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Mageiros L, Megremis S, Papadopoulos NG. The virome in allergy and asthma: A nascent, ineffable player. J Allergy Clin Immunol 2023; 152:1347-1351. [PMID: 37778473 DOI: 10.1016/j.jaci.2023.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/28/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
Allergic diseases can be affected by virus-host interactions and are increasingly linked with the tissue-specific microbiome. High-throughput metagenomic sequencing has offered the opportunity to study the presence of viruses as an ecologic system, namely, the virome. Even though virome studies are technically challenging conceptually and analytically, they are already producing novel data expanding our understanding of the pathophysiologic mechanisms related to chronic inflammation and allergy. The importance of interspecies and intraspecies interactions is becoming apparent, as they can significantly, directly or indirectly, affect the host's response and antigenic state. Here, we emphasize the challenges and potential insights related to study of the virome in the context of allergy and asthma. We review the limited number of studies that have investigated the virome in these conditions, underlining the need for prospective, repeated sampling designs to unravel the virome's impact on disease development and its interplay with microbiota and immunity. The potential therapeutic use of bacteriophages, which are highly complex components of the virome, is discussed. There is clearly a need for further in-depth investigation of the virome as a system in allergic diseases.
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Affiliation(s)
- Leonardos Mageiros
- Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Nikolaos G Papadopoulos
- Allergy Department, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece; University of Manchester, Manchester, United Kingdom.
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2
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Gao J, Yi X, Wang Z. The application of multi-omics in the respiratory microbiome: Progresses, challenges and promises. Comput Struct Biotechnol J 2023; 21:4933-4943. [PMID: 37867968 PMCID: PMC10585227 DOI: 10.1016/j.csbj.2023.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/24/2023] Open
Abstract
The study of the respiratory microbiome has entered a multi-omic era. Through integrating different omic data types such as metagenome, metatranscriptome, metaproteome, metabolome, culturome and radiome surveyed from respiratory specimens, holistic insights can be gained on the lung microbiome and its interaction with host immunity and inflammation in respiratory diseases. The power of multi-omics have moved the field forward from associative assessment of microbiome alterations to causative understanding of the lung microbiome in the pathogenesis of chronic, acute and other types of respiratory diseases. However, the application of multi-omics in respiratory microbiome remains with unique challenges from sample processing, data integration, and downstream validation. In this review, we first introduce the respiratory sample types and omic data types applicable to studying the respiratory microbiome. We next describe approaches for multi-omic integration, focusing on dimensionality reduction, multi-omic association and prediction. We then summarize progresses in the application of multi-omics to studying the microbiome in respiratory diseases. We finally discuss current challenges and share our thoughts on future promises in the field.
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Affiliation(s)
- Jingyuan Gao
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
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3
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Romero-Tapia SDJ, Guzmán Priego CG, Del-Río-Navarro BE, Sánchez-Solis M. Advances in the Relationship between Respiratory Viruses and Asthma. J Clin Med 2023; 12:5501. [PMID: 37685567 PMCID: PMC10488270 DOI: 10.3390/jcm12175501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/02/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023] Open
Abstract
Several studies have reported that viral infection is closely associated with the onset, progression, and exacerbation of asthma. The purpose of this review is to summarize the role that viral infections have in the pathogenesis of asthma onset and exacerbations, as well as discuss interrelated protective and risk factors of asthma and current treatment options. Furthermore, we present current knowledge of the innate immunological pathways driving host defense, including changes in the epithelial barrier. In addition, we highlight the importance of the genetics and epigenetics of asthma and virus susceptibility. Moreover, the involvement of virus etiology from bronchiolitis and childhood wheezing to asthma is described. The characterization and mechanisms of action of the respiratory viruses most frequently related to asthma are mentioned.
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Affiliation(s)
- Sergio de Jesús Romero-Tapia
- Health Sciences Academic Division (DACS), Juarez Autonomous University of Tabasco (UJAT), Villahermosa 86040, Tabasco, Mexico
| | - Crystell Guadalupe Guzmán Priego
- Cardiometabolism Laboratory, Research Center, Health Sciences Academic Division (DACS), Juarez Autonomous University of Tabasco (UJAT), Villahermosa 86040, Tabasco, Mexico;
| | | | - Manuel Sánchez-Solis
- Paediatric Pulmonology Unit, Virgen de la Arrixaca University Children’s Hospital, University of Murcia, 30120 Murcia, Spain;
- Biomedical Research Institute of Murcia (IMIB), 30120 Murcia, Spain
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4
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Megremis S, Constantinides B, Xepapadaki P, Yap CF, Sotiropoulos AG, Bachert C, Finotto S, Jartti T, Tapinos A, Vuorinen T, Andreakos E, Robertson DL, Papadopoulos NG. Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma. Sci Rep 2023; 13:8319. [PMID: 37221274 PMCID: PMC10205716 DOI: 10.1038/s41598-023-34730-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/06/2023] [Indexed: 05/25/2023] Open
Abstract
Asthma development and exacerbation is linked to respiratory virus infections. There is limited information regarding the presence of viruses during non-exacerbation/infection periods. We investigated the nasopharyngeal/nasal virome during a period of asymptomatic state, in a subset of 21 healthy and 35 asthmatic preschool children from the Predicta cohort. Using metagenomics, we described the virome ecology and the cross-species interactions within the microbiome. The virome was dominated by eukaryotic viruses, while prokaryotic viruses (bacteriophages) were independently observed with low abundance. Rhinovirus B species consistently dominated the virome in asthma. Anelloviridae were the most abundant and rich family in both health and asthma. However, their richness and alpha diversity were increased in asthma, along with the co-occurrence of different Anellovirus genera. Bacteriophages were richer and more diverse in healthy individuals. Unsupervised clustering identified three virome profiles that were correlated to asthma severity and control and were independent of treatment, suggesting a link between the respiratory virome and asthma. Finally, we observed different cross-species ecological associations in the healthy versus the asthmatic virus-bacterial interactome, and an expanded interactome of eukaryotic viruses in asthma. Upper respiratory virome "dysbiosis" appears to be a novel feature of pre-school asthma during asymptomatic/non-infectious states and merits further investigation.
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Affiliation(s)
- Spyridon Megremis
- University of Manchester, Manchester, UK.
- University of Leicester, Leicester, UK.
| | | | | | | | | | | | - Susetta Finotto
- Friedrich Alexander University Erlangen-Nurnberg, Erlangen, Germany
| | - Tuomas Jartti
- University of Turku, Turku, Finland
- University of Oulu, Oulu, Finland
| | | | | | | | | | - Nikolaos G Papadopoulos
- University of Manchester, Manchester, UK.
- National and Kapodistrian University of Athens, Athens, Greece.
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5
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Liu Z, Wang C, Zheng S, Yang X, Han H, Dai Y, Xiao R. Simultaneously ultrasensitive and quantitative detection of influenza A virus, SARS-CoV-2, and respiratory syncytial virus via multichannel magnetic SERS-based lateral flow immunoassay. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2023; 47:102624. [PMID: 36328340 PMCID: PMC9622431 DOI: 10.1016/j.nano.2022.102624] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/30/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Respiratory viruses usually induced similar clinical symptoms at early infection. Herein, we presented a multichannel surface-enhanced Raman scattering-based lateral flow immunoassay (SERS-based LFA) using high-performance magnetic SERS tags for the simultaneous ultrasensitive detection of respiratory viruses, namely influenza A virus (H1N1), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and respiratory syncytial virus (RSV) in biological samples. As-prepared magnetic SERS tags can directly enrich and capture target viruses without pretreatment of samples, avoiding the interference of impurities in the samples as well as improving the sensitivity. With the capture-detection method, the detection limits of the proposed assay reached 85 copies mL-1, 8 pg mL-1, and 8 pg mL-1 for H1N1, SARS-CoV-2 and RSV, respectively. Moreover, the detection properties of the proposed method for target viruses in throat swab samples were verified, suggesting its remarkable potential for the early and rapid differential diagnosis of respiratory viruses.
