trends Microbiol 2021; 30:34-46. [PMID: 34052095 DOI: 10.1016/j.tim.2021.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/13/2022]
Abstract
A comprehensive understanding of the microbiome-host relationship in respiratory diseases can be elucidated by exploring the landscape of virome-bacteriome-host metabolome data through unsupervised 'multi-omics' approaches. Here, we describe how the composition and function of airway and gut virome and bacteriome may contribute to pathogen establishment and propagation in airway districts and how the virome-bacteriome communities may react to respiratory diseases. A new systems medicine approach, including the characterization of respiratory and gut microbiome, may be crucial to demonstrate the likelihood and odds of respiratory disease pathophysiology, opening new avenues to the discovery of a chain of causation for key bacteria and viruses in disease severity.
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Affiliation(s)
- Andrea Iorio
- Department of Diagnostic and Laboratory Medicine, Unit of Parasitology and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Manuele Biazzo
- The BioArte Ltd, The Victoria Centre, Mosta, Malta; SienaBioActive, University of Siena, Siena, Italy
| | | | - Andrea Onetti Muda
- Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Carlo Federico Perno
- Unit of Microbiology and Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Bruno Dallapiccola
- Scientific Directorate, Children's Hospital and Research Institute 'Bambino Gesù', IRCCS, Rome
| | - Lorenza Putignani
- Department of Diagnostic and Laboratory Medicine, Unit of Parasitology and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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12
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Abade Dos Santos FA, Portela SJ, Nogueira T, Carvalho CL, de Sousa R, Duarte MD. Harmless or Threatening? Interpreting the Results of Molecular Diagnosis in the Context of Virus-Host Relationships. Front Microbiol 2021; 12:647730. [PMID: 34093464 PMCID: PMC8175621 DOI: 10.3389/fmicb.2021.647730] [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: 12/30/2020] [Accepted: 04/27/2021] [Indexed: 01/15/2023] Open
Abstract
Molecular methods, established in the 1980s, expanded and delivered tools for the detection of vestigial quantities of nucleic acids in biological samples. Nucleotide sequencing of these molecules reveals the identity of the organism it belongs to. However, the implications of such detection are often misinterpreted as pathogenic, even in the absence of corroborating clinical evidence. This is particularly significant in the field of virology where the concepts of commensalism, and other benign or neutral relationships, are still very new. In this manuscript, we review some fundamental microbiological concepts including commensalism, mutualism, pathogenicity, and infection, giving special emphasis to their application in virology, in order to clarify the difference between detection and infection. We also propose a system for the correct attribution of terminology in this context.
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Affiliation(s)
- Fábio A Abade Dos Santos
- National Institute for Agrarian and Veterinary Research, Oeiras, Portugal.,Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Sara J Portela
- Harrogate District Hospital NHS Foundation Trust, Harrogate, United Kingdom
| | - Teresa Nogueira
- National Institute for Agrarian and Veterinary Research, Oeiras, Portugal.,Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Carina L Carvalho
- National Institute for Agrarian and Veterinary Research, Oeiras, Portugal
| | - Rita de Sousa
- National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Margarida D Duarte
- National Institute for Agrarian and Veterinary Research, Oeiras, Portugal.,Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
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13
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Waeijen-Smit K, Houben-Wilke S, DiGiandomenico A, Gehrmann U, Franssen FME. Unmet needs in the management of exacerbations of chronic obstructive pulmonary disease. Intern Emerg Med 2021; 16:559-569. [PMID: 33616876 PMCID: PMC7897880 DOI: 10.1007/s11739-020-02612-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022]
Abstract
Exacerbations of chronic obstructive pulmonary disease (COPD) are episodes of acute worsening of respiratory symptoms that require additional therapy. These events play a pivotal role in the natural course of the disease and are associated with a progressive decline in lung function, reduced health status, a low physical activity level, tremendous health care costs, and increased mortality. Although most exacerbations have an infectious origin, the underlying mechanisms are heterogeneous and specific predictors of their occurrence in individual patients are currently unknown. Accurate prediction and early diagnosis of exacerbations is essential to develop novel targets for prevention and personalized treatments to reduce the impact of these events. Several potential biomarkers have previously been studied, these however lack specificity, accuracy and do not add value to the available clinical predictors. At present, microbial composition and host-microbiome interactions in the lung are increasingly recognized for their role in affecting the susceptibility to exacerbations, and may steer towards a novel direction in the management of COPD exacerbations. This narrative review describes the current challenges and unmet needs in the management of acute exacerbations of COPD. Exacerbation triggers, biological clusters, current treatment strategies, and their limitations, previously studied biomarkers and prediction tools, the lung microbiome and its role in COPD exacerbations as well as future directions are discussed.
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Affiliation(s)
- Kiki Waeijen-Smit
- Department of Research and Education, Ciro, Horn, NM, 6085, The Netherlands.
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht, The Netherlands.
- Department of Respiratory Medicine, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands.
| | - Sarah Houben-Wilke
- Department of Research and Education, Ciro, Horn, NM, 6085, The Netherlands
| | - Antonio DiGiandomenico
- Discovery Microbiome, Microbial Sciences, Biopharmaceuticals R&D, AstraZeneca, Gaithersburg, USA
| | - Ulf Gehrmann
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Frits M E Franssen
- Department of Research and Education, Ciro, Horn, NM, 6085, The Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht, The Netherlands
- Department of Respiratory Medicine, Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
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14
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Metagenomic Analysis of the Respiratory Microbiome of a Broiler Flock from Hatching to Processing. Microorganisms 2021; 9:microorganisms9040721. [PMID: 33807233 PMCID: PMC8065701 DOI: 10.3390/microorganisms9040721] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/30/2021] [Indexed: 12/15/2022] Open
Abstract
Elucidating the complex microbial interactions in biological environments requires the identification and characterization of not only the bacterial component but also the eukaryotic viruses, bacteriophage, and fungi. In a proof of concept experiment, next generation sequencing approaches, accompanied by the development of novel computational and bioinformatics tools, were utilized to examine the evolution of the microbial ecology of the avian trachea during the growth of a healthy commercial broiler flock. The flock was sampled weekly, beginning at placement and concluding at 49 days, the day before processing. Metagenomic sequencing of DNA and RNA was utilized to examine the bacteria, virus, bacteriophage, and fungal components during flock growth. The utility of using a metagenomic approach to study the avian respiratory virome was confirmed by detecting the dysbiosis in the avian respiratory virome of broiler chickens diagnosed with infection with infectious laryngotracheitis virus. This study provides the first comprehensive analysis of the ecology of the avian respiratory microbiome and demonstrates the feasibility for the use of this approach in future investigations of avian respiratory diseases.
