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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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Goolam Mahomed T, Peters RPH, Allam M, Ismail A, Mtshali S, Goolam Mahomed A, Ueckermann V, Kock MM, Ehlers MM. Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa. Sci Rep 2021; 11:19758. [PMID: 34611216 PMCID: PMC8492659 DOI: 10.1038/s41598-021-99127-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.
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Affiliation(s)
- T. Goolam Mahomed
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - R. P. H. Peters
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.442327.40000 0004 7860 2538Foundation for Professional Development, Research Unit, East London, South Africa
| | - M. Allam
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - A. Ismail
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - S. Mtshali
- grid.416657.70000 0004 0630 4574National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | | | - V. Ueckermann
- grid.49697.350000 0001 2107 2298Department of Internal Medicine, University of Pretoria, Pretoria, South Africa
| | - M. M. Kock
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.416657.70000 0004 0630 4574Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
| | - M. M. Ehlers
- grid.49697.350000 0001 2107 2298Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa ,grid.416657.70000 0004 0630 4574Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Johannesburg, South Africa
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Santoro A, Tomino C, Prinzi G, Cardaci V, Fini M, Macera L, Russo P, Maggi F. Microbiome in Chronic Obstructive Pulmonary Disease: Role of Natural Products Against Microbial Pathogens. Curr Med Chem 2020; 27:2931-2948. [PMID: 31838985 DOI: 10.2174/0929867327666191213110551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/11/2019] [Accepted: 11/25/2019] [Indexed: 12/28/2022]
Abstract
The "microbiome" is the operative term to refer to a collection of all taxa constituting microbial communities, such as bacteria, archaea, fungi and protists (originally microbiota). The microbiome consists of the indigenous microbial communities and of the host environment that they inhabit. Actually, it has been shown that there is a close relationship between the microbiome and human health and disease condition. Although, initially, the lung was considered sterile, actually, the existence of a healthy lung microbiome is usually accepted. Lung microbiome changes are reported in Chronic Obstructive Pulmonary Disease (COPD) and in its exacerbation. Viral and bacterial infections of the respiratory system are a major cause of COPD exacerbations (AECOPD) leading to increased local and systemic inflammation. Detection rates of virus in AECOPD are variable between 25-62% according to the detection method. The study of human airway and lung disease virome is quite recent and still very limited. The purpose of this review is to summarize recent findings on the lung microbiome composition with a special emphasis on virome in COPD and in AECOPD. Some drugs of natural origins active against resistant bacteria and virus are described.
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Affiliation(s)
- Alessia Santoro
- Clinical and Molecular Epidemiology, IRCSS San Raffaele Pisana, Via di Val Cannuta, 247, I-00166 Rome, Italy
| | - Carlo Tomino
- Scientific Direction, IRCSS San Raffaele Pisana,Via di Val Cannuta, 247, I-00166 Rome, Italy
| | - Giulia Prinzi
- Clinical and Molecular Epidemiology, IRCSS San Raffaele Pisana, Via di Val Cannuta, 247, I-00166 Rome, Italy
| | - Vittorio Cardaci
- Unit of Pulmonary Rehabilitation, IRCCS San Raffaele Pisana, Via della Pisana, 235, I-00163 Rome, Italy
| | - Massimo Fini
- Scientific Direction, IRCSS San Raffaele Pisana,Via di Val Cannuta, 247, I-00166 Rome, Italy
| | - Lisa Macera
- Department of Translational Research, University of Pisa, Via Savi, 10, I-56126 Pisa, Italy
| | - Patrizia Russo
- Clinical and Molecular Epidemiology, IRCSS San Raffaele Pisana, Via di Val Cannuta, 247, I-00166 Rome, Italy
| | - Fabrizio Maggi
- Department of Translational Research, University of Pisa, Via Savi, 10, I-56126 Pisa, Italy.,Virology Division, Pisa University Hospital, Via Paradisa, 2, I-56127 Pisa, Italy
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