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Tiew PY, Narayana JK, Quek MSL, Ang YY, Ko FWS, Poh ME, Jaggi TK, Xu H, Thng KX, Koh MS, Tee A, Hui DSC, Abisheganaden JA, Tsaneva-Atanasova K, Chew FT, Chotirmall SH. Sensitisation to recombinant Aspergillus fumigatus allergens and clinical outcomes in COPD. Eur Respir J 2023; 61:13993003.00507-2022. [PMID: 35926878 PMCID: PMC9816419 DOI: 10.1183/13993003.00507-2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/24/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Variable clinical outcomes are reported with fungal sensitisation in chronic obstructive pulmonary disease (COPD), and it remains unclear which fungi and what allergens associate with the poorest outcomes. The use of recombinant as opposed to crude allergens for such assessment is unknown. METHODS A prospective multicentre assessment of stable COPD (n=614) was undertaken in five hospitals across three countries: Singapore, Malaysia and Hong Kong. Clinical and serological assessment was performed against a panel of 35 fungal allergens including crude and recombinant Aspergillus and non-Aspergillus allergens. Unsupervised clustering and topological data analysis (TDA) approaches were employed using the measured sensitisation responses to elucidate if sensitisation subgroups exist and their related clinical outcomes. RESULTS Aspergillus fumigatus sensitisation was associated with increased exacerbations in COPD. Unsupervised cluster analyses revealed two "fungal sensitisation" groups. The first was characterised by Aspergillus sensitisation and increased exacerbations, poorer lung function and worse prognosis. Polysensitisation in this group conferred even poorer outcome. The second group, characterised by Cladosporium sensitisation, was more symptomatic. Significant numbers of individuals demonstrated sensitisation responses to only recombinant (as opposed to crude) A. fumigatus allergens f 1, 3, 5 and 6, and exhibited increased exacerbations, poorer lung function and an overall worse prognosis. TDA validated these findings and additionally identified a subgroup within Aspergillus-sensitised COPD of patients with frequent exacerbations. CONCLUSION Aspergillus sensitisation is a treatable trait in COPD. Measuring sensitisation responses to recombinant Aspergillus allergens identifies an important patient subgroup with poor COPD outcomes that remains overlooked by assessment of only crude Aspergillus allergens.
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Affiliation(s)
- Pei Yee Tiew
- Dept of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | | | | | - Yan Ying Ang
- Dept of Biological Sciences, National University of Singapore, Singapore
| | - Fanny Wai San Ko
- Dept of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Mau Ern Poh
- Dept of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Huiying Xu
- Dept of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Mariko Siyue Koh
- Dept of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Augustine Tee
- Dept of Respiratory and Critical Care Medicine, Changi General Hospital, Singapore
| | - David Shu Cheong Hui
- Dept of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - John Arputhan Abisheganaden
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Dept of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Krasimira Tsaneva-Atanasova
- Living Systems Institute and Department of Mathematics, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
- EPSRC Hub for Quantitative Modelling in Healthcare, University of Exeter, Exeter, UK
| | - Fook Tim Chew
- Dept of Biological Sciences, National University of Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Dept of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
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7
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Ottmann M. [These viruses that inhabit and visit us: The human virome]. Med Sci (Paris) 2022; 38:1028-1038. [PMID: 36692282 DOI: 10.1051/medsci/2022161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Recent advances in new sequencing technologies have opened the way to the deciphering of human virome. So far, human virome is defined as the complete list of viruses found in human body. Those viruses could be endogenous, prokaryotic, archaeal and eukaryotic. In addition, each compartment of the human body constitutes a different microenvironment with its own virome. Viral infections can be categorized according to the outcome of the acute phase and until recently, only symptomatic and pathological infections were studied. It is now well established that a healthy person has an extremely diverse virome. This review summarizes the current state of our knowledge and also proposes another classification of the human virome based on principles of ecology.
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Affiliation(s)
- Michèle Ottmann
- Centre international de recherche en infectiologie (CIRI), université Claude Bernard-Lyon 1, université de Lyon, Inserm U1111 - CNRS UMR 5308 - ENS, Laboratoire de virologie et pathologies humaines, Faculté de médecine RTH Laennec, 7 rue Guillaume Paradin, 69372 Lyon cedex 08, France
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8
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Sandybayev N, Beloussov V, Strochkov V, Solomadin M, Granica J, Yegorov S. Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome. Microorganisms 2022; 10:microorganisms10122327. [PMID: 36557580 PMCID: PMC9785614 DOI: 10.3390/microorganisms10122327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
The COVID-19 pandemic and heightened perception of the risk of emerging viral infections have boosted the efforts to better understand the virome or complete repertoire of viruses in health and disease, with a focus on infectious respiratory diseases. Next-generation sequencing (NGS) is widely used to study microorganisms, allowing the elucidation of bacteria and viruses inhabiting different body systems and identifying new pathogens. However, NGS studies suffer from a lack of standardization, in particular, due to various methodological approaches and no single format for processing the results. Here, we review the main methodological approaches and key stages for studies of the human virome, with an emphasis on virome changes during acute respiratory viral infection, with applications for clinical diagnostics and epidemiologic analyses.
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Affiliation(s)
- Nurlan Sandybayev
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
- Correspondence: ; Tel.: +7-778312-2058
| | - Vyacheslav Beloussov
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
- Molecular Genetics Laboratory TreeGene, Almaty 050009, Kazakhstan
| | - Vitaliy Strochkov
- Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty 050010, Kazakhstan
| | - Maxim Solomadin
- School of Pharmacy, Karaganda Medical University, Karaganda 100000, Kazakhstan
| | - Joanna Granica
- Molecular Genetics Laboratory TreeGene, Almaty 050009, Kazakhstan
| | - Sergey Yegorov
- Michael G. DeGroote Institute for Infectious Disease Research, Faculty of Health Sciences, McMaster University, Hamilton, ON L8S 4LB, Canada
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Ogunbayo AE, Mogotsi MT, Sondlane H, Nkwadipo KR, Sabiu S, Nyaga MM. Metagenomic Analysis of Respiratory RNA Virome of Children with and without Severe Acute Respiratory Infection from the Free State, South Africa during COVID-19 Pandemic Reveals Higher Diversity and Abundance in Summer Compared with Winter Period. Viruses 2022; 14:v14112516. [PMID: 36423125 PMCID: PMC9692838 DOI: 10.3390/v14112516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/04/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Viral respiratory infections contribute to significant morbidity and mortality in children. Currently, there are limited reports on the composition and abundance of the normal commensal respiratory virome in comparison to those in severe acute respiratory infections (SARIs) state. This study characterised the respiratory RNA virome in children ≤ 5 years with (n = 149) and without (n = 139) SARI during the summer and winter of 2020/2021 seasons in South Africa. Nasopharyngeal swabs were, collected, pooled, enriched for viral RNA detection, sequenced using Illumina MiSeq, and analysed using the Genome Detective bioinformatic tool. Overall, Picornaviridae, Paramoxyviridae, Pneumoviridae, Picobirnaviridae, Totiviridae, and Retroviridae families were the most abundant viral population in both groups across both seasons. Human rhinovirus and endogenous retrovirus K113 were detected in most pools, with exclusive detection of Pneumoviridae in SARI pools. Generally, higher viral diversity/abundance was seen in children with SARI and in the summer pools. Several plant/animal viruses, eukaryotic viruses with unclear pathogenicity including a distinct rhinovirus A type, were detected. This study provides remarkable data on the respiratory RNA virome in children with and without SARI with a degree of heterogeneity of known viruses colonizing their respiratory tract. The implication of the detected viruses in the dynamics/progression of SARI requires further investigations.
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Affiliation(s)
- Ayodeji E. Ogunbayo
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Milton T. Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Hlengiwe Sondlane
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Kelebogile R. Nkwadipo
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
- Correspondence: ; Tel.: +27-51-401-9158
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10
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Yi X, Gao J, Wang Z. The human lung microbiome-A hidden link between microbes and human health and diseases. IMETA 2022; 1:e33. [PMID: 38868714 PMCID: PMC10989958 DOI: 10.1002/imt2.33] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/10/2022] [Accepted: 05/25/2022] [Indexed: 06/14/2024]
Abstract
Once thought to be sterile, the human lung is now well recognized to harbor a consortium of microorganisms collectively known as the lung microbiome. The lung microbiome is altered in an array of lung diseases, including chronic lung diseases such as chronic obstructive pulmonary disease, asthma, and bronchiectasis, acute lung diseases caused by pneumonia, sepsis, and COVID-19, and other lung complications such as those related to lung transplantation, lung cancer, and human immunodeficiency virus. The effects of lung microbiome in modulating host immunity and inflammation in the lung and distal organs are being elucidated. However, the precise mechanism by which members of microbiota produce structural ligands that interact with host genes and pathways remains largely uncharacterized. Multiple unique challenges, both technically and biologically, exist in the field of lung microbiome, necessitating the development of tailored experimental and analytical approaches to overcome the bottlenecks. In this review, we first provide an overview of the principles and methodologies in studying the lung microbiome. We next review current knowledge of the roles of lung microbiome in human diseases, highlighting mechanistic insights. We finally discuss critical challenges in the field and share our thoughts on broad topics for future investigation.