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15
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Harper A, Vijayakumar V, Ouwehand AC, ter Haar J, Obis D, Espadaler J, Binda S, Desiraju S, Day R. Viral Infections, the Microbiome, and Probiotics. Front Cell Infect Microbiol 2021; 10:596166. [PMID: 33643929 PMCID: PMC7907522 DOI: 10.3389/fcimb.2020.596166] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/23/2020] [Indexed: 01/07/2023] Open
Abstract
Viral infections continue to cause considerable morbidity and mortality around the world. Recent rises in these infections are likely due to complex and multifactorial external drivers, including climate change, the increased mobility of people and goods and rapid demographic change to name but a few. In parallel with these external factors, we are gaining a better understanding of the internal factors associated with viral immunity. Increasingly the gastrointestinal (GI) microbiome has been shown to be a significant player in the host immune system, acting as a key regulator of immunity and host defense mechanisms. An increasing body of evidence indicates that disruption of the homeostasis between the GI microbiome and the host immune system can adversely impact viral immunity. This review aims to shed light on our understanding of how host-microbiota interactions shape the immune system, including early life factors, antibiotic exposure, immunosenescence, diet and inflammatory diseases. We also discuss the evidence base for how host commensal organisms and microbiome therapeutics can impact the prevention and/or treatment of viral infections, such as viral gastroenteritis, viral hepatitis, human immunodeficiency virus (HIV), human papilloma virus (HPV), viral upper respiratory tract infections (URTI), influenza and SARS CoV-2. The interplay between the gastrointestinal microbiome, invasive viruses and host physiology is complex and yet to be fully characterized, but increasingly the evidence shows that the microbiome can have an impact on viral disease outcomes. While the current evidence base is informative, further well designed human clinical trials will be needed to fully understand the array of immunological mechanisms underlying this intricate relationship.
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Affiliation(s)
- Ashton Harper
- ADM Health & Wellness, Medical Affairs Department, Somerset, United Kingdom
| | | | - Arthur C. Ouwehand
- Global Health and Nutrition Sciences, DuPont Nutrition and Biosciences, Kantvik, Finland
| | | | - David Obis
- Innovation Science & Nutrition Department, Danone Nutricia Research, Palaiseau, France
| | | | - Sylvie Binda
- Lallemand Health Solutions, Montreal, QC, Canada
| | | | - Richard Day
- ADM Health & Wellness, Medical Affairs Department, Somerset, United Kingdom
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16
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Piggott DA, Tuddenham S. The gut microbiome and frailty. Transl Res 2020; 221:23-43. [PMID: 32360945 PMCID: PMC8487348 DOI: 10.1016/j.trsl.2020.03.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 12/12/2022]
Abstract
The human microbiome is constituted by an extensive network of organisms that lie at the host/environment interface and transduce signals that play vital roles in human health and disease across the lifespan. Frailty is a critical aging-related syndrome marked by diminished physiological reserve and heightened vulnerability to stress, predictive of major adverse clinical outcomes including death. While recent studies suggest the microbiome may impact key pathways critical to frailty pathophysiology, direct evaluation of the microbiome-frailty relationship remains limited. In this article, we review the complex interplay of biological, behavioral, and environmental factors that may influence shifts in gut microbiome composition and function in aging populations and the putative implications of such shifts for progression to frailty. We discuss HIV infection as a key prototype for elucidating the complex pathways via which the microbiome may precipitate frailty. Finally, we review considerations for future research efforts.
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Affiliation(s)
- Damani A Piggott
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Epidemiology, Johns Hopkins University School of Public Health, Baltimore, Maryland.
| | - Susan Tuddenham
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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17
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Kumata R, Ito J, Takahashi K, Suzuki T, Sato K. A tissue level atlas of the healthy human virome. BMC Biol 2020; 18:55. [PMID: 32493363 PMCID: PMC7269688 DOI: 10.1186/s12915-020-00785-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Human-resident microbes can influence both health and disease. Investigating the microbiome using next-generation sequencing technology has revealed examples of mutualism and conflict between microbes and humans. Comparing to bacteria, the viral component of the microbiome (i.e., the "virome") is understudied. Somatic tissues of healthy individuals are usually inaccessible for the virome sampling; therefore, there is limited understanding of the presence and distribution of viruses in tissues in healthy individuals and how virus infection associates with human gene expression and perturbs immunological homeostasis. RESULTS To characterize the human virome in a tissue-specific manner, here we performed meta-transcriptomic analysis using the RNA-sequencing dataset from the Genotype-Tissue Expression (GTEx) Project. We analyzed the 8991 RNA-sequencing data obtained from 51 somatic tissues from 547 individuals and successfully detected 39 viral species in at least one tissue. We then investigated associations between virus infection and human gene expression and human disease onset. We detected some expected relationships; for instance, hepatitis C virus infection in the liver was strongly associated with interferon-stimulated gene upregulation and pathological findings of chronic hepatitis. The presence of herpes simplex virus type 1 in one subject's brain strongly associated with immune gene expression. While torque teno virus was detected in a broad range of human tissues, it was not associated with interferon responses. Being notable in light of its association with lymphoproliferative disorders, Epstein-Barr virus infection in the spleen and blood was associated with an increase in plasma cells in healthy subjects. Human herpesvirus 7 was often detected in the stomach; intriguingly, it associated with the proportion of human leukocytes in the stomach as well as digestive gene expression. Moreover, virus infections in the local tissues associated with systemic immune responses in circulating blood. CONCLUSIONS To our knowledge, this study is the first comprehensive investigation of the human virome in a variety of tissues in healthy individuals through meta-transcriptomic analysis. Further investigation of the associations described here, and application of this analytical pipeline to additional datasets, will be useful to reveal the impact of viral infections on human health.
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Affiliation(s)
- Ryuichi Kumata
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan
| | - Kenta Takahashi
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 1628640, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 1628640, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan. .,CREST, Japan Science and Technology Agency, Saitama, 3220012, Japan.
