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Dora D, Szőcs E, Soós Á, Halasy V, Somodi C, Mihucz A, Rostás M, Mógor F, Lohinai Z, Nagy N. From bench to bedside: an interdisciplinary journey through the gut-lung axis with insights into lung cancer and immunotherapy. Front Immunol 2024; 15:1434804. [PMID: 39301033 PMCID: PMC11410641 DOI: 10.3389/fimmu.2024.1434804] [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: 05/18/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024] Open
Abstract
This comprehensive review undertakes a multidisciplinary exploration of the gut-lung axis, from the foundational aspects of anatomy, embryology, and histology, through the functional dynamics of pathophysiology, to implications for clinical science. The gut-lung axis, a bidirectional communication pathway, is central to understanding the interconnectedness of the gastrointestinal- and respiratory systems, both of which share embryological origins and engage in a continuous immunological crosstalk to maintain homeostasis and defend against external noxa. An essential component of this axis is the mucosa-associated lymphoid tissue system (MALT), which orchestrates immune responses across these distant sites. The review delves into the role of the gut microbiome in modulating these interactions, highlighting how microbial dysbiosis and increased gut permeability ("leaky gut") can precipitate systemic inflammation and exacerbate respiratory conditions. Moreover, we thoroughly present the implication of the axis in oncological practice, particularly in lung cancer development and response to cancer immunotherapies. Our work seeks not only to synthesize current knowledge across the spectrum of science related to the gut-lung axis but also to inspire future interdisciplinary research that bridges gaps between basic science and clinical application. Our ultimate goal was to underscore the importance of a holistic understanding of the gut-lung axis, advocating for an integrated approach to unravel its complexities in human health and disease.
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Affiliation(s)
- David Dora
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Emőke Szőcs
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Ádám Soós
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Viktória Halasy
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Csenge Somodi
- Translational Medicine Institute, Semmelweis University, Budapest, Hungary
| | - Anna Mihucz
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Melinda Rostás
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Fruzsina Mógor
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Zoltan Lohinai
- Translational Medicine Institute, Semmelweis University, Budapest, Hungary
| | - Nándor Nagy
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
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Wang H, Wang Y. What Makes the Gut-Lung Axis Working? From the Perspective of Microbiota and Traditional Chinese Medicine. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2024; 2024:8640014. [PMID: 38274122 PMCID: PMC10810697 DOI: 10.1155/2024/8640014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/21/2023] [Accepted: 01/08/2024] [Indexed: 01/27/2024]
Abstract
Background An increasing number of studies have proved that gut microbiota is involved in the occurrence and development of various lung diseases and can interact with the diseased lung. The concept of the gut-lung axis (GLA) provides a new idea for the subsequent clinical treatment of lung diseases through human microbiota. This review aims to summarize the microbiota in the lung and gut and the interaction between them from the perspectives of traditional Chinese medicine and modern medicine. Method We conducted a literature search by using the search terms "GLA," "gut microbiota," "spleen," and "Chinese medicine" in the databases PubMed, Web of Science, and CNKI. We then explored the mechanism of action of the gut-lung axis from traditional Chinese medicine and modern medicine. Results The lung and gut microbiota enable the GLA to function through immune regulation, while metabolites of the gut microbiota also play an important role. The spleen can improve the gut microbiota to achieve the regulation of the GLA. Conclusion Improving the gut microbiota through qi supplementation and spleen fortification provides a new approach to the clinical treatment of lung diseases by regulating the GLA. Currently, our understanding of the GLA is limited, and more research is needed to explain its working principle.
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Affiliation(s)
- Hui Wang
- Zhejiang Chinese Medical University, Hangzhou 310000, China
| | - Ying Wang
- Zhejiang Chinese Medical University, Hangzhou 310000, China
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3
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Zhang Y, Chen X, Wang Y, Li L, Ju Q, Zhang Y, Xi H, Wang F, Qiu D, Liu X, Chang N, Zhang W, Zhang C, Wang K, Li L, Zhang J. Alterations of lower respiratory tract microbiome and short-chain fatty acids in different segments in lung cancer: a multiomics analysis. Front Cell Infect Microbiol 2023; 13:1261284. [PMID: 37915846 PMCID: PMC10617678 DOI: 10.3389/fcimb.2023.1261284] [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: 07/19/2023] [Accepted: 09/20/2023] [Indexed: 11/03/2023] Open
Abstract
Introduction The lower respiratory tract microbiome is widely studied to pinpoint microbial dysbiosis of diversity or abundance that is linked to a number of chronic respiratory illnesses. However, it is vital to clarify how the microbiome, through the release of microbial metabolites, impacts lung health and oncogenesis. Methods In order to discover the powerful correlations between microbial metabolites and disease, we collected, under electronic bronchoscopy examinations, samples of paired bronchoalveolar lavage fluids (BALFs) from tumor-burden lung segments and ipsilateral non-tumor sites from 28 lung cancer participants, further performing metagenomic sequencing, short-chain fatty acid (SCFA) metabolomics, and multiomics analysis to uncover the potential correlations of the microbiome and SCFAs in lung cancer. Results In comparison to BALFs from normal lung segments of the same participant, those from lung cancer burden lung segments had slightly decreased microbial diversity in the lower respiratory tract. With 18 differentially prevalent microbial species, including the well-known carcinogens Campylobacter jejuni and Nesseria polysaccharea, the relative species abundance in the lower respiratory tract microbiome did not significantly differ between the two groups. Additionally, a collection of commonly recognized probiotic metabolites called short-chain fatty acids showed little significance in either group independently but revealed a strong predictive value when using an integrated model by machine learning. Multiomics also discovered particular species related to SCFAs, showing a positive correlation with Brachyspira hydrosenteriae and a negative one with Pseudomonas at the genus level, despite limited detection in lower airways. Of note, these distinct microbiota and metabolites corresponded with clinical traits that still required confirmation. Conclusions Further analysis of metagenome functional capacity revealed that genes encoding environmental information processing and metabolism pathways were enriched in the lower respiratory tract metagenomes of lung cancer patients, further supporting the oncogenesis function of various microbial species by different metabolites. These findings point to a potent relationship between particular components of the integrated microbiota-metabolites network and lung cancer, with implications for screening and diagnosis in clinical settings.
