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Hosgood HD, Mongodin EF, Wan Y, Hua X, Rothman N, Hu W, Vermeulen R, Seow WJ, Rohan T, Xu J, Li J, He J, Huang Y, Yang K, Wu G, Wei F, Shi J, Sapkota AR, Lan Q. The respiratory tract microbiome and its relationship to lung cancer and environmental exposures found in rural china. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:617-623. [PMID: 30942501 PMCID: PMC8259386 DOI: 10.1002/em.22291] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/30/2019] [Accepted: 03/26/2019] [Indexed: 06/09/2023]
Abstract
We previously reported that bacterial diversity in sputum samples from never-smoking women in rural China varied by lung cancer status and household air pollution (HAP) exposure type. Here, we expand on our associations between environmental exposures and respiratory tract microbiota with an additional 90 never-smoking women from Xuanwei, China. DNA from sputum samples of cases (n = 45) and controls (n = 45) was extracted using a multistep enzymatic and physical lysis, followed by a standardized clean up. V1-V2 regions of 16S rRNA genes were Polymerase chain reaction (PCR) amplified. Purified amplicons were sequenced by 454 FLX Titanium pyrosequencing and high-quality sequences were evaluated for diversity and taxonomic membership. In our population of never-smokers, increased risk of lung cancer was associated with lower alpha diversity compared to higher alpha diversity (Shannon: ORhigh = 1.00 [reference], ORmedium = 3.84 [1.02-14.48], ORlow = 3.78 [1.03-13.82]; observed species: ORhigh = 1.00 [reference], ORmedium = 2.37 [0.67-8.48], ORlow = 2.01 [0.58-6.97]; Phylogenetic Diversity (PD) whole tree: ORhigh = 1.00 [reference], ORmedium = 3.04 [0.85-10.92], ORlow = 2.53 [0.72-8.96]), as well as a decreased relative abundance of Fusobacteria (ORhigh = 1.00 [reference], ORmedium = 1.24 [0.42-3.66], ORlow = 2.01 [0.63-6.44], ptrend = 0.03). Increasing alpha diversity was associated with smoky coal use compared to clean fuel use among all subjects (observed species, P = 0.001; PD whole tree, P = 0.006; Shannon, P = 0.0002), as well as cases (observed species, P = 0.02; PD whole tree, P = 0.03; Shannon, P = 0.03) and controls (observed species, P = 0.01; PD whole tree, P = 0.05; Shannon, P = 0.002). Increased diversity was also associated with presence of livestock (observed species, P = 0.02; PD whole tree, P = 0.02; Shannon, P = 0.03) in the home for cases. Our study is the first to report that decreased microbial diversity is associated with risk of lung cancer. Larger studies are necessary to elucidate the direct and indirect effects attributed to the disease-specific, HAP-specific, and animal-specific associations. Environ. Mol. Mutagen. 2019. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- H. Dean Hosgood
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Emmanuel F. Mongodin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland
| | - Yunhu Wan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Wei Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, Netherlands
| | - Wei Jie Seow
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Thomas Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Jun Xu
- School of Public Health, The University of Hong Kong, Pokfulam, Hong Kong
| | - Jihua Li
- Qujing Center for Diseases Control and Prevention, Qujing, China
| | - Jun He
- Qujing Center for Diseases Control and Prevention, Qujing, China
| | - Yunchao Huang
- Third Affiliated Hospital of Kunming Medical University (Yunnan Tumor Hospital), Kunming, China
| | - Kaiyun Yang
- Third Affiliated Hospital of Kunming Medical University (Yunnan Tumor Hospital), Kunming, China
| | - Guoping Wu
- China National Environmental Monitoring Center, Beijing, China
| | - Fusheng Wei
- China National Environmental Monitoring Center, Beijing, China
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Amy R. Sapkota
- Maryland Institute for Applied Environmental Health, University of Maryland, School of Public Health, College Park, Maryland
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
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102
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Wu Z, Gatesoupe FJ, Zhang Q, Wang X, Feng Y, Wang S, Feng D, Li A. High-throughput sequencing reveals the gut and lung prokaryotic community profiles of the Chinese giant salamander (Andrias davidianus). Mol Biol Rep 2019; 46:5143-5154. [PMID: 31364018 DOI: 10.1007/s11033-019-04972-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/05/2019] [Indexed: 12/27/2022]
Abstract
Increasing attention has been attracted to host microbiota, due to their vital impact on host health. Little is known about the microbiota of the Chinese giant salamander (Andrias davidianus), in spite of the high economic and scientific value of this endangered species. This study was designed to characterise and compare the gut and lung prokaryotic communities of the Chinese giant salamander by high-throughput sequencing. Our study showed that the giant salamander had a lung prokaryotic community that clustered separately from its intestinal microbiota. Statistical analysis (LEfSe) revealed that the bacterial populations were dominated by Geobacter, Sulfurimonas, and Dechloromonas from Proteobacteria phylum, and Corynebacterium from Actinobacteria phylum in the lung, while Parabacteroides, Bacteroides, and PW3 from Bacteroidetes phylum, and Oscillospira from Firmicutes phylum were predominant in the intestine. A particularly innovative finding was the fairly high abundance of Archaea, especially methanogenic Euryarchaeota. The gut dominant Archaea were Methanocorpusculum and Thermoplasmata vadinCA11, while Methanosaeta and Methanoculleus were the main Archaea in the lung. PICRUSt analysis revealed differentiated functional profiles between the intestinal miacrobiota and the lung microbiota. Specially, some microbial metabolic functions were significantly more active in the intestinal microbiota, while the functional genes involved in infectious diseases were much richer in the lung microbiota. This study characterized the prokaryotic microbial community profiles in the gut and lung of the Chinese giant salamander, providing foundational support for future study seeking to understand microbiota of the giant salamander and the role of its microbiota on infectious diseases.
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Affiliation(s)
- Zhenbing Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - François-Joël Gatesoupe
- INRA, Nutrition Metabolism and Aquaculture, Center de Bretagne, Ifremer, 29280, Plouzané, France
| | - Qianqian Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,Freshwater Aquaculture Collaborative Innovation Centre of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiehao Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yuqing Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuyi Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dongyue Feng
- National Fisheries Technical Extension Center, Ministry of Agriculture, Beijing, 100125, China.
| | - Aihua Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. .,Freshwater Aquaculture Collaborative Innovation Centre of Hubei Province, Huazhong Agricultural University, Wuhan, 430070, China.
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103
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Human Lung Microbiome on the Way to Cancer. J Immunol Res 2019; 2019:1394191. [PMID: 31485458 PMCID: PMC6710786 DOI: 10.1155/2019/1394191] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/21/2019] [Accepted: 06/17/2019] [Indexed: 12/13/2022] Open
Abstract
Recent research on cancer-associated microbial communities led to the accumulation of data on the interplay between bacteria, immune and tumor cells, the pathways of bacterial induction of carcinogenesis, and its meaningfulness for medicine. Microbial communities that have any kind of impact on tumor progression and microorganisms associated with tumors have been defined as oncobiome. Over the last decades, a number of studies were dedicated to Helicobacter pylori and its role in the progression of stomach tumors, so this correlation can be regarded as proven. Involvement of bacteria in the induction of lung cancer has been largely ignored for a long time, though some correlations between this type of cancer and lung microbiome were established. Despite the fact that in the present the microbial impact on lung cancer progression has many confirmations, the underlying mechanisms are poorly understood. Microorganisms can contribute to tumor initiation and progression through production of bacteriotoxins and other proinflammatory factors. The purpose of this review is to organize the available data on lung cancer microbiome and its role in malignant tumor progression.
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104
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Selective pressures during chronic infection drive microbial competition and cooperation. NPJ Biofilms Microbiomes 2019; 5:16. [PMID: 31263568 PMCID: PMC6555799 DOI: 10.1038/s41522-019-0089-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/15/2019] [Indexed: 12/14/2022] Open
Abstract
Chronic infections often contain complex mixtures of pathogenic and commensal microorganisms ranging from aerobic and anaerobic bacteria to fungi and viruses. The microbial communities present in infected tissues are not passively co-existing but rather actively interacting with each other via a spectrum of competitive and/or cooperative mechanisms. Competition versus cooperation in these microbial interactions can be driven by both the composition of the microbial community as well as the presence of host defense strategies. These interactions are typically mediated via the production of secreted molecules. In this review, we will explore the possibility that microorganisms competing for nutrients at the host–pathogen interface can evolve seemingly cooperative mechanisms by controlling the production of subsets of secreted virulence factors. We will also address interspecies versus intraspecies utilization of community resources and discuss the impact that this phenomenon might have on co-evolution at the host–pathogen interface.
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105
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Kim HJ, Jo A, Jeon YJ, An S, Lee KM, Yoon SS, Choi JY. Nasal commensal Staphylococcus epidermidis enhances interferon-λ-dependent immunity against influenza virus. MICROBIOME 2019; 7:80. [PMID: 31146794 PMCID: PMC6542144 DOI: 10.1186/s40168-019-0691-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 05/08/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Staphylococcus epidermidis is one of the most abundant colonizers of healthy human mucosa including that in the respiratory tract. As the respiratory microbiome has been linked to host immune responses, this study sought to determine the role of nasal mucosa-associated S. epidermidis in innate immune responses against the influenza A virus (IAV). S. epidermidis strains were isolated from nasal mucus samples of healthy individuals. The effects of these mucosa-derived commensal strains on interferon (IFN)-dependent innate immunity and IAV infection dynamics were tested in vitro using normal human nasal epithelial (NHNE) cells and human turbinate mucosa. The effects of S. epidermidis on antiviral immunity were also tested in vivo using an acute IAV infection mouse model. RESULTS Exposure of NHNE cells to nasal mucosa-derived S. epidermidis increased IFN-λ mRNA and secreted protein levels in the absence of viral stimulation. In the context of IAV infection, NHNE exposure to S. epidermidis prevented an increase in the viral burden, as revealed by IAV PA mRNA abundance, IAV nucleoprotein levels, and viral titers. S. epidermidis also enhanced transcription of IFN-stimulated genes independently of Toll-like receptor 2 and further induced IFN-λ production in IAV-infected cells by promoting phosphorylation of interferon regulatory factor 7. In a murine infection model, S. epidermidis prevented the spread of IAV to the lungs by stimulating IFN-λ innate immunity and suppressing IAV replication in the nasal mucosa. CONCLUSION The human nasal commensal S. epidermidis mediates front-line antiviral protection against IAV infection through modulation of IFN-λ-dependent innate immune mechanisms in the nasal mucosa, thereby demonstrating the role of host-bacterial commensalism in shaping human antiviral responses.