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18
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Cao J, Zhang Y, Dai M, Xu J, Chen L, Zhang F, Zhao N, Wang J. Profiling of Human Gut Virome with Oxford Nanopore Technology. MEDICINE IN MICROECOLOGY 2020. [DOI: 10.1016/j.medmic.2020.100012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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19
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Nazareth R, Chasqueira MJ, Rodrigues ML, Paulino C, Conceição C, Lêdo L, Segura Ú, Santos M, Messias A, Póvoa P, Paixão P. Respiratory viruses in mechanically ventilated patients: a pilot study. BMC Pulm Med 2020; 20:39. [PMID: 32054471 PMCID: PMC7020345 DOI: 10.1186/s12890-020-1082-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 02/07/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Respiratory virome is an integral part of the human microbiome and its characterization may contribute to a better understanding of the changes that arise in the disease and, consequently, influence the approach and treatment of patients with acute lower respiratory infections. The aim of this study was to evaluate the presence of respiratory viruses in the lower airways of individuals undergoing invasive mechanical ventilation, with and without acute lower respiratory infection (respectively WRI and WORI groups). METHODS We studied 44 mini-bronchoalveolar lavage samples (collected with a double catheter, Combicath® kit) from patients with mean age in the seventh decade, 20 from WORI group and 24 from WRI group, who were hospitalized for acute respiratory failure in Intensive Care Units of two hospitals in the Lisbon area. Real-time PCR was applied to verify analyse the presence of 15 common respiratory viruses (adenovirus, human bocavirus, influenza virus A and B, repiratory syncytial virus, human parainfluenza virus types 1, 2, 3 and 4, human enterovirus, human rhinovirus, human metapneumovirus, human coronavirus group 1 (229E, NL63) and 2 (OC43, HKU1). RESULTS Respiratory viruses were detected in six of the 20 patients in the WORI group: influenza AH3 (n = 2), parainfluenza virus 1/3 (n = 2), human rhinovirus (n = 2), respiratory syncytial virus (n = 1) and human metapneumovirus (n = 1). In the WRI group, respiratory viruses were detected in 12 of the 24 patients: influenza AH3 (n = 3), human rhinovirus (n = 3), respiratory syncytial virus (n = 3), human metapneumovirus (n = 3), human bocavirus (n = 2) and human enterovirus (n = 1). Simultaneous detection of two viruses was recorded in two samples in both groups. CONCLUSIONS The results of this study suggest the presence of common respiratory viruses in the lower respiratory tract without causing symptomatic infection, even in carefully collected lower samples. This may have important implications on the interpretation of the results on the diagnostic setting.
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Affiliation(s)
- Raquel Nazareth
- Hospital Beatriz Ângelo, Avenida Carlos Teixeira, 3, 2674-514, Loures, Portugal. .,Centro de Estudos de Doenças Crónicas, CEDOC, Faculdade de Ciências Médicas
- NOVA Medical School, Campo Mártires da Pátria, 130, 1169-056, Lisbon, Portugal.
| | - Maria-Jesus Chasqueira
- Centro de Estudos de Doenças Crónicas, CEDOC, Faculdade de Ciências Médicas
- NOVA Medical School, Campo Mártires da Pátria, 130, 1169-056, Lisbon, Portugal
| | - Maria-Lúcia Rodrigues
- Centro de Estudos de Doenças Crónicas, CEDOC, Faculdade de Ciências Médicas
- NOVA Medical School, Campo Mártires da Pátria, 130, 1169-056, Lisbon, Portugal
| | - Carolina Paulino
- Hospital São Francisco de Xavier, Estrada Forte do Alto Duque, 1449-005, Lisbon, Portugal
| | - Catarina Conceição
- Hospital São Francisco de Xavier, Estrada Forte do Alto Duque, 1449-005, Lisbon, Portugal
| | - Lia Lêdo
- Hospital São Francisco de Xavier, Estrada Forte do Alto Duque, 1449-005, Lisbon, Portugal
| | - Úrsula Segura
- Hospital Beatriz Ângelo, Avenida Carlos Teixeira, 3, 2674-514, Loures, Portugal
| | - Madalena Santos
- Hospital Curry Cabral, Centro Hospitalar de Lisboa Central, Rua da Beneficiência n° 8, 1069-166, Lisbon, Portugal
| | - António Messias
- Hospital Beatriz Ângelo, Avenida Carlos Teixeira, 3, 2674-514, Loures, Portugal
| | - Pedro Póvoa
- Centro de Estudos de Doenças Crónicas, CEDOC, Faculdade de Ciências Médicas
- NOVA Medical School, Campo Mártires da Pátria, 130, 1169-056, Lisbon, Portugal.,Hospital São Francisco de Xavier, Estrada Forte do Alto Duque, 1449-005, Lisbon, Portugal.,Center for Clinical Epidemiology and Research Unit of Clinical Epidemiology, OUH Odense University Hospital, Odense, Denmark
| | - Paulo Paixão
- Centro de Estudos de Doenças Crónicas, CEDOC, Faculdade de Ciências Médicas
- NOVA Medical School, Campo Mártires da Pátria, 130, 1169-056, Lisbon, Portugal.,Clinical Pathology Laboratory (Synlab), Hospital da Luz, Av Lusíada, 100, 1500-650, Lisbon, Portugal
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20
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Pausan MR, Csorba C, Singer G, Till H, Schöpf V, Santigli E, Klug B, Högenauer C, Blohs M, Moissl-Eichinger C. Exploring the Archaeome: Detection of Archaeal Signatures in the Human Body. Front Microbiol 2019; 10:2796. [PMID: 31866971 PMCID: PMC6906140 DOI: 10.3389/fmicb.2019.02796] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/18/2019] [Indexed: 01/18/2023] Open
Abstract
Due to their fundamentally different biology, archaea are consistently overlooked in conventional microbiome surveys. Using amplicon sequencing, we evaluated methodological set-ups to detect archaea in samples from five different body sites: respiratory tract (nasal cavity), digestive tract (mouth, appendix, and stool) and skin. With optimized protocols, the detection of archaeal ribosomal sequence variants (RSVs) was increased from one (found in currently used, so-called "universal" approach) to 81 RSVs in a representative sample set. The results from this extensive primer-evaluation led to the identification of the primer pair combination 344f-1041R/519F-806R which performed superior for the analysis of the archaeome of gastrointestinal tract, oral cavity and skin. The proposed protocol might not only prove useful for analyzing the human archaeome in more detail but could also be used for other holobiont samples.