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Affiliation(s)
- Xinzhu Yi
- Institute of Ecological Sciences, School of Life SciencesSouth China Normal UniversityGuangzhouGuangdongChina
| | - Jingyuan Gao
- Institute of Ecological Sciences, School of Life SciencesSouth China Normal UniversityGuangzhouGuangdongChina
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life SciencesSouth China Normal UniversityGuangzhouGuangdongChina
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11
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Broderick DTJ, Waite DW, Marsh RL, Camargo CA, Cardenas P, Chang AB, Cookson WOC, Cuthbertson L, Dai W, Everard ML, Gervaix A, Harris JK, Hasegawa K, Hoffman LR, Hong SJ, Josset L, Kelly MS, Kim BS, Kong Y, Li SC, Mansbach JM, Mejias A, O’Toole GA, Paalanen L, Pérez-Losada M, Pettigrew MM, Pichon M, Ramilo O, Ruokolainen L, Sakwinska O, Seed PC, van der Gast CJ, Wagner BD, Yi H, Zemanick ET, Zheng Y, Pillarisetti N, Taylor MW. Bacterial Signatures of Paediatric Respiratory Disease: An Individual Participant Data Meta-Analysis. Front Microbiol 2021; 12:711134. [PMID: 35002989 PMCID: PMC8733647 DOI: 10.3389/fmicb.2021.711134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 12/01/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction: The airway microbiota has been linked to specific paediatric respiratory diseases, but studies are often small. It remains unclear whether particular bacteria are associated with a given disease, or if a more general, non-specific microbiota association with disease exists, as suggested for the gut. We investigated overarching patterns of bacterial association with acute and chronic paediatric respiratory disease in an individual participant data (IPD) meta-analysis of 16S rRNA gene sequences from published respiratory microbiota studies. Methods: We obtained raw microbiota data from public repositories or via communication with corresponding authors. Cross-sectional analyses of the paediatric (<18 years) microbiota in acute and chronic respiratory conditions, with >10 case subjects were included. Sequence data were processed using a uniform bioinformatics pipeline, removing a potentially substantial source of variation. Microbiota differences across diagnoses were assessed using alpha- and beta-diversity approaches, machine learning, and biomarker analyses. Results: We ultimately included 20 studies containing individual data from 2624 children. Disease was associated with lower bacterial diversity in nasal and lower airway samples and higher relative abundances of specific nasal taxa including Streptococcus and Haemophilus. Machine learning success in assigning samples to diagnostic groupings varied with anatomical site, with positive predictive value and sensitivity ranging from 43 to 100 and 8 to 99%, respectively. Conclusion: IPD meta-analysis of the respiratory microbiota across multiple diseases allowed identification of a non-specific disease association which cannot be recognised by studying a single disease. Whilst imperfect, machine learning offers promise as a potential additional tool to aid clinical diagnosis.
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Affiliation(s)
| | - David W. Waite
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Robyn L. Marsh
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
| | - Carlos A. Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, United States
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Paul Cardenas
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Anne B. Chang
- Child Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- Department of Respiratory and Sleep Medicine, Queensland Children’s Hospital, Brisbane, QLD, Australia
- Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - William O. C. Cookson
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom
| | - Leah Cuthbertson
- Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom
| | - Wenkui Dai
- Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Mark L. Everard
- School of Medicine, University of Western Australia, Perth, WA, Australia
| | - Alain Gervaix
- Department of Pediatrics, Gynecology and Obstetrics, Faculty of Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - J. Kirk Harris
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, United States
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Lucas R. Hoffman
- Seattle Children’s Hospital, Seattle, WA, United States
- Department of Pediatrics and Microbiology, University of Washington, Seattle, WA, United States
| | - Soo-Jong Hong
- Department of Pediatrics, Childhood Asthma Atopy Center, Humidifier Disinfectant Health Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | | | - Matthew S. Kelly
- Division of Pediatric Infectious Diseases, Duke University, Durham, NC, United States
| | - Bong-Soo Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, South Korea
| | - Yong Kong
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, United States
| | - Shuai C. Li
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Jonathan M. Mansbach
- Harvard Medical School, Boston, MA, United States
- Department of Pediatrics, Boston Children’s Hospital, Boston, MA, United States
| | - Asuncion Mejias
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, The Ohio State University College of Medicine, Columbus, OH, United States
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Laura Paalanen
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Marcos Pérez-Losada
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Melinda M. Pettigrew
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States
| | - Maxime Pichon
- CHU Poitiers, Infectious Agents Department, Poitiers, France
- University of Poitiers, INSERM U1070, Poitiers, France
| | - Octavio Ramilo
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Lasse Ruokolainen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Patrick C. Seed
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | | | - Brandie D. Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, Aurora, CO, United States
| | - Hana Yi
- School of Biosystem and Biomedical Science, Korea University, Seoul, South Korea
| | - Edith T. Zemanick
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
| | | | | | - Michael W. Taylor
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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12
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Narayana JK, Mac Aogáin M, Goh WWB, Xia K, Tsaneva-Atanasova K, Chotirmall SH. Mathematical-based microbiome analytics for clinical translation. Comput Struct Biotechnol J 2021; 19:6272-6281. [PMID: 34900137 PMCID: PMC8637001 DOI: 10.1016/j.csbj.2021.11.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 12/20/2022] Open
Abstract
Traditionally, human microbiology has been strongly built on the laboratory focused culture of microbes isolated from human specimens in patients with acute or chronic infection. These approaches primarily view human disease through the lens of a single species and its relevant clinical setting however such approaches fail to account for the surrounding environment and wide microbial diversity that exists in vivo. Given the emergence of next generation sequencing technologies and advancing bioinformatic pipelines, researchers now have unprecedented capabilities to characterise the human microbiome in terms of its taxonomy, function, antibiotic resistance and even bacteriophages. Despite this, an analysis of microbial communities has largely been restricted to ordination, ecological measures, and discriminant taxa analysis. This is predominantly due to a lack of suitable computational tools to facilitate microbiome analytics. In this review, we first evaluate the key concerns related to the inherent structure of microbiome datasets which include its compositionality and batch effects. We describe the available and emerging analytical techniques including integrative analysis, machine learning, microbial association networks, topological data analysis (TDA) and mathematical modelling. We also present how these methods may translate to clinical settings including tools for implementation. Mathematical based analytics for microbiome analysis represents a promising avenue for clinical translation across a range of acute and chronic disease states.
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Affiliation(s)
- Jayanth Kumar Narayana
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James’s Hospital, Dublin, Ireland
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Wilson Wen Bin Goh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kelin Xia
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Krasimira Tsaneva-Atanasova
- Department of Mathematics & Living Systems Institute, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter EX4 4QF, UK
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
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13
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Arunasri K, Sai Prashanthi G, Tyagi M, Pappuru RR, Shivaji S. Intraocular Viral Communities Associated With Post-fever Retinitis. Front Med (Lausanne) 2021; 8:724195. [PMID: 34869420 PMCID: PMC8639604 DOI: 10.3389/fmed.2021.724195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 09/27/2021] [Indexed: 01/14/2023] Open
Abstract
The virome of ocular fluids is naive. The results of this study highlight the virome in the vitreous fluid of the eye of individuals without any ocular infection and compare it with the virome of the vitreous fluid of individuals with retinitis. A total of 1,016,037 viral reads were generated from 25 vitreous fluid samples comprising control and post-fever retinitis (PFR) samples. The top 10 viral families in the vitreous fluids comprised of Myoviridae, Siphoviridae, Phycodnaviridae, Herpesviridae, Poxviridae, Iridoviridae, Podoviridae, Retroviridae, Baculoviridae, and Flaviviridae. Principal coordinate analysis and heat map analysis clearly discriminated the virome of the vitreous fluid of the controls from that of the PFR virome. The abundance of 10 viral genera increased significantly in the vitreous fluid virome of the post-fever retinitis group compared with the control group. Genus Lymphocryptovirus, comprising the human pathogen Epstein-Barr virus (EBV) that is also implicated in ocular infections was significantly abundant in eight out of the nine vitreous fluid viromes of post-fever retinitis group samples compared with the control viromes. Human viruses, such as Hepacivirus, Circovirus, and Kobuvirus, were also significantly increased in abundance in the vitreous fluid viromes of post-fever retinitis group samples compared with the control viromes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analysis and the network analysis depicted an increase in the immune response by the host in the post-fever retinitis group compared with the control group. All together, the results of the study indicate changes in the virome in the vitreous fluid of patients with the post-fever retinitis group compared to the control group.
