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Sherrard LJ, Bell SC. Lower airway microbiota for ‘biomarker’ measurements of cystic fibrosis disease progression? Thorax 2018; 73:1001-1003. [DOI: 10.1136/thoraxjnl-2018-212165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2018] [Indexed: 11/03/2022]
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52
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Marsh RL, Nelson MT, Pope CE, Leach AJ, Hoffman LR, Chang AB, Smith-Vaughan HC. How low can we go? The implications of low bacterial load in respiratory microbiota studies. Pneumonia (Nathan) 2018; 10:7. [PMID: 30003009 PMCID: PMC6033291 DOI: 10.1186/s41479-018-0051-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/21/2018] [Indexed: 12/18/2022] Open
Abstract
Background Culture-independent sequencing methods are increasingly used to investigate the microbiota associated with human mucosal surfaces, including sites that have low bacterial load in healthy individuals (e.g. the lungs). Standard microbiota methods developed for analysis of high bacterial load specimens (e.g. stool) may require modification when bacterial load is low, as background contamination derived from sterile laboratory reagents and kits can dominate sequence data when few bacteria are present. Main body Bacterial load in respiratory specimens may vary depending on the specimen type, specimen volume, the anatomic site sampled and clinical parameters. This review discusses methodological issues inherent to analysis of low bacterial load specimens and recommends strategies for successful respiratory microbiota studies. The range of methods currently used to process DNA from low bacterial load specimens, and the strategies used to identify and exclude background contamination are also discussed. Conclusion Microbiota studies that include low bacterial load specimens require additional tests to ensure that background contamination does not bias the results or interpretation. Several methods are currently used to analyse the microbiota in low bacterial load respiratory specimens; however, there is scant literature comparing the effectiveness and biases of different methods. Further research is needed to define optimal methods for analysing the microbiota in low bacterial load specimens.
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Affiliation(s)
- Robyn L Marsh
- 1Child Health Division, Menzies School of Health Research, Darwin, Northern Territory Australia
| | - Maria T Nelson
- 2Respiratory Medicine, Seattle Children's Hospital and University of Washington, Seattle, Washington USA
| | - Chris E Pope
- 2Respiratory Medicine, Seattle Children's Hospital and University of Washington, Seattle, Washington USA
| | - Amanda J Leach
- 1Child Health Division, Menzies School of Health Research, Darwin, Northern Territory Australia
| | - Lucas R Hoffman
- 2Respiratory Medicine, Seattle Children's Hospital and University of Washington, Seattle, Washington USA
| | - Anne B Chang
- 1Child Health Division, Menzies School of Health Research, Darwin, Northern Territory Australia.,3Department of Respiratory and Sleep Medicine, Children's Health Queensland and Queensland University of Technology, Brisbane, QLD Australia
| | - Heidi C Smith-Vaughan
- 1Child Health Division, Menzies School of Health Research, Darwin, Northern Territory Australia
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Hahn A, Bendall ML, Gibson KM, Chaney H, Sami I, Perez GF, Koumbourlis AC, McCaffrey TA, Freishtat RJ, Crandall KA. Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity. Front Microbiol 2018; 9:1069. [PMID: 29887843 PMCID: PMC5980964 DOI: 10.3389/fmicb.2018.01069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/04/2018] [Indexed: 11/30/2022] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease associated with recurrent lung infections that can lead to morbidity and mortality. The impact of antibiotics for treatment of acute pulmonary exacerbations on the CF airway microbiome remains unclear with prior studies giving conflicting results and being limited by their use of 16S ribosomal RNA sequencing. Our primary objective was to validate the use of true single molecular sequencing (tSMS) and PathoScope in the analysis of the CF airway microbiome. Three control samples were created with differing amounts of Burkholderia cepacia, Pseudomonas aeruginosa, and Prevotella melaninogenica, three common bacteria found in cystic fibrosis lungs. Paired sputa were also obtained from three study participants with CF before and >6 days after initiation of antibiotics. Antibiotic resistant B. cepacia and P. aeruginosa were identified in concurrently obtained respiratory cultures. Direct sequencing was performed using tSMS, and filtered reads were aligned to reference genomes from NCBI using PathoScope and Kraken and unique clade-specific marker genes using MetaPhlAn. A total of 180–518 K of 6–12 million filtered reads were aligned for each sample. Detection of known pathogens in control samples was most successful using PathoScope. In the CF sputa, alpha diversity measures varied based on the alignment method used, but similar trends were found between pre- and post-antibiotic samples. PathoScope outperformed Kraken and MetaPhlAn in our validation study of artificial bacterial community controls and also has advantages over Kraken and MetaPhlAn of being able to determine bacterial strains and the presence of fungal organisms. PathoScope can be confidently used when evaluating metagenomic data to determine CF airway microbiome diversity.
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Affiliation(s)
- Andrea Hahn
- Division of Infectious Diseases, Children's National Health System, Washington, DC, United States.,Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Matthew L Bendall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States.,Department of Microbiology, Immunology and Tropical Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Keylie M Gibson
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
| | - Hollis Chaney
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, United States
| | - Iman Sami
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, United States
| | - Geovanny F Perez
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, United States
| | - Anastassios C Koumbourlis
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, United States
| | - Timothy A McCaffrey
- Division of Genomic Medicine, The George Washington University, Washington, DC, United States.,Department of Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Robert J Freishtat
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Division of Emergency Medicine, Children's National Health System, Washington, DC, United States
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, The George Washington University, Washington, DC, United States
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54
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How can the cystic fibrosis respiratory microbiome influence our clinical decision-making? Curr Opin Pulm Med 2018; 23:536-543. [PMID: 28786882 DOI: 10.1097/mcp.0000000000000419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW Almost 15 years have now passed since bacterial community profiling techniques were first used to analyse respiratory samples from people with cystic fibrosis. Since then, many different analytical approaches have been used to try to better understand the contribution of the cystic fibrosis lung microbiota to disease, with varying degrees of success. We examine the extent to which cystic fibrosis respiratory microbiome research has been successful in informing clinical decision-making, and highlight areas that we believe have the potential to yield important insight. RECENT FINDINGS Recent research on the cystic fibrosis lung microbiome can be broadly divided into efforts to better characterize microbiota composition, particularly relative to key clinical events, and attempts to understand the cystic fibrosis lung microbiology as an interactive microbial system. The latter, in particular, has led to the development of a number of models in which microbiome-mediated processes precipitate clinical events. SUMMARY Growing technological sophistication is enabling increasingly detailed microbiological data to be generated from cystic fibrosis respiratory samples. However, translating these data into clinically useful measures that accurately predict outcomes and guide treatments remains a formidable challenge. The development of systems biology approaches that enable the integration of complex microbiome and host-derived data provide an exciting opportunity to address this goal.