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Affiliation(s)
- Manuela R. Pausan
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Cintia Csorba
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Georg Singer
- Department of Pediatrics and Adolescent Surgery, Medical University of Graz, Graz, Austria
| | - Holger Till
- Department of Pediatrics and Adolescent Surgery, Medical University of Graz, Graz, Austria
| | - Veronika Schöpf
- Institute of Psychology, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Elisabeth Santigli
- Department of Dental Medicine and Oral Health, Medical University Graz, Graz, Austria
| | - Barbara Klug
- Department of Dental Medicine and Oral Health, Medical University Graz, Graz, Austria
| | | | - Marcus Blohs
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Christine Moissl-Eichinger
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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21
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Stefanaki C. The Gut Microbiome Beyond the Bacteriome—The Neglected Role of Virome and Mycobiome in Health and Disease. MICROBIOME AND METABOLOME IN DIAGNOSIS, THERAPY, AND OTHER STRATEGIC APPLICATIONS 2019. [DOI: 10.1016/b978-0-12-815249-2.00003-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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The human archaeome: methodological pitfalls and knowledge gaps. Emerg Top Life Sci 2018; 2:469-482. [PMID: 33525835 DOI: 10.1042/etls20180037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/20/2018] [Accepted: 10/01/2018] [Indexed: 02/07/2023]
Abstract
Forty years ago, archaea were described as a separate domain of life, distinct from bacteria and eukarya. Although it is known for quite a long time that methanogenic archaea are substantial components of the human gastrointestinal tract (GIT) and the oral cavity, the knowledge on the human archaeome is very limited. Various methodological problems contribute to the invisibility of the human archaeome, resulting in severe knowledge gaps and contradictory information. Similar to the bacteriome, the archaeal biogeography was found to be site-specific, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal GIT landscape, (iii) a mixed skin/GIT landscape in nose, and (iv) a woesearchaeal lung landscape, including numerous unknown archaeal clades. Compared with so-called universal microbiome approaches, archaea-specific protocols reveal a wide diversity and high quantity of archaeal signatures in various human tissues, with up to 1 : 1 ratios of bacteria and archaea in appendix and nose samples. The archaeome interacts closely with the bacteriome and the human body cells, whereas the roles of the human-associated archaea with respect to human health are only sparsely described. Methanogenic archaea and methane production were correlated with many health issues, including constipation, periodontitis and multiple sclerosis. However, one of the most burning questions - do archaeal pathogens exist? - still remains obscure to date.
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23
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Proal A, Marshall T. Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity. Front Pediatr 2018; 6:373. [PMID: 30564562 PMCID: PMC6288442 DOI: 10.3389/fped.2018.00373] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/14/2018] [Indexed: 12/16/2022] Open
Abstract
The illness ME/CFS has been repeatedly tied to infectious agents such as Epstein Barr Virus. Expanding research on the human microbiome now allows ME/CFS-associated pathogens to be studied as interacting members of human microbiome communities. Humans harbor these vast ecosystems of bacteria, viruses and fungi in nearly all tissue and blood. Most well-studied inflammatory conditions are tied to dysbiosis or imbalance of the human microbiome. While gut microbiome dysbiosis has been identified in ME/CFS, microbes and viruses outside the gut can also contribute to the illness. Pathobionts, and their associated proteins/metabolites, often control human metabolism and gene expression in a manner that pushes the body toward a state of illness. Intracellular pathogens, including many associated with ME/CFS, drive microbiome dysbiosis by directly interfering with human transcription, translation, and DNA repair processes. Molecular mimicry between host and pathogen proteins/metabolites further complicates this interference. Other human pathogens disable mitochondria or dysregulate host nervous system signaling. Antibodies and/or clonal T cells identified in patients with ME/CFS are likely activated in response to these persistent microbiome pathogens. Different human pathogens have evolved similar survival mechanisms to disable the host immune response and host metabolic pathways. The metabolic dysfunction driven by these organisms can result in similar clusters of inflammatory symptoms. ME/CFS may be driven by this pathogen-induced dysfunction, with the nature of dysbiosis and symptom presentation varying based on a patient's unique infectious and environmental history. Under such conditions, patients would benefit from treatments that support the human immune system in an effort to reverse the infectious disease process.
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Affiliation(s)
- Amy Proal
- Autoimmunity Research Foundation, Thousand Oaks, CA, United States
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Versluys AB, Boelens JJ. Morbidity and Mortality Associated With Respiratory Virus Infections in Allogeneic Hematopoietic Cell Transplant: Too Little Defense or Harmful Immunity? Front Microbiol 2018; 9:2795. [PMID: 30519222 PMCID: PMC6258814 DOI: 10.3389/fmicb.2018.02795] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 10/31/2018] [Indexed: 12/29/2022] Open
Abstract
The impact on morbidity and mortality of Community Acquired Respiratory Virus (CARV) infections in patients undergoing Allogeneic Hematopoietic Cell Transplant (HCT) is widely studied. Here we give an overview of the current literature on the incidence and chance of progression to severe disease in this highly immune compromised population. We discuss the issue whether it is predominantly direct viral damage that causes clinical deterioration, or that it is in fact the allogeneic immuneresponse to the virus that is most important. This is an important question as it will guide therapeutic decision making. It asks for further collaborative studies focusing on sensitive surveillance with PCR techniques and relating clinical data with parameters of immune reconstitution.
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Affiliation(s)
- Anne Birgitta Versluys
- Blood and Marrow Transplantation Program, Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Jaap Jan Boelens
- Stem Cell Transplant and Cellular Therapies Program, Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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25
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Ungaro F, Massimino L, Furfaro F, Rimoldi V, Peyrin-Biroulet L, D’Alessio S, Danese S. Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease. Gut Microbes 2018; 10:149-158. [PMID: 30252582 PMCID: PMC6546319 DOI: 10.1080/19490976.2018.1511664] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 07/17/2018] [Accepted: 08/07/2018] [Indexed: 02/07/2023] Open
Abstract
Intestinal dysbiosis is one of the causes underlying the pathogenesis of inflammatory bowel disease (IBD), encompassing ulcerative colitis (UC) and Crohn's disease (CD). Besides bacteria, microbiota comprises both prokaryotic and eukaryotic viruses, that together compose the gut virome. Few works have defined the viral composition of stools, while the virome populating intestinal mucosae from early-diagnosed IBD patients has never been studied. Here we show that, by in-depth metagenomic analysis of RNA-Seq data obtained from gut mucosae of young treatment-naïve patients, early-diagnosed for CD and UC, and from healthy subjects (Ctrl), UC patients display significantly higher levels of eukaryotic Hepadnaviridae transcripts by comparison with both Ctrl and CD patients, whereas CD patients show increased abundance of Hepeviridae versus Ctrl. Moreover, we found that UC gut mucosa is characterized by lower levels of Polydnaviridae and Tymoviridae, whereas the mucosa of patients with CD showed a reduced abundance of Virgaviridae. Our findings support the idea that certain eukaryotic viruses might trigger intestinal inflammation and contribute to IBD pathogenesis and pave the way not only for the discovery of novel diagnostic biomarkers but also for the development of anti-viral drugs for the treatment of IBD.