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Affiliation(s)
- Yong Zhang
- Department of Pulmonary and Critical Care of Medicine, The First Affiliated Hospital of Fourth Military Medical University, Xi’an, China
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi’an, China
| | - Xiangxiang Chen
- Department of Pulmonary and Critical Care of Medicine, The First Affiliated Hospital of Fourth Military Medical University, Xi’an, China
| | - Yuan Wang
- Department of Microbiology, School of Basic Medicine of Fourth Military Medical University, Xi’an, China
| | - Ling Li
- Department of Pediatrics, The First Affiliated Hospital of Fourth Military Medical University, Xi’an, China
| | - Qing Ju
- Department of Pulmonary and Critical Care of Medicine, The First Affiliated Hospital of Fourth Military Medical University, Xi’an, China
| | - Yan Zhang
- Department of Pulmonary and Critical Care of Medicine, The First Affiliated Hospital of Fourth Military Medical University, Xi’an, China
| | - Hangtian Xi
- Department of Pulmonary and Critical Care of Medicine, The First Affiliated Hospital of Fourth Military Medical University, Xi’an, China
| | - Fahan Wang
- School of Basic Medicine, Fourth Military Medical University, Xi’an, China
| | - Dan Qiu
- Department of Pulmonary and Critical Care of Medicine, The First Affiliated Hospital of Fourth Military Medical University, Xi’an, China
| | - Xingchen Liu
- School of Basic Medicine, Fourth Military Medical University, Xi’an, China
| | - Ning Chang
- Department of Pulmonary and Critical Care of Medicine, The First Affiliated Hospital of Fourth Military Medical University, Xi’an, China
| | - Weiqi Zhang
- Department of Radiology, The First Affiliated Hospital of Fourth Military Medical University, Xi’an, China
| | - Cong Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of Fourth Military Medical University, Xi’an, China
| | - Ke Wang
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi’an, China
| | - Ling Li
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi’an, China
| | - Jian Zhang
- Department of Pulmonary and Critical Care of Medicine, The First Affiliated Hospital of Fourth Military Medical University, Xi’an, China
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Pérez-Cobas AE, Ginevra C, Rusniok C, Jarraud S, Buchrieser C. The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia. Cell Rep Med 2023; 4:101167. [PMID: 37633274 PMCID: PMC10518590 DOI: 10.1016/j.xcrm.2023.101167] [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: 12/05/2022] [Revised: 06/18/2023] [Accepted: 08/02/2023] [Indexed: 08/28/2023]
Abstract
Bacterial pneumonia is a considerable problem worldwide. Here, we follow the inter-kingdom respiratory tract microbiome (RTM) of a unique cohort of 38 hospitalized patients (n = 97 samples) with pneumonia caused by Legionella pneumophila. The RTM composition is characterized by diversity drops early in hospitalization and ecological species replacement. RTMs with the highest bacterial and fungal loads show low diversity and pathogen enrichment, suggesting high biomass as a biomarker for secondary and/or co-infections. The RTM structure is defined by a "commensal" cluster associated with a healthy RTM and a "pathogen" enriched one, suggesting that the cluster equilibrium drives the microbiome to recovery or dysbiosis. Legionella biomass correlates with disease severity and co-morbidities, while clinical interventions influence the RTM dynamics. Fungi, archaea, and protozoa seem to contribute to progress of pneumonia. Thus, the interplay of the RTM equilibrium, the pathogen load dynamics, and clinical interventions play a critical role in patient recovery.
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Affiliation(s)
- Ana Elena Pérez-Cobas
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, Paris, France; CNRS UMR 6047, 75724 Paris, France.
| | - Christophe Ginevra
- Hospices Civils de Lyon, Centre National de Référence des Légionelles, Bron, France; Centre International de Recherche en Infectiologie, Université Lyon 1, UMR CNRS 5308, U1111 Inserm, École Normale Supérieure de Lyon, Lyon, France
| | - Christophe Rusniok
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, Paris, France; CNRS UMR 6047, 75724 Paris, France
| | - Sophie Jarraud
- Hospices Civils de Lyon, Centre National de Référence des Légionelles, Bron, France; Centre International de Recherche en Infectiologie, Université Lyon 1, UMR CNRS 5308, U1111 Inserm, École Normale Supérieure de Lyon, Lyon, France
| | - Carmen Buchrieser
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, Paris, France; CNRS UMR 6047, 75724 Paris, France.
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Xie L, Zhang X, Gao X, Wang L, Cheng Y, Zhang S, Yue J, Tang Y, Deng Y, Zhang B, He X, Tang M, Yang H, Zheng T, You J, Song X, Xiong J, Zuo H, Pei X. Microbiota and mycobiota in bronchoalveolar lavage fluid of silicosis patients. J Occup Med Toxicol 2023; 18:10. [PMID: 37430310 DOI: 10.1186/s12995-023-00377-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/29/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND The contribution of bronchoalveolar lavage fluid (BALF) microbiota and mycobiota to silicosis has recently been noticed. However, many confounding factors can influence the accuracy of BALF microbiota and mycobiota studies, resulting in inconsistencies in the published results. In this cross-sectional study, we systematically investigated the effects of "sampling in different rounds of BALF" on its microbiota and mycobiota. We further explored the relationship between silicosis fatigue and the microbiota and mycobiota. METHODS After obtaining approval from the ethics board, we collected 100 BALF samples from 10 patients with silicosis. Demographic data, clinical information, and blood test results were also collected from each patient. The characteristics of the microbiota and mycobiota were defined using next-generation sequencing. However, no non-silicosis referent group was examined, which was a major limitation of this study. RESULTS Our analysis indicated that subsampling from different rounds of BALF did not affect the alpha- and beta-diversities of microbial and fungal communities when the centrifuged BALF sediment was sufficient for DNA extraction. In contrast, fatigue status significantly influenced the beta-diversity of microbes and fungi (Principal Coordinates Analysis, P = 0.001; P = 0.002). The abundance of Vibrio alone could distinguish silicosis patients with fatigue from those without fatigue (area under the curve = 0.938, 95% confidence interval [CI] 0.870-1.000). Significant correlations were found between Vibrio and haemoglobin levels (P < 0.001, ρ = -0.64). CONCLUSIONS Sampling in different rounds of BALF showed minimal effect on BALF microbial and fungal diversities; the first round of BALF collection was recommended for microbial and fungal analyses for convenience. In addition, Vibrio may be a potential biomarker for silicosis fatigue screening.
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Affiliation(s)
- Linshen Xie
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaoyan Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaosi Gao
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Linyao Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Yiyang Cheng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Shirong Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Ji Yue
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Yingru Tang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Yufeng Deng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Baochao Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Xun He
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Mingyuan Tang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Hua Yang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Tianli Zheng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Jia You
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Xuejiao Song
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Jingyuan Xiong
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
| | - Haojiang Zuo
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province, Chengdu, 610041, China.
| | - Xiaofang Pei
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
- Food Safety Monitoring and Risk Assessment Key Laboratory of Sichuan Province, Chengdu, 610041, China
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Association Studies on Gut and Lung Microbiomes in Patients with Lung Adenocarcinoma. Microorganisms 2023; 11:microorganisms11030546. [PMID: 36985120 PMCID: PMC10059697 DOI: 10.3390/microorganisms11030546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Lung adenocarcinoma (LADC) is a prevalent type of lung cancer that is associated with lung and gut microbiota. However, the interactions between these microbiota and cancer development remain unclear. In this study, a microbiome study was performed on paired fecal and bronchoalveolar lavage fluid (BALF) samples from 42 patients with LADC and 64 healthy controls using 16S rRNA gene amplicon and shotgun metagenome sequencing, aiming to correlate the lung and gut microbiota with LADC. Patients with LADC had reduced α-diversity in the gut microbiome and altered β-diversity compared with healthy controls, and the abundances of Flavonifractor, Eggerthella, and Clostridium were higher in the gut microbiome of LADC patients. The increased abundance of microbial species, such as Flavonifractor plautii, was associated with advanced-stage LADC and a higher metastasis rate. Phylogenetically, Haemophilus parainfluenzae was the most frequently shared taxon in the lung and gut microbiota of LADC patients. Gut microbiome functional pathways involving leucine, propanoate, and fatty acids were associated with LADC progression. In conclusion, the low diversity of the gut microbiota and the presence of H. parainfluenzae in gut and lung microbiota were linked to LADC development, while an increased abundance of F. plautii and the enriched metabolic pathways could be associated with the progression of LADC.