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Impact of Long-Term Erythromycin Therapy on the Oropharyngeal Microbiome and Resistance Gene Reservoir in Non-Cystic Fibrosis Bronchiectasis. mSphere 2018; 3:3/2/e00103-18. [PMID: 29669883 PMCID: PMC5907653 DOI: 10.1128/msphere.00103-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 03/29/2018] [Indexed: 01/06/2023] Open
Abstract
Recent demonstrations that long-term macrolide therapy can prevent exacerbations in chronic airways diseases have led to a dramatic increase in their use. However, little is known about the wider, potentially adverse impacts of these treatments. Substantial disruption of the upper airway commensal microbiota might reduce its contribution to host defense and local immune regulation, while increases in macrolide resistance carriage would represent a serious public health concern. Using samples from a randomized controlled trial, we show that low-dose erythromycin given over 48 weeks influences the composition of the oropharyngeal commensal microbiota. We report that macrolide therapy is associated with significant changes in the relative abundances of members of the Actinomyces genus and with significant increases in the carriage of transmissible macrolide resistance. Determining the clinical significance of these changes, relative to treatment benefit, now represents a research priority. Long-term macrolide therapy reduces rates of pulmonary exacerbation in bronchiectasis. However, little is known about the potential for macrolide therapy to alter the composition and function of the oropharyngeal commensal microbiota or to increase the carriage of transmissible antimicrobial resistance. We assessed the effect of long-term erythromycin on oropharyngeal microbiota composition and the carriage of transmissible macrolide resistance genes in 84 adults with bronchiectasis, enrolled in the Bronchiectasis and Low-dose Erythromycin Study (BLESS) 48-week placebo-controlled trial of twice-daily erythromycin ethylsuccinate (400 mg). Oropharyngeal microbiota composition and macrolide resistance gene carriage were determined by 16S rRNA gene amplicon sequencing and quantitative PCR, respectively. Long-term erythromycin treatment was associated with a significant increase in the relative abundance of oropharyngeal Haemophilus parainfluenzae (P = 0.041) and with significant decreases in the relative abundances of Streptococcus pseudopneumoniae (P = 0.024) and Actinomyces odontolyticus (P = 0.027). Validation of the sequencing results by quantitative PCR confirmed a significant decrease in the abundance of Actinomyces spp. (P = 0.046). Erythromycin treatment did not result in a significant increase in the number of subjects who carried erm(A), erm(B), erm(C), erm(F), mef(A/E), and msrA macrolide resistance genes. However, the abundance of erm(B) and mef(A/E) gene copies within carriers who had received erythromycin increased significantly (P < 0.05). Our findings indicate that changes in oropharyngeal microbiota composition resulting from long-term erythromycin treatment are modest and are limited to a discrete group of taxa. Associated increases in levels of transmissible antibiotic resistance genes within the oropharyngeal microbiota highlight the potential for this microbial system to act as a reservoir for resistance. IMPORTANCE Recent demonstrations that long-term macrolide therapy can prevent exacerbations in chronic airways diseases have led to a dramatic increase in their use. However, little is known about the wider, potentially adverse impacts of these treatments. Substantial disruption of the upper airway commensal microbiota might reduce its contribution to host defense and local immune regulation, while increases in macrolide resistance carriage would represent a serious public health concern. Using samples from a randomized controlled trial, we show that low-dose erythromycin given over 48 weeks influences the composition of the oropharyngeal commensal microbiota. We report that macrolide therapy is associated with significant changes in the relative abundances of members of the Actinomyces genus and with significant increases in the carriage of transmissible macrolide resistance. Determining the clinical significance of these changes, relative to treatment benefit, now represents a research priority.
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56
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Fu X, Zeng B, Wang P, Wang L, Wen B, Li Y, Liu H, Bai S, Jia G. Microbiome of Total Versus Live Bacteria in the Gut of Rex Rabbits. Front Microbiol 2018; 9:733. [PMID: 29692775 PMCID: PMC5902543 DOI: 10.3389/fmicb.2018.00733] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/28/2018] [Indexed: 12/12/2022] Open
Abstract
Gastrointestinal bacteria are essential for host health, and only viable microorganisms contribute to gastrointestinal functions. When evaluating the gut microbiota by next generation sequencing method, dead bacteria, which compose a proportion of gut bacteria, may distort analysis of the live gut microbiota. We collected stomach, jejunum, ileum, cecum, and colon contents from Rex rabbits. A modified propidium monoazide (PMA) treatment protocol was used to exclude DNA from dead bacteria. Analysis of untreated samples yielded total bacteria, and analysis of PMA-treated samples yielded live bacteria. Quantitative polymerase chain reaction and 16S rRNA gene sequencing were performed to evaluate the live-to-total bacteria ratio and compare the difference between live and total microbiota in the entire digestive tract. A low proportion of live bacteria in the foregut (stomach 1.12%, jejunum 1.2%, ileum 2.84%) and a high proportion of live bacteria in the hindgut (cecum 24.66%, colon 19.08%) were observed. A significant difference existed between total and live microbiota. Clostridiales, Ruminococcaceae, and S24-7 dominated the hindgut of both groups, while Acinetobacter and Cupriavidus dominated only in live foregut microbiota. Clostridiales and Ruminococcaceae abundance decreased, while S24-7 increased in live hindgut microbiota. The alpha- and beta-diversities differed significantly between groups. Analysis of networks showed the mutual relationship between live bacteria differed vastly when compared with total bacteria. Our study revealed a large number of dead bacteria existed in the digestive tract of Rex rabbits and distorted the community profile of the live microbiota. Total bacteria is an improper representation of the live gut microbiota, particularly in the foregut.
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Affiliation(s)
- Xiangchao Fu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China.,Sichuan Academy of Grassland Science, Chengdu, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Ping Wang
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Lihuan Wang
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Bin Wen
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Ying Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hanzhong Liu
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Gang Jia
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
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57
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Hakansson AP, Orihuela CJ, Bogaert D. Bacterial-Host Interactions: Physiology and Pathophysiology of Respiratory Infection. Physiol Rev 2018; 98:781-811. [PMID: 29488821 PMCID: PMC5966719 DOI: 10.1152/physrev.00040.2016] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 02/06/2023] Open
Abstract
It has long been thought that respiratory infections are the direct result of acquisition of pathogenic viruses or bacteria, followed by their overgrowth, dissemination, and in some instances tissue invasion. In the last decades, it has become apparent that in contrast to this classical view, the majority of microorganisms associated with respiratory infections and inflammation are actually common members of the respiratory ecosystem and only in rare circumstances do they cause disease. This suggests that a complex interplay between host, environment, and properties of colonizing microorganisms together determines disease development and its severity. To understand the pathophysiological processes that underlie respiratory infectious diseases, it is therefore necessary to understand the host-bacterial interactions occurring at mucosal surfaces, along with the microbes inhabiting them, during symbiosis. Current knowledge regarding host-bacterial interactions during asymptomatic colonization will be discussed, including a plausible role for the human microbiome in maintaining a healthy state. With this as a starting point, we will discuss possible disruptive factors contributing to dysbiosis, which is likely to be a key trigger for pathobionts in the development and pathophysiology of respiratory diseases. Finally, from this renewed perspective, we will reflect on current and potential new approaches for treatment in the future.