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Affiliation(s)
- Federica Ungaro
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Luca Massimino
- Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Federica Furfaro
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Milan, Italy
| | - Valeria Rimoldi
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Laurent Peyrin-Biroulet
- Institut National de la Santé et de la Recherche Médicale U954 and Department of Gastroenterology, Nancy University Hospital, Lorraine University, Nancy, France
| | - Silvia D’Alessio
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Silvio Danese
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
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26
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Strouse C, Mangalam A, Zhang J. Bugs in the system: bringing the human microbiome to bear in cancer immunotherapy. Gut Microbes 2018; 10:109-112. [PMID: 30183502 PMCID: PMC6546317 DOI: 10.1080/19490976.2018.1511665] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/01/2018] [Accepted: 08/07/2018] [Indexed: 02/03/2023] Open
Abstract
The influence of the composition of the human microbiome on the efficacy of cancer directed immunotherapies, such as antibodies directed against the programmed cell death 1 protein (PD-1) or its ligand (PD-L1), has garnered increasing attention as the role of immunotherapies in the care of cancer has grown. Dysbiosis (altered microbiota) has recently been reported to adversely affect the efficacy of cancer directed immunotherapies, and correction of this dysbiosis has the potential to improve the efficacy of these treatments. However, the exact mechanisms underlying this relationship remains unknown. Current methods for characterizing the microbiome likely capture only a small portion of the highly complex interaction between the microbiome and the immune system. Here we discuss the recent reports of the influence of dysbiosis on cancer immunotherapy, methods to more fully characterize the interaction between the microbiome and the immune system, and methods of modulating the immune system to improve the efficacy of cancer immunotherapy.
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Affiliation(s)
- Christopher Strouse
- Division of Hematology, Oncology and Blood & Marrow Transplantation, Department of Internal Medicine, Holden Comprehensive Cancer Center, Iowa City, IA, USA
| | - Ashutosh Mangalam
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Jun Zhang
- Division of Hematology, Oncology and Blood & Marrow Transplantation, Department of Internal Medicine, Holden Comprehensive Cancer Center, Iowa City, IA, USA
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Chatterjee A, Duerkop BA. Beyond Bacteria: Bacteriophage-Eukaryotic Host Interactions Reveal Emerging Paradigms of Health and Disease. Front Microbiol 2018; 9:1394. [PMID: 29997604 PMCID: PMC6030379 DOI: 10.3389/fmicb.2018.01394] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 06/07/2018] [Indexed: 12/28/2022] Open
Abstract
For decades, a wealth of information has been acquired to define how host associated microbial communities contribute to health and disease. Within the human microbiota this has largely focused on bacteria, yet there is a myriad of viruses that occupy various tissue sites, the most abundant being bacteriophages that infect bacteria. Animal hosts are colonized with niche specific microbial communities where bacteria are continuously co-evolving with phages. Bacterial growth, metabolic activity, pathogenicity, antibiotic resistance, interspecies competition and evolution can all be influenced by phage infection and the beneficial nature of such interactions suggests that to an extent phages are tolerated by their hosts. With the understanding that phage-specific host–microbe interactions likely contribute to bacterial interactions with their mammalian hosts, phages and their communities may also impact aspects of mammalian health and disease that have gone unrecognized. Here, we review recent progress in understanding how bacteria acquire and tolerate phage in both pure culture and within complex communities. We apply these findings to discuss how intra-body phages interact with bacteria to influence their eukaryotic hosts through potential contributions to microbial homeostasis, mucosal immunity, immune tolerance and autoimmunity.
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Affiliation(s)
- Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Breck A Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
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28
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Elbehery AHA, Feichtmayer J, Singh D, Griebler C, Deng L. The Human Virome Protein Cluster Database (HVPC): A Human Viral Metagenomic Database for Diversity and Function Annotation. Front Microbiol 2018; 9:1110. [PMID: 29896176 PMCID: PMC5987705 DOI: 10.3389/fmicb.2018.01110] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 05/09/2018] [Indexed: 12/19/2022] Open
Abstract
Human virome, including those of bacteria (bacteriophages) have received an increasing attention recently, owing to the rapid developments in human microbiome research and the awareness of the far-reaching influence of microbiomes on health and disease. Nevertheless, human viromes are still underrepresented in literature making viruses a virtually untapped resource of diversity, functional and physiological information. Here we present the human virome protein cluster database as an effort to improve functional annotation and characterization of human viromes. The database was built out of hundreds of virome datasets from six different body sites. We also show the utility of this database through its use for the characterization of three bronchoalveolar lavage (BAL) viromes from one healthy control in addition to one moderate and one severe chronic obstructive pulmonary disease (COPD) patients. The use of the database allowed for a better functional annotation, which were otherwise poorly characterized when limited to annotation using sequences from full-length viral genomes. In addition, our BAL samples gave a first insight into viral communities of COPD patients and confirm a state of dysbiosis for viruses that increases with disease progression. Moreover, they shed light on the potential role of phages in the horizontal gene transfer of bacterial virulence factors, a phenomenon that highlights a possible contribution of phages to etiopathology.
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Affiliation(s)
- Ali H A Elbehery
- Institute of Virology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
| | - Judith Feichtmayer
- Institute of Groundwater Ecology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
| | - Dave Singh
- EvA Consortium, Manchester, United Kingdom.,Medicines Evaluation Unit, University Hospital of South Manchester Foundation Trust, University of Manchester, Manchester, United Kingdom
| | - Christian Griebler
- Institute of Groundwater Ecology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
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29
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Abstract
PURPOSE OF REVIEW Resident microbial communities likely modify risk for allergic disorders, including food allergy. We review epidemiologic studies linking microbial exposures to food allergy risk and discuss the mechanisms by which the microbiome may modulate oral tolerance. We additionally address ongoing translational efforts in human microbiome studies. RECENT FINDINGS Epidemiologic studies and murine models support that altered microbial exposures and colonization in early life modify food allergy risk. Differential microbiota confer protection or susceptibility to food allergy by modulating the regulatory tone of the mucosal immune system. Recent efforts are focused on the identification of bacterial strains necessary for oral tolerance in human and microbial-based clinical trials. Early childhood appears to be critical for the colonization of a diverse microbiota necessary for the induction and maintenance of oral tolerance. Identification and functional evaluation of protective commensal microbes will inform strategies for the prevention and treatment of food allergy.
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Affiliation(s)
- Hsi-En Ho
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Supinda Bunyavanich
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Genomics and Multiscale Biology, Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L Levy Place, Box 1498, New York, NY, 10029, USA.