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Abotsi RE, Dube FS, Rehman AM, Claassen-Weitz S, Xia Y, Simms V, Mwaikono KS, Gardner-Lubbe S, McHugh G, Ngwira LG, Kwambana-Adams B, Heyderman RS, Odland JØ, Ferrand RA, Nicol MP. Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease. MICROBIOME 2023; 11:29. [PMID: 36803868 PMCID: PMC9940396 DOI: 10.1186/s40168-023-01460-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Long-term azithromycin (AZM) treatment reduces the frequency of acute respiratory exacerbation in children and adolescents with HIV-associated chronic lung disease (HCLD). However, the impact of this treatment on the respiratory bacteriome is unknown. METHOD African children with HCLD (defined as forced expiratory volume in 1 s z-score (FEV1z) less than - 1.0 with no reversibility) were enrolled in a placebo-controlled trial of once-weekly AZM given for 48-weeks (BREATHE trial). Sputum samples were collected at baseline, 48 weeks (end of treatment) and 72 weeks (6 months post-intervention in participants who reached this timepoint before trial conclusion). Sputum bacterial load and bacteriome profiles were determined using 16S rRNA gene qPCR and V4 region amplicon sequencing, respectively. The primary outcomes were within-participant and within-arm (AZM vs placebo) changes in the sputum bacteriome measured across baseline, 48 weeks and 72 weeks. Associations between clinical or socio-demographic factors and bacteriome profiles were also assessed using linear regression. RESULTS In total, 347 participants (median age: 15.3 years, interquartile range [12.7-17.7]) were enrolled and randomised to AZM (173) or placebo (174). After 48 weeks, participants in the AZM arm had reduced sputum bacterial load vs placebo arm (16S rRNA copies/µl in log10, mean difference and 95% confidence interval [CI] of AZM vs placebo - 0.54 [- 0.71; - 0.36]). Shannon alpha diversity remained stable in the AZM arm but declined in the placebo arm between baseline and 48 weeks (3.03 vs. 2.80, p = 0.04, Wilcoxon paired test). Bacterial community structure changed in the AZM arm at 48 weeks compared with baseline (PERMANOVA test p = 0.003) but resolved at 72 weeks. The relative abundances of genera previously associated with HCLD decreased in the AZM arm at 48 weeks compared with baseline, including Haemophilus (17.9% vs. 25.8%, p < 0.05, ANCOM ω = 32) and Moraxella (1% vs. 1.9%, p < 0.05, ANCOM ω = 47). This reduction was sustained at 72 weeks relative to baseline. Lung function (FEV1z) was negatively associated with bacterial load (coefficient, [CI]: - 0.09 [- 0.16; - 0.02]) and positively associated with Shannon diversity (0.19 [0.12; 0.27]). The relative abundance of Neisseria (coefficient, [standard error]: (2.85, [0.7], q = 0.01), and Haemophilus (- 6.1, [1.2], q < 0.001) were positively and negatively associated with FEV1z, respectively. An increase in the relative abundance of Streptococcus from baseline to 48 weeks was associated with improvement in FEV1z (3.2 [1.11], q = 0.01) whilst an increase in Moraxella was associated with decline in FEV1z (-2.74 [0.74], q = 0.002). CONCLUSIONS AZM treatment preserved sputum bacterial diversity and reduced the relative abundances of the HCLD-associated genera Haemophilus and Moraxella. These bacteriological effects were associated with improvement in lung function and may account for reduced respiratory exacerbations associated with AZM treatment of children with HCLD. Video Abstract.
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Affiliation(s)
- Regina E Abotsi
- Department of Molecular and Cell Biology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Felix S Dube
- Department of Molecular and Cell Biology & Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Andrea M Rehman
- International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
| | - Shantelle Claassen-Weitz
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yao Xia
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Victoria Simms
- International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine, London, UK
- Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Kilaza S Mwaikono
- Computational Biology Group and H3ABioNet, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Department of Science and Laboratory Technology, Dar es Salaam Institute of Technology, Dar es Salaam, Tanzania
| | - Sugnet Gardner-Lubbe
- Department of Statistics and Actuarial Science, Stellenbosch University, Stellenbosch, South Africa
| | - Grace McHugh
- Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Lucky G Ngwira
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Brenda Kwambana-Adams
- NIHR Global Health Research Unit on Mucosal Pathogens, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Robert S Heyderman
- NIHR Global Health Research Unit on Mucosal Pathogens, Research Department of Infection, Division of Infection and Immunity, University College London, London, UK
| | - Jon Ø Odland
- Department of Community Medicine, University of Tromsø, Tromsø, Norway
- International Research Laboratory for Reproductive Ecotoxicology (IL RET), The National Research University Higher School of Economics, Moscow, Russia
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Rashida A Ferrand
- Biomedical Research and Training Institute, Harare, Zimbabwe
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Mark P Nicol
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
- Marshall Centre, Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia.
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Schneeberger PHH, Zhang CYK, Santilli J, Chen B, Xu W, Lee Y, Wijesinha Z, Reguera-Nuñez E, Yee N, Ahmed M, Boonstra K, Ramendra R, Frankel CW, Palmer SM, Todd JL, Martinu T, Coburn B. Lung Allograft Microbiome Association with Gastroesophageal Reflux, Inflammation, and Allograft Dysfunction. Am J Respir Crit Care Med 2022; 206:1495-1507. [PMID: 35876129 PMCID: PMC9757088 DOI: 10.1164/rccm.202110-2413oc] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Rationale: It remains unclear how gastroesophageal reflux disease (GERD) affects allograft microbial community composition in lung transplant recipients and its impact on lung allograft inflammation and function. Objectives: Our objective was to compare the allograft microbiota in lung transplant recipients with or without clinically diagnosed GERD in the first year after transplant and assess associations between GERD, allograft microbiota, inflammation, and acute and chronic lung allograft dysfunction (ALAD and CLAD). Methods: A total of 268 BAL samples were collected from 75 lung transplant recipients at a single transplant center every 3 months after transplant for 1 year. Ten transplant recipients from a separate transplant center provided samples before and after antireflux Nissen fundoplication surgery. Microbial community composition and density were measured using 16S ribosomal RNA gene sequencing and quantitative polymerase chain reaction, respectively, and inflammatory markers and bile acids were quantified. Measurements and Main Results: We observed a range of allograft community composition with three discernible types (labeled community state types [CSTs] 1-3). Transplant recipients with GERD were more likely to have CST1, characterized by high bacterial density and relative abundance of the oropharyngeal colonizing genera Prevotella and Veillonella. GERD was associated with more frequent transitions to CST1. CST1 was associated with lower inflammatory cytokine concentrations than pathogen-dominated CST3 across the range of microbial densities observed. Cox proportional hazard models revealed associations between CST3 and the development of ALAD/CLAD. Nissen fundoplication decreased bacterial load and proinflammatory cytokines. Conclusions: GERD was associated with a high bacterial density, Prevotella- and Veillonella-dominated CST1. CST3, but not CST1 or GERD, was associated with inflammation and early development of ALAD and CLAD. Nissen fundoplication was associated with a reduction in microbial density in BAL fluid samples, especially the CST1-specific genus, Prevotella.