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Affiliation(s)
- Kotakonda Arunasri
- Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Hyderabad, India
| | | | - Mudit Tyagi
- Smt. Kanuri Santhamma Center for Vitreo Retinal Diseases, L. V. Prasad Eye Institute, Hyderabad, India
| | - Rajeev R. Pappuru
- Smt. Kanuri Santhamma Center for Vitreo Retinal Diseases, L. V. Prasad Eye Institute, Hyderabad, India
| | - Sisinthy Shivaji
- Brien Holden Eye Research Centre, L. V. Prasad Eye Institute, Hyderabad, India
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14
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Rajagopala SV, Bakhoum NG, Pakala SB, Shilts MH, Rosas-Salazar C, Mai A, Boone HH, McHenry R, Yooseph S, Halasa N, Das SR. Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples. CELL REPORTS METHODS 2021; 1:100091. [PMID: 34790908 PMCID: PMC8594859 DOI: 10.1016/j.crmeth.2021.100091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/18/2021] [Accepted: 09/10/2021] [Indexed: 12/23/2022]
Abstract
We developed a metatranscriptomics method that can simultaneously capture the respiratory virome, microbiome, and host response directly from low biomass samples. Using nasal swab samples, we capture RNA virome with sufficient sequencing depth required to assemble complete genomes. We find a surprisingly high frequency of respiratory syncytial virus (RSV) and coronavirus (CoV) in healthy children, and a high frequency of RSV-A and RSV-B co-detections in children with symptomatic RSV. In addition, we have identified commensal and pathogenic bacteria and fungi at the species level. Functional analysis revealed that H. influenzae was highly active in symptomatic RSV subjects. The host nasal transcriptome reveled upregulation of the innate immune system, anti-viral response and inflammasome pathway, and downregulation of fatty acid pathways in children with symptomatic RSV. Overall, we demonstrate that our method is broadly applicable to infer the transcriptome landscape of an infected system, surveil respiratory infections, and to sequence RNA viruses directly from clinical samples.
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Affiliation(s)
- Seesandra V. Rajagopala
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nicole G. Bakhoum
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Suman B. Pakala
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Meghan H. Shilts
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Christian Rosas-Salazar
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Annie Mai
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Helen H. Boone
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rendie McHenry
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Shibu Yooseph
- Department of Computer Science, Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA
| | - Natasha Halasa
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Suman R. Das
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Otolaryngology and Head and Neck Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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15
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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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16
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Huntley KS, Raber J, Fine L, Bernstein JA. Influence of the Microbiome on Chronic Rhinosinusitis With and Without Polyps: An Evolving Discussion. FRONTIERS IN ALLERGY 2021; 2:737086. [PMID: 35386978 PMCID: PMC8974788 DOI: 10.3389/falgy.2021.737086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022] Open
Abstract
Chronic rhinosinusitis (CRS) is widely prevalent within the population and often leads to decreased quality of life, among other related health complications. CRS has classically been stratified by the presence of nasal polyps (CRSwNP) or the absence nasal polyps (CRSsNP). Management of these conditions remains a challenge as investigators continue to uncover potential etiologies and therapeutic targets. Recently, attention has been given to the sinunasal microbiota as both an inciting and protective influence of CRS development. The healthy sinunasal microbiologic environment is largely composed of bacteria, with the most frequent strains including Staphylococcus aureus, Streptococcus epidermidis, and Corynebacterium genera. Disruptions in this milieu, particularly increases in S. aureus concentration, have been hypothesized to perpetuate both Th1 and Th2 inflammatory changes within the nasal mucosa, leading to CRS exacerbation and potential polyp formation. Other contributors to the sinunasal microbiota include fungi, viruses, and bacteriophages which may directly contribute to underlying inflammation or impact bacterial prevalence. Modifiable risk factors, such as smoking, have also been linked to microbiota alterations. Research interest in CRS continues to expand, and thus the goal of this review is to provide clinicians and investigators alike with a current discussion on the microbiologic influence on CRS development, particularly with respect to the expression of various phenotypes. Although this subject is rapidly evolving, a greater understanding of these potential factors may lead to novel research and targeted therapies for this often difficult to treat condition.
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Affiliation(s)
- Kyle S. Huntley
- Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Joshua Raber
- Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Lauren Fine
- Dr. Kiran C. Patel College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Jonathan A. Bernstein
- Department of Internal Medicine, Division of Immunology/Allergy Section, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- *Correspondence: Jonathan A. Bernstein
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17
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Ding L, Liu Y, Wu X, Wu M, Luo X, Ouyang H, Xia J, Liu X, Ding T. Pathogen Metagenomics Reveals Distinct Lung Microbiota Signatures Between Bacteriologically Confirmed and Negative Tuberculosis Patients. Front Cell Infect Microbiol 2021; 11:708827. [PMID: 34589441 PMCID: PMC8475726 DOI: 10.3389/fcimb.2021.708827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the dynamics of lung microbiota in tuberculosis patients, especially those who cannot be confirmed bacteriologically in clinical practice, is imperative for accurate diagnosis and effective treatment. This study aims to characterize the distinct lung microbial features between bacteriologically confirmed and negative tuberculosis patients to understand the influence of microbiota on tuberculosis patients. We collected specimens of bronchoalveolar lavage fluid from 123 tuberculosis patients. Samples were subjected to metagenomic next-generation sequencing to reveal the lung microbial signatures. By combining conventional bacterial detection and metagenomic sequencing, 101/123 (82%) tuberculosis patients were bacteriologically confirmed. In addition to Mycobacterium tuberculosis, Staphylococcus aureus, Kluyveromyces lactis, and Pyricularia pennisetigena were also enriched in the bacteriological confirmation group. In contrast, Haemophilus parainfluenzae was enriched in the bacteriologically negative group. Besides, microbial interaction exhibits a different state between bacteriologically confirmed and negative tuberculosis patients. Mycobacterium tuberculosis was confirmed correlated with clinical characteristics such as albumin and chest cavities. Our study comprehensively demonstrates the correlation between unique features of lung microbial dynamics and the clinical characteristics of tuberculosis patients, suggesting the importance of studying the pulmonary microbiome in tuberculosis disease and providing new insights for future precision diagnosis and treatment.
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Affiliation(s)
- Li Ding
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Yanmin Liu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaorong Wu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Minhao Wu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaoqing Luo
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Hui Ouyang
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Jinyu Xia
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Xi Liu
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Tao Ding
- Program of Infectious Diseases, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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18
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Eskind CC, Shilts MH, Shaver CM, Das SR, Satyanarayana G. The respiratory microbiome after lung transplantation: Reflection or driver of respiratory disease? Am J Transplant 2021; 21:2333-2340. [PMID: 33749996 PMCID: PMC8926303 DOI: 10.1111/ajt.16568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 02/17/2021] [Accepted: 03/05/2021] [Indexed: 01/25/2023]
Abstract
With the introduction of high-throughput sequencing methods, our understanding of the human lower respiratory tract's inhabitants has expanded significantly in recent years. What is now termed the "lung microbiome" has been described for healthy patients, as well as people with chronic lung diseases and lung transplants. The lung microbiome of lung transplant recipients (LTRs) has proven to be unique compared with nontransplant patients, with characteristic findings associated with disease states, such as pneumonia, acute rejection, and graft failure. In this review, we summarize the current understanding of the lung microbiome in LTRs, not only focusing on bacteria but also highlighting key findings of the viral and the fungal community. Based on our knowledge of the lung microbiome in LTRs, we propose multiple opportunities for clinical use of the microbiome to improve outcomes in this population.
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Affiliation(s)
- Caroline Cohen Eskind
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Meghan H. Shilts
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ciara M. Shaver
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Suman R. Das
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Otolaryngology and Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Gowri Satyanarayana
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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19
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Dodi G, Attanasi M, Di Filippo P, Di Pillo S, Chiarelli F. Virome in the Lungs: The Role of Anelloviruses in Childhood Respiratory Diseases. Microorganisms 2021; 9:microorganisms9071357. [PMID: 34201449 PMCID: PMC8307813 DOI: 10.3390/microorganisms9071357] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/24/2022] Open
Abstract
More recently, increasing attention has been directed to exploring the function of the global virome in health and disease. Currently, by new molecular techniques, such as metagenomic DNA sequencing, the virome has been better unveiled. By investigating the human lung virome, we could provide novel insights into respiratory diseases. The virome, as a part of the microbiome, is characterized by a constant change in composition related to the type of diet, environment, and our genetic code, and other incalculable factors. The virome plays a substantial role in modulating human immune defenses and contributing to the inflammatory processes. Anelloviruses (AVs) are new components of the virome. AVs are already present during early life and reproduce without apparently causing harm to the host. The role of AVs is still unknown, but several reports have shown that AVs could activate the inflammasomes, intracellular multiprotein oligomers of the innate immune system, which show a crucial role in the host defense to several pathogens. In this narrative revision, we summarize the epidemiological data related to the possible link between microbial alterations and chronic respiratory diseases in children. Briefly, we also describe the characteristics of the most frequent viral family present in the lung virome, Anelloviridae. Furthermore, we discuss how AVs could modulate the immune system in children, affecting the development of chronic respiratory diseases, particularly asthma, the most common chronic inflammatory disease in childhood.