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Affiliation(s)
- A P Hakansson
- Division of Experimental Infection Medicine, Department of Translational Medicine, Lund University , Lund , Sweden ; Department of Microbiology, University of Alabama at Birmingham , Birmingham, Alabama ; and Center for Inflammation Research, Queens Medical Research Institute, University of Edinburgh , Edinburgh , United Kingdom
| | - C J Orihuela
- Division of Experimental Infection Medicine, Department of Translational Medicine, Lund University , Lund , Sweden ; Department of Microbiology, University of Alabama at Birmingham , Birmingham, Alabama ; and Center for Inflammation Research, Queens Medical Research Institute, University of Edinburgh , Edinburgh , United Kingdom
| | - D Bogaert
- Division of Experimental Infection Medicine, Department of Translational Medicine, Lund University , Lund , Sweden ; Department of Microbiology, University of Alabama at Birmingham , Birmingham, Alabama ; and Center for Inflammation Research, Queens Medical Research Institute, University of Edinburgh , Edinburgh , United Kingdom
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58
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Abstract
PURPOSE OF REVIEW Progression of lung disease in cystic fibrosis (CF) is punctuated by Pseudomonas aeruginosa infection and recurrent pulmonary exacerbations, and is the major determinant of a patient's life expectancy. With the advent of novel deep-sequencing techniques, polymicrobial bacterial assemblages rather than single pathogens seem to be responsible for the deterioration of pulmonary function. This review summarizes recent insights into the development of the CF respiratory tract microbiome, with its determinants and its relations to clinical parameters. RECENT FINDINGS Research has moved from microbiota snapshots to intensive sampling over time, in an attempt to identify biomarkers of progression of CF lung disease. The developing respiratory tract microbiota in CF is perturbed by various endogenous and exogenous factors from the first months of life on. This work has revealed that both major pathogens such as P. aeruginosa and newly discovered players such as anaerobic species seem to contribute to CF lung disease. However, their interrelations remain to be unraveled. SUMMARY Long-term follow-up of microbiome development and alterations in relation to progression of lung disease and treatment is recommended. Moreover, integrating this information with other systems such as the metabolome, genome, mycome and virome is likely to contribute significantly to insights into host-microbiome interactions and thereby CF lung disease pathogenesis.
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59
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Abstract
PURPOSE OF REVIEW Anaerobic bacteria are not only normal commensals, but are also considered opportunistic pathogens and have been identified as persistent members of the lower airway community in people with cystic fibrosis of all ages and stages of disease. Currently, the role of anaerobic bacteria in cystic fibrosis lower airway disease is not well understood. Therefore, this review describes the recent studies relating to the potential pathophysiological role(s) of anaerobes within the cystic fibrosis lungs. RECENT FINDINGS The most frequently identified anaerobic bacteria in the lower airways are common to both cystic fibrosis and healthy lungs. Studies have shown that in cystic fibrosis, the relative abundance of anaerobes fluctuates in the lower airways with reduced lung function and increased inflammation associated with a decreased anaerobic load. However, anaerobes found within the lower airways also produce virulence factors, may cause a host inflammatory response and interact synergistically with recognized pathogens. SUMMARY Anaerobic bacteria are potentially members of the airway microbiota in health but could also contribute to the pathogenesis of lower airway disease in cystic fibrosis via both direct and indirect mechanisms. A personalized treatment strategy that maintains a normal microbial community may be possible in the future.
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60
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Guilloux CA, Lamoureux C, Héry-Arnaud G. [Anaerobic bacteria, the unknown members of the lung microbiota]. Med Sci (Paris) 2018; 34:253-260. [PMID: 29547112 DOI: 10.1051/medsci/20183403014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Lungs were considered as sterile for a long time. However, it is now evident that the lungs of healthy people are colonized by microorganisms. Among the bacteria present in the pulmonary microbiota, a significant proportion is anaerobic (strict or facultative). Even though interest in the pulmonary microbiota is increasing, few studies have focused on these unknowns that represent the lung resident anaerobic bacteria. This review describes the biodiversity of anaerobes in physiological conditions, and in different chronic respiratory diseases (cystic fibrosis, COPD, asthma). It also explains anaerobes' roles in the barrier flora effect, in inflammation, or as potential biomarkers in disease progression.
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Affiliation(s)
- Charles-Antoine Guilloux
- UMR1078, Génétique, Génomique Fonctionnelle et Biotechnologies, Inserm, Université de Brest, EFS, IBSAM, 22, avenue Camille Desmoulins, 29238 Brest, France
| | - Claudie Lamoureux
- UMR1078, Génétique, Génomique Fonctionnelle et Biotechnologies, Inserm, Université de Brest, EFS, IBSAM, 22, avenue Camille Desmoulins, 29238 Brest, France - Unité de Bactériologie, Pôle de Biologie-Pathologie, Hôpital La Cavale Blanche, CHRU de Brest, 29238 Brest, France
| | - Geneviève Héry-Arnaud
- UMR1078, Génétique, Génomique Fonctionnelle et Biotechnologies, Inserm, Université de Brest, EFS, IBSAM, 22, avenue Camille Desmoulins, 29238 Brest, France - Unité de Bactériologie, Pôle de Biologie-Pathologie, Hôpital La Cavale Blanche, CHRU de Brest, 29238 Brest, France
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Cystic Fibrosis Airway Microbiome: Overturning the Old, Opening the Way for the New. J Bacteriol 2018; 200:JB.00561-17. [PMID: 29084859 DOI: 10.1128/jb.00561-17] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The genetic disease cystic fibrosis (CF) is associated with chronic airway infections that are a proximal cause of death in many patients with this affliction. Classic microbiology studies focusing on canonical pathogens resulted in the development of a common set of views regarding the nature of the airway infections associated with this disease, and these ideas have influenced everything from the way infections are treated to how clinical trials for new CF-targeted antibiotics are designed and the focus of CF-related research topics. Recent culture-independent studies have prompted us to rethink, and in some cases discard, some of these long-held views. In this piece, I argue that an updated view of the complicated chronic infections associated with CF, thanks in large part to culture-independent studies of sputum and bronchoalveolar lavage fluid samples, should be leveraged to develop new strategies to treat these recalcitrant infections.