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Affiliation(s)
- Pierre H. H. Schneeberger
- Department of Medicine,,Department of Laboratory Medicine & Pathobiology, and,Department of Medicine and,Swiss Tropical and Public Health Institute, University of Basel, Allschwil, Switzerland; and
| | - Chen Yang Kevin Zhang
- Department of Medicine,,Department of Laboratory Medicine & Pathobiology, and,Toronto Lung Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Jessica Santilli
- Department of Medicine,,Department of Laboratory Medicine & Pathobiology, and,Department of Medicine and
| | - Bo Chen
- Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Youngho Lee
- Department of Medicine,,Department of Laboratory Medicine & Pathobiology, and,Department of Medicine and
| | - Zonelle Wijesinha
- Department of Medicine,,Department of Laboratory Medicine & Pathobiology, and,Department of Medicine and
| | - Elaine Reguera-Nuñez
- Department of Medicine,,Department of Laboratory Medicine & Pathobiology, and,Department of Medicine and
| | - Noelle Yee
- Department of Medicine,,Department of Laboratory Medicine & Pathobiology, and,Department of Medicine and
| | - Musawir Ahmed
- Department of Medicine and,Toronto Lung Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Kristen Boonstra
- Toronto Lung Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Rayoun Ramendra
- Toronto Lung Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Courtney W. Frankel
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Scott M. Palmer
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Jamie L. Todd
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Tereza Martinu
- Department of Medicine,,Department of Laboratory Medicine & Pathobiology, and,Department of Medicine and,Toronto Lung Transplant Program, University Health Network, Toronto, Ontario, Canada
| | - Bryan Coburn
- Department of Medicine,,Department of Laboratory Medicine & Pathobiology, and,Department of Medicine and
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9
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Bacteriomes in lesions of pulmonary tuberculosis and its association with status of Mycobacterium tuberculosis excretion. BMC Microbiol 2022; 22:280. [PMID: 36418957 PMCID: PMC9686068 DOI: 10.1186/s12866-022-02698-5] [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: 07/04/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Bacteria in lung play an important role in sustaining lung health. Understanding the characteristics of bacteriomes in lesions of pulmonary tuberculosis (TB) patients, who excrete Mycobacterium tuberculosis (MTB), is important for TB prevention and effective treatment. METHODS: In this study, bacteriomes in lesions from TB patients excreting bacteria (TB-E) and those from TB patients not excreting bacteria (TB-NE) with matched normal lung tissues (NT) were compared by 16S rRNA sequencing. Bacterial MetaCyc functions in TB lesions were also predicted by PICRUSt2 tool. RESULTS Alpha diversity of bacteria, including Chao 1 and Shannon indexes, for TB-E was significantly higher than those in TB-NE and NT; while for TB-NE group, Chao 1 index was higher than that in NT group. Predominant phyla in TB lesions and NT were Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes, but analysis of similarity (ANOSIM, p < 0.001) revealed significantly different bacterial compositions among TB-E, TB-NE and NT samples. As for bacteriomes in TB lesions, a strong association (ANOSIM, p < 0.001) was observed with the status of MTB excretion. Indicator genera identified in TB-E and TB-NE demonstrated distinctive micro-ecological environments of TB lesions from patients with different clinical manifestations. Co-occurrence analysis revealed a densely-linked bacterial community in TB-NE compared to that in TB-E. MetaCyc functions responsible for menaquinone synthesis and chorismate metabolism that could potentially impact the persistent-state and nutrient metabolism of MTB were enriched in TB-E samples. While in TB-NE samples, enrichment of bacterial MetaCyc function responsible for heme b synthesis might contribute to TB pathology through ferroptosis. CONCLUSION Bacteriomes and their MetaCyc functions in TB lesions are elucidated, and they are associated with status of MTB excretion among pulmonary TB patients. These results serve as a basis for designing novel strategies for preventing and treating pulmonary TB disease.
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10
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Zhang J, Wu Y, Liu J, Yang Y, Li H, Wu X, Zheng X, Liang Y, Tu C, Chen M, Tan C, Chang B, Huang Y, Wang Z, Tian G, Ding T. Differential Oral Microbial Input Determines Two Microbiota Pneumo-Types Associated with Health Status. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203115. [PMID: 36031410 PMCID: PMC9661847 DOI: 10.1002/advs.202203115] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/02/2022] [Indexed: 05/09/2023]
Abstract
The oral and upper respiratory tracts are closely linked anatomically and physiologically with the lower respiratory tract and lungs, and the influence of oral and upper respiratory microbes on the lung microbiota is increasingly being recognized. However, the ecological process and individual heterogeneity of the oral and upper respiratory tract microbes shaping the lung microbiota remain unclear owing to the lack of controlled analyses with sufficient sample sizes. Here, the microbiomes of saliva, nasal cavity, oropharyngeal area, and bronchoalveolar lavage samples are profiled and the shaping process of multisource microbes on the lung microbiota is measured. It is found that oral and nasal microbial inputs jointly shape the lung microbiota by occupying different ecological niches. It is also observed that the spread of oral microbes to the lungs is heterogeneous, with more oral microbes entering the lungs being associated with decreased lung function and increased lung proinflammatory cytokines. These results depict the external shaping process of lung microbiota and indicate the great value of oral samples, such as saliva, in monitoring and assessing lung microbiota status in clinical settings.
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Affiliation(s)
- Jingxiang Zhang
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Yiping Wu
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Jing Liu
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Yongqiang Yang
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Hui Li
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Xiaorong Wu
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Xiaobin Zheng
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Yingjian Liang
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Changli Tu
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Meizhu Chen
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Cuiyan Tan
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Bozhen Chang
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
| | - Yiying Huang
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Zhengguo Wang
- Department of Respiratory MedicineThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhai519000China
| | - Guo‐Bao Tian
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
- School of MedicineXizang Minzu UniversityXianyangShaanxi712082China
| | - Tao Ding
- Department of Immunology and MicrobiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080China
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University)Ministry of EducationGuangzhou510080China
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11
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Xia X, Chen J, Cheng Y, Chen F, Lu H, Liu J, Wang L, Pu F, Wang Y, Liu H, Cao D, Zhang Z, Xia Z, Fan M, Ling Z, Zhao L. Comparative analysis of the lung microbiota in patients with respiratory infections, tuberculosis, and lung cancer: A preliminary study. Front Cell Infect Microbiol 2022; 12:1024867. [PMID: 36389135 PMCID: PMC9663837 DOI: 10.3389/fcimb.2022.1024867] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/06/2022] [Indexed: 11/29/2022] Open
Abstract
Recent evidence suggests that lung microbiota can be recognized as one of the ecological determinants of various respiratory diseases. However, alterations in the lung microbiota and associated lung immunity in these respiratory diseases remain unclear. To compare the lung microbiota and lung immune profiles in common respiratory diseases, a total of 78 patients were enrolled in the present study, including 21 patients with primary pulmonary tuberculosis (PTB), eight patients with newly diagnosed lung cancer (LC), and 49 patients with community-acquired pneumonia (CAP). Bronchoalveolar lavage fluid (BALF) was collected for microbiota and cytokine analyses. With MiSeq sequencing system, increased bacterial alpha-diversity and richness were observed in patients with LC than in those with PTB and CAP. Linear discriminant analysis effect size revealed that CAP-associated pulmonary microbiota were significantly different between the PTB and LC groups. More key functionally different genera were found in the PTB and LC groups than in the CAP group. The interaction network revealed stronger positive and negative correlations among these genera in the LC group than in the other two groups. However, increased BALF cytokine profiles were observed in the PTB group than in the other two groups, while BALF cytokines were correlated with key functional bacteria. This comparative study provides evidence for the associations among altered lung microbiota, BALF inflammation, and different respiratory disorders, which provides insight into the possible roles and mechanisms of pulmonary microbiota in the progression of respiratory disorders.