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20
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Hendaus MA, Jomha FA. Can virus-virus interactions impact the dynamics of the covid-19 pandemic? J Biomol Struct Dyn 2021; 40:9571-9575. [PMID: 33998968 DOI: 10.1080/07391102.2021.1926327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Viral respiratory infections can occur in pandemics and can spread rapidly within communities resulting in health concerns globally. Several respiratory viruses co-circulate at one specific time. However, interface between different viruses has not been clearly established. This interaction is crucial to delineate, especially during pandemics, including the one relate to covid-19. This commentary will provide a brief description of how respiratory viruses interact and the outcome of this interaction on a pandemic.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohamed A Hendaus
- Department of Pediatrics, Sidra Medicine, Doha, Qatar.,Weill Cornell Medicine, Ar-Rayyan, Qatar
| | - Fatima A Jomha
- School of Pharmacy, Lebanese International University, Beirut, Lebanon
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21
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Jin T, Yin J. Patterns of virus growth across the diversity of life. Integr Biol (Camb) 2021; 13:44-59. [PMID: 33616184 DOI: 10.1093/intbio/zyab001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/24/2020] [Accepted: 01/04/2021] [Indexed: 01/14/2023]
Abstract
Although viruses in their natural habitats add up to less than 10% of the biomass, they contribute more than 90% of the genome sequences [1]. These viral sequences or 'viromes' encode viruses that populate the Earth's oceans [2, 3] and terrestrial environments [4, 5], where their infections impact life across diverse ecological niches and scales [6, 7], including humans [8-10]. Most viruses have yet to be isolated and cultured [11-13], and surprisingly few efforts have explored what analysis of available data might reveal about their nature. Here, we compiled and analyzed seven decades of one-step growth and other data for viruses from six major families, including their infections of archaeal, bacterial and eukaryotic hosts [14-191]. We found that the use of host cell biomass for virus production was highest for archaea at 10%, followed by bacteria at 1% and eukarya at 0.01%, highlighting the degree to which viruses of archaea and bacteria exploit their host cells. For individual host cells, the yield of virus progeny spanned a relatively narrow range (10-1000 infectious particles per cell) compared with the million-fold difference in size between the smallest and largest cells. Furthermore, healthy and infected host cells were remarkably similar in the time they needed to multiply themselves or their virus progeny. Specifically, the doubling time of healthy cells and the delay time for virus release from infected cells were not only correlated (r = 0.71, p < 10-10, n = 101); they also spanned the same range from tens of minutes to about a week. These results have implications for better understanding the growth, spread and persistence of viruses in complex natural habitats that abound with diverse hosts, including humans and their associated microbes.
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Affiliation(s)
- Tianyi Jin
- Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - John Yin
- Chemical and Biological Engineering, Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA
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22
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Beyond Cytomegalovirus and Epstein-Barr Virus: a Review of Viruses Composing the Blood Virome of Solid Organ Transplant and Hematopoietic Stem Cell Transplant Recipients. Clin Microbiol Rev 2020; 33:33/4/e00027-20. [PMID: 32847820 DOI: 10.1128/cmr.00027-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Viral primary infections and reactivations are common complications in patients after solid organ transplantation (SOT) and hematopoietic stem cell transplantation (HSCT) and are associated with high morbidity and mortality. Among these patients, viral infections are frequently associated with viremia. Beyond the usual well-known viruses that are part of the routine clinical management of transplant recipients, numerous other viral signatures or genomes can be identified in the blood of these patients. The identification of novel viral species and variants by metagenomic next-generation sequencing has opened up a new field of investigation and new paradigms. Thus, there is a need to thoroughly describe the state of knowledge in this field with a review of all viral infections that should be scrutinized in high-risk populations. Here, we review the eukaryotic DNA and RNA viruses identified in blood, plasma, or serum samples of pediatric and adult SOT/HSCT recipients and the prevalence of their detection, with a particular focus on recently identified viruses and those for which their potential association with disease remains to be investigated, such as members of the Polyomaviridae, Anelloviridae, Flaviviridae, and Astroviridae families. Current knowledge of the clinical significance of these viral infections with associated viremia among transplant recipients is also discussed. To ensure a comprehensive description in these two populations, individuals described as healthy (mostly blood donors) are considered for comparative purposes. The list of viruses that should be on the clinicians' radar is certainly incomplete and will expand, but the challenge is to identify those of possible clinical significance.
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23
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Gosens R, Hiemstra PS, Adcock IM, Bracke KR, Dickson RP, Hansbro PM, Krauss-Etschmann S, Smits HH, Stassen FRM, Bartel S. Host-microbe cross-talk in the lung microenvironment: implications for understanding and treating chronic lung disease. Eur Respir J 2020; 56:13993003.02320-2019. [PMID: 32430415 PMCID: PMC7439216 DOI: 10.1183/13993003.02320-2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/20/2020] [Indexed: 12/15/2022]
Abstract
Chronic respiratory diseases are highly prevalent worldwide and will continue to rise in the foreseeable future. Despite intensive efforts over recent decades, the development of novel and effective therapeutic approaches has been slow. However, there is new and increasing evidence that communities of micro-organisms in our body, the human microbiome, are crucially involved in the development and progression of chronic respiratory diseases. Understanding the detailed mechanisms underlying this cross-talk between host and microbiota is critical for development of microbiome- or host-targeted therapeutics and prevention strategies. Here we review and discuss the most recent knowledge on the continuous reciprocal interaction between the host and microbes in health and respiratory disease. Furthermore, we highlight promising developments in microbiome-based therapies and discuss the need to employ more holistic approaches of restoring both the pulmonary niche and the microbial community. The reciprocal interaction between microbes and host in the lung is increasingly recognised as an important determinant of health. The complexity of this cross-talk needs to be taken into account when studying diseases and developing future new therapies.https://bit.ly/2VKYUfT
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Affiliation(s)
- Reinoud Gosens
- University of Groningen, Dept of Molecular Pharmacology, GRIAC Research Institute, Groningen, The Netherlands
| | - Pieter S Hiemstra
- Dept of Pulmonology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Ian M Adcock
- Airways Disease, National Heart and Lung Institute, Imperial College London, London, UK
| | - Ken R Bracke
- Dept of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Dept of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.,Michigan Center for Integrative Research in Critical Care, Ann Arbor, MI, USA
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and the University of Newcastle, Newcastle, Australia.,Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
| | - Susanne Krauss-Etschmann
- Early Life Origins of Chronic Lung Disease, Research Center Borstel, Leibniz Lung Center, Airway Research Center North, Member of the German Center for Lung Research (DZL), Borstel, Germany.,Institute for Experimental Medicine, Christian-Albrechts-Universitaet zu Kiel, Kiel, Germany
| | - Hermelijn H Smits
- Dept of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Frank R M Stassen
- Dept of Medical Microbiology, NUTRIM - School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Sabine Bartel
- Early Life Origins of Chronic Lung Disease, Research Center Borstel, Leibniz Lung Center, Airway Research Center North, Member of the German Center for Lung Research (DZL), Borstel, Germany .,University of Groningen, University Medical Center Groningen, Dept of Pathology and Medical Biology, GRIAC Research Institute, Groningen, The Netherlands
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24
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Kostoff RN, Briggs MB, Porter AL, Hernández AF, Abdollahi M, Aschner M, Tsatsakis A. The under-reported role of toxic substance exposures in the COVID-19 pandemic. Food Chem Toxicol 2020; 145:111687. [PMID: 32805343 PMCID: PMC7426727 DOI: 10.1016/j.fct.2020.111687] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 12/16/2022]
Abstract
Coronavirus disease 2019 (COVID-19) and previous pandemics have been viewed almost exclusively as virology problems, with toxicology problems mostly being ignored. This perspective is not supported by the evolution of COVID-19, where the impact of real-life exposures to multiple toxic stressors degrading the immune system is followed by the SARS-CoV-2 virus exploiting the degraded immune system to trigger a chain of events ultimately leading to COVID-19. This immune system degradation from multiple toxic stressors (chemical, physical, biological, psychosocial stressors) means that attribution of serious consequences from COVID-19 should be made to the virus-toxic stressors nexus, not to any of the nexus constituents in isolation. The leading toxic stressors (identified in this study as contributing to COVID-19) are pervasive, contributing to myriad chronic diseases as well as immune system degradation. They increase the likelihood for comorbidities and mortality associated with COVID-19. For the short-term, tactical/reactive virology-focused treatments are of higher priority than strategic/proactive toxicology-focused treatments, although both could be implemented in parallel to reinforce each other. However, for long-term pandemic prevention, toxicology-based approaches should be given higher priority than virology-based approaches. Since current COVID-19 treatments globally ignore the toxicology component almost completely, only limited benefits can be expected from these treatments. Toxicology contributions to COVID-19 are mostly ignored relative to virology contributions. Exposure to myriad toxic substances degrades the immune system, whose resulting dysfunction is then exploited by SARS-CoV-2 to result in COVID-19. Attribution of serious consequences from COVID-19 should be made to the virus-toxic stressors combination nexus, not to any of the nexus constituents in isolation. Effective treatments need to address toxicology and virology interactions.