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Affiliation(s)
- Hyun Jik Kim
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Seoul National University Hospital, Seoul, Republic of Korea
| | - Ara Jo
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yung Jin Jeon
- Department of Otorhinolaryngology, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Sujin An
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kang-Mu Lee
- Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Sciences, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Sang Sun Yoon
- Department of Microbiology and Immunology, Brain Korea 21 PLUS Project for Medical Sciences, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Jae Young Choi
- Department of Otorhinolaryngology, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
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106
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Sangiovanni M, Granata I, Thind AS, Guarracino MR. From trash to treasure: detecting unexpected contamination in unmapped NGS data. BMC Bioinformatics 2019; 20:168. [PMID: 30999839 PMCID: PMC6472186 DOI: 10.1186/s12859-019-2684-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background Next Generation Sequencing (NGS) experiments produce millions of short sequences that, mapped to a reference genome, provide biological insights at genomic, transcriptomic and epigenomic level. Typically the amount of reads that correctly maps to the reference genome ranges between 70% and 90%, leaving in some cases a consistent fraction of unmapped sequences. This ’misalignment’ can be ascribed to low quality bases or sequence differences between the sample reads and the reference genome. Investigating the source of the unmapped reads is definitely important to better assess the quality of the whole experiment and to check for possible downstream or upstream ’contamination’ from exogenous nucleic acids. Results Here we propose DecontaMiner, a tool to unravel the presence of contaminating sequences among the unmapped reads. It uses a subtraction approach to identify bacteria, fungi and viruses genome contamination. DecontaMiner generates several output files to track all the processed reads, and to provide a complete report of their characteristics. The good quality matches on microorganism genomes are counted and compared among samples. DecontaMiner builds an offline HTML page containing summary statistics and plots. The latter are obtained using the state-of-the-art D3 javascript libraries. DecontaMiner has been mainly used to detect contamination in human RNA-Seq data. The software is freely available at http://www-labgtp.na.icar.cnr.it/decontaminer. Conclusions DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further investigation and experimental validation. The novelty of DecontaMiner is mainly represented by its easy integration with the standard procedures of NGS data analysis, while providing a complete, reliable, and automatic pipeline. Electronic supplementary material The online version of this article (10.1186/s12859-019-2684-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mara Sangiovanni
- Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, 80121, Italy
| | - Ilaria Granata
- High Performance Computing and Networking Institute, National Research Council of Italy, Via P. Castellino, 111, Napoli, 80131, Italy.
| | - Amarinder Singh Thind
- High Performance Computing and Networking Institute, National Research Council of Italy, Via P. Castellino, 111, Napoli, 80131, Italy
| | - Mario Rosario Guarracino
- High Performance Computing and Networking Institute, National Research Council of Italy, Via P. Castellino, 111, Napoli, 80131, Italy
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107
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Wang K, Huang Y, Zhang Z, Liao J, Ding Y, Fang X, Liu L, Luo J, Kong J. A Preliminary Study of Microbiota Diversity in Saliva and Bronchoalveolar Lavage Fluid from Patients with Primary Bronchogenic Carcinoma. Med Sci Monit 2019; 25:2819-2834. [PMID: 30994108 PMCID: PMC6482867 DOI: 10.12659/msm.915332] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background The present study aimed to evaluate the difference in microbiota diversity in the oral cavity and fluid bronchoalveolar lavage (BALF) of patients with lung cancer. Material/Methods Buccal (saliva) and lower respiratory tract BALF samples were collected from 51 patients with primary bronchogenic carcinoma and 15 healthy controls, and bacterial genomic DNA was extracted. High-throughput 16S rDNA amplicon sequencing was performed, and microbial diversity, composition, and functions of microbiota were analyzed by bioinformatics methods. Results Patients with lung cancer have lower microbial diversity than healthy controls in both saliva and BALF samples. Significant segregation was observed between the different pathological types of lung cancer groups and the control group regardless of the sampling site. Treponema and Filifactor were identified as potential bacterial biomarkers in BALF samples, while Filifactor was ideal to distinguish healthy controls from lung cancer patients. Moreover, the predictive variation analysis of the KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathway showed that the metabolic differences in microbiota varied by sampling site. Conclusions Lung cancer patients carry a different and less diverse microorganism community than healthy controls. Certain bacterial taxa might be associated with lung cancer, but the exact species depends on the sampling site and the pathological type. This study provides basic data on the microbiota diversity in BALF and saliva samples from lung cancer patients. Further investigation with a larger sample size should help validate the enriched species in different pathological types of lung cancers.
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Affiliation(s)
- Ke Wang
- Pulmonary and Critical Care Medicine Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Yufen Huang
- BGI Genomics, BGI-Shenzhen University, Shenzhen, Guangdong, China (mainland)
| | - Zhenqiang Zhang
- Pulmonary and Critical Care Medicine Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Jinling Liao
- Pulmonary and Critical Care Medicine Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Yudi Ding
- Pulmonary and Critical Care Medicine Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Xiaodong Fang
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China (mainland)
| | - Lihua Liu
- Pulmonary and Critical Care Medicine Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Jing Luo
- Pulmonary and Critical Care Medicine Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
| | - Jinliang Kong
- Pulmonary and Critical Care Medicine Ward, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland)
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108
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Cross talk between neutrophils and the microbiota. Blood 2019; 133:2168-2177. [PMID: 30898860 DOI: 10.1182/blood-2018-11-844555] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 12/24/2018] [Indexed: 12/18/2022] Open
Abstract
The microbiota has emerged as an important regulator of the host immunity by the induction, functional modulation, or suppression of local and systemic immune responses. In return, the host immune system restricts translocation and fine tunes the composition and distribution of the microbiota to maintain a beneficial symbiosis. This paradigm applies to neutrophils, a critical component of the innate immunity, allowing their production and function to be influenced by microbial components and metabolites derived from the microbiota, and engaging them in the process of microbiota containment and regulation. The cross talk between neutrophils and the microbiota adjusts the magnitude of neutrophil-mediated inflammation on challenge while preventing neutrophil responses against commensals under steady state. Here, we review the major molecular and cellular mediators of the interactions between neutrophils and the microbiota and discuss their interplay and contribution in chronic inflammatory diseases and cancer.
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109
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Huang T, Zhang M, Tong X, Chen J, Yan G, Fang S, Guo Y, Yang B, Xiao S, Chen C, Huang L, Ai H. Microbial communities in swine lungs and their association with lung lesions. Microb Biotechnol 2019; 12:289-304. [PMID: 30556308 PMCID: PMC6389860 DOI: 10.1111/1751-7915.13353] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 12/26/2022] Open
Abstract
Under natural farming, environmental pathogenic microorganisms may invade and affect swine lungs, further resulting in lung lesions. However, few studies on swine lung microbiota and their potential relationship with lung lesions were reported. Here, we sampled 20 pigs from a hybrid herd raised under natural conditions; we recorded a lung-lesion phenotype and investigated lung microbial communities by sequencing the V3-V4 region of 16S rRNA gene for each individual. We found reduced microbial diversity but more biomass in the severe-lesion lungs. Methylotenera, Prevotella, Sphingobium and Lactobacillus were the prominent bacteria in the healthy lungs, while Mycoplasma, Ureaplasma, Sphingobium, Haemophilus and Phyllobacterium were the most abundant microbes in the severe-lesion lungs. Notably, we identified 64 lung-lesion-associated OTUs, of which two classified to Mycoplasma were positively associated with lung lesions and 62 showed negative association including thirteen classified to Prevotella and six to Ruminococcus. Cross-validation analysis showed that lung microbiota explained 23.7% phenotypic variance of lung lesions, suggesting that lung microbiota had large effects on promoting lung healthy. Furthermore, 22 KEGG pathways correlated with lung lesions were predicted. Altogether, our findings improve the knowledge about swine lung microbial communities and give insights into the relationship between lung microbiota and lung lesions.
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Affiliation(s)
- Tao Huang
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Mingpeng Zhang
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Xinkai Tong
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Jiaqi Chen
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Guorong Yan
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Shaoming Fang
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Yuanmei Guo
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Bin Yang
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Shijun Xiao
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Congying Chen
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Lusheng Huang
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
| | - Huashui Ai
- State Key Laboratory for Swine Genetic Improvement and Production TechnologyJiangxi Agricultural UniversityNanchang330045China
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Limoli DH, Hoffman LR. Help, hinder, hide and harm: what can we learn from the interactions between Pseudomonas aeruginosa and Staphylococcus aureus during respiratory infections? Thorax 2019; 74:684-692. [PMID: 30777898 PMCID: PMC6585302 DOI: 10.1136/thoraxjnl-2018-212616] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/10/2019] [Accepted: 01/14/2019] [Indexed: 12/15/2022]
Abstract
Recent studies of human respiratory secretions using culture-independent techniques have found a surprisingly diverse array of microbes. Interactions among these community members can profoundly impact microbial survival, persistence and antibiotic susceptibility and, consequently, disease progression. Studies of polymicrobial interactions in the human microbiota have shown that the taxonomic and structural compositions, and resulting behaviours, of microbial communities differ substantially from those of the individual constituent species and in ways of clinical importance. These studies primarily involved oral and gastrointestinal microbiomes. While the field of polymicrobial respiratory disease is relatively young, early findings suggest that respiratory tract microbiota members also compete and cooperate in ways that may influence disease outcomes. Ongoing efforts therefore focus on how these findings can inform more 'enlightened', rational approaches to combat respiratory infections. Among the most common respiratory diseases involving polymicrobial infections are cystic fibrosis (CF), non-CF bronchiectasis, COPD and ventilator-associated pneumonia. While respiratory microbiota can be diverse, two of the most common and best-studied members are Staphylococcus aureus and Pseudomonas aeruginosa, which exhibit a range of competitive and cooperative interactions. Here, we review the state of research on pulmonary coinfection with these pathogens, including their prevalence, combined and independent associations with patient outcomes, and mechanisms of those interactions that could influence lung health. Because P. aeruginosa-S. aureus coinfection is common and well studied in CF, this disease serves as the paradigm for our discussions on these two organisms and inform our recommendations for future studies of polymicrobial interactions in pulmonary disease.