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Affiliation(s)
- Xiaoxue Xia
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Jiang Chen
- Department of Neurosurgery, Changxing People’s Hospital, Huzhou, China
| | - Yiwen Cheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China,Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Feng Chen
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Huoquan Lu
- Department of Respiratory, Changxing People’s Hospital, Huzhou, China
| | - Jianfeng Liu
- Department of Respiratory, Changxing People’s Hospital, Huzhou, China
| | - Ling Wang
- Department of Laboratory Medicine, Lishui Second People’s Hospital, Lishui, China
| | - Fengxia Pu
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Ying Wang
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Hua Liu
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Daxing Cao
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Zhengye Zhang
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Zeping Xia
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Meili Fan
- Department of Infectious Diseases, Changxing People’s Hospital, Huzhou, China
| | - Zongxin Ling
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China,Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China,*Correspondence: Zongxin Ling, ; Longyou Zhao,
| | - Longyou Zhao
- Department of Laboratory Medicine, Lishui Second People’s Hospital, Lishui, China,*Correspondence: Zongxin Ling, ; Longyou Zhao,
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12
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Du W, Zhao Y, Wang C, Dong Y, Qu X, Liu Z, Li K, Che N. Spatial bacterial subpopulations of a human lung lobe and their potential impact on the progression of pulmonary tuberculosis. Microb Pathog 2022; 169:105656. [PMID: 35777521 DOI: 10.1016/j.micpath.2022.105656] [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: 01/19/2022] [Revised: 05/16/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022]
Abstract
Better understanding the spatial variation in resident pulmonary bacteria can help to link the disease severity of pulmonary tuberculosis (TB) with lung bacteriomes. This study aimed to investigate bacterial compositions in subniches of a lung lobe from pulmonary TB patient with two separate visible lesions. There were no significant differences between the bacterial compositions in normal tissue and TB lesions, but the bacterial compositions of the two TB lesions differed significantly (P = 0.009). Interestingly, 52 OTUs (relative abundance >1%) that specifically inhabiting certain lung niches were observed and they were affiliated with five phyla. Specific OTUs affiliated with Firmicutes mainly inhabited normal tissues. The dominant phylum in the lung subniches was Proteobacteria, with a relative abundance between 67.03% and 99.99%. Ralstonia, Achromobacter, and Pseudomonas were the most abundant genera, collectively accounting for 34.02% of total bacterial species. A total of 667 of the 700 bacterial connections in a co-correlation network of 145 OTUs (Operational Taxonomic Unit) were positive, indicating a cooperative relationship between bacterial members. Using PICRUSt tool, we do predict bacterial MetaCyc functions responsible for lipid synthesis and heme biosynthesis across the lung lobe that are essential for generation of caseous necrosis and TB disease pathology. MetaCyc pathways responsible for the degradation of aromatic biogenic amines, sulfur oxidation, and denitrification were all related to M.tb growth status, and they were significantly enriched in the lesion with necrosis than that with inflammation. These results open a new insight for us to comprehend the spatial profile of bacteriomes in a pulmonary TB human lung lobe, and shed light on the design of future diagnosis and treatment for pulmonary TB disease.
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Affiliation(s)
- Weili Du
- Department of Pathology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beiguandajie 9#, Tongzhou Dist, Beijing, 101149, China
| | - Yingli Zhao
- Department of Pathology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beiguandajie 9#, Tongzhou Dist, Beijing, 101149, China
| | - Chong Wang
- Minimally Invasive Treatment Center, Beiguandajie 9#, Tongzhou Dist, Beijing, 101149, China
| | - Yujie Dong
- Department of Pathology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beiguandajie 9#, Tongzhou Dist, Beijing, 101149, China
| | - Xiaodie Qu
- Department of Pathology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beiguandajie 9#, Tongzhou Dist, Beijing, 101149, China
| | - Zichen Liu
- Department of Pathology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beiguandajie 9#, Tongzhou Dist, Beijing, 101149, China
| | - Kun Li
- Department of Pathology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beiguandajie 9#, Tongzhou Dist, Beijing, 101149, China
| | - Nanying Che
- Department of Pathology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beiguandajie 9#, Tongzhou Dist, Beijing, 101149, China.
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13
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Mancabelli L, Milani C, Fontana F, Lugli GA, Tarracchini C, Turroni F, van Sinderen D, Ventura M. Mapping bacterial diversity and metabolic functionality of the human respiratory tract microbiome. J Oral Microbiol 2022; 14:2051336. [PMID: 35309410 PMCID: PMC8933033 DOI: 10.1080/20002297.2022.2051336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 02/07/2023] Open
Abstract
Background The Human Respiratory Tract (HRT) is colonized by various microbial taxa, known as HRT microbiota, in a manner that is indicative of mutualistic interaction between such microorganisms and their host. Aim To investigate the microbial composition of the HRT and its possible correlation with the different compartments of the respiratory tract. Methods In the current study, we performed an in-depth meta-analysis of 849 HRT samples from public shotgun metagenomic datasets obtained through several distinct collection methods. Results The statistical robustness provided by this meta-analysis allowed the identification of 13 possible HRT-specific Community State Types (CSTs), which appear to be specific to each anatomical region of the respiratory tract. Furthermore, functional characterization of the metagenomic datasets revealed specific microbial metabolic features correlating with the different compartments of the respiratory tract. Conclusion The meta-analysis here performed suggested that the variable presence of certain bacterial species seems to be linked to a location-related abundance gradient in the HRT and seems to be characterized by a specific microbial metabolic capability.
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Affiliation(s)
- Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Interdepartmental Research Centre “Microbiome Research Hub”, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Interdepartmental Research Centre “Microbiome Research Hub”, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Interdepartmental Research Centre “Microbiome Research Hub”, University of Parma, Parma, Italy
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14
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Pérez-Cobas AE, Baquero F, de Pablo R, Soriano MC, Coque TM. Altered Ecology of the Respiratory Tract Microbiome and Nosocomial Pneumonia. Front Microbiol 2022; 12:709421. [PMID: 35222291 PMCID: PMC8866767 DOI: 10.3389/fmicb.2021.709421] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 12/21/2021] [Indexed: 12/23/2022] Open
Abstract
Nosocomial pneumonia is one of the most frequent infections in critical patients. It is primarily associated with mechanical ventilation leading to severe illness, high mortality, and prolonged hospitalization. The risk of mortality has increased over time due to the rise in multidrug-resistant (MDR) bacterial infections, which represent a global public health threat. Respiratory tract microbiome (RTM) research is growing, and recent studies suggest that a healthy RTM positively stimulates the immune system and, like the gut microbiome, can protect against pathogen infection through colonization resistance (CR). Physiological conditions of critical patients and interventions as antibiotics administration and mechanical ventilation dramatically alter the RTM, leading to dysbiosis. The dysbiosis of the RTM of ICU patients favors the colonization by opportunistic and resistant pathogens that can be part of the microbiota or acquired from the hospital environments (biotic or built ones). Despite recent evidence demonstrating the significance of RTM in nosocomial infections, most of the host-RTM interactions remain unknown. In this context, we present our perspective regarding research in RTM altered ecology in the clinical environment, particularly as a risk for acquisition of nosocomial pneumonia. We also reflect on the gaps in the field and suggest future research directions. Moreover, expected microbiome-based interventions together with the tools to study the RTM highlighting the "omics" approaches are discussed.
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Affiliation(s)
- Ana Elena Pérez-Cobas
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain
| | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain.,CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Raúl de Pablo
- Intensive Care Department, Ramón y Cajal University Hospital, Madrid, Spain
| | - María Cruz Soriano
- Intensive Care Department, Ramón y Cajal University Hospital, Madrid, Spain
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain.,CIBER in Infectious Diseases (CIBERINFEC), Madrid, Spain
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15
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Different gut microbial communities correlate with efficacy of albendazole-ivermectin against soil-transmitted helminthiases. Nat Commun 2022; 13:1063. [PMID: 35217670 PMCID: PMC8881608 DOI: 10.1038/s41467-022-28658-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/04/2022] [Indexed: 01/10/2023] Open
Abstract
Soil-transmitted helminth infections represent a large burden with over a quarter of the world’s population at risk. Low cure rates are observed with standard of care (albendazole); therefore, a more effective combination therapy (albendazole and ivermectin) is being investigated but showed variable treatment efficacies without evidence of intrinsic parasite resistance. Here, we analyzed the microbiome of Trichuris trichiura and hookworm-infected patients and found an association of different enterotypes with treatment efficacy. 80 T. trichiura-infected patients with hookworm co-infections from Pak-Khan, Laos, received either albendazole (n = 41) or albendazole and ivermectin combination therapy (n = 39). Pre-/post-treatment stool samples were collected to monitor treatment efficacy and microbial communities were profiled using 16S rRNA gene sequencing, qPCR, and shotgun sequencing. We identified three bacterial enterotypes and show that pre-treatment enterotype is associated with efficacy of the combination treatment for both T. trichiura (CRET1 = 5.8%; CRET2 = 16.6%; CRET3 = 68.8%) and hookworm (CRET1 = 31.3%; CRET2 = 16.6%; CRET3 = 78.6%). This study shows that pre-treatment enterotype enables predicting treatment outcome of combination therapy for T. trichiura and hookworm infections. Trial registration: ClinicalTrials.gov, NCT03527732. Registered 17 May 2018, https://clinicaltrials.gov/ct2/show/NCT03527732. Little is known about the cause of treatment failure of soil-transmitted helminth infections. Here, the authors show that pre-treatment gut microbial community composition enables predicting treatment outcome for Trichuris trichiura and hookworm infections.