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Affiliation(s)
- Ronald N Kostoff
- Research Affiliate, School of Public Policy, Georgia Institute of Technology, Gainesville, VA, USA.
| | | | - Alan L Porter
- School of Public Policy, Georgia Institute of Technology, Atlanta, GA, USA; Search Technology, Peachtree Corners, GA, USA
| | - Antonio F Hernández
- Department of Legal Medicine and Toxicology, University of Granada School of Medicine, Health Sciences Technological Park, Granada, Spain
| | - Mohammad Abdollahi
- Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, New York, NY, USA; IM Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Aristidis Tsatsakis
- IM Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia; Laboratory of Toxicolgy and Forensic Sciences, Faculty of Medicine, University of Crete, 71003, Heraklion, Greece
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25
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Gupta P, Singh MP, Goyal K. Diversity of Vaginal Microbiome in Pregnancy: Deciphering the Obscurity. Front Public Health 2020; 8:326. [PMID: 32793540 PMCID: PMC7393601 DOI: 10.3389/fpubh.2020.00326] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/15/2020] [Indexed: 12/12/2022] Open
Abstract
Human microbiota plays an indispensable role in physiology, nutrition and most significantly, in imparting immunity. The role of microbiota has remained cryptic for years, until recently meticulous studies revealed the interaction and dynamics of these microbial communities. This diversified state is governed by hormonal, behavioral and physio-chemical changes in the genital tract. Many inclusive studies have revealed "Lactobacillus" to be the most dominant member of vaginal flora in most of the healthy, reproductive age group and pregnant females. A total of five community state types have been described, out of which four are dominated by Lactobacillus while the fifth one by facultative or strict anaerobic species. A variation between species stability and gestational age has also been revealed. Studies have divulged a significant higher stability of vaginal microbiota in early stages of pregnancy and the same increased subsequently. Inter-species and racial variation has shown women belonging to White, Asian, and Caucasian race to harbor more of the anaerobic flora. The vaginal microbiome in pregnancy play a significant role in preterm and spontaneous labor. This Lactobacillus-rich microbiome falls tremendously, becoming more diverse in post-partum period. Apart from these known bacterial communities in human vagina, other microbial communities have also been traced. The major fragment is constituted by vaginal viral virome and very little information exists in relation to vaginal mycobiome. Studies have revealed the abundance of ds DNA viruses in vaginal microbiome, followed by ssDNA, and few unidentified viruses. The eukaryotic viruses detected were very few, with Herpesvirales, and Papillomaviridae being the only pathogenic ones. This flora is transmitted to infants either via maternal gut, vagina or breast milk. Recent studies have given an insight for vaginal microbiome, dissociating the old concept of "healthy" and "diseased." However, more extensive studies are required to study evolution of virome and mycobiome in relation to their association with bacterial communities; to establish and decode full array of vaginal virome under the influence of genotypic and environmental factors, using novel bioinformatic, multi-omic, statistical model, and CRISPR/Cas approaches.
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26
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Liu B, Shao N, Wang J, Zhou S, Su H, Dong J, Sun L, Li L, Zhang T, Yang F. An Optimized Metagenomic Approach for Virome Detection of Clinical Pharyngeal Samples With Respiratory Infection. Front Microbiol 2020; 11:1552. [PMID: 32754134 PMCID: PMC7366072 DOI: 10.3389/fmicb.2020.01552] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/16/2020] [Indexed: 12/23/2022] Open
Abstract
Respiratory virus infections are one of the major causes of acute respiratory disease or exacerbation of chronic obstructive pulmonary disease (COPD). However, next-generation sequencing has not been used for routine viral detection in clinical respiratory samples owing to its sophisticated technology. Here, several pharyngeal samples with COPD were collected to enrich viral particles using an optimized method (M3), which involved M1 with centrifugation, filtration, and concentration, M2 (magnetic beads) combined with mixed nuclease digestion, and M4 with no pretreatment as a control. Metagenomic sequencing and bioinformatics analyses showed that the M3 method for viral enrichment was superior in both viral sequencing composition and viral taxa when compared to M1, M2, and M4. M3 acquired the most viral reads and more complete sequences within 15-h performance, indicating that it might be feasible for viral detection in multiple respiratory samples in clinical practice. Based on sequence similarity analysis, 12 human viruses, including nine Anelloviruses and three coronaviruses, were characterized. Coronavirus OC43 with the largest number of viral reads accounted for nearly complete (99.8%) genome sequences, indicating that it may be a major viral pathogen involved in exacerbation of COPD.
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Affiliation(s)
- Bo Liu
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Shao
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Wang
- Division of Pulmonary and Critical Care Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - SiYu Zhou
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - HaoXiang Su
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Dong
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - LiLian Sun
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Li
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Zhang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fan Yang
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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27
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Reckziegel M, Weber-Osel C, Egerer R, Gruhn B, Kubek F, Walther M, Wilhelm S, Zell R, Krumbholz A. Viruses and atypical bacteria in the respiratory tract of immunocompromised and immunocompetent patients with airway infection. Eur J Clin Microbiol Infect Dis 2020; 39:1581-1592. [PMID: 32462500 PMCID: PMC7253234 DOI: 10.1007/s10096-020-03878-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/24/2020] [Indexed: 01/08/2023]
Abstract
Respiratory tract infections (RTI) can take a serious course under immunosuppression. Data on the impact of the underlying pathogens are still controversial. Samples from the upper (n = 322) and lower RT (n = 169) were collected from 136 children and 355 adults; 225 among them have been immunocompromised patients. Exclusion criteria were presence of relevant cultivable microorganisms, C-reactive protein > 20 mg/dl, or procalcitonin > 2.0 ng/ml. Samples were tested by PCR for the presence of herpesviruses (HSV-1/-2; VZV; CMV; HHV6; EBV), adenoviruses, bocaviruses, entero-/rhinoviruses (HRV), parechoviruses, coronaviruses, influenza viruses (IV), parainfluenza viruses as well as for pneumoviruses (HMPV and RSV), and atypical bacteria (Mycoplasma pneumoniae, M.p.; Chlamydia pneumoniae, C.p.). Viral/bacterial genome equivalents were detected in more than two-thirds of specimens. Under immunosuppression, herpesviruses (EBV 30.9%/14.6%, p < 0.001; CMV 19.6%/7.9%, p < 0.001; HSV-1: 14.2%/7.1%, p = 0.012) were frequently observed, mainly through their reactivation in adults. Immunocompromised adults tended to present a higher RSV prevalence (6.4%/2.4%, p = 0.078). Immunocompetent patients were more frequently tested positive for IV (15.0%/5.8%, p = 0.001) and M.p. (6.4%/0.4%, p < 0.001), probably biased due to the influenza pandemic of 2009 and an M.p. epidemic in 2011. About 41.8% of samples were positive for a single pathogen, and among them EBV (19.9%) was most prevalent followed by HRV (18.2%) and IV (16.6%). HSV-2 and C.p. were not found. Marked seasonal effects were observed for HRV, IV, and RSV. Differences in pathogen prevalence were demonstrated between immunocompetent and immunocompromised patients. The exact contribution of some herpesviruses to the development of RTI remains unclear.
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Affiliation(s)
- Maria Reckziegel
- Section of Experimental Virology, Institute of Medical Microbiology, Jena University Hospital, Jena, Germany.,Department of Hematology/Oncology, Clinic of Internal Medicine II, Jena University Hospital, Jena, Germany
| | - Claudia Weber-Osel
- Section of Experimental Virology, Institute of Medical Microbiology, Jena University Hospital, Jena, Germany.,Department of Medicine II, Catholic Hospital 'St. Johann Nepomuk', Erfurt, Germany
| | - Renate Egerer
- Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Bernd Gruhn
- Department of Pediatrics, Jena University Hospital, Jena, Germany
| | - Florian Kubek
- Section of Experimental Virology, Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Mario Walther
- Department of Fundamental Sciences, Jena University of Applied Sciences, Jena, Germany
| | - Stefanie Wilhelm
- Section of Experimental Virology, Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Roland Zell
- Section of Experimental Virology, Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Andi Krumbholz
- Institute of Infection Medicine, Christian-Albrechts-Universität zu Kiel and University Medical Center Schleswig-Holstein, Brunswiker Straße 4, D-24105, Kiel, Germany.