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Affiliation(s)
- Dominique Hope Limoli
- Microbiology and Immunology, University of Iowa Roy J and Lucille A Carver College of Medicine, Iowa City, Iowa, USA
| | - Lucas R Hoffman
- Departments of Pediatrics and Microbiology, University of Washington, Seattle, Washington, USA
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111
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Finamore P, Scarlata S, Incalzi RA. Breath analysis in respiratory diseases: state-of-the-art and future perspectives. Expert Rev Mol Diagn 2018; 19:47-61. [PMID: 30575423 DOI: 10.1080/14737159.2019.1559052] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION The vast majority of respiratory diseases are associated with the production of volatile organic compounds (VOCs), the analysis of which might improve our knowledge about these disorders and their clinical management. The aim of this narrative review is to provide a comprehensive summary of current evidence supporting the application of breath analysis in the field of respiratory diseases, as well as suggesting potential applications available in the near future. Areas covered: A computerized literature search was performed to identify relevant articles reporting original data on the clinical use of breath analysis in respiratory diseases. Papers focusing on diseases other than respiratory, technical issues of VOC sampling and analysis, in vitro experiments or exogenous compounds were excluded. Expert commentary: Currently available evidence on the application of breath analysis in respiratory diseases is encouraging; however, it is mostly based on single-center studies without external validation. The standardization of the technique, together with multicenter clinical trials with external validation, will ensure it is ready for clinical use. Current and new applications in respiratory diseases may represent a major breakthrough in the field, so much so as to deserve further efforts in outlining the most effective way to apply VOC analysis for clinical purposes.
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Affiliation(s)
| | - Simone Scarlata
- a Unit of Geriatrics , Campus Bio-Medico University, Rome, Italy
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112
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Yatera K, Noguchi S, Mukae H. The microbiome in the lower respiratory tract. Respir Investig 2018; 56:432-439. [PMID: 30392534 DOI: 10.1016/j.resinv.2018.08.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 12/31/2022]
Abstract
With the advent of new technologies evaluating the microbiome in the sample such as next-generation sequencer (NGS), current increase of an interest in understanding of the lung microbiome and its roles in lung diseases are marked. Gathering the data of bacterial flora in the lung and their changes during disease courses is unraveling the pathogenesis and the mechanism of disease progression particularly in patients with bronchial asthma, chronic obstructive pulmonary disease and infectious lung diseases. To clarify the relationship between the lung microbiome and pulmonary diseases, new information may help us to create new treatment and prevention strategies of some pulmonary diseases by controlling the lung microbiome. Using bacterial 16S ribosomal RNA gene sequence, NGS can rapidly estimate large amount of bacterial sequences in the phylum and genus levels, and some of them in species levels in a very short period of time. In addition to new information of the microbiome using NGS in the respiratory tract, other techniques using basically Sanger method in combination with the clone library construction can also be useful to identify pathogenic bacterial species with their ratio in the respiratory samples such as bacterial pneumonia, lung abscess and nontuberculous mycobacteriosis. These modalities to identify and semi-quantify bacterial burden in the respiratory tract have revealed new bacterial information in each infectious lung disease. This review describes current understanding of the lung microbiome in several representative lung diseases.
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Affiliation(s)
- Kazuhiro Yatera
- Department of Respiratory Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishiku, Kitakyushu City, Fukuoka, 807-8555, Japan.
| | - Shingo Noguchi
- Department of Respiratory Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishiku, Kitakyushu City, Fukuoka, 807-8555, Japan.
| | - Hiroshi Mukae
- Department of Respiratory Medicine, Unit of Translational Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki City, Nagasaki, Japan.
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113
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Liu Y, O’Brien JL, Ajami NJ, Scheurer ME, Amirian ES, Armstrong G, Tsavachidis S, Thrift AP, Jiao L, Wong MC, Smith DP, Spitz MR, Bondy ML, Petrosino JF, Kheradmand F. Lung tissue microbial profile in lung cancer is distinct from emphysema. Am J Cancer Res 2018; 8:1775-1787. [PMID: 30323970 PMCID: PMC6176189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 02/11/2018] [Indexed: 06/08/2023] Open
Abstract
OBJECTIVES The composition and structure of site-specific microbiota have been investigated as potential biomarkers for a variety of chronic inflammatory diseases and cancers. While many studies have focused on the changes in the airway microbiota using respiratory specimens from patients with various respiratory diseases, more research is needed to explore the microbial profiles within the distal lung parenchyma in smokers with lung cancer and/or emphysema. MATERIALS AND METHODS To describe and contrast lung tissue-associated microbial signatures in smokers with lung cancer and/or emphysema, we employed culture-independent pyrosequencing of 16S rRNA gene hypervariable V4 region and compositional analysis in non-malignant lung tissue samples obtained from 40 heavy smokers, including 10 emphysema-only, 11 lung cancer-only, and 19 with both lung cancer and emphysema. RESULTS AND CONCLUSION The emphysema-only group presented a lower bacterial community evenness defined by a significantly lower Shannon diversity index compared to the lung cancer patients with or without emphysema (P = 0.006). Furthermore, community compositions of lung cancer patients with or without emphysema were characterized by a significantly lower abundance of Proteobacteria (primary the genera Acinetobacter and Acidovorax) and higher prevalence of Firmicutes (Streptococcus) and Bacteroidetes (Prevotella), compared to emphysema-only patients. In conclusion, the lung microbial composition and communities structures of smokers with lung cancer are distinct from the emphysema-only patients. Although preliminary, our findings suggest that lung microbiome changes could be a biomarker of lung cancer that could eventually be used to help screening for the disease.
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Affiliation(s)
- Yanhong Liu
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of MedicineHouston, TX 77030, USA
- Department of Medicine, Baylor College of MedicineHouston, TX 77030, USA
| | - Jacqueline L O’Brien
- Department of Molecular Virology and Microbiology, Baylor College of MedicineHouston, TX 77030, USA
- The Alkek Center for Metagenomics and Microbiome Research, Baylor College of MedicineHouston, TX 77030, USA
| | - Nadim J Ajami
- Department of Molecular Virology and Microbiology, Baylor College of MedicineHouston, TX 77030, USA
- The Alkek Center for Metagenomics and Microbiome Research, Baylor College of MedicineHouston, TX 77030, USA
| | - Michael E Scheurer
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of MedicineHouston, TX 77030, USA
- Department of Pediatrics, Baylor College of MedicineHouston, TX 77030, USA
| | - E Susan Amirian
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of MedicineHouston, TX 77030, USA
| | - Georgina Armstrong
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of MedicineHouston, TX 77030, USA
| | - Spiridon Tsavachidis
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of MedicineHouston, TX 77030, USA
| | - Aaron P Thrift
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of MedicineHouston, TX 77030, USA
- Department of Medicine, Baylor College of MedicineHouston, TX 77030, USA
| | - Li Jiao
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of MedicineHouston, TX 77030, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Baylor College of MedicineHouston, TX 77030, USA
| | - Matthew C Wong
- Department of Molecular Virology and Microbiology, Baylor College of MedicineHouston, TX 77030, USA
- The Alkek Center for Metagenomics and Microbiome Research, Baylor College of MedicineHouston, TX 77030, USA
| | - Daniel P Smith
- Department of Molecular Virology and Microbiology, Baylor College of MedicineHouston, TX 77030, USA
- The Alkek Center for Metagenomics and Microbiome Research, Baylor College of MedicineHouston, TX 77030, USA
| | - Margaret R Spitz
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of MedicineHouston, TX 77030, USA
- Department of Medicine, Baylor College of MedicineHouston, TX 77030, USA
| | - Melissa L Bondy
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of MedicineHouston, TX 77030, USA
- Department of Medicine, Baylor College of MedicineHouston, TX 77030, USA
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of MedicineHouston, TX 77030, USA
- The Alkek Center for Metagenomics and Microbiome Research, Baylor College of MedicineHouston, TX 77030, USA
| | - Farrah Kheradmand
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of MedicineHouston, TX 77030, USA
- Department of Medicine, Baylor College of MedicineHouston, TX 77030, USA
- Michael E. DeBakey Veterans Affairs Medical Center, Baylor College of MedicineHouston, TX 77030, USA
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114
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Hasan S, Sebo P, Osicka R. A guide to polarized airway epithelial models for studies of host-pathogen interactions. FEBS J 2018; 285:4343-4358. [PMID: 29896776 DOI: 10.1111/febs.14582] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/21/2018] [Accepted: 06/11/2018] [Indexed: 11/28/2022]
Abstract
Mammalian lungs are organs exhibiting the cellular and spatial complexity required for gas exchange to support life. The respiratory epithelium internally lining the airways is susceptible to infections due to constant exposure to inhaled microbes. Biomedical research into respiratory bacterial infections in humans has been mostly carried out using small mammalian animal models or two-dimensional, submerged cultures of undifferentiated epithelial cells. These experimental model systems have considerable limitations due to host specificity of bacterial pathogens and lack of cellular and morphological complexity. This review describes the in vitro differentiated and polarized airway epithelial cells of human origin that are used as a model to study respiratory bacterial infections. Overall, these models recapitulate key aspects of the complexity observed in vivo and can help in elucidating the molecular details of disease processes observed during respiratory bacterial infections.