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16
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Abstract
When determining human microbiota composition, shotgun sequencing is a powerful tool that can generate high-resolution taxonomic and functional information at once. However, the technique is limited by missing information about host-to-microbe ratios observed in different body compartments. This limitation makes it difficult to plan shotgun sequencing assays, especially in the context of high sample multiplexing and limited sequencing output and is of particular importance for studies employing the recently described shallow shotgun sequencing technique. In this study, we evaluated the use of a quantitative PCR (qPCR)-based assay to predict host-to-microbe ratio prior to sequencing. Combining a two-target assay involving the bacterial 16S rRNA gene and the human beta-actin gene, we derived a model to predict human-to-microbe ratios from two sample types, including stool samples and oropharyngeal swabs. We then validated it on two independently collected sample types, including rectal swabs and vaginal secretion samples. This assay enabled accurate prediction in the validation set in a range of sample compositions between 4% and 98% nonhuman reads and observed proportions varied between −18.8% and +19.2% from the expected values. We hope that this easy-to-use assay will help researchers to plan their shotgun sequencing experiments in a more efficient way. IMPORTANCE When determining human microbiota composition, shotgun sequencing is a powerful tool that can generate large amounts of data. However, in sample compositions with low or variable microbial density, shallowing sequencing can negatively affect microbial community metrics. Here, we show that variable sequencing depth decreases measured alpha diversity at differing rates based on community composition. We then derived a model that can determine sample composition prior to sequencing using quantitative PCR (qPCR) data and validated the model using a separate sample set. We have included a tool that uses this model to be available for researchers to use when gauging shallow sequencing viability of samples.
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17
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Systems Biology and Bile Acid Signalling in Microbiome-Host Interactions in the Cystic Fibrosis Lung. Antibiotics (Basel) 2021; 10:antibiotics10070766. [PMID: 34202495 PMCID: PMC8300688 DOI: 10.3390/antibiotics10070766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/14/2021] [Accepted: 06/21/2021] [Indexed: 12/16/2022] Open
Abstract
The study of the respiratory microbiota has revealed that the lungs of healthy and diseased individuals harbour distinct microbial communities. Imbalances in these communities can contribute to the pathogenesis of lung disease. How these imbalances occur and establish is largely unknown. This review is focused on the genetically inherited condition of Cystic Fibrosis (CF). Understanding the microbial and host-related factors that govern the establishment of chronic CF lung inflammation and pathogen colonisation is essential. Specifically, dissecting the interplay in the inflammation–pathogen–host axis. Bile acids are important host derived and microbially modified signal molecules that have been detected in CF lungs. These bile acids are associated with inflammation and restructuring of the lung microbiota linked to chronicity. This community remodelling involves a switch in the lung microbiota from a high biodiversity/low pathogen state to a low biodiversity/pathogen-dominated state. Bile acids are particularly associated with the dominance of Proteobacterial pathogens. The ability of bile acids to impact directly on both the lung microbiota and the host response offers a unifying principle underpinning the pathogenesis of CF. The modulating role of bile acids in lung microbiota dysbiosis and inflammation could offer new potential targets for designing innovative therapeutic approaches for respiratory disease.
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18
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Refinement of 16S rRNA gene analysis for low biomass biospecimens. Sci Rep 2021; 11:10741. [PMID: 34031485 PMCID: PMC8144411 DOI: 10.1038/s41598-021-90226-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/05/2021] [Indexed: 02/04/2023] Open
Abstract
High-throughput phylogenetic 16S rRNA gene analysis has permitted to thoroughly delve into microbial community complexity and to understand host-microbiota interactions in health and disease. The analysis comprises sample collection and storage, genomic DNA extraction, 16S rRNA gene amplification, high-throughput amplicon sequencing and bioinformatic analysis. Low biomass microbiota samples (e.g. biopsies, tissue swabs and lavages) are receiving increasing attention, but optimal standardization for analysis of low biomass samples has yet to be developed. Here we tested the lower bacterial concentration required to perform 16S rRNA gene analysis using three different DNA extraction protocols, three different mechanical lysing series and two different PCR protocols. A mock microbiota community standard and low biomass samples (108, 107, 106, 105 and 104 microbes) from two healthy donor stools were employed to assess optimal sample processing for 16S rRNA gene analysis using paired-end Illumina MiSeq technology. Three DNA extraction protocols tested in our study performed similar with regards to representing microbiota composition, but extraction yield was better for silica columns compared to bead absorption and chemical precipitation. Furthermore, increasing mechanical lysing time and repetition did ameliorate the representation of bacterial composition. The most influential factor enabling appropriate representation of microbiota composition remains sample biomass. Indeed, bacterial densities below 106 cells resulted in loss of sample identity based on cluster analysis for all tested protocols. Finally, we excluded DNA extraction bias using a genomic DNA standard, which revealed that a semi-nested PCR protocol represented microbiota composition better than classical PCR. Based on our results, starting material concentration is an important limiting factor, highlighting the need to adapt protocols for dealing with low biomass samples. Our study suggests that the use of prolonged mechanical lysing, silica membrane DNA isolation and a semi-nested PCR protocol improve the analysis of low biomass samples. Using the improved protocol we report a lower limit of 106 bacteria per sample for robust and reproducible microbiota analysis.
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19
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Choi S, Sohn KH, Jung JW, Kang MG, Yang MS, Kim S, Choi JH, Cho SH, Kang HR, Yi H. Lung virome: New potential biomarkers for asthma severity and exacerbation. J Allergy Clin Immunol 2021; 148:1007-1015.e9. [PMID: 33757721 DOI: 10.1016/j.jaci.2021.03.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/08/2021] [Accepted: 03/11/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Although some respiratory virus infections are known to contribute to the development and exacerbation of asthma, commensal viromes in airway have not been extensively studied due to technical challenges. OBJECTIVES This study investigated the characteristics of the virome in asthmatic airways. METHODS Both the bacteriome and virome profiles in sputum from 12 healthy individuals, 15 patients with nonsevere asthma, and 15 patients with severe asthma were analyzed and assessed for the association with clinical characteristics such as severity, exacerbation, Asthma Control Test (ACT), and lung function. RESULTS While analysis of the 16S ribosomal RNA bacteriome in the airway showed no differences, clear contrasts in the diversity and composition of airway viromes were observed between healthy controls and patients with asthma. Herpesviruses were the most abundant type of virus in the asthma group (44.6 ± 4.6%), mainly with cytomegalovirus (CMV) and EBV accounting for 24.5 ± 3.3% and 16.9 ± 3.5%, respectively, in contrast to those in the healthy controls (5.4 ± 2.5% and 7.1 ± 3.0%, respectively). CMV and EBV were more abundant in patients with asthma who experienced exacerbation, and their abundance showed correlation with more severe asthma, lower ACT score, and lower lung function. On the contrary, bacteriophage that is abundant in healthy controls was severely reduced in patients with asthma in the order of nonsevere and severe asthma and presented significant positive correlation with ACT and FEV1/forced vital capacity. CONCLUSIONS Lung viromes, especially, CMV, EBV, and bacteriophage may be potential biomarkers of asthma severity and exacerbation.