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28
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Lejeune S, Deschildre A, Le Rouzic O, Engelmann I, Dessein R, Pichavant M, Gosset P. Childhood asthma heterogeneity at the era of precision medicine: Modulating the immune response or the microbiota for the management of asthma attack. Biochem Pharmacol 2020; 179:114046. [PMID: 32446884 PMCID: PMC7242211 DOI: 10.1016/j.bcp.2020.114046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/19/2020] [Indexed: 12/12/2022]
Abstract
Exacerbations are a main characteristic of asthma. In childhood, the risk is increasing with severity. Exacerbations are a strong phenotypic marker, particularly of severe and therapy-resistant asthma. These early-life events may influence the evolution and be involved in lung function decline. In children, asthma attacks are facilitated by exposure to allergens and pollutants, but are mainly triggered by microbial agents. Multiple studies have assessed immune responses to viruses, and to a lesser extend bacteria, during asthma exacerbation. Research has identified impairment of innate immune responses in children, related to altered pathogen recognition, interferon release, or anti-viral response. Influence of this host-microbiota dialog on the adaptive immune response may be crucial, leading to the development of biased T helper (Th)2 inflammation. These dynamic interactions may impact the presentations of asthma attacks, and have long-term consequences. The aim of this review is to synthesize studies exploring immune mechanisms impairment against viruses and bacteria promoting asthma attacks in children. The potential influence of the nature of infectious agents and/or preexisting microbiota on the development of exacerbation is also addressed. We then discuss our understanding of how these diverse host-microbiota interactions in children may account for the heterogeneity of endotypes and clinical presentations. Finally, improving the knowledge of the pathophysiological processes induced by infections has led to offer new opportunities for the development of preventive or curative therapeutics for acute asthma. A better definition of asthma endotypes associated with precision medicine might lead to substantial progress in the management of severe childhood asthma.
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Affiliation(s)
- Stéphanie Lejeune
- CHU Lille, Univ. Lille, Pediatric Pulmonology and Allergy Department, Hôpital Jeanne de Flandre, F-59000 Lille, France; Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France
| | - Antoine Deschildre
- CHU Lille, Univ. Lille, Pediatric Pulmonology and Allergy Department, Hôpital Jeanne de Flandre, F-59000 Lille, France; Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France
| | - Olivier Le Rouzic
- Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France; CHU Lille, Univ. Lille, Department of Respiratory Diseases, F-59000 Lille Cedex, France
| | - Ilka Engelmann
- Univ. Lille, Virology Laboratory, EA3610, Institute of Microbiology, CHU Lille, F-59037 Lille Cedex, France
| | - Rodrigue Dessein
- Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France; Univ. Lille, Bacteriology Department, Institute of Microbiology, CHU Lille, F-59037 Lille Cedex, France
| | - Muriel Pichavant
- Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France
| | - Philippe Gosset
- Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France.
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29
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Abstract
Aspergillus fumigatus is a saprotrophic fungus; its primary habitat is the soil. In its ecological niche, the fungus has learned how to adapt and proliferate in hostile environments. This capacity has helped the fungus to resist and survive against human host defenses and, further, to be responsible for one of the most devastating lung infections in terms of morbidity and mortality. In this review, we will provide (i) a description of the biological cycle of A. fumigatus; (ii) a historical perspective of the spectrum of aspergillus disease and the current epidemiological status of these infections; (iii) an analysis of the modes of immune response against Aspergillus in immunocompetent and immunocompromised patients; (iv) an understanding of the pathways responsible for fungal virulence and their host molecular targets, with a specific focus on the cell wall; (v) the current status of the diagnosis of different clinical syndromes; and (vi) an overview of the available antifungal armamentarium and the therapeutic strategies in the clinical context. In addition, the emergence of new concepts, such as nutritional immunity and the integration and rewiring of multiple fungal metabolic activities occurring during lung invasion, has helped us to redefine the opportunistic pathogenesis of A. fumigatus.
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Affiliation(s)
- Jean-Paul Latgé
- School of Medicine, University of Crete, Heraklion, Crete, Greece
| | - Georgios Chamilos
- School of Medicine, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Crete, Greece
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30
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Naidoo CC, Nyawo GR, Wu BG, Walzl G, Warren RM, Segal LN, Theron G. The microbiome and tuberculosis: state of the art, potential applications, and defining the clinical research agenda. THE LANCET. RESPIRATORY MEDICINE 2019; 7:892-906. [PMID: 30910543 DOI: 10.1016/s2213-2600(18)30501-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 01/26/2023]
Abstract
The diverse microbial communities within our bodies produce metabolites that modulate host immune responses. Even the microbiome at distal sites has an important function in respiratory health. However, the clinical importance of the microbiome in tuberculosis, the biggest infectious cause of death worldwide, is only starting to be understood. Here, we critically review research on the microbiome's association with pulmonary tuberculosis. The research indicates five main points: (1) susceptibility to infection and progression to active tuberculosis is altered by gut Helicobacter co-infection, (2) aerosol Mycobacterium tuberculosis infection changes the gut microbiota, (3) oral anaerobes in the lung make metabolites that decrease pulmonary immunity and predict progression, (4) the increased susceptibility to reinfection of patients who have previously been treated for tuberculosis is likely due to the depletion of T-cell epitopes on commensal gut non-tuberculosis mycobacteria, and (5) the prolonged antibiotic treatment required for cure of tuberculosis has long-term detrimental effects on the microbiome. We highlight knowledge gaps, considerations for addressing these knowledge gaps, and describe potential targets for modifying the microbiome to control tuberculosis.
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Affiliation(s)
- Charissa C Naidoo
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Georgina R Nyawo
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Gerhard Walzl
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Robin M Warren
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Grant Theron
- Department of Science and Technology-National Research Foundation (DST-NRF) Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; African Microbiome Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
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31
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Ghose C, Ly M, Schwanemann LK, Shin JH, Atab K, Barr JJ, Little M, Schooley RT, Chopyk J, Pride DT. The Virome of Cerebrospinal Fluid: Viruses Where We Once Thought There Were None. Front Microbiol 2019; 10:2061. [PMID: 31555247 PMCID: PMC6742758 DOI: 10.3389/fmicb.2019.02061] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/21/2019] [Indexed: 01/21/2023] Open
Abstract
Traditionally, medicine has held that some human body sites are sterile and that the introduction of microbes to these sites results in infections. This paradigm shifted significantly with the discovery of the human microbiome and acceptance of these commensal microbes living across the body. However, the central nervous system (CNS) is still believed by many to be sterile in healthy people. Using culture-independent methods, we examined the virome of cerebrospinal fluid (CSF) from a cohort of mostly healthy human subjects. We identified a community of DNA viruses, most of which were identified as bacteriophages. Compared to other human specimen types, CSF viromes were not ecologically distinct. There was a high alpha diversity cluster that included feces, saliva, and urine, and a low alpha diversity cluster that included CSF, body fluids, plasma, and breast milk. The high diversity cluster included specimens known to have many bacteria, while other specimens traditionally assumed to be sterile formed the low diversity cluster. There was an abundance of viruses shared among CSF, breast milk, plasma, and body fluids, while each generally shared less with urine, feces, and saliva. These shared viruses ranged across different virus families, indicating that similarities between these viromes represent more than just a single shared virus family. By identifying a virome in the CSF of mostly healthy individuals, it is now less likely that any human body site is devoid of microbes, which further highlights the need to decipher the role that viral communities may play in human health.
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Affiliation(s)
| | - Melissa Ly
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Leila K Schwanemann
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Ji Hyun Shin
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Katayoon Atab
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Jeremy J Barr
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Mark Little
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Robert T Schooley
- Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Jessica Chopyk
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - David T Pride
- Department of Pathology, University of California, San Diego, San Diego, CA, United States.,Department of Medicine, University of California, San Diego, San Diego, CA, United States
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32
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Davis JS, Magin PJ, van Driel ML. The false dichotomy of viral versus bacterial aetiology in upper respiratory tract infections. Med J Aust 2019; 211:108-109.e1. [PMID: 31232463 DOI: 10.5694/mja2.50250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Joshua S Davis
- Menzies School of Health Research, Darwin, NT.,John Hunter Hospital, Newcastle, NSW
| | - Parker J Magin
- University of Newcastle, Newcastle, NSW.,GP Synergy, Newcastle, NSW
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33
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Altered respiratory virome and serum cytokine profile associated with recurrent respiratory tract infections in children. Nat Commun 2019; 10:2288. [PMID: 31123265 PMCID: PMC6533328 DOI: 10.1038/s41467-019-10294-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 04/29/2019] [Indexed: 12/12/2022] Open
Abstract
Recurrent acute respiratory tract infections (ARTIs) affect a large population, yet the specific decisive factors are largely unknown. Here we study a population of 4407 children diagnosed with ARTI, comparing respiratory virome and serum cytokine profiles associated with multiple ARTIs and single ARTI during a six-year period. The relative abundance of Propionibacterium phages is significantly elevated in multiple ARTIs compared to single ARTI group. Serum levels of TIMP-1 and PDGF-BB are markedly increased in multiple ARTIs compared to single-ARTI and non-ARTI controls, making these two cytokines potential predictors for multiple ARTIs. The presence of Propionibacterium phages is associated with higher levels of TIMP-1 and PDGF-BB. Receiver operating characteristic (ROC) curve analyses show that the combination of TIMP-1, PDGF-BB and Propionibacterium phages could be a strong predictor for multiple ARTIs. These findings indicate that respiratory microbe homeostasis and specific cytokines are associated with the onset of multiple ARTIs over time. Here, the authors determine the respiratory virome and serum cytokine profile in children diagnosed with acute respiratory tract infections (ARTI) and show that relative abundance of Propionibacterium phages as well as serum levels of TIMP-1 and PDGF-BB are increased in multiple ARTIs compared with single ARTI.