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62
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Inflammatory phenotypes in patients with severe asthma are associated with distinct airway microbiology. J Allergy Clin Immunol 2018; 141:94-103.e15. [DOI: 10.1016/j.jaci.2017.03.044] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 02/28/2017] [Accepted: 03/15/2017] [Indexed: 12/31/2022]
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Mao Q, Jiang F, Yin R, Wang J, Xia W, Dong G, Ma W, Yang Y, Xu L, Hu J. Interplay between the lung microbiome and lung cancer. Cancer Lett 2017; 415:40-48. [PMID: 29197615 DOI: 10.1016/j.canlet.2017.11.036] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/23/2017] [Accepted: 11/27/2017] [Indexed: 12/31/2022]
Abstract
The human microbiome confers benefits or disease susceptibility to the human body through multiple pathways. Disruption of the symbiotic balance of the human microbiome is commonly found in systematic diseases such as diabetes, obesity, and chronic gastric diseases. Emerging evidence has suggested that dysbiosis of the microbiota may also play vital roles in carcinogenesis at multiple levels, e.g., by affecting metabolic, inflammatory, or immune pathways. Although the impact of the gut microbiome on the digestive cancer has been widely explored, few studies have investigated the interplay between the microbiome and lung cancer. Some recent studies have shown that certain microbes and microbiota dysbiosis are correlated with development of lung cancer. In this mini-review, we briefly summarize current research findings describing the relationship between the lung microbiome and lung cancer. We further discuss the potential mechanisms through which the lung microbiome may play a role in lung carcinogenesis and impact lung cancer treatment. A better knowledge of the interplay between the lung microbiome and lung cancer may promote the development of innovative strategies for early prevention and personalized treatment in lung cancer.
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Affiliation(s)
- Qixing Mao
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, 210009, PR China; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY10029, USA; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, PR China; The Fourth Clinical College of Nanjing Medical University, Graduated College of Nanjing Medical University, Nanjing 210000, PR China
| | - Feng Jiang
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, 210009, PR China; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, PR China
| | - Rong Yin
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, 210009, PR China; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, PR China
| | - Jie Wang
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, 210009, PR China; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, PR China
| | - Wenjie Xia
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, 210009, PR China; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, PR China; The Fourth Clinical College of Nanjing Medical University, Graduated College of Nanjing Medical University, Nanjing 210000, PR China
| | - Gaochao Dong
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, 210009, PR China; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, PR China
| | - Weidong Ma
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, 210009, PR China; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, PR China; The Fourth Clinical College of Nanjing Medical University, Graduated College of Nanjing Medical University, Nanjing 210000, PR China
| | - Yao Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY10029, USA
| | - Lin Xu
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, 210009, PR China; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, PR China.
| | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York NY10029, USA.
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Abstract
The Human Microbiome Project began 10 years ago, leading to a significant growth in understanding of the role the human microbiome plays in health and disease. In this article, we explain with an emphasis on the lung, the origins of microbiome research. We discuss how 16S rRNA gene sequencing became the first major molecular tool to examine the bacterial communities present within the human body. We highlight the pitfalls of molecular-based studies, such as false findings resulting from contamination, and the limitations of 16S rRNA gene sequencing. Knowledge about the lung microbiome has evolved from initial scepticism to the realisation that it might have a significant influence on many illnesses. We also discuss the lung microbiome in the context of disease by giving examples of important respiratory conditions. In addition, we draw attention to the challenges for metagenomic studies of respiratory samples and the importance of systematic bacterial isolation to enable host-microbiome interactions to be understood. We conclude by discussing how knowledge of the lung microbiome impacts current clinical diagnostics.
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65
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Chotirmall SH, Gellatly SL, Budden KF, Mac Aogain M, Shukla SD, Wood DLA, Hugenholtz P, Pethe K, Hansbro PM. Microbiomes in respiratory health and disease: An Asia-Pacific perspective. Respirology 2017; 22:240-250. [PMID: 28102970 DOI: 10.1111/resp.12971] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 10/30/2016] [Accepted: 11/17/2016] [Indexed: 02/06/2023]
Abstract
There is currently enormous interest in studying the role of the microbiome in health and disease. Microbiome's role is increasingly being applied to respiratory diseases, in particular COPD, asthma, cystic fibrosis and bronchiectasis. The changes in respiratory microbiomes that occur in these diseases and how they are modified by environmental challenges such as cigarette smoke, air pollution and infection are being elucidated. There is also emerging evidence that gut microbiomes play a role in lung diseases through the modulation of systemic immune responses and can be modified by diet and antibiotic treatment. There are issues that are particular to the Asia-Pacific region involving diet and prevalence of specific respiratory diseases. Each of these issues is further complicated by the effects of ageing. The challenges now are to elucidate the cause and effect relationships between changes in microbiomes and respiratory diseases and how to translate these into new treatments and clinical care. Here we review the current understanding and progression in these areas.
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Affiliation(s)
- Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Shaan L Gellatly
- Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Kurtis F Budden
- Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Micheál Mac Aogain
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Shakti D Shukla
- Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - David L A Wood
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Kevin Pethe
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs, University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia
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66
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The lung microbiome. Emerg Top Life Sci 2017; 1:313-324. [PMID: 33525774 DOI: 10.1042/etls20170043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/31/2017] [Accepted: 09/29/2017] [Indexed: 12/17/2022]
Abstract
Historically, our understanding of lung microbiology has relied on insight gained through culture-based diagnostic approaches that employ selective culture conditions to isolate specific pathogens. The relatively recent development of culture-independent microbiota-profiling techniques, particularly 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing, has enabled more comprehensive characterisation of the microbial content of respiratory samples. The widespread application of such techniques has led to a fundamental shift in our view of respiratory microbiology. Rather than a sterile lung environment that can become colonised by microbes during infection, it appears that a more nuanced balance exists between what we consider respiratory health and disease, mediated by mechanisms that influence the clearance of microbes from the lungs. Where airway defences are compromised, the ongoing transient exposure of the lower airways to microbes can lead to the establishment of complex microbial communities within the lung. Importantly, the characteristics of these communities, and the manner in which they influence lung pathogenesis, can be very different from those of their constituent members when viewed in isolation. The lung microbiome, a construct that incorporates microbes, their genetic material, and the products of microbial genes, is increasingly central to our understanding of the regulation of respiratory physiology and the processes that underlie lung pathogenesis.