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Affiliation(s)
- Sungmi Choi
- Institute for Biomaterials, Korea University, Seoul, Korea; Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Korea
| | - Kyoung-Hee Sohn
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Korea; Department of Internal Medicine, Kyung Hee University Hospital, Seoul, Korea
| | - Jae-Woo Jung
- Department of Internal Medicine, Chung-Ang University College of Medicine, Seoul, Korea
| | - Min-Gyu Kang
- Department of Internal Medicine, Chungbuk National University College of Medicine, Chungbuk National University Hospital, Cheongju, Korea
| | - Min-Suk Yang
- Department of Internal Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Sujeong Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Korea
| | - Jeong-Hee Choi
- Department of Pulmonology and Allergy, Hallym University Dongtan Sacred Heart Hospital, Hwaseong, Korea; Allergy and Clinical Immunology Research Center, Hallym University College of Medicine, Chuncheon, Korea
| | - Sang-Heon Cho
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Korea; Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Hye-Ryun Kang
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul National University College of Medicine, Seoul, Korea; Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.
| | - Hana Yi
- Institute for Biomaterials, Korea University, Seoul, Korea; Interdisciplinary Program in Precision Public Health, Korea University, Seoul, Korea; School of Biosystems and Biomedical Sciences, Korea University, Seoul, Korea.
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20
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Oliva M, Schneeberger PHH, Rey V, Cho M, Taylor R, Hansen AR, Taylor K, Hosni A, Bayley A, Hope AJ, Bratman SV, Ringash J, Singh S, Weinreb I, Perez-Ordoñez B, Chepeha D, Waldron J, Xu W, Guttman D, Siu LL, Coburn B, Spreafico A. Transitions in oral and gut microbiome of HPV+ oropharyngeal squamous cell carcinoma following definitive chemoradiotherapy (ROMA LA-OPSCC study). Br J Cancer 2021; 124:1543-1551. [PMID: 33750907 PMCID: PMC8076306 DOI: 10.1038/s41416-020-01253-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 11/25/2020] [Accepted: 12/17/2020] [Indexed: 02/07/2023] Open
Abstract
Background Oral and gut microbiomes have emerged as potential biomarkers in cancer. We characterised the oral and gut microbiomes in a prospective observational cohort of HPV+ oropharyngeal squamous cell carcinoma (OPSCC) patients and evaluated the impact of chemoradiotherapy (CRT). Methods Saliva, oropharyngeal swabs over the tumour site and stool were collected at baseline and post-CRT. 16S RNA and shotgun metagenomic sequencing were used to generate taxonomic profiles, including relative abundance (RA), bacterial density, α-diversity and β-diversity. Results A total of 132 samples from 22 patients were analysed. Baseline saliva and swabs had similar taxonomic composition (R2 = 0.006; p = 0.827). Oropharyngeal swabs and stool taxonomic composition varied significantly by stage, with increased oral RA of Fusobacterium nucleatum observed in stage III disease (p < 0.05). CRT significantly reduced the species richness and increased the RA of gut-associated taxa in oropharyngeal swabs (p < 0.05), while it had no effect in stool samples. These findings remained significant when adjusted by stage, smoking status and antibiotic use. Conclusions Baseline oral and gut microbiomes differ by stage in this HPV+ cohort. CRT caused a shift towards a gut-like microbiome composition in oropharyngeal swabs. Stage-specific features and the transitions in oral microbiome might have prognostic and therapeutic implications.
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Affiliation(s)
- Marc Oliva
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada.,Department of Medical Oncology, Catalan Institute of Oncology (ICO), Barcelona, Spain
| | - Pierre H H Schneeberger
- Division of Infectious Diseases and Toronto General Hospital Research Institute, University Health Network, Departments of Medicine, Immunology and Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Victor Rey
- Division of Infectious Diseases and Toronto General Hospital Research Institute, University Health Network, Departments of Medicine, Immunology and Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Matthew Cho
- Division of Infectious Diseases and Toronto General Hospital Research Institute, University Health Network, Departments of Medicine, Immunology and Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Rachel Taylor
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Aaron R Hansen
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Kirsty Taylor
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Ali Hosni
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Andrew Bayley
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Andrew J Hope
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Scott V Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Jolie Ringash
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Simron Singh
- Department of Pathology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Ilan Weinreb
- Department of Medical Oncology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Bayardo Perez-Ordoñez
- Department of Medical Oncology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Douglas Chepeha
- Department of Surgical Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - John Waldron
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - David Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Lillian L Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Bryan Coburn
- Division of Infectious Diseases and Toronto General Hospital Research Institute, University Health Network, Departments of Medicine, Immunology and Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Anna Spreafico
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada.
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21
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Saladié M, Caparrós-Martín JA, Agudelo-Romero P, Wark PAB, Stick SM, O'Gara F. Microbiomic Analysis on Low Abundant Respiratory Biomass Samples; Improved Recovery of Microbial DNA From Bronchoalveolar Lavage Fluid. Front Microbiol 2020; 11:572504. [PMID: 33123104 PMCID: PMC7573210 DOI: 10.3389/fmicb.2020.572504] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years the study of the commensal microbiota is driving a remarkable paradigm shift in our understanding of human physiology. However, intrinsic technical difficulties associated with investigating the Microbiomics of some body niches are hampering the development of new knowledge. This is particularly the case when investigating the functional role played by the human microbiota in modulating the physiology of key organ systems. A major hurdle in investigating specific Microbiome communities is linked to low bacterial density and susceptibility to bias caused by environmental contamination. To prevent such inaccuracies due to background processing noise, harmonized tools for Microbiomic and bioinformatics practices have been recommended globally. The fact that the impact of this undesirable variability is negatively correlated with the DNA concentration in the sample highlights the necessity to improve existing DNA isolation protocols. In this report, we developed and tested a protocol to more efficiently recover bacterial DNA from low volumes of bronchoalveolar lavage fluid obtained from infants and adults. We have compared the efficiency of the described method with that of a commercially available kit for microbiome analysis in body fluids. We show that this new methodological approach performs better in terms of extraction efficiency. As opposed to commercial kits, the DNA extracts obtained with this new protocol were clearly distinguishable from the negative extraction controls in terms of 16S copy number and Microbiome community profiles. Altogether, we described a cost-efficient protocol that can facilitate microbiome research in low-biomass human niches.
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Affiliation(s)
- Montserrat Saladié
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Jose Antonio Caparrós-Martín
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Patricia Agudelo-Romero
- Telethon Kids Institute, Perth, WA, Australia.,ARC Centre for Plant Energy Biology, Faculty of Science, School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia.,Wal-yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia
| | - Peter A B Wark
- Centre of Excellence in Severe Asthma and Priority Research, Centre for Healthy Lungs, Faculty of Health, University of Newcastle, Newcastle, NSW, Australia.,Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW, Australia
| | - Stephen M Stick
- Telethon Kids Institute, Perth, WA, Australia.,Wal-yan Respiratory Research Centre, Telethon Kids Institute, Perth, WA, Australia.,Department of Respiratory and Sleep Medicine, Perth Children's Hospital, Perth, WA, Australia
| | - Fergal O'Gara
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, Australia.,Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia.,Telethon Kids Institute, Perth, WA, Australia.,BIOMERIT Research Centre, School of Microbiology, University College Cork, Cork, Ireland
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22
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Fernández-Barat L, López-Aladid R, Torres A. Reconsidering ventilator-associated pneumonia from a new dimension of the lung microbiome. EBioMedicine 2020; 60:102995. [PMID: 32950001 PMCID: PMC7492164 DOI: 10.1016/j.ebiom.2020.102995] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/25/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Complex microbial communities that reside in the lungs, skin and gut are now appreciated for their role in maintaining organ, tissue and immune homoeostasis. As lungs are currently seen as an ecosystem, the shift in paradigm calls for the consideration of new algorithms related to lung ecology in pulmonology. Evidence of lung microbiota does not solely challenge the traditional physiopathology of ventilator-associated pneumonia (VAP); indeed, it also reinforces the need to include molecular techniques in VAP diagnosis and accelerate the use of immunomodulatory drugs, including corticosteroids, and other supplements such as probiotics for VAP prevention and/or treatment. With that stated, both microbiome and virome, including phageome, can lead to new opportunities in further understanding the relationship between health and dysbiosis in VAP. Previous knowledge may be, however, reconsidered at a microbiome scale.