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Affiliation(s)
- Shakir Hasan
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
| | - Peter Sebo
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
| | - Radim Osicka
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic
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115
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Reece E, Doyle S, Greally P, Renwick J, McClean S. Aspergillus fumigatus Inhibits Pseudomonas aeruginosa in Co-culture: Implications of a Mutually Antagonistic Relationship on Virulence and Inflammation in the CF Airway. Front Microbiol 2018; 9:1205. [PMID: 29922270 PMCID: PMC5996130 DOI: 10.3389/fmicb.2018.01205] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/17/2018] [Indexed: 11/26/2022] Open
Abstract
Many cystic fibrosis (CF) airway infections are considered to be polymicrobial and microbe–microbe interactions may play an important role in disease pathology. Pseudomonas aeruginosa and Aspergillus fumigatus are the most prevalent bacterial and fungal pathogens isolated from the CF airway, respectively. We have previously shown that patients co-colonized with these pathogens had comparable outcomes to those chronically colonized with P. aeruginosa. Our objective was to examine the interactions between A. fumigatus and P. aeruginosa, specifically the effects of co-colonization on biofilm formation, virulence and host pro-inflammatory responses. Our findings suggest that co-infections of A. fumigatus and P. aeruginosa in the Galleria mellonella acute infection model showed that pre-exposure of larvae to sub-lethal inocula of A. fumigatus increased the mortality caused by subsequent P. aeruginosa infection. Co-infection of human bronchial epithelial cells (CFBE41o-) with both pathogens did not enhance IL-6 and IL-8 production beyond the levels observed following single infections. In addition, both pathogens stimulated cytokine secretion via the same two mitogen-activated protein kinases (MAPKs) signaling pathways, ERK and p38. Mixed species biofilms showed overall reduced biofilm development with crystal violet staining. Quantification by species-specific qPCR revealed that both pathogens had mutually antagonistic effects on each other. A. fumigatus supernatants showed strong anti-Pseudomonal activity and gliotoxin was the main active agent. Gliotoxin resulted in varying levels of anti-biofilm activity toward other bacteria commonly found in the CF airways. Gliotoxin produced by A. fumigatus colonizing the CF airways may have a significant impact on the CF airway microbiome composition with potential clinical implications.
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Affiliation(s)
- Emma Reece
- Department of Clinical Microbiology, Trinity College Dublin - Trinity Centre for Health Science, Tallaght Hospital, Dublin, Ireland
| | - Sean Doyle
- Department of Biology, Maynooth University, Maynooth, Ireland
| | - Peter Greally
- Department of Respiratory Medicine, The National Children's Hospital, Tallaght Hospital, Dublin, Ireland
| | - Julie Renwick
- Department of Clinical Microbiology, Trinity College Dublin - Trinity Centre for Health Science, Tallaght Hospital, Dublin, Ireland
| | - Siobhán McClean
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
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116
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Lu D, Yao X, Abulimiti A, Cai L, Zhou L, Hong J, Li N. Profiling of lung microbiota in the patients with obstructive sleep apnea. Medicine (Baltimore) 2018; 97:e11175. [PMID: 29952967 PMCID: PMC6039595 DOI: 10.1097/md.0000000000011175] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Lung microbiota may affect innate immunity and treatment consequence in the obstructive sleep apnea (OSA) patients. Bronchoalveolar lavage fluid (BALF) was obtained from 11 OSA patients and 8 patients with other lung diseases as control, and used for lung microbiota profiling by PCR amplification and sequencing of the microbial samples. It was demonstrated that phyla of Firmicutes, Fusobacteria, and Bacteriodetes were relatively abundant in the lung microbiota. Alpha-diversity comparison between OSA and control group revealed that Proteobacteria and Fusobacteria were significantly higher in OSA patients (0.3863 ± 0.0631 and 0.0682 ± 0.0159, respectively) than that in control group (0.119 ± 0.074 and 0.0006 ± 0.0187, respectively, P < .05 for both phyla). In contrast, Firmicutes was significantly less in OSA patients (0.1371 ± 0.0394) compared with that in the control group (0.384 ± 0.046, P < .05). Comparison within a group (ß-diversity) indicated that the top 5 phyla in the OSA lung were Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Acidobacteria, while the top 5 phyla in the control group were Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Acidobacteria. These findings indicated that lung microbiota in OSA is distinct from that of non-OSA patients. Manipulation of the microbiota may be an alternative strategy to augment airway immunity and to reduce susceptibility to airway infection.
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Affiliation(s)
- Dongmei Lu
- The Center of Hypertension of the People's Hospital of Xinjiang Uygur Autonomous Region, The Center of Diagnosis, Treatment and Research of Hypertension in Xinjiang
- Pulmonary and Critical Care Medicine Department, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Xiaoguang Yao
- The Center of Hypertension of the People's Hospital of Xinjiang Uygur Autonomous Region, The Center of Diagnosis, Treatment and Research of Hypertension in Xinjiang
| | - Ayinigeer Abulimiti
- The Center of Hypertension of the People's Hospital of Xinjiang Uygur Autonomous Region, The Center of Diagnosis, Treatment and Research of Hypertension in Xinjiang
| | - Li Cai
- The Center of Hypertension of the People's Hospital of Xinjiang Uygur Autonomous Region, The Center of Diagnosis, Treatment and Research of Hypertension in Xinjiang
| | - Ling Zhou
- The Center of Hypertension of the People's Hospital of Xinjiang Uygur Autonomous Region, The Center of Diagnosis, Treatment and Research of Hypertension in Xinjiang
| | - Jing Hong
- The Center of Hypertension of the People's Hospital of Xinjiang Uygur Autonomous Region, The Center of Diagnosis, Treatment and Research of Hypertension in Xinjiang
| | - Nanfang Li
- The Center of Hypertension of the People's Hospital of Xinjiang Uygur Autonomous Region, The Center of Diagnosis, Treatment and Research of Hypertension in Xinjiang
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117
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Kim KH, Kabir E, Jahan SA. Airborne bioaerosols and their impact on human health. J Environ Sci (China) 2018; 67:23-35. [PMID: 29778157 PMCID: PMC7128579 DOI: 10.1016/j.jes.2017.08.027] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 08/24/2017] [Accepted: 08/30/2017] [Indexed: 05/19/2023]
Abstract
Bioaerosols consist of aerosols originated biologically such as metabolites, toxins, or fragments of microorganisms that are present ubiquitously in the environment. International interests in bioaerosols have increased rapidly to broaden the pool of knowledge on their identification, quantification, distribution, and health impacts (e.g., infectious and respiratory diseases, allergies, and cancer). However, risk assessment of bioaerosols based on conventional culture methods has been hampered further by several factors such as: (1) the complexity of microorganisms or derivatives to be investigated; (2) the purpose, techniques, and locations of sampling; and (3) the lack of valid quantitative criteria (e.g., exposure standards and dose/effect relationships). Although exposure to some microbes is considered to be beneficial for health, more research is needed to properly assess their potential health hazards including inter-individual susceptibility, interactions with non-biological agents, and many proven/unproven health effects (e.g., atopy and atopic diseases).
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Affiliation(s)
- Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seoul 04763, Republic of Korea.
| | - Ehsanul Kabir
- Department of Farm, Power & Machinery, Bangladesh Agricultural University, Mymensingh, Bangladesh
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118
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Gupta N, Kumar R, Agrawal B. New Players in Immunity to Tuberculosis: The Host Microbiome, Lung Epithelium, and Innate Immune Cells. Front Immunol 2018; 9:709. [PMID: 29692778 PMCID: PMC5902499 DOI: 10.3389/fimmu.2018.00709] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/22/2018] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis (TB) is a highly contagious infection and devastating chronic disease, causing 10.4 million new infections and 1.8 million deaths every year globally. Efforts to control and eradicate TB are hampered by the rapid emergence of drug resistance and limited efficacy of the only available vaccine, BCG. Immunological events in the airways and lungs are of major importance in determining whether exposure to Mycobacterium tuberculosis (Mtb) results in successful infection or protective immunity. Several studies have demonstrated that the host microbiota is in constant contact with the immune system, and thus continually directs the nature of immune responses occurring during new infections. However, little is known about its role in the eventual outcome of the mycobacterial infection. In this review, we highlight the changes in microbial composition in the respiratory tract and gut that have been linked to the alteration of immune responses, and to the risk, prevention, and treatment of TB. In addition, we summarize our current understanding of alveolar epithelial cells and the innate immune system, and their interaction with Mtb during early infection. Extensive studies are warranted to fully understand the all-inclusive role of the lung microbiota, its interaction with epithelium and innate immune responses and resulting adaptive immune responses, and in the pathogenesis and/or protection from Mtb infection. Novel interventions aimed at influencing the microbiota, the alveolar immune system and innate immunity will shape future strategies of prevention and treatment for TB.
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Affiliation(s)
- Nancy Gupta
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Rakesh Kumar
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Babita Agrawal
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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119
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Endotracheal Tube Biofilm and its Impact on the Pathogenesis of Ventilator-Associated Pneumonia. ACTA ACUST UNITED AC 2018; 4:50-55. [PMID: 30581995 PMCID: PMC6294989 DOI: 10.2478/jccm-2018-0011] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 04/30/2018] [Indexed: 01/18/2023]
Abstract
Ventilator-associated pneumonia (VAP) is a common and serious nosocomial infection in mechanically ventilated patients and results in high mortality, prolonged intensive care unit- (ICU) and hospital-length of stay and increased costs. In order to reduce its incidence, it is imperative to better understand the involved mechanisms and to identify the source of infection. The role of the endotracheal tube (ET) in VAP pathogenesis became more prominent over the last decades, along with extensive research dedicated to medical device-related infections and biofilms. ET biofilm formation is an early and constant process in intubated patients. New data regarding its temporal dynamics, composition, germ identification and consequences enhance knowledge about VAP occurrence, microbiology, treatment response and recurrence. This paper presents a structured analysis of the medical literature to date, in order to outline the role of ET biofilm in VAP pathogenesis and to review recommended methods to identify ET biofilm microorganisms and to prevent or decrease VAP incidence.
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120
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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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121
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Veli M, Ozcan A. Computational Sensing of Staphylococcus aureus on Contact Lenses Using 3D Imaging of Curved Surfaces and Machine Learning. ACS NANO 2018; 12:2554-2559. [PMID: 29522316 PMCID: PMC5871588 DOI: 10.1021/acsnano.7b08375] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We present a cost-effective and portable platform based on contact lenses for noninvasively detecting Staphylococcus aureus, which is part of the human ocular microbiome and resides on the cornea and conjunctiva. Using S. aureus-specific antibodies and a surface chemistry protocol that is compatible with human tears, contact lenses are designed to specifically capture S. aureus. After the bacteria capture on the lens and right before its imaging, the captured bacteria are tagged with surface-functionalized polystyrene microparticles. These microbeads provide sufficient signal-to-noise ratio for the quantification of the captured bacteria on the contact lens, without any fluorescent labels, by 3D imaging of the curved surface of each lens using only one hologram taken with a lens-free on-chip microscope. After the 3D surface of the contact lens is computationally reconstructed using rotational field transformations and holographic digital focusing, a machine learning algorithm is employed to automatically count the number of beads on the lens surface, revealing the count of the captured bacteria. To demonstrate its proof-of-concept, we created a field-portable and cost-effective holographic microscope, which weighs 77 g, controlled by a laptop. Using daily contact lenses that are spiked with bacteria, we demonstrated that this computational sensing platform provides a detection limit of ∼16 bacteria/μL. This contact-lens-based wearable sensor can be broadly applicable to detect various bacteria, viruses, and analytes in tears using a cost-effective and portable computational imager that might be used even at home by consumers.