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67
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Kramná L, Dřevínek P, Lin J, Kulich M, Cinek O. Changes in the lung bacteriome in relation to antipseudomonal therapy in children with cystic fibrosis. Folia Microbiol (Praha) 2017; 63:237-248. [PMID: 29127619 DOI: 10.1007/s12223-017-0562-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 10/30/2017] [Indexed: 12/28/2022]
Abstract
The lung in cystic fibrosis (CF) is home to numerous pathogens that shorten the lives of patients. The aim of the present study was to assess changes in the lung bacteriome following antibiotic therapy targeting Pseudomonas aeruginosa in children with CF. The study included nine children (9-18 years) with CF who were treated for their chronic or intermittent positivity for Pseudomonas aeruginosa. The bacteriomes were determined in 16 pairs of sputa collected at the beginning and at the end of a course of intravenous antibiotic therapy via deep sequencing of the variable region 4 of the 16S rRNA gene, and the total bacterial load and selected specific pathogens were assessed using quantitative real-time PCR. The effect of antipseudomonal antibiotics was observable as a profound decrease in the total 16S rDNA load (p = 0.001) as well as in a broad range of individual taxa including Staphylococcus aureus (p = 0.03) and several members of the Streptococcus mitis group (S. oralis, S. mitis, and S. infantis) (p = 0.003). Improvements in forced expiratory volume (FEV1) were associated with an increase in Granulicatella sp. (p = 0.004), whereas a negative association was noted between the total bacterial load and white blood cell count (p = 0.007). In conclusion, the data show how microbial communities differ in reaction to antipseudomonal treatment, suggesting that certain rare species may be associated with clinical parameters. Our work also demonstrates the utility of absolute quantification of bacterial load in addition to the 16S rDNA profiling.
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Affiliation(s)
- Lenka Kramná
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, V Úvalu 84, 15006, Prague 5, Czech Republic
| | - Pavel Dřevínek
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Jake Lin
- BioMediTech, Computational Biology, University of Tampere, Tampere, Finland
| | - Michal Kulich
- Department of Probability and Mathematical Statistics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Ondrej Cinek
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University in Prague and University Hospital Motol, V Úvalu 84, 15006, Prague 5, Czech Republic.
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68
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Lopes SP, Azevedo NF, Pereira MO. Developing a model for cystic fibrosis sociomicrobiology based on antibiotic and environmental stress. Int J Med Microbiol 2017; 307:460-470. [PMID: 29033313 DOI: 10.1016/j.ijmm.2017.09.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 08/30/2017] [Accepted: 09/28/2017] [Indexed: 02/06/2023] Open
Abstract
Cystic fibrosis (CF) infections are invariably biofilm-mediated and polymicrobial, being safe to assume that a myriad of factors affects the sociomicrobiology within the CF infection site and modulate the CF community dynamics, by shaping their social activities, overall functions, virulence, ultimately affecting disease outcome. This work aimed to assess changes in the dynamics (particularly on the microbial composition) of dual-/three-species biofilms involving CF-classical (Pseudomonas aeruginosa) and unusual species (Inquilinus limosus and Dolosigranulum pigrum), according to variable oxygen conditions and antibiotic exposure. Low fluctuations in biofilm compositions were observed across distinct oxygen environments, with dual-species biofilms exhibiting similar relative proportions and P. aeruginosa and/or D. pigrum populations dominating three-species consortia. Once exposed to antibiotics, biofilms displayed high resistance profiles, and microbial compositions, distributions, and microbial interactions significantly challenged. The antibiotic/oxygen environment supported such fluctuations, which enhanced for three-species communities. In conclusion, antibiotic therapy hugely disturbed CF communities' dynamics, inducing significant compositional changes on multispecies consortia. Clearly, multiple perturbations may disturb this dynamic, giving rise to various microbiological scenarios in vivo, and affecting disease phenotype. Therefore, an appreciation of the ecological/evolutionary nature within CF communities will be useful for the optimal use of current therapies and for newer breakthroughs on CF antibiotherapy.
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Affiliation(s)
- Susana Patrícia Lopes
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Nuno Filipe Azevedo
- LEPABE - Dep. of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal
| | - Maria Olívia Pereira
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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69
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Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period. mBio 2017; 8:mBio.00959-17. [PMID: 28951476 PMCID: PMC5615197 DOI: 10.1128/mbio.00959-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cystic fibrosis (CF) lung microbiota composition has recently been redefined by the application of next-generation sequencing (NGS) tools, identifying, among others, previously undescribed anaerobic and uncultivable bacteria. In the present study, we monitored the fluctuations of this ecosystem in 15 CF patients during a 1-year follow-up period, describing for the first time, as far as we know, the presence of predator bacteria in the CF lung microbiome. In addition, a new computational model was developed to ascertain the hypothetical ecological repercussions of a prey-predator interaction in CF lung microbial communities. Fifteen adult CF patients, stratified according to their pulmonary function into mild (n = 5), moderate (n = 9), and severe (n = 1) disease, were recruited at the CF unit of the Ramón y Cajal University Hospital (Madrid, Spain). Each patient contributed three or four induced sputum samples during a 1-year follow-up period. Lung microbiota composition was determined by both cultivation and NGS techniques and was compared with the patients’ clinical variables. Results revealed a particular microbiota composition for each patient that was maintained during the study period, although some fluctuations were detected without any clinical correlation. For the first time, Bdellovibrio and Vampirovibrio predator bacteria were shown in CF lung microbiota and reduced-genome bacterial parasites of the phylum Parcubacteria were also consistently detected. The newly designed computational model allows us to hypothesize that inoculation of predators into the pulmonary microbiome might contribute to the control of chronic colonization by CF pathogens in early colonization stages. The application of NGS to sequential samples of CF patients demonstrated the complexity of the organisms present in the lung (156 species) and the constancy of basic individual colonization patterns, although some differences between samples from the same patient were observed, probably related to sampling bias. Bdellovibrio and Vampirovibrio predator bacteria were found for the first time by NGS as part of the CF lung microbiota, although their ecological significance needs to be clarified. The newly designed computational model allows us to hypothesize that inoculation of predators into the lung microbiome can eradicate CF pathogens in early stages of the process. Our data strongly suggest that lower respiratory microbiome fluctuations are not necessarily related to the patient’s clinical status.
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70
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Esposito S, Principi N. Impact of nasopharyngeal microbiota on the development of respiratory tract diseases. Eur J Clin Microbiol Infect Dis 2017; 37:1-7. [PMID: 28795339 DOI: 10.1007/s10096-017-3076-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/24/2017] [Indexed: 12/31/2022]
Abstract
Knowledge of whether and how respiratory microbiota composition can prime the immune system and provide colonisation resistance, limiting consecutive pathobiont overgrowth and infections, is essential to improving the prevention and therapy of respiratory disorders. Modulation of dysbiotic ecosystems or reconstitution of missing microbes might be a possible measure to reduce respiratory diseases. The aim of this review is to analyse the role of nasopharyngeal microbiota in the development of respiratory tract disease in paediatric-age subjects. PubMed was used to search for all studies published over the last 15 years using the following key words: "microbiota" or "microbioma" and "nasopharyngeal" or "respiratory" or "nasal" and "children" or "paediatric" or "infant". Analysis of the literature showed that respiratory microbiota can regulate health and disease development in the respiratory tract. Like the gut microbiota, the respiratory microbiota is established at birth, and early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children. Protective and dangerous bacteria have been identified, and this can be considered the base for developing new approaches to diseases that respond poorly to traditional interventions. Reconstitution of missing microbes can be achieved by the administration of pre- and probiotics. Modulation of respiratory microbiota by favouring colonisation of the upper respiratory tract by beneficial commensals can interfere with the proliferation and activity of resident pathobionts and is a possible new measure to reduce the risk of disease. However, further studies are needed because a deeper understanding of these and related issues can be transferred to clinical practice.