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Affiliation(s)
- Laia Fernández-Barat
- Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, 06/06/0028), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spain; School of Medicine, University of Barcelona, Barcelona, Spain.
| | - Ruben López-Aladid
- Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, 06/06/0028), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spain
| | - Antoni Torres
- Cellex Laboratory, CibeRes (Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, 06/06/0028), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spain; School of Medicine, University of Barcelona, Barcelona, Spain; Department of Pneumology, Thorax Institute, Hospital Clinic of Barcelona, Spain.
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23
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Davidson KR, Ha DM, Schwarz MI, Chan ED. Bronchoalveolar lavage as a diagnostic procedure: a review of known cellular and molecular findings in various lung diseases. J Thorac Dis 2020; 12:4991-5019. [PMID: 33145073 PMCID: PMC7578496 DOI: 10.21037/jtd-20-651] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bronchoalveolar lavage (BAL) is a commonly used procedure in the evaluation of lung disease as it allows for sampling of the lower respiratory tract. In many circumstances, BAL differential cell counts have been reported to be typical of specific lung disorders. In addition, more specific diagnostic tests including molecular assays such as polymerase chain reaction (PCR) or enzyme-linked immunosorbent assay, special cytopathologic stains, or particular microscopic findings have been described as part of BAL fluid analysis. This review focuses on common cellular and molecular findings of BAL in a wide range of lung diseases. Since the performance of the first lung irrigation in 1927, BAL has become a common and important diagnostic tool. While some pulmonary disorders have a highly characteristic signature of BAL findings, BAL results alone often lack specificity and require interpretation along with other clinical and radiographic details. Development of new diagnostic assays is certain to reinforce the utility of BAL in the future. Our review of the BAL literature is intended to serve as a resource to assist clinicians in the care of patients with lung disorders.
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Affiliation(s)
- Kevin R Davidson
- Division of Pulmonary Sciences & Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Duc M Ha
- Division of Pulmonary Sciences & Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, Colorado, USA.,Institute for Health Research, Kaiser Permanente Colorado, Aurora, Colorado, USA
| | - Marvin I Schwarz
- Division of Pulmonary Sciences & Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Edward D Chan
- Division of Pulmonary Sciences & Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.,Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, Colorado, USA.,National Jewish Health, Denver, Colorado, USA
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24
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Persistent Legionnaires' Disease and Associated Antibiotic Treatment Engender a Highly Disturbed Pulmonary Microbiome Enriched in Opportunistic Microorganisms. mBio 2020; 11:mBio.00889-20. [PMID: 32430469 PMCID: PMC7240155 DOI: 10.1128/mbio.00889-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Despite the importance of pneumonia to public health, little is known about the composition of the lung microbiome during infectious diseases, such as pneumonia, and how it evolves during antibiotic therapy. To study the possible relation of the pulmonary microbiome to the severity and outcome of this respiratory disease, we analyzed the dynamics of the pathogen and the human lung microbiome during persistent infections caused by the bacterium Legionella pneumophila and their evolution during antimicrobial treatment. We collected 10 bronchoalveolar lavage fluid samples from three patients during long-term hospitalization due to pneumonia and performed a unique longitudinal study of the interkingdom microbiome, analyzing the samples for presence of bacteria, archaea, fungi, and protozoa by high-throughput Illumina sequencing of marker genes. The lung microbiome of the patients was characterized by a strong predominance of the pathogen, a low diversity of the bacterial fraction, and an increased presence of opportunistic microorganisms. The fungal fraction was more stable than the bacterial fraction. During long-term treatment, no genomic changes or antibiotic resistance-associated mutations that could explain the persistent infection occurred, according to whole-genome sequencing analyses of the pathogen. After antibiotic treatment, the microbiome did not recover rapidly but was mainly constituted of antibiotic-resistant species and enriched in bacteria, archaea, fungi, or protozoa associated with pathogenicity. The lung microbiome seems to contribute to nonresolving Legionella pneumonia, as it is strongly disturbed during infection and enriched in opportunistic and/or antibiotic-resistant bacteria and microorganisms, including fungi, archaea, and protozoa that are often associated with infections.IMPORTANCE The composition and dynamics of the lung microbiome during pneumonia are not known, although the lung microbiome might influence the severity and outcome of this infectious disease, similar to what was shown for the microbiome at other body sites. Here we report the findings of a comprehensive analysis of the lung microbiome composition of three patients with long-term pneumonia due to L. pneumophila and its evolution during antibiotic treatment. This work adds to our understanding of how the microbiome changes during disease and antibiotic treatment and points to microorganisms and their interactions that might be beneficial. In addition to bacteria and fungi, our analyses included archaea and eukaryotes (protozoa), showing that both are present in the pulmonary microbiota and that they might also play a role in the response to the microbiome disturbance.
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25
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Optimizing 16S rRNA gene profile analysis from low biomass nasopharyngeal and induced sputum specimens. BMC Microbiol 2020; 20:113. [PMID: 32397992 PMCID: PMC7218582 DOI: 10.1186/s12866-020-01795-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/20/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Careful consideration of experimental artefacts is required in order to successfully apply high-throughput 16S ribosomal ribonucleic acid (rRNA) gene sequencing technology. Here we introduce experimental design, quality control and "denoising" approaches for sequencing low biomass specimens. RESULTS We found that bacterial biomass is a key driver of 16S rRNA gene sequencing profiles generated from bacterial mock communities and that the use of different deoxyribonucleic acid (DNA) extraction methods [DSP Virus/Pathogen Mini Kit® (Kit-QS) and ZymoBIOMICS DNA Miniprep Kit (Kit-ZB)] and storage buffers [PrimeStore® Molecular Transport medium (Primestore) and Skim-milk, Tryptone, Glucose and Glycerol (STGG)] further influence these profiles. Kit-QS better represented hard-to-lyse bacteria from bacterial mock communities compared to Kit-ZB. Primestore storage buffer yielded lower levels of background operational taxonomic units (OTUs) from low biomass bacterial mock community controls compared to STGG. In addition to bacterial mock community controls, we used technical repeats (nasopharyngeal and induced sputum processed in duplicate, triplicate or quadruplicate) to further evaluate the effect of specimen biomass and participant age at specimen collection on resultant sequencing profiles. We observed a positive correlation (r = 0.16) between specimen biomass and participant age at specimen collection: low biomass technical repeats (represented by < 500 16S rRNA gene copies/μl) were primarily collected at < 14 days of age. We found that low biomass technical repeats also produced higher alpha diversities (r = - 0.28); 16S rRNA gene profiles similar to no template controls (Primestore); and reduced sequencing reproducibility. Finally, we show that the use of statistical tools for in silico contaminant identification, as implemented through the decontam package in R, provides better representations of indigenous bacteria following decontamination. CONCLUSIONS We provide insight into experimental design, quality control steps and "denoising" approaches for 16S rRNA gene high-throughput sequencing of low biomass specimens. We highlight the need for careful assessment of DNA extraction methods and storage buffers; sequence quality and reproducibility; and in silico identification of contaminant profiles in order to avoid spurious results.
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