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Affiliation(s)
- Muhammed Veli
- Department of Electrical and Computer Engineering, University of California Los Angeles (UCLA), California 90095, USA
| | - Aydogan Ozcan
- Department of Electrical and Computer Engineering, University of California Los Angeles (UCLA), California 90095, USA
- Department of Bioengineering, University of California Los Angeles (UCLA), California 90095, USA
- California NanoSystems Institute (CNSI), University of California Los Angeles (UCLA), California 90095, USA
- Department of Surgery, David Geffen School of Medicine, University of California Los Angeles (UCLA), California 90095, USA
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122
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Goodman B, Gardner H. The microbiome and cancer. J Pathol 2018; 244:667-676. [PMID: 29377130 DOI: 10.1002/path.5047] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/11/2018] [Accepted: 01/17/2018] [Indexed: 12/12/2022]
Abstract
Humans coexist with a vast bacterial, fungal and viral microbiome with which we have coevolved for millions of years. Several long recognized epidemiological associations between particular bacteria and cancer are now understood at the molecular level. At the same time, the arrival of next-generation sequencing technology has permitted a thorough exploration of microbiomes such as that of the human gut, enabling observation of taxonomic and metabolomic relationships between the microbiome and cancer. These studies have revealed causal mechanisms for both microbes within tumours and microbes in other host niches separated from tumours, mediated through direct and immunological mechanisms. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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123
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Pimponi D, Chinappi M, Gualtieri P. Flagellated microswimmers: Hydrodynamics in thin liquid films. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:28. [PMID: 29488023 DOI: 10.1140/epje/i2018-11635-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 02/09/2018] [Indexed: 06/08/2023]
Abstract
The hydrodynamics of a flagellated microswimmer moving in thin films is discussed. The fully resolved hydrodynamics is exploited by solving the Stokes equations for the actual geometry of the swimmer. Two different interfaces are used to confine the swimmer: a bottom solid wall and a top air-liquid interface, as appropriate for a thin film. The swimmer follows curved clockwise trajectories that can converge towards an asymptotically stable circular path or can result in a collision with one of the two interfaces. A bias towards the air-liquid interface emerges. Slight changes in the swimmer geometry and film thickness strongly affect the resulting dynamics suggesting that a very reach phenomenology occurs in the presence of confinement. Under specific conditions, the swimmer follows a "crown-like" path. Implications for the motion of bacteria close to an air bubble moving in a microchannel are discussed.
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Affiliation(s)
- Daniela Pimponi
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, via Eudossiana 18, 00184, Roma, Italy
| | - Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, via del Politecnico 1, 00133, Roma, Italy
| | - Paolo Gualtieri
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, via Eudossiana 18, 00184, Roma, Italy.
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124
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Kamariza M, Shieh P, Ealand CS, Peters JS, Chu B, Rodriguez-Rivera FP, Babu Sait MR, Treuren WV, Martinson N, Kalscheuer R, Kana BD, Bertozzi CR. Rapid detection of Mycobacterium tuberculosis in sputum with a solvatochromic trehalose probe. Sci Transl Med 2018; 10:eaam6310. [PMID: 29491187 PMCID: PMC5985656 DOI: 10.1126/scitranslmed.aam6310] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/06/2018] [Indexed: 01/05/2023]
Abstract
Tuberculosis (TB) is the leading cause of death from an infectious bacterial disease. Poor diagnostic tools to detect active disease plague TB control programs and affect patient care. Accurate detection of live Mycobacterium tuberculosis (Mtb), the causative agent of TB, could improve TB diagnosis and patient treatment. We report that mycobacteria and other corynebacteria can be specifically detected with a fluorogenic trehalose analog. We designed a 4-N,N-dimethylamino-1,8-naphthalimide-conjugated trehalose (DMN-Tre) probe that undergoes >700-fold increase in fluorescence intensity when transitioned from aqueous to hydrophobic environments. This enhancement occurs upon metabolic conversion of DMN-Tre to trehalose monomycolate and incorporation into the mycomembrane of Actinobacteria. DMN-Tre labeling enabled the rapid, no-wash visualization of mycobacterial and corynebacterial species without nonspecific labeling of Gram-positive or Gram-negative bacteria. DMN-Tre labeling was detected within minutes and was inhibited by heat killing of mycobacteria. Furthermore, DMN-Tre labeling was reduced by treatment with TB drugs, unlike the clinically used auramine stain. Lastly, DMN-Tre labeled Mtb in TB-positive human sputum samples comparably to auramine staining, suggesting that this operationally simple method may be deployable for TB diagnosis.
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Affiliation(s)
| | - Peyton Shieh
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Christopher S Ealand
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Health Sciences, University of Witwatersrand, National Health Laboratory Service, Johannesburg, South Africa
| | - Julian S Peters
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Health Sciences, University of Witwatersrand, National Health Laboratory Service, Johannesburg, South Africa
| | - Brian Chu
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Mohammed R Babu Sait
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Duesseldorf, Universitätsstrasse 1, 40225 Duesseldorf, Germany
| | - William V Treuren
- Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Neil Martinson
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Health Sciences, University of Witwatersrand, National Health Laboratory Service, Johannesburg, South Africa
- Perinatal HIV Research Unit (PHRU), SA MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa
| | - Rainer Kalscheuer
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University Duesseldorf, Universitätsstrasse 1, 40225 Duesseldorf, Germany
| | - Bavesh D Kana
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Health Sciences, University of Witwatersrand, National Health Laboratory Service, Johannesburg, South Africa
- Medical Research Council-Centre for the AIDS Programme of Research in South Africa (CAPRISA) HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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125
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Mangul S, Yang HT, Strauli N, Gruhl F, Porath HT, Hsieh K, Chen L, Daley T, Christenson S, Wesolowska-Andersen A, Spreafico R, Rios C, Eng C, Smith AD, Hernandez RD, Ophoff RA, Santana JR, Levanon EY, Woodruff PG, Burchard E, Seibold MA, Shifman S, Eskin E, Zaitlen N. ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues. Genome Biol 2018; 19:36. [PMID: 29548336 PMCID: PMC5857127 DOI: 10.1186/s13059-018-1403-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 02/02/2018] [Indexed: 11/22/2022] Open
Abstract
High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin Protocol (ROP), a tool for discovering the source of all reads originating from complex RNA molecules. We apply ROP to samples across 2630 individuals from 54 diverse human tissues. Our approach can account for 99.9% of 1 trillion reads of various read length. Additionally, we use ROP to investigate the functional mechanisms underlying connections between the immune system, microbiome, and disease. ROP is freely available at https://github.com/smangul1/rop/wiki.
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Affiliation(s)
- Serghei Mangul
- Department of Computer Science, University of California, Los Angeles, CA, USA. .,Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA.
| | - Harry Taegyun Yang
- Department of Computer Science, University of California, Los Angeles, CA, USA
| | - Nicolas Strauli
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - Franziska Gruhl
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hagit T Porath
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Kevin Hsieh
- Department of Computer Science, University of California, Los Angeles, CA, USA
| | - Linus Chen
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Timothy Daley
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanie Christenson
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | | | - Roberto Spreafico
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA
| | - Cydney Rios
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Andrew D Smith
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.,Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Roel A Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California, Los Angeles, CA, USA.,Department of Human Genetics, University of California, Los Angeles, CA, USA.,Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Prescott G Woodruff
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Esteban Burchard
- Schools of Pharmacy and Medicine, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Max A Seibold
- Department of Pediatrics, National Jewish Health, Denver, CO, USA.,University of Colorado School of Medicine, Denver, CO, USA
| | - Sagiv Shifman
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, CA, USA.,Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Noah Zaitlen
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Cardiovascular Research Institute, University of California, San Francisco, CA, USA.
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126
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Yildiz S, Mazel-Sanchez B, Kandasamy M, Manicassamy B, Schmolke M. Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis. MICROBIOME 2018; 6:9. [PMID: 29321057 PMCID: PMC5763955 DOI: 10.1186/s40168-017-0386-z] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/14/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Microbiota integrity is essential for a growing number of physiological processes. Consequently, disruption of microbiota homeostasis correlates with a variety of pathological states. Importantly, commensal microbiota provide a shield against invading bacterial pathogens, probably by direct competition. The impact of viral infections on host microbiota composition and dynamics is poorly understood. Influenza A viruses (IAV) are common respiratory pathogens causing acute infections. Here, we show dynamic changes in respiratory and intestinal microbiota over the course of a sublethal IAV infection in a mouse model. RESULTS Using a combination of 16S rRNA gene-specific next generation sequencing and qPCR as well as culturing of bacterial organ content, we found body site-specific and transient microbiota responses. In the lower respiratory tract, we observed only minor qualitative changes in microbiota composition. No quantitative impact on bacterial colonization after IAV infection was detectable, despite a robust antimicrobial host response and increased sensitivity to bacterial super infection. In contrast, in the intestine, IAV induced robust depletion of bacterial content, disruption of mucus layer integrity, and higher levels of antimicrobial peptides in Paneth cells. As a functional consequence of IAV-mediated microbiota depletion, we demonstrated that the small intestine is rendered more susceptible to bacterial pathogen invasion, in a Salmonella typhimurium super infection model. CONCLUSION We show for the first time the consequences of IAV infection for lower respiratory tract and intestinal microbiobiota in a qualitative and quantitative fashion. The discrepancy of relative 16S rRNA gene next-generation sequencing (NGS) and normalized 16S rRNA gene-specific qPCR stresses the importance of combining qualitative and quantitative approaches to correctly analyze composition of organ associated microbial communities. The transiently induced dysbiosis underlines the overall stability of microbial communities to effects of acute infection. However, during a short-time window, specific ecological niches might lose their microbiota shield and remain vulnerable to bacterial invasion.