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34
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Dumas A, Bernard L, Poquet Y, Lugo-Villarino G, Neyrolles O. The role of the lung microbiota and the gut-lung axis in respiratory infectious diseases. Cell Microbiol 2018; 20:e12966. [PMID: 30329198 DOI: 10.1111/cmi.12966] [Citation(s) in RCA: 242] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/05/2018] [Accepted: 10/14/2018] [Indexed: 12/13/2022]
Abstract
The pulmonary microbial community, described only a few years ago, forms a discreet part of the human host microbiota. The airway microbiota has been found to be substantially altered in the context of numerous respiratory disorders; nonetheless, its role in health and disease is as yet only poorly understood. Another important parameter to consider is the gut-lung axis, where distal (gut) immune modulation during respiratory disease is mediated by the gut microbiota. The use of specific microbiota strains, termed "probiotics," with beneficial effects on the host immunity and/or against pathogens, has proven successful in the treatment of intestinal disorders and is also showing promise in the context of airway diseases. In this review, we highlight the beneficial role of the body's commensal bacteria during airway infectious diseases, including recent evidence highlighting their local (lung) or distal (gut) contribution in this process.
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Affiliation(s)
- Alexia Dumas
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Lucie Bernard
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yannick Poquet
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Geanncarlo Lugo-Villarino
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Olivier Neyrolles
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
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35
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Jankauskaitė L, Misevičienė V, Vaidelienė L, Kėvalas R. Lower Airway Virology in Health and Disease-From Invaders to Symbionts. MEDICINA (KAUNAS, LITHUANIA) 2018; 54:E72. [PMID: 30344303 PMCID: PMC6262431 DOI: 10.3390/medicina54050072] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/10/2018] [Accepted: 10/10/2018] [Indexed: 12/13/2022]
Abstract
Studies of human airway virome are relatively recent and still very limited. Culture-independent microbial techniques showed growing evidence of numerous viral communities in the respiratory microbial ecosystem. The significance of different acute respiratory viruses is already known in the pathogenesis of chronic conditions, such as asthma, cystic fibrosis (CF), or chronic obstructive lung disease (COPD), and their exacerbations. Viral pathogens, such as influenza, metapneumovirus, parainfluenza, respiratory syncytial virus, or rhinovirus, have been associated with impaired immune response, acute exacerbations, and decrease in lung function in chronic lung diseases. However, more data have attributed a role to Herpes family viruses or the newly identified Anelloviridae family of viruses in chronic diseases, such as asthma, idiopathic pulmonary fibrosis (IPF), or CF. Impaired antiviral immunity, bacterial colonization, or used medication, such as glucocorticoids or antibiotics, contribute to the imbalance of airway microbiome and may shape the local viral ecosystem. A specific part of virome, bacteriophages, frames lung microbial communities through direct contact with its host, the specific bacteria known as Pseudomonas aeruginosa or their biofilm formation. Moreover, antibiotic resistance is induced through phages via horizontal transfer and leads to more severe exacerbations of chronic airway conditions. Morbidity and mortality of asthma, COPD, CF, and IPF remains high, despite an increased understanding and knowledge about the impact of respiratory virome in the pathogenesis of these conditions. Thus, more studies focus on new prophylactic methods or therapeutic agents directed toward viral⁻host interaction, microbial metabolic function, or lung microbial composition rearrangement.
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Affiliation(s)
- Lina Jankauskaitė
- Department of Paediatrics, Medical Academy, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania.
| | - Valdonė Misevičienė
- Department of Paediatrics, Medical Academy, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania.
| | - Laimutė Vaidelienė
- Department of Paediatrics, Medical Academy, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania.
| | - Rimantas Kėvalas
- Department of Paediatrics, Medical Academy, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania.
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36
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Pannaraj PS, Ly M, Cerini C, Saavedra M, Aldrovandi GM, Saboory AA, Johnson KM, Pride DT. Shared and Distinct Features of Human Milk and Infant Stool Viromes. Front Microbiol 2018; 9:1162. [PMID: 29910789 PMCID: PMC5992295 DOI: 10.3389/fmicb.2018.01162] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/14/2018] [Indexed: 01/01/2023] Open
Abstract
Infants acquire many of their microbes from their mothers during the birth process. The acquisition of these microbes is believed to be critical in the development of the infant immune system. Bacteria also are transmitted to the infant through breastfeeding, and help to form the microbiome of the infant gastrointestinal (GI) tract; it is unknown whether viruses in human milk serve to establish an infant GI virome. We examined the virome contents of milk and infant stool in a cohort of mother-infant pairs to discern whether milk viruses colonize the infant GI tract. We observed greater viral alpha diversity in milk than in infant stool, similar to the trend we found for bacterial communities from both sites. When comparing beta diversity, viral communities were mostly distinguishable between milk and infant stool, but each was quite distinct from adult stool, urine, and salivary viromes. There were significant differences in viral families in the infant stool (abundant bacteriophages from the family Siphoviridae) compared to milk (abundant bacteriophages from the family Myoviridae), which may reflect significant differences in the bacterial families identified from both sites. Despite the differences in viral taxonomy, we identified a significant number of shared viruses in the milk and stool from all mother-infant pairs. Because of the significant proportion of bacteriophages transmitted in these mother-infant pairs, we believe the transmission of milk phages to the infant GI tract may help to shape the infant GI microbiome.
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Affiliation(s)
- Pia S Pannaraj
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States.,Department of Pediatrics, Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Melissa Ly
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Chiara Cerini
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Monica Saavedra
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Grace M Aldrovandi
- Department of Pediatrics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Abdul A Saboory
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - Kevin M Johnson
- Department of Pathology, University of California, San Diego, San Diego, CA, United States
| | - David T Pride
- Department of Pathology, University of California, San Diego, San Diego, CA, United States.,Department of Medicine, University of California, San Diego, San Diego, CA, United States
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37
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Guilloux CA, Lamoureux C, Héry-Arnaud G. [Anaerobic bacteria, the unknown members of the lung microbiota]. Med Sci (Paris) 2018; 34:253-260. [PMID: 29547112 DOI: 10.1051/medsci/20183403014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Lungs were considered as sterile for a long time. However, it is now evident that the lungs of healthy people are colonized by microorganisms. Among the bacteria present in the pulmonary microbiota, a significant proportion is anaerobic (strict or facultative). Even though interest in the pulmonary microbiota is increasing, few studies have focused on these unknowns that represent the lung resident anaerobic bacteria. This review describes the biodiversity of anaerobes in physiological conditions, and in different chronic respiratory diseases (cystic fibrosis, COPD, asthma). It also explains anaerobes' roles in the barrier flora effect, in inflammation, or as potential biomarkers in disease progression.
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Affiliation(s)
- Charles-Antoine Guilloux
- UMR1078, Génétique, Génomique Fonctionnelle et Biotechnologies, Inserm, Université de Brest, EFS, IBSAM, 22, avenue Camille Desmoulins, 29238 Brest, France
| | - Claudie Lamoureux
- UMR1078, Génétique, Génomique Fonctionnelle et Biotechnologies, Inserm, Université de Brest, EFS, IBSAM, 22, avenue Camille Desmoulins, 29238 Brest, France - Unité de Bactériologie, Pôle de Biologie-Pathologie, Hôpital La Cavale Blanche, CHRU de Brest, 29238 Brest, France
| | - Geneviève Héry-Arnaud
- UMR1078, Génétique, Génomique Fonctionnelle et Biotechnologies, Inserm, Université de Brest, EFS, IBSAM, 22, avenue Camille Desmoulins, 29238 Brest, France - Unité de Bactériologie, Pôle de Biologie-Pathologie, Hôpital La Cavale Blanche, CHRU de Brest, 29238 Brest, France
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The Human Virome: Implications for Clinical Practice in Transplantation Medicine. J Clin Microbiol 2017; 55:2884-2893. [PMID: 28724557 DOI: 10.1128/jcm.00489-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Advances in DNA sequencing technology have provided an unprecedented opportunity to study the human virome. Transplant recipients and other immunocompromised hosts are at particular risk for developing virus-related pathology; thus, the impact of the virome on health and disease may be even more relevant in this population. Here, we discuss technical considerations in studying the human virome, the current literature on the virome in transplant recipients, and near-future applications of sequence-based findings that can further our understanding of viruses in transplantation medicine.
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