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Affiliation(s)
- S Esposito
- Pediatric Clinic, Università degli Studi di Perugia, Piazza Menghini 1, 06129, Perugia, Italy.
| | - N Principi
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
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71
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Bacci G, Mengoni A, Fiscarelli E, Segata N, Taccetti G, Dolce D, Paganin P, Morelli P, Tuccio V, De Alessandri A, Lucidi V, Bevivino A. A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease. Int J Mol Sci 2017; 18:E1654. [PMID: 28758937 PMCID: PMC5578044 DOI: 10.3390/ijms18081654] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 12/12/2022] Open
Abstract
In recent years, next-generation sequencing (NGS) was employed to decipher the structure and composition of the microbiota of the airways in cystic fibrosis (CF) patients. However, little is still known about the overall gene functions harbored by the resident microbial populations and which specific genes are associated with various stages of CF lung disease. In the present study, we aimed to identify the microbial gene repertoire of CF microbiota in twelve patients with severe and normal/mild lung disease by performing sputum shotgun metagenome sequencing. The abundance of metabolic pathways encoded by microbes inhabiting CF airways was reconstructed from the metagenome. We identified a set of metabolic pathways differently distributed in patients with different pulmonary function; namely, pathways related to bacterial chemotaxis and flagellar assembly, as well as genes encoding efflux-mediated antibiotic resistance mechanisms and virulence-related genes. The results indicated that the microbiome of CF patients with low pulmonary function is enriched in virulence-related genes and in genes encoding efflux-mediated antibiotic resistance mechanisms. Overall, the microbiome of severely affected adults with CF seems to encode different mechanisms for the facilitation of microbial colonization and persistence in the lung, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in patients with severe lung disease.
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Affiliation(s)
- Giovanni Bacci
- Department of Biology, University of Florence, Florence 50019, Italy.
| | - Alessio Mengoni
- Department of Biology, University of Florence, Florence 50019, Italy.
| | - Ersilia Fiscarelli
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, "Bambino Gesù" Children's Hospital and Research Institute, Rome 00165, Italy.
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, Trento 38123, Italy.
| | - Giovanni Taccetti
- Department of Pediatric Medicine, Cystic Fibrosis Center, Anna Meyer Children's University Hospital, Florence 50139, Italy.
| | - Daniela Dolce
- Department of Pediatric Medicine, Cystic Fibrosis Center, Anna Meyer Children's University Hospital, Florence 50139, Italy.
| | - Patrizia Paganin
- Territorial and Production Systems Sustainability Department, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Rome 00123, Italy.
| | - Patrizia Morelli
- Cystic Fibrosis Center, IRCCS G. Gaslini Institute, Genoa 16146, Italy.
| | - Vanessa Tuccio
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, "Bambino Gesù" Children's Hospital and Research Institute, Rome 00165, Italy.
| | | | - Vincenzina Lucidi
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, "Bambino Gesù" Children's Hospital and Research Institute, Rome 00165, Italy.
| | - Annamaria Bevivino
- Territorial and Production Systems Sustainability Department, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Rome 00123, Italy.
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72
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Finch S, Keir HR, Dicker AJ, Chalmers JD. The past decade in bench research into pulmonary infectious diseases: What do clinicians need to know? Respirology 2017; 22:1062-1072. [PMID: 28657170 DOI: 10.1111/resp.13106] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/07/2017] [Accepted: 05/14/2017] [Indexed: 12/12/2022]
Abstract
Respiratory infections are primarily treated with antibiotics, drugs that are mostly inexpensive and have been widely available since the 1940s and 1950s. Nevertheless, despite antibiotics, the burden of disease in pneumonia, bronchiectasis, cystic fibrosis, COPD and rare respiratory infections remains exceptionally high. There is an urgent need for translational studies to develop new treatments or new biomarkers to improve outcomes in these conditions. The 'translational gaps' between bench science and clinical practice are particularly challenging in respiratory infections. This is partly due to the poor representativeness of animal models of infection to human disease, and a long-term lack of investment into pulmonary infection research. The revolution in genomics and other omics technologies, however, is beginning to unlock clinically important information about the host response to infection, the behaviour of bacterial communities and the development of new antibiotics. It is not possible to review the extensive progress made in the last decade into the pathophysiology of the different respiratory infections and so here, we focus on major technologies that are now changing respiratory infection research, specifically bacterial whole-genome sequencing, the microbiota, personalized medicine with omics technologies, new antibiotic development and host inflammatory cell biology.
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Affiliation(s)
- Simon Finch
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Holly R Keir
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Alison J Dicker
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - James D Chalmers
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
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73
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Faner R, Sibila O, Agustí A, Bernasconi E, Chalmers JD, Huffnagle GB, Manichanh C, Molyneaux PL, Paredes R, Pérez Brocal V, Ponomarenko J, Sethi S, Dorca J, Monsó E. The microbiome in respiratory medicine: current challenges and future perspectives. Eur Respir J 2017; 49:49/4/1602086. [PMID: 28404649 DOI: 10.1183/13993003.02086-2016] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/08/2017] [Indexed: 12/15/2022]
Abstract
The healthy lung has previously been considered to be a sterile organ because standard microbiological culture techniques consistently yield negative results. However, culture-independent techniques report that large numbers of microorganisms coexist in the lung. There are many unknown aspects in the field, but available reports show that the lower respiratory tract microbiota: 1) is similar in healthy subjects to the oropharyngeal microbiota and dominated by members of the Firmicutes, Bacteroidetes and Proteobacteria phyla; 2) shows changes in smokers and well-defined differences in chronic respiratory diseases, although the temporal and spatial kinetics of these changes are only partially known; and 3) shows relatively abundant non-cultivable bacteria in chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, cystic fibrosis and bronchiectasis, with specific patterns for each disease. In all of these diseases, a loss of diversity, paralleled by an over-representation of Proteobacteria (dysbiosis), has been related to disease severity and exacerbations. However, it is unknown whether dysbiosis is a cause or a consequence of the damage to bronchoalveolar surfaces.Finally, little is known about bacterial functionality and the interactions between viruses, fungi and bacteria. It is expected that future research in bacterial gene expressions, metagenomics longitudinal analysis and host-microbiome animal models will help to move towards targeted microbiome interventions in respiratory diseases.
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Affiliation(s)
- Rosa Faner
- Hospital Clinic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain.,CIBER de Enfermedades Respiratorias - CIBERES, Madrid, Spain.,These co-primary authors contributed equally to this work
| | - Oriol Sibila
- Hospital Universitari de la Santa Creu i Sant Pau, Universitat Autónoma Barcelona, Barcelona, Spain.,These co-primary authors contributed equally to this work
| | - Alvar Agustí
- Hospital Clinic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain.,CIBER de Enfermedades Respiratorias - CIBERES, Madrid, Spain
| | - Eric Bernasconi
- Service de Pneumologie, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | | | | | - Chaysavanh Manichanh
- Dept of Gastroenterology, Vall d'Hebron Research Institute, Barcelona, Spain.,CIBER de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | | | - Roger Paredes
- Hospital Universitari Germans Trias i Pujol, Universitat Autónoma Barcelona, Barcelona, Spain
| | - Vicente Pérez Brocal
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.,Joint Research Unit on Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health) and Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
| | - Julia Ponomarenko
- Centro de Regulación Genómica, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Jordi Dorca
- Hospital Universitari de Bellvitge, IDIBELL, Universitat de Barcelona, Hospitalet del Llobregat, Barcelona, Spain.,These co-senior authors contributed equally to this work
| | - Eduard Monsó
- CIBER de Enfermedades Respiratorias - CIBERES, Madrid, Spain .,Hospital Universitari Parc Taulí, Universitat Autònoma de Barcelona, Barcelona, Spain.,These co-senior authors contributed equally to this work
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74
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Strong incidence of Pseudomonas aeruginosa on bacterial rrs and ITS genetic structures of cystic fibrosis sputa. PLoS One 2017; 12:e0173022. [PMID: 28282386 PMCID: PMC5345789 DOI: 10.1371/journal.pone.0173022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 02/14/2017] [Indexed: 11/20/2022] Open
Abstract
Cystic fibrosis (CF) lungs harbor a complex community of interacting microbes, including pathogens like Pseudomonas aeruginosa. Meta-taxogenomic analysis based on V5-V6 rrs PCR products of 52 P. aeruginosa-positive (Pp) and 52 P. aeruginosa-negative (Pn) pooled DNA extracts from CF sputa suggested positive associations between P. aeruginosa and Stenotrophomonas and Prevotella, but negative ones with Haemophilus, Neisseria and Burkholderia. Internal Transcribed Spacer analyses (RISA) from individual DNA extracts identified three significant genetic structures within the CF cohorts, and indicated an impact of P. aeruginosa. RISA clusters Ip and IIIp contained CF sputa with a P. aeruginosa prevalence above 93%, and of 24.2% in cluster IIp. Clusters Ip and IIIp showed lower RISA genetic diversity and richness than IIp. Highly similar cluster IIp RISA profiles were obtained from two patients harboring isolates of a same P. aeruginosa clone, suggesting convergent evolution in the structure of their microbiota. CF patients of cluster IIp had received significantly less antibiotics than patients of clusters Ip and IIIp but harbored the most resistant P. aeruginosa strains. Patients of cluster IIIp were older than those of Ip. The effects of P. aeruginosa on the RISA structures could not be fully dissociated from the above two confounding factors but several trends in these datasets support the conclusion of a strong incidence of P. aeruginosa on the genetic structure of CF lung microbiota.
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75
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Whelan FJ, Heirali AA, Rossi L, Rabin HR, Parkins MD, Surette MG. Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis. PLoS One 2017; 12:e0172811. [PMID: 28253277 PMCID: PMC5333848 DOI: 10.1371/journal.pone.0172811] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/09/2017] [Indexed: 02/01/2023] Open
Abstract
Cystic fibrosis (CF) manifests in the lungs resulting in chronic microbial infection. Most morbidity and mortality in CF is due to cycles of pulmonary exacerbations-episodes of acute inflammation in response to the lung microbiome-which are difficult to prevent and treat because their cause is not well understood. We hypothesized that longitudinal analyses of the bacterial component of the CF lung microbiome may elucidate causative agents within this community for pulmonary exacerbations. In this study, 6 participants were sampled thrice-weekly for up to one year. During sampling, sputum, and data (antibiotic usage, spirometry, and symptom scores) were collected. Time points were categorized based on relation to exacerbation as Stable, Intermediate, and Treatment. Retrospectively, a subset of were interrogated via 16S rRNA gene sequencing. When samples were examined categorically, a significant difference between the lung microbiota in Stable, Intermediate, and Treatment samples was observed in a subset of participants. However, when samples were examined longitudinally, no correlations between microbial composition and collected data (antibiotic usage, spirometry, and symptom scores) were observed upon exacerbation onset. In this study, we identified no universal indicator within the lung microbiome of exacerbation onset but instead showed that changes to the CF lung microbiome occur outside of acute pulmonary episodes and are patient-specific.
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Affiliation(s)
- Fiona J. Whelan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Alya A. Heirali
- Department of Microbiology, Immunology and Infectious Diseases, The University of Calgary, Calgary, Canada
| | - Laura Rossi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Harvey R. Rabin
- Department of Microbiology, Immunology and Infectious Diseases, The University of Calgary, Calgary, Canada
- Department of Medicine, The University of Calgary, Calgary, Canada
| | - Michael D. Parkins
- Department of Microbiology, Immunology and Infectious Diseases, The University of Calgary, Calgary, Canada
- Department of Medicine, The University of Calgary, Calgary, Canada
| | - Michael G. Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Department of Microbiology, Immunology and Infectious Diseases, The University of Calgary, Calgary, Canada
- Department of Medicine, McMaster University, Hamilton, Canada
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76
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Antimicrobial-resistant Escherichia coli and Enterococcus spp. isolated from Miranda donkey (Equus asinus): an old problem from a new source with a different approach. J Med Microbiol 2017; 66:191-202. [DOI: 10.1099/jmm.0.000423] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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77
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Boutin S, Dalpke AH. Acquisition and adaptation of the airway microbiota in the early life of cystic fibrosis patients. Mol Cell Pediatr 2017; 4:1. [PMID: 28097632 PMCID: PMC5241261 DOI: 10.1186/s40348-016-0067-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/15/2016] [Indexed: 12/26/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease in which bacterial infections of the airways play a major role in the long-term clinical outcome. In recent years, a number of next-generation sequencing (NGS)-based studies aimed at deciphering the structure and composition of the airways’ microbiota. It was shown that the nasal cavity of CF patients displays dysbiosis early in life indicating a failure in the first establishment of a healthy microbiota. In contrast, within the conducting and lower airways, the establishment occurs normally first, but is sensitive to future dysbiosis including chronic infections with classical pathogens in later life. The objective of this mini-review is to give an update on the current knowledge about the development of the microbiota in the early life of CF patients. Microbial acquisition in the human airways can be described by the island model: Microbes found in the lower airways of CF patients represent “islands” that are at first populated from the upper airways reflecting the “mainland.” Colonization can be modeled following the neutral theory in which the most abundant bacteria in the mainland are also frequently found in the lower airways initially. At later times, however, the colonization process of the lower airways segregates by active selection of specific microbes. Future research should focus on those processes of microbial and host interactions to understand how microbial communities are shaped on short- and long-term scales. We point out what therapeutic consequences arise from the microbiome data obtained within ecological framework models.
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Affiliation(s)
- Sébastien Boutin
- Department of Infectious Disease, Medical Microbiology and Hygiene, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Alexander H Dalpke
- Department of Infectious Disease, Medical Microbiology and Hygiene, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany. .,Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany.
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78
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Cystic fibrosis lung environment and Pseudomonas aeruginosa infection. BMC Pulm Med 2016; 16:174. [PMID: 27919253 PMCID: PMC5139081 DOI: 10.1186/s12890-016-0339-5] [Citation(s) in RCA: 225] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/24/2016] [Indexed: 12/20/2022] Open
Abstract
Background The airways of patients with cystic fibrosis (CF) are highly complex, subject to various environmental conditions as well as a distinct microbiota. Pseudomonas aeruginosa is recognized as one of the most important pulmonary pathogens and the predominant cause of morbidity and mortality in CF. A multifarious interplay between the host, pathogens, microbiota, and the environment shapes the course of the disease. There have been several excellent reviews detailing CF pathology, Pseudomonas and the role of environment in CF but only a few reviews connect these entities with regards to influence on the overall course of the disease. A holistic understanding of contributing factors is pertinent to inform new research and therapeutics. Discussion In this article, we discuss the deterministic alterations in lung physiology as a result of CF. We also revisit the impact of those changes on the microbiota, with special emphasis on P. aeruginosa and the influence of other non-genetic factors on CF. Substantial past and current research on various genetic and non-genetic aspects of cystic fibrosis has been reviewed to assess the effect of different factors on CF pulmonary infection. A thorough review of contributing factors in CF and the alterations in lung physiology indicate that CF lung infection is multi-factorial with no isolated cause that should be solely targeted to control disease progression. A combinatorial approach may be required to ensure better disease outcomes. Conclusion CF lung infection is a complex disease and requires a broad multidisciplinary approach to improve CF disease outcomes. A holistic understanding of the underlying mechanisms and non-genetic contributing factors in CF is central to development of new and targeted therapeutic strategies.
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Caverly LJ, Caverly TJ, Kalikin LM, Foster BK, Simon RH, LiPuma JJ. Episodic oral antibiotic use in CF: Discordance between the electronic medical record and self-report. J Cyst Fibros 2016; 15:630-3. [PMID: 27156045 DOI: 10.1016/j.jcf.2016.04.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 04/19/2016] [Indexed: 11/18/2022]
Abstract
BACKGROUND Accurate accounting of antibiotic use is necessary for studies comparing the CF airway microbiota across clinically relevant disease states. While poor adherence to chronic therapies is well described for individuals with CF, use patterns of episodic oral antibiotics are less clear. METHODS Eleven individuals with CF completed daily questionnaires regarding antibiotic use for a mean of 458days. Self-report of episodic oral antibiotic use was compared to antibiotic prescription data in the electronic medical record (EMR). RESULTS Self-reported use of episodic oral antibiotics differed from EMR data an average of 8.3% of days per subject. The majority of these discrepancies were due to self-reported use of oral antibiotics outside of the EMR-documented dates of antibiotic prescription. CONCLUSIONS Discrepancies exist between self-reported use of episodic oral antibiotics and EMR data that have implications for studies of the CF airway microbiota.
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Affiliation(s)
- Lindsay J Caverly
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109, United States.
| | - Tanner J Caverly
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, United States; Center for Clinical Management Research, Veterans Affairs, Ann Arbor, MI 48105, United States
| | - Linda M Kalikin
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Bridget K Foster
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Richard H Simon
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - John J LiPuma
- Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109, United States
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80
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Langdon A, Crook N, Dantas G. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Med 2016; 8:39. [PMID: 27074706 PMCID: PMC4831151 DOI: 10.1186/s13073-016-0294-z] [Citation(s) in RCA: 521] [Impact Index Per Article: 65.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The widespread use of antibiotics in the past 80 years has saved millions of human lives, facilitated technological progress and killed incalculable numbers of microbes, both pathogenic and commensal. Human-associated microbes perform an array of important functions, and we are now just beginning to understand the ways in which antibiotics have reshaped their ecology and the functional consequences of these changes. Mounting evidence shows that antibiotics influence the function of the immune system, our ability to resist infection, and our capacity for processing food. Therefore, it is now more important than ever to revisit how we use antibiotics. This review summarizes current research on the short-term and long-term consequences of antibiotic use on the human microbiome, from early life to adulthood, and its effect on diseases such as malnutrition, obesity, diabetes, and Clostridium difficile infection. Motivated by the consequences of inappropriate antibiotic use, we explore recent progress in the development of antivirulence approaches for resisting infection while minimizing resistance to therapy. We close the article by discussing probiotics and fecal microbiota transplants, which promise to restore the microbiota after damage of the microbiome. Together, the results of studies in this field emphasize the importance of developing a mechanistic understanding of gut ecology to enable the development of new therapeutic strategies and to rationally limit the use of antibiotic compounds.
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Affiliation(s)
- Amy Langdon
- Center for Genome Sciences, Washington University School of Medicine, Campus Box 8510, 4515 McKinley Research Building, St. Louis, MO, 63108, USA
- Clinical Research Training Center, Washington University School of Medicine, Campus Box 8051, 660 South Euclid Avenue, St. Louis, MO, 63110-1093, USA
| | - Nathan Crook
- Center for Genome Sciences, Washington University School of Medicine, Campus Box 8510, 4515 McKinley Research Building, St. Louis, MO, 63108, USA
- Department of Pathology & Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Ave, St. Louis, MO, 63110, USA
| | - Gautam Dantas
- Center for Genome Sciences, Washington University School of Medicine, Campus Box 8510, 4515 McKinley Research Building, St. Louis, MO, 63108, USA.
- Department of Pathology & Immunology, Washington University School of Medicine, Campus Box 8118, 660 South Euclid Ave, St. Louis, MO, 63110, USA.
- Department of Biomedical Engineering, Washington University in Saint Louis, Campus Box 1097, 1 Brookings Drive, Saint Louis, MO, 63130, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, Campus Box 8230, 660 S. Euclid Ave, St. Louis, MO, 63110, USA.
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