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Affiliation(s)
- Soner Yildiz
- Department of Microbiology and Molecular Medicine, University Medical Center (CMU), University of Geneva, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
| | - Béryl Mazel-Sanchez
- Department of Microbiology and Molecular Medicine, University Medical Center (CMU), University of Geneva, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
| | | | - Balaji Manicassamy
- Department of Microbiology, University of Chicago, Chicago, IL 60637 USA
| | - Mirco Schmolke
- Department of Microbiology and Molecular Medicine, University Medical Center (CMU), University of Geneva, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
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127
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Abstract
Over the last decade, biologists have come to appreciate that the human body is inhabited by thousands of bacterial species in diverse communities unique to each body site. Moreover, due to high-throughput sequencing methods for microbial characterization in a culture-independent manner, it is becoming evident that the microbiome plays an important role in human health and disease. This chapter focuses on the most common form of bacterial microbiome profiling, targeted amplicon sequencing of the 16S ribosomal RNA (rRNA) subunit encoded by 16S rDNA. We discuss important features for designing and performing microbiome experiments on human specimens, including experimental design, sample collection, DNA preparation, and selection of the 16S rDNA sequencing target. We also provide details for designing fusion primers required for targeted amplicon sequencing and selecting the most appropriate high-throughput sequencing platform. We conclude with a review of the fundamental concepts of data analysis and interpretation for these kinds of experiments. Our goal is to provide the reader with the essential knowledge needed to undertake microbiome experiments for application to human disease research questions.
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Affiliation(s)
- Rebecca M Davidson
- Department of Biomedical Research, Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA.
| | - L Elaine Epperson
- Department of Biomedical Research, Center for Genes, Environment and Health, National Jewish Health, 1400 Jackson Street, Denver, CO, 80206, USA
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128
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Samuelson DR, Burnham EL, Maffei VJ, Vandivier RW, Blanchard EE, Shellito JE, Luo M, Taylor CM, Welsh DA. The respiratory tract microbial biogeography in alcohol use disorder. Am J Physiol Lung Cell Mol Physiol 2018; 314:L107-L117. [PMID: 28860145 PMCID: PMC5866426 DOI: 10.1152/ajplung.00277.2017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/24/2017] [Accepted: 08/24/2017] [Indexed: 11/22/2022] Open
Abstract
Individuals with alcohol use disorders (AUDs) are at an increased risk of pneumonia and acute respiratory distress syndrome. Data of the lung microbiome in the setting of AUDs are lacking. The objective of this study was to determine the microbial biogeography of the upper and lower respiratory tract in individuals with AUDs compared with non-AUD subjects. Gargle, protected bronchial brush, and bronchoalveolar lavage specimens were collected during research bronchoscopies. Bacterial 16S gene sequencing and phylogenetic analysis was performed, and the alterations to the respiratory tract microbiota and changes in microbial biogeography were determined. The microbial structure of the upper and lower respiratory tract was significantly altered in subjects with AUDs compared with controls. Subjects with AUD have greater microbial diversity [ P < 0.0001, effect size = 16 ± 1.7 observed taxa] and changes in microbial species relative abundances. Furthermore, microbial communities in the upper and lower respiratory tract displayed greater similarity in subjects with AUDs. Alcohol use is associated with an altered composition of the respiratory tract microbiota. Subjects with AUDs demonstrate convergence of the microbial phylogeny and taxonomic communities between distinct biogeographical sites within the respiratory tract. These results support a mechanistic pathway potentially explaining the increased incidence of pneumonia and lung diseases in patients with AUDs.
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Affiliation(s)
- Derrick R. Samuelson
- Department of Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Ellen L. Burnham
- Department of Medicine, Division of Pulmonary Sciences & Critical Care, University of Colorado-Anschutz Medical Campus, Aurora, Colorado
| | - Vincent J. Maffei
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - R. William Vandivier
- Department of Medicine, Division of Pulmonary Sciences & Critical Care, University of Colorado-Anschutz Medical Campus, Aurora, Colorado
| | - Eugene E. Blanchard
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Judd E. Shellito
- Department of Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Sciences Center, New Orleans, Louisiana
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Meng Luo
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Christopher M. Taylor
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - David A. Welsh
- Department of Medicine, Section of Pulmonary/Critical Care & Allergy/Immunology, Louisiana State University Health Sciences Center, New Orleans, Louisiana
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana
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129
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Lu J, Xiong L, Zhang X, Liu Z, Wang S, Zhang C, Zheng J, Wang G, Zheng R, Simpson JL, Wang F. The Role of Lower Airway Dysbiosis in Asthma: Dysbiosis and Asthma. Mediators Inflamm 2017; 2017:3890601. [PMID: 29386750 PMCID: PMC5745728 DOI: 10.1155/2017/3890601] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/13/2017] [Accepted: 10/04/2017] [Indexed: 12/12/2022] Open
Abstract
With the development of culture-independent techniques, numerous studies have demonstrated that the lower airway is not sterile in health and harbors diverse microbial communities. Furthermore, new evidence suggests that there is a distinct lower airway microbiome in those with chronic respiratory disease. To understand the role of lower airway dysbiosis in the pathogenesis of asthma, in this article, we review the published reports about the lung microbiome of healthy controls, provide an outlook on the contribution of lower airway dysbiosis to asthma, especially steroid-resistant asthma, and discuss the potential therapies targeted for lower airway dysbiosis.
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Affiliation(s)
- Junying Lu
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
- Department of Intensive Care Unit, First Hospital of Jilin University, Changchun 130021, China
| | - Lingxin Xiong
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Xiaohao Zhang
- Department of Cardiology, Second Hospital of Jilin University, Changchun 130041, China
| | - Zhongmin Liu
- Department of Intensive Care Unit, First Hospital of Jilin University, Changchun 130021, China
| | - Shiji Wang
- Department of Intensive Care Unit, First Hospital of Jilin University, Changchun 130021, China
| | - Chao Zhang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Jingtong Zheng
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Guoqiang Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
| | - Ruipeng Zheng
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
- Department of Interventional Therapy, First Hospital of Jilin University, Changchun 130021, China
| | - Jodie L. Simpson
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
- Department of Respiratory and Sleep Medicine, University of Newcastle, New Lambton, NSW, Australia
| | - Fang Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China
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130
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Upregulation of bacterial-specific Th1 and Th17 responses that are enriched in CXCR5 + CD4 + T cells in non-small cell lung cancer. Int Immunopharmacol 2017; 52:305-309. [DOI: 10.1016/j.intimp.2017.09.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/24/2017] [Accepted: 09/26/2017] [Indexed: 12/12/2022]
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131
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Sinibaldi G, Iebba V, Chinappi M. Swimming and rafting of E.coli microcolonies at air-liquid interfaces. Microbiologyopen 2017; 7. [PMID: 29057610 PMCID: PMC5822344 DOI: 10.1002/mbo3.532] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/22/2017] [Accepted: 07/27/2017] [Indexed: 02/05/2023] Open
Abstract
The dynamics of swimming microorganisms is strongly affected by solid‐liquid and air‐liquid interfaces. In this paper, we characterize the motion of both single bacteria and microcolonies at an air‐liquid interface. Both of them follow circular trajectories. Single bacteria preferentially show a counter‐clockwise motion, in agreement with previous experimental and theoretical findings. Instead, no preferential rotation direction is observed for microcolonies suggesting that their motion is due to a different physical mechanism. We propose a simple mechanical model where the microcolonies move like rafts constrained to the air‐liquid interface. Finally, we observed that the microcolony growth is due to the aggregation of colliding single‐swimmers, suggesting that the microcolony formation resembles a condensation process where the first nucleus originates by the collision between two single‐swimmers. Implications of microcolony splitting and aggregation on biofilm growth and dispersion at air‐liquid interface are discussed.
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Affiliation(s)
- Giorgia Sinibaldi
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, Rome, Italy
| | - Valerio Iebba
- Public Health and Infectious Diseases Dept, Istituto Pasteur Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Mauro Chinappi
- Center for Life Nano Science, Istituto Italiano di Tecnologia, Rome, Italy.,Department of Industrial Engineering, University of Rome Tor Vergata, Rome, Italy
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132
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Extensive Core Microbiome in Drone-Captured Whale Blow Supports a Framework for Health Monitoring. mSystems 2017; 2:mSystems00119-17. [PMID: 29034331 PMCID: PMC5634792 DOI: 10.1128/msystems.00119-17] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 09/13/2017] [Indexed: 01/21/2023] Open
Abstract
The pulmonary system is a common site for bacterial infections in cetaceans, but very little is known about their respiratory microbiome. We used a small, unmanned hexacopter to collect exhaled breath condensate (blow) from two geographically distinct populations of apparently healthy humpback whales (Megaptera novaeangliae), sampled in the Massachusetts coastal waters off Cape Cod (n = 17) and coastal waters around Vancouver Island (n = 9). Bacterial and archaeal small-subunit rRNA genes were amplified and sequenced from blow samples, including many of sparse volume, as well as seawater and other controls, to characterize the associated microbial community. The blow microbiomes were distinct from the seawater microbiomes and included 25 phylogenetically diverse bacteria common to all sampled whales. This core assemblage comprised on average 36% of the microbiome, making it one of the more consistent animal microbiomes studied to date. The closest phylogenetic relatives of 20 of these core microbes were previously detected in marine mammals, suggesting that this core microbiome assemblage is specialized for marine mammals and may indicate a healthy, noninfected pulmonary system. Pathogen screening was conducted on the microbiomes at the genus level, which showed that all blow and few seawater microbiomes contained relatives of bacterial pathogens; no known cetacean respiratory pathogens were detected in the blow. Overall, the discovery of a shared large core microbiome in humpback whales is an important advancement for health and disease monitoring of this species and of other large whales. IMPORTANCE The conservation and management of large whales rely in part upon health monitoring of individuals and populations, and methods generally necessitate invasive sampling. Here, we used a small, unmanned hexacopter drone to noninvasively fly above humpback whales from two populations, capture their exhaled breath (blow), and examine the associated microbiome. In the first extensive examination of the large-whale blow microbiome, we present surprising results about the discovery of a large core microbiome that was shared across individual whales from geographically separated populations in two ocean basins. We suggest that this core microbiome, in addition to other microbiome characteristics, could be a useful feature for health monitoring of large whales worldwide.