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30
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Elimination of Viral Hepatitis and an Update on Blood Safety Technology. HEPATITIS MONTHLY 2018. [DOI: 10.5812/hepatmon.66577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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31
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D'arc M, Furtado C, Siqueira JD, Seuánez HN, Ayouba A, Peeters M, Soares MA. Assessment of the gorilla gut virome in association with natural simian immunodeficiency virus infection. Retrovirology 2018; 15:19. [PMID: 29402305 PMCID: PMC5800045 DOI: 10.1186/s12977-018-0402-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 01/28/2018] [Indexed: 01/10/2023] Open
Abstract
Background Simian immunodeficiency viruses (SIVs) of chimpanzees and gorillas from Central Africa crossed the species barrier at least four times giving rise to human immunodeficiency virus type 1 (HIV-1) groups M, N, O and P. The paradigm of non-pathogenic lentiviral infections has been challenged by observations of naturally infected chimpanzees with SIVcpz associated with a negative impact on their life span and reproduction, CD4+ T-lymphocyte loss and lymphoid tissue destruction. With the advent and dissemination of new generation sequencing technologies, novel promising markers of immune deficiency have been explored in human and nonhuman primate species, showing changes in the microbiome (dysbiosis) that might be associated with pathogenic conditions. The aim of the present study was to identify and compare enteric viromes of SIVgor-infected and uninfected gorillas using noninvasive sampling and ultradeep sequencing, and to assess the association of virome composition with potential SIVgor pathogenesis in their natural hosts. Results We analyzed both RNA and DNA virus libraries of 23 fecal samples from 11 SIVgor-infected (two samples from one animal) and 11 uninfected western lowland gorillas from Campo-Ma’an National Park (CP), in southwestern Cameroon. Three bacteriophage families (Siphoviridae, Myoviridae and Podoviridae) represented 67.5 and 68% of the total annotated reads in SIVgor-infected and uninfected individuals, respectively. Conversely, mammalian viral families, such as Herpesviridae and Reoviridae, previously associated with gut- and several mammalian diseases were significantly more abundant (p < 0.003) in the SIVgor-infected group. In the present study, we analyzed, for the first time, the enteric virome of gorillas and their association with SIVgor status. This also provided the first evidence of association of specific mammalian viral families and SIVgor in a putative dysbiosis context. Conclusions Our results suggested that viromes might be potentially used as markers of lentiviral disease progression in wild gorilla populations. The diverse mammalian viral families, herein described in SIVgor-infected gorillas, may play a pivotal role in a disease progression still unclear in these animals but already well characterized in pathogenic lentiviral infections in other organisms. Larger sample sets should be further explored to reduce intrinsic sampling variation.
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Affiliation(s)
- Mirela D'arc
- Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil.,Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | | | | | - Héctor N Seuánez
- Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil.,Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Ahidjo Ayouba
- UMI233/INSERM1175 Institut de Recherche pour le Développement (IRD), University of Montpellier, Montpellier, France
| | - Martine Peeters
- UMI233/INSERM1175 Institut de Recherche pour le Développement (IRD), University of Montpellier, Montpellier, France
| | - Marcelo A Soares
- Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil. .,Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin. mBio 2017; 8:mBio.00824-17. [PMID: 29138298 PMCID: PMC5686531 DOI: 10.1128/mbio.00824-17] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Human-associated archaea remain understudied in the field of microbiome research, although in particular methanogenic archaea were found to be regular commensals of the human gut, where they represent keystone species in metabolic processes. Knowledge on the abundance and diversity of human-associated archaea is extremely limited, and little is known about their function(s), their overall role in human health, or their association with parts of the human body other than the gastrointestinal tract and oral cavity. Currently, methodological issues impede the full assessment of the human archaeome, as bacteria-targeting protocols are unsuitable for characterization of the full spectrum of Archaea. The goal of this study was to establish conservative protocols based on specifically archaea-targeting, PCR-based methods to retrieve first insights into the archaeomes of the human gastrointestinal tract, lung, nose, and skin. Detection of Archaea was highly dependent on primer selection and the sequence processing pipeline used. Our results enabled us to retrieve a novel picture of the human archaeome, as we found for the first time Methanobacterium and Woesearchaeota (DPANN superphylum) to be associated with the human gastrointestinal tract and the human lung, respectively. Similar to bacteria, human-associated archaeal communities were found to group biogeographically, forming (i) the thaumarchaeal skin landscape, (ii) the (methano)euryarchaeal gastrointestinal tract, (iii) a mixed skin-gastrointestinal tract landscape for the nose, and (iv) a woesearchaeal lung landscape. On the basis of the protocols we used, we were able to detect unexpectedly high diversity of archaea associated with different body parts. In summary, our study highlights the importance of the primers and NGS data processing pipeline used to study the human archaeome. We were able to establish protocols that revealed the presence of previously undetected Archaea in all of the tissue samples investigated and to detect biogeographic patterns of the human archaeome in the gastrointestinal tract, on the skin, and for the first time in the respiratory tract, i.e., the nose and lungs. Our results are a solid basis for further investigation of the human archaeome and, in the long term, discovery of the potential role of archaea in human health and disease.
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Denner J. The porcine virome and xenotransplantation. Virol J 2017; 14:171. [PMID: 28874166 PMCID: PMC5585927 DOI: 10.1186/s12985-017-0836-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/27/2017] [Indexed: 12/29/2022] Open
Abstract
The composition of the porcine virome includes viruses that infect pig cells, ancient virus-derived elements including endogenous retroviruses inserted in the pig chromosomes, and bacteriophages that infect a broad array of bacteria that inhabit pigs. Viruses infecting pigs, among them viruses also infecting human cells, as well as porcine endogenous retroviruses (PERVs) are of importance when evaluating the virus safety of xenotransplantation. Bacteriophages associated with bacteria mainly in the gut are not relevant in this context. Xenotransplantation using pig cells, tissues or organs is under development in order to alleviate the shortage of human transplants. Here for the first time published data describing the viromes in different pigs and their relevance for the virus safety of xenotransplantation is analysed. In conclusion, the analysis of the porcine virome has resulted in numerous new viruses being described, although their impact on xenotransplantation is unclear. Most importantly, viruses with known or suspected zoonotic potential were often not detected by next generation sequencing, but were revealed by more sensitive methods.
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Affiliation(s)
- Joachim Denner
- Robert Koch Fellow, Robert Koch Institute, Nordufer, 20, Berlin, Germany.
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34
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Watanabe T, Shibasaki M, Maruyama F, Sekizaki T, Nakagawa I. Investigation of potential targets of Porphyromonas CRISPRs among the genomes of Porphyromonas species. PLoS One 2017; 12:e0183752. [PMID: 28837670 PMCID: PMC5570325 DOI: 10.1371/journal.pone.0183752] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/10/2017] [Indexed: 12/13/2022] Open
Abstract
The oral bacterial species Porphyromonas gingivalis, a periodontal pathogen, has plastic genomes that may be driven by homologous recombination with exogenous deoxyribonucleic acid (DNA) that is incorporated by natural transformation and conjugation. However, bacteriophages and plasmids, both of which are main resources of exogenous DNA, do not exist in the known P. gingivalis genomes. This could be associated with an adaptive immunity system conferred by clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated (cas) genes in P. gingivalis as well as innate immune systems such as a restriction-modification system. In a previous study, few immune targets were predicted for P. gingivalis CRISPR/Cas. In this paper, we analyzed 51 P. gingivalis genomes, which were newly sequenced, and publicly available genomes of 13 P. gingivalis and 46 other Porphyromonas species. We detected 6 CRISPR/Cas types (classified by sequence similarity of repeat) in P. gingivalis and 12 other types in the remaining species. The Porphyromonas CRISPR spacers with potential targets in the genus Porphyromonas were approximately 23 times more abundant than those with potential targets in other genus taxa (1,720/6,896 spacers vs. 74/6,896 spacers). Porphyromonas CRISPR/Cas may be involved in genome plasticity by exhibiting selective interference against intra- and interspecies nucleic acids.
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Affiliation(s)
- Takayasu Watanabe
- Laboratory of Food-borne Pathogenic Microbiology, Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
- * E-mail:
| | - Masaki Shibasaki
- Department of Oral Implantology and Regenerative Dental Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Tsutomu Sekizaki
- Laboratory of Food-borne Pathogenic Microbiology, Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
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35
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Shankar J. Insights into study design and statistical analyses in translational microbiome studies. ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:249. [PMID: 28706917 DOI: 10.21037/atm.2017.01.13] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Research questions in translational microbiome studies are substantially more complex than their counterparts in basic science. Robust study designs with appropriate statistical analysis frameworks are pivotal to the success of these translational studies. This review considers how study designs can account for heterogeneous phenotypes by adopting representative sampling schemes for recruiting the study population and making careful choices about the control population. Advantages and limitations of 16S profiling and whole-genome sequencing, the two primary techniques for measuring the microbiome, are discussed followed by an overview of bioinformatic processing of high-throughput sequencing data from these measurements. Practical insights into the downstream statistical analyses including data processing and integration, variable transformations, and data exploration are provided. The merits of regularization and ensemble modeling for analyzing microbiome data are discussed along with a recommendation for selecting modeling approaches based on data-driven simulations and objective evaluation. The review builds on several recent discussions of study design issues in microbiome research but with a stronger emphasis on the downstream and often-ignored aspects of statistical analyses that are crucial for bridging the gap between basic science and translation.
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36
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Eid HM, Wright ML, Anil Kumar NV, Qawasmeh A, Hassan STS, Mocan A, Nabavi SM, Rastrelli L, Atanasov AG, Haddad PS. Significance of Microbiota in Obesity and Metabolic Diseases and the Modulatory Potential by Medicinal Plant and Food Ingredients. Front Pharmacol 2017; 8:387. [PMID: 28713266 PMCID: PMC5493053 DOI: 10.3389/fphar.2017.00387] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/02/2017] [Indexed: 01/11/2023] Open
Abstract
Metabolic syndrome is a cluster of three or more metabolic disorders including insulin resistance, obesity, and hyperlipidemia. Obesity has become the epidemic of the twenty-first century with more than 1.6 billion overweight adults. Due to the strong connection between obesity and type 2 diabetes, obesity has received wide attention with subsequent coining of the term "diabesity." Recent studies have identified unique contributions of the immensely diverse gut microbiota in the pathogenesis of obesity and diabetes. Several mechanisms have been proposed including altered glucose and fatty acid metabolism, hepatic fatty acid storage, and modulation of glucagon-like peptide (GLP)-1. Importantly, the relationship between unhealthy diet and a modified gut microbiota composition observed in diabetic or obese subjects has been recognized. Similarly, the role of diet rich in polyphenols and plant polysaccharides in modulating gut bacteria and its impact on diabetes and obesity have been the subject of investigation by several research groups. Gut microbiota are also responsible for the extensive metabolism of polyphenols thus modulating their biological activities. The aim of this review is to shed light on the composition of gut microbes, their health importance and how they can contribute to diseases as well as their modulation by polyphenols and polysaccharides to control obesity and diabetes. In addition, the role of microbiota in improving the oral bioavailability of polyphenols and hence in shaping their antidiabetic and antiobesity activities will be discussed.
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Affiliation(s)
- Hoda M. Eid
- Natural Health Products and Metabolic Diseases Laboratory, Department of Pharmacology and Physiology, Université de MontréalMontréal, QC, Canada
- Canadian Institutes of Health Research Team in Aboriginal Antidiabetic MedicinesMontréal, QC, Canada
- Department of Pharmacognosy, University of Beni-SuefBeni-Suef, Egypt
| | - Michelle L. Wright
- Nell Hodgson Woodruff School of Nursing, Emory UniversityAtlanta, GA, United States
| | - N. V. Anil Kumar
- Department of Chemistry, Manipal Institute of Technology, Manipal UniversityManipal, India
| | | | - Sherif T. S. Hassan
- Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences BrnoBrno, Czechia
| | - Andrei Mocan
- Department of Pharmaceutical Botany, Iuliu Hatieganu University of Medicine and PharmacyCluj-Napoca, Romania
- ICHAT and Institute for Life Sciences, University of Agricultural Sciences and Veterinary MedicineCluj-Napoca, Romania
| | - Seyed M. Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical SciencesTehran, Iran
| | - Luca Rastrelli
- Dipartimento di Farmacia, University of SalernoFisciano, Italy
| | - Atanas G. Atanasov
- Institute of Genetics and Animal Breeding, Polish Academy of SciencesJastrzebiec, Poland
- Department of Pharmacognosy, University of ViennaVienna, Austria
- Department of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of ViennaVienna, Austria
| | - Pierre S. Haddad
- Natural Health Products and Metabolic Diseases Laboratory, Department of Pharmacology and Physiology, Université de MontréalMontréal, QC, Canada
- Canadian Institutes of Health Research Team in Aboriginal Antidiabetic MedicinesMontréal, QC, Canada
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37
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Watkins SC, Putonti C. The use of informativity in the development of robust viromics-based examinations. PeerJ 2017; 5:e3281. [PMID: 28480148 PMCID: PMC5417064 DOI: 10.7717/peerj.3281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 04/07/2017] [Indexed: 01/08/2023] Open
Abstract
Metagenomics-based studies have provided insight into many of the complex microbial communities responsible for maintaining life on this planet. Sequencing efforts often uncover novel genetic content; this is most evident for phage communities, in which upwards of 90% of all sequences exhibit no similarity to any sequence in current data repositories. For the small fraction that can be identified, the top BLAST hit is generally posited as being representative of a viral taxon present in the sample of origin. Homology-based classification, however, can be misleading as sequence repositories capture but a small fraction of phage diversity. Furthermore, lateral gene transfer is pervasive within phage communities. As such, the presence of a particular gene may not be indicative of the presence of a particular viral species. Rather, it is just that: an indication of the presence of a specific gene. To circumvent this limitation, we have developed a new method for the analysis of viral metagenomic datasets. BLAST hits are weighted, integrating the sequence identity and length of alignments as well as a taxonomic signal, such that each gene is evaluated with respect to its information content. Through this quantifiable metric, predictions of viral community structure can be made with confidence. As a proof-of-concept, the approach presented here was implemented and applied to seven freshwater viral metagenomes. While providing a robust method for evaluating viral metagenomic data, the tool is versatile and can easily be customized to investigations of any environment or biome.
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Affiliation(s)
- Siobhan C Watkins
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, United States of America.,Department of Biology, Loyola University of Chicago, Chicago, IL, United States of America
| | - Catherine Putonti
- Department of Biology, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Computer Science, Loyola University of Chicago, Chicago, IL, United States of America.,Bioinformatics Program, Loyola University of Chicago, Chicago, IL, United States of America.,Department of Microbiology and Immunology, Loyola University of Chicago, Maywood, IL, United States of America
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Moustafa A, Xie C, Kirkness E, Biggs W, Wong E, Turpaz Y, Bloom K, Delwart E, Nelson KE, Venter JC, Telenti A. The blood DNA virome in 8,000 humans. PLoS Pathog 2017; 13:e1006292. [PMID: 28328962 PMCID: PMC5378407 DOI: 10.1371/journal.ppat.1006292] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 04/03/2017] [Accepted: 03/14/2017] [Indexed: 02/06/2023] Open
Abstract
The characterization of the blood virome is important for the safety of blood-derived transfusion products, and for the identification of emerging pathogens. We explored non-human sequence data from whole-genome sequencing of blood from 8,240 individuals, none of whom were ascertained for any infectious disease. Viral sequences were extracted from the pool of sequence reads that did not map to the human reference genome. Analyses sifted through close to 1 Petabyte of sequence data and performed 0.5 trillion similarity searches. With a lower bound for identification of 2 viral genomes/100,000 cells, we mapped sequences to 94 different viruses, including sequences from 19 human DNA viruses, proviruses and RNA viruses (herpesviruses, anelloviruses, papillomaviruses, three polyomaviruses, adenovirus, HIV, HTLV, hepatitis B, hepatitis C, parvovirus B19, and influenza virus) in 42% of the study participants. Of possible relevance to transfusion medicine, we identified Merkel cell polyomavirus in 49 individuals, papillomavirus in blood of 13 individuals, parvovirus B19 in 6 individuals, and the presence of herpesvirus 8 in 3 individuals. The presence of DNA sequences from two RNA viruses was unexpected: Hepatitis C virus is revealing of an integration event, while the influenza virus sequence resulted from immunization with a DNA vaccine. Age, sex and ancestry contributed significantly to the prevalence of infection. The remaining 75 viruses mostly reflect extensive contamination of commercial reagents and from the environment. These technical problems represent a major challenge for the identification of novel human pathogens. Increasing availability of human whole-genome sequences will contribute substantial amounts of data on the composition of the normal and pathogenic human blood virome. Distinguishing contaminants from real human viruses is challenging. Novel sequencing technologies offer insight into the virome in human samples. Here, we identify the viral DNA sequences in blood of over 8,000 individuals undergoing whole genome sequencing. This approach serves to identify 94 viruses; however, many are shown to reflect widespread DNA contamination of commercial reagents or of environmental origin. While this represents a significant limitation to reliably identify novel viruses infecting humans, we could confidently detect sequences and quantify abundance of 19 human viruses in 42% of individuals. Ancestry, sex, and age were important determinants of viral prevalence. This large study calls attention on the challenge of interpreting next generation sequencing data for the identification of novel viruses. However, it serves to categorize the abundance of human DNA viruses using an unbiased technique.
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Affiliation(s)
- Ahmed Moustafa
- Human Longevity Inc., San Diego, California, United States of America
| | - Chao Xie
- Human Longevity Singapore Pte. Ltd., Singapore
| | - Ewen Kirkness
- Human Longevity Inc., San Diego, California, United States of America
| | - William Biggs
- Human Longevity Inc., San Diego, California, United States of America
| | - Emily Wong
- Human Longevity Inc., San Diego, California, United States of America
| | | | - Kenneth Bloom
- Human Longevity Inc., San Diego, California, United States of America
| | - Eric Delwart
- Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Karen E. Nelson
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - J. Craig Venter
- Human Longevity Inc., San Diego, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: (JCV); (AT)
| | - Amalio Telenti
- Human Longevity Inc., San Diego, California, United States of America
- J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: (JCV); (AT)
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39
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Tipton L, Ghedin E, Morris A. The lung mycobiome in the next-generation sequencing era. Virulence 2016; 8:334-341. [PMID: 27687858 DOI: 10.1080/21505594.2016.1235671] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The fungi that reside in the human lungs represent an understudied, but medically relevant comm-unity. From the few studies published on the lung mycobiome, we find that there are fungi in both the healthy and diseased respiratory tract, that these fungi vary widely between individuals, and that there is a trend toward lower fungal diversity among individuals with disease. This review discusses the few studies of the lung mycobiome and details the challenges that accompany lung mycobiome studies. These challenges include sample collection and processing, sequence amplification and processing, and a history of multiple names for species. Some challenges may never be solved, but others can be solved with more data and additional studies of the lung mycobiome.
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Affiliation(s)
- Laura Tipton
- a Department of Computational and Systems Biology , University of Pittsburgh School of Medicine , Pittsburgh , PA , USA.,b Department of Biology , New York University , New York , NY , USA
| | - Elodie Ghedin
- b Department of Biology , New York University , New York , NY , USA
| | - Alison Morris
- c Departments of Medicine and Immunology , University of Pittsburgh School of Medicine , Pittsburgh , PA , USA
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