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133
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Wang J, Li F, Tian Z. Role of microbiota on lung homeostasis and diseases. SCIENCE CHINA-LIFE SCIENCES 2017; 60:1407-1415. [PMID: 29019144 PMCID: PMC7089139 DOI: 10.1007/s11427-017-9151-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/12/2017] [Indexed: 12/13/2022]
Abstract
The lungs, as a place of gas exchange, are continuously exposed to environmental stimuli, such as allergens, microbes, and pollutants. The development of the culture-independent technique for microbiological analysis, such as 16S rRNA sequencing, has uncovered that the lungs are not sterile and, in fact, colonized by diverse communities of microbiota. The function of intestinal microbiota in modulating mucosal homeostasis and defense has been widely studied; however, the potential function of lung microbiota in regulating immunity and homeostasis has just begun. Increasing evidence indicates the relevance of microbiota to lung homeostasis and disease. In this review, we describe the distribution and composition of microbiota in the respiratory system and discuss the potential function of lung microbiota in both health and acute/chronic lung disease. In addition, we also discuss the recent understanding of the gut-lung axis, because several studies have revealed that the immunological interaction among the gut, the lung, and the microbiota was involved in this issue.
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Affiliation(s)
- Jian Wang
- Institute of Immunology and the Key Laboratory of Innate Immunity and Chronic Disease (Chinese Academy of Sciences), School of Life Science and Medical Center, University of Science and Technology of China, Hefei, 230027, China. .,Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University Zurich, Zurich, 8091, Switzerland.
| | - Fengqi Li
- Institute of Immunology and the Key Laboratory of Innate Immunity and Chronic Disease (Chinese Academy of Sciences), School of Life Science and Medical Center, University of Science and Technology of China, Hefei, 230027, China
| | - Zhigang Tian
- Institute of Immunology and the Key Laboratory of Innate Immunity and Chronic Disease (Chinese Academy of Sciences), School of Life Science and Medical Center, University of Science and Technology of China, Hefei, 230027, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China.
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134
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Abstract
INTRODUCTION The respiratory tract is constantly exposed to various environmental and endogenous microbes; however, unlike other similar mucosal surfaces, there has been limited investigation of the microbiome of the respiratory tract. AREAS COVERED In this review, we summarize the current state of knowledge of the bacterial, fungal, and viral respiratory microbiomes during HIV infection and how the microbiome might relate to HIV-associated lung disease. Expert commentary: HIV infection is associated with alterations in the respiratory microbiome. The clinical implications of lung microbial dysbiosis are however currently unknown. Mechanistic studies are needed to establish causality between shifts in the respiratory microbiome and pulmonary complications in HIV-infected individuals.
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Affiliation(s)
- M B Lawani
- a University of Pittsburgh , School of Medicine, Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine , Pittsburgh , PA , USA
| | - A Morris
- a University of Pittsburgh , School of Medicine, Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine , Pittsburgh , PA , USA
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135
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Kugadas A, Wright Q, Geddes-McAlister J, Gadjeva M. Role of Microbiota in Strengthening Ocular Mucosal Barrier Function Through Secretory IgA. Invest Ophthalmol Vis Sci 2017; 58:4593-4600. [PMID: 28892827 PMCID: PMC5595225 DOI: 10.1167/iovs.17-22119] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Purpose The purpose of this study was to evaluate mechanisms controlling secretory IgA (SIgA) production, thereby ensuring maintenance of ocular surface health. Methods To determine whether the presence of specific gut commensal species regulates SIgA levels and IgA transcripts in the eye-associated lymphoid tissues (EALT), specific-pathogen-free (SPF) Swiss Webster (SW) mice were treated with antibiotic cocktails, germ-free (GF) SW mice were reconstituted with diverse commensal gut microbiota, or monocolonized with gut-specific commensals. Proteomic profiling and quantitative real-time polymerase chain reaction (qRT-PCR) were used to quantify SIgA and IgA levels. 16S rDNA sequencing was carried out to characterize commensal microbiota. Results Commensal presence regulated ocular surface SIgA levels and mRNA IgA transcripts in EALT. Oral antibiotic cocktail intake significantly reduced gut commensal presence, while maintaining ocular surface commensal levels reduced SIgA and IgA transcripts in EALT. Analysis of gut microbial communities revealed that SPF SW mice carried abundant Bacteroides organisms when compared to SPF C57BL6/N mice, with B. acidifaciens being the most prominent species in SPF SW mice. Monocolonization of GF SW mice with B. acidifaciens, a strict gut anaerobe, resulted in significant increase of IgA transcripts in the EALT, implying generation of B-cell memory. Conclusions These data illustrated a “gut-eye” axis of immune regulation. Exposure of the host to gut commensal species may serve as a priming signal to generate B-cell repertoires at sites different from the gut, such as EALT, thereby ensuring broad protection.
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Affiliation(s)
- Abirami Kugadas
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States
| | - Quentin Wright
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States
| | - Jennifer Geddes-McAlister
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Mihaela Gadjeva
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States
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136
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Wirsdörfer F, Jendrossek V. Modeling DNA damage-induced pneumopathy in mice: insight from danger signaling cascades. Radiat Oncol 2017; 12:142. [PMID: 28836991 PMCID: PMC5571607 DOI: 10.1186/s13014-017-0865-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/07/2017] [Indexed: 02/08/2023] Open
Abstract
Radiation-induced pneumonitis and fibrosis represent severe and dose-limiting side effects in the radiotherapy of thorax-associated neoplasms leading to decreased quality of life or - as a consequence of treatment with suboptimal radiation doses - to fatal outcomes by local recurrence or metastatic disease. It is assumed that the initial radiation-induced damage to the resident cells triggers a multifaceted damage-signalling cascade in irradiated normal tissues including a multifactorial secretory program. The resulting pro-inflammatory and pro-angiogenic microenvironment triggers a cascade of events that can lead within weeks to a pronounced lung inflammation (pneumonitis) or after months to excessive deposition of extracellular matrix molecules and tissue scarring (pulmonary fibrosis).The use of preclinical in vivo models of DNA damage-induced pneumopathy in genetically modified mice has helped to substantially advance our understanding of molecular mechanisms and signalling molecules that participate in the pathogenesis of radiation-induced adverse late effects in the lung. Herein, murine models of whole thorax irradiation or hemithorax irradiation nicely reproduce the pathogenesis of the human disease with respect to the time course and the clinical symptoms. Alternatively, treatment with the radiomimetic DNA damaging chemotherapeutic drug Bleomycin (BLM) has frequently been used as a surrogate model of radiation-induced lung disease. The advantage of the BLM model is that the symptoms of pneumonitis and fibrosis develop within 1 month.Here we summarize and discuss published data about the role of danger signalling in the response of the lung tissue to DNA damage and its cross-talk with the innate and adaptive immune systems obtained in preclinical studies using immune-deficient inbred mouse strains and genetically modified mice. Interestingly we observed differences in the role of molecules involved in damage sensing (TOLL-like receptors), damage signalling (MyD88) and immune regulation (cytokines, CD73, lymphocytes) for the pathogenesis and progression of DNA damage-induced pneumopathy between the models of pneumopathy induced by whole thorax irradiation or treatment with the radiomimetic drug BLM. These findings underline the importance to pursue studies in the radiation model(s) if we are to unravel the mechanisms driving radiation-induced adverse late effects.A better understanding of the cross-talk of danger perception and signalling with immune activation and repair mechanisms may allow a modulation of these processes to prevent or treat radiation-induced adverse effects. Vice-versa an improved knowledge of the normal tissue response to injury is also particularly important in view of the increasing interest in combining radiotherapy with immune checkpoint blockade or immunotherapies to avoid exacerbation of radiation-induced normal tissue toxicity.
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Affiliation(s)
- Florian Wirsdörfer
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Virchowstrasse 173, Essen, Germany
| | - Verena Jendrossek
- Institute of Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Virchowstrasse 173, Essen, Germany.
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137
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Neudecker V, Yuan X, Bowser JL, Eltzschig HK. MicroRNAs in mucosal inflammation. J Mol Med (Berl) 2017; 95:935-949. [PMID: 28726085 DOI: 10.1007/s00109-017-1568-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/28/2017] [Accepted: 07/04/2017] [Indexed: 12/12/2022]
Abstract
Of the total human body's surface, the majority is internal surface, belonging to the lungs (100 m2) and intestinal tract (400 m2). In comparison, the external surface area, belonging to the skin, comprises less than 1% (2 m2). Continuous exposure of the mucosal surface to external factors (e.g., pathogens, food particles) requires tight regulation to maintain homeostasis. MicroRNAs (miRNAs) have gained noticeable attention as playing important roles in maintaining the steady-state of tissues by modulating immune functions and inflammatory responses. Accordingly, associations have been found between miRNA expression levels and human health conditions and diseases. These findings have important implications in inflammatory diseases involving pulmonary and intestinal mucosa, such as acute lung injury or inflammatory bowel disease. In this review, we highlight the known biology of miRNAs and discuss the role of miRNAs in modulating mucosal defense and homeostasis. Additionally, we discuss miRNAs serving as potential therapeutic targets to treat immunological conditions, particularly mucosal inflammation.
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Affiliation(s)
- Viola Neudecker
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany.
| | - Xiaoyi Yuan
- Department of Anesthesiology, the University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Jessica L Bowser
- Department of Anesthesiology, the University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Holger K Eltzschig
- Department of Anesthesiology, the University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
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Zeineldin MM, Lowe JF, Grimmer ED, de Godoy MRC, Ghanem MM, Abd El-Raof YM, Aldridge BM. Relationship between nasopharyngeal and bronchoalveolar microbial communities in clinically healthy feedlot cattle. BMC Microbiol 2017; 17:138. [PMID: 28645257 PMCID: PMC5481913 DOI: 10.1186/s12866-017-1042-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/02/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The importance of upper airway structure in the susceptibility of the lower respiratory tract to colonization with potential pathogens is well established. With the advent of rapid, high throughput, next generation sequencing, there is a growing appreciation of the importance of commensal microbial populations in maintaining mucosal health, and a realization that bacteria colonize anatomical locations that were previously considered to be sterile. While upper respiratory tract microbial populations have been described, there are currently no published studies describing the normal microbial populations of the bovine lower respiratory tract. Consequently, we have little understanding of the relationship between upper and lower respiratory tract microbiota in healthy cattle. The primary objective of our study was to characterize the composition, structure and relationship of the lower and upper respiratory microbial communities in clinically healthy feedlot cattle. Nasopharyngeal swabs (NPS), and bronchoalveolar lavage (BAL) fluid, were collected from clinically healthy feedlot calves (n = 8). Genomic DNA from each sample was extracted, and the V3-V4 hypervariable region of the bacterial 16S rRNA gene was amplified and sequenced using Illumina Miseq platform. RESULTS Across all samples, the most predominant phyla were Proteobacteria, Actinobacteria and Firmicutes. The most common genera were Rathayibacter, Mycoplasma, Bibersteinia and Corynebacterium. The microbial community structure was distinct between these two biogeographical sites. Most of the bacterial genera identified in the BAL samples were also present in the NPS, but biogeographical-specific genera were enriched in both the NPS (Rathayibacter) and BAL (Bibersteinia) samples. There were strong associations between the presence of certain taxa at each specific location, and strong correlations between the presence of specific taxa in both the NPS and BAL samples. CONCLUSIONS The correlation between the presence of specific taxa in both the NPS and BAL samples, supports the notion of a mutualistic interrelationship between these microbial communities. Future studies, in large cohorts of animals, are needed to determine the role and clinical importance of the relationships of respiratory tract microbial communities with health, productivity, and susceptibility to the development of respiratory disease, in growing cattle.
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Affiliation(s)
- Mohamed M Zeineldin
- Integrated Food Animal Management Systems, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, 241 LAC, 1008 W Hazelwood Dr, Urbana, IL, 61802, USA
| | - James F Lowe
- Integrated Food Animal Management Systems, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, 241 LAC, 1008 W Hazelwood Dr, Urbana, IL, 61802, USA
| | - Elsbeth D Grimmer
- Integrated Food Animal Management Systems, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, 241 LAC, 1008 W Hazelwood Dr, Urbana, IL, 61802, USA
| | - Maria R C de Godoy
- Department of Animal Sciences and Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Mohamed M Ghanem
- Department of Animal Medicine, College of Veterinary Medicine, Benha University, Benha, Egypt
| | - Yassein M Abd El-Raof
- Department of Animal Medicine, College of Veterinary Medicine, Benha University, Benha, Egypt
| | - Brian M Aldridge
- Integrated Food Animal Management Systems, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, 241 LAC, 1008 W Hazelwood Dr, Urbana, IL, 61802, USA.
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Singh N, Vats A, Sharma A, Arora A, Kumar A. The development of lower respiratory tract microbiome in mice. MICROBIOME 2017; 5:61. [PMID: 28637485 PMCID: PMC5479047 DOI: 10.1186/s40168-017-0277-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 05/17/2017] [Indexed: 05/22/2023]
Abstract
BACKGROUND Although culture-independent methods have paved the way for characterization of the lung microbiome, the dynamic changes in the lung microbiome from neonatal stage to adult age have not been investigated. RESULTS In this study, we tracked changes in composition and diversity of the lung microbiome in C57BL/6N mice, starting from 1-week-old neonates to 8-week-old mice. Towards this, the lungs were sterilely excised from mice of different ages from 1 to 8 weeks. High-throughput DNA sequencing of the 16S rRNA gene followed by composition and diversity analysis was utilized to decipher the microbiome in these samples. Microbiome analysis suggests that the changes in the lung microbiome correlated with age. The lung microbiome was primarily dominated by phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria in all the stages from week 1 to week 8 after birth. Although Defluvibacter was the predominant genus in 1-week-old neonatal mice, Streptococcus became the dominant genus at the age of 2 weeks. Lactobacillus, Defluvibacter, Streptococcus, and Achromobacter were the dominant genera in 3-week-old mice, while Lactobacillus and Achromobacter were the most abundant genera in 4-week-old mice. Interestingly, relatively greater diversity (at the genus level) during the age of 5 to 6 weeks was observed as compared to the earlier weeks. The diversity of the lung microbiome remained stable between 6 and 8 weeks of age. CONCLUSIONS In summary, we have tracked the development of the lung microbiome in mice from an early age of 1 week to adulthood. The lung microbiome is dominated by the phyla Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. However, dynamic changes were observed at the genus level. Relatively higher richness in the microbial diversity was achieved by age of 6 weeks and then maintained at later ages. We believe that this study improves our understanding of the development of the mice lung microbiome and will facilitate further analyses of the role of the lung microbiome in chronic lung diseases.
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Affiliation(s)
- Nisha Singh
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Sector 39 A, Chandigarh, 160036, India
| | - Asheema Vats
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Sector 39 A, Chandigarh, 160036, India
| | - Aditi Sharma
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Sector 39 A, Chandigarh, 160036, India
| | - Amit Arora
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Sector 39 A, Chandigarh, 160036, India.
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Microbial Type Culture Collection and Gene Bank (MTCC), Chandigarh, India.
- Present Address: Department of Medical Microbiology, PGIMER, Sector 12, Chandigarh, 160012, India.
| | - Ashwani Kumar
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Sector 39 A, Chandigarh, 160036, India.
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Wu X, Chen J, Xu M, Zhu D, Wang X, Chen Y, Wu J, Cui C, Zhang W, Yu L. 16S rDNA analysis of periodontal plaque in chronic obstructive pulmonary disease and periodontitis patients. J Oral Microbiol 2017; 9:1324725. [PMID: 28748030 PMCID: PMC5508401 DOI: 10.1080/20002297.2017.1324725] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/24/2017] [Indexed: 12/14/2022] Open
Abstract
This study investigated if chronic obstructive pulmonary disease (COPD) is correlated with periodontitis via periodontal microbiota and if certain bacteria affect periodontitis as well as COPD. Moreover, the study investigated whether suffering from COPD is associated with a decrease in the richness and diversity of periodontal microbiota. Subgingival plaque was obtained from 105 patients. Bacterial DNA was isolated from 55 COPD and 50 non-COPD participants (either with or without periodontitis). 16S rRNA gene metagenomic sequencing was used to characterize the microbiota and to determine taxonomic classification. In the non-periodontitis patients, suffering from COPD resulted in a decrease in bacteria richness and diversity in the periodontal microenvironment. An increase in the genera Dysgonomonas, Desulfobulbus, and Catonella and in four species (Porphyromonas endodontalis, Dysgonomonas wimpennyi, Catonella morbi, and Prevotella intermedia) in both COPD and periodontitis patients suggests that an increase in these periodontitis-associated microbiota may be related to COPD. Three genera (Johnsonella, Campylobacter, and Oribacterium) were associated with COPD but not with periodontitis. The decrease in the genera Arcanobacterium, Oribacterium, and Streptomyces in COPD patients implies that these genera may be health-associated genera, and the decrease in these genera may be related to disease. These data support the hypothesis that COPD is correlated with periodontitis via these significantly changed specific bacteria.
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Affiliation(s)
- Xingwen Wu
- Department of Dentistry, Huashan Hospital, Fudan University, Shanghai, P.R. China.,Department of Dentistry, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Jiazhen Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Meng Xu
- Department of Dentistry, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Danting Zhu
- Department of Dentistry, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Xuyang Wang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Yulin Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Jing Wu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Chenghao Cui
- Department of Dentistry, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, P.R. China
| | - Liying Yu
- Department of Dentistry, Huashan Hospital, Fudan University, Shanghai, P.R. China
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141
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Ames NJ, Ranucci A, Moriyama B, Wallen GR. The Human Microbiome and Understanding the 16S rRNA Gene in Translational Nursing Science. Nurs Res 2017; 66:184-197. [PMID: 28252578 PMCID: PMC5535273 DOI: 10.1097/nnr.0000000000000212] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND As more is understood regarding the human microbiome, it is increasingly important for nurse scientists and healthcare practitioners to analyze these microbial communities and their role in health and disease. 16S rRNA sequencing is a key methodology in identifying these bacterial populations that has recently transitioned from use primarily in research to having increased utility in clinical settings. OBJECTIVES The objectives of this review are to (a) describe 16S rRNA sequencing and its role in answering research questions important to nursing science; (b) provide an overview of the oral, lung, and gut microbiomes and relevant research; and (c) identify future implications for microbiome research and 16S sequencing in translational nursing science. DISCUSSION Sequencing using the 16S rRNA gene has revolutionized research and allowed scientists to easily and reliably characterize complex bacterial communities. This type of research has recently entered the clinical setting, one of the best examples involving the use of 16S sequencing to identify resistant pathogens, thereby improving the accuracy of bacterial identification in infection control. Clinical microbiota research and related requisite methods are of particular relevance to nurse scientists-individuals uniquely positioned to utilize these techniques in future studies in clinical settings.
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Affiliation(s)
- Nancy J Ames
- Nancy J. Ames, RN, PhD, is Clinical Nurse Scientist, Nursing Department, National Institutes of Health Clinical Center, Bethesda, Maryland. Alexandra Ranucci, BS, is MD/MPH Candidate, Tulane University School of Medicine, New Orleans, Louisiana. She was a Post-Baccalaureate Intramural Research Award Recipient, Nursing Department, National Institutes of Health Clinical Center, Bethesda, Maryland, at the time this paper was prepared. Brad Moriyama, PharmD, is Clinical Pharmacist, Pharmacy Department, National Institutes of Health Clinical Center, Bethesda, Maryland. Gwenyth R. Wallen, RN, PhD, is Chief Nurse Officer (Acting), Nursing Department, National Institutes of Health Clinical Center, Bethesda, Maryland
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Johnston D, Earley B, Cormican P, Murray G, Kenny DA, Waters SM, McGee M, Kelly AK, McCabe MS. Illumina MiSeq 16S amplicon sequence analysis of bovine respiratory disease associated bacteria in lung and mediastinal lymph node tissue. BMC Vet Res 2017; 13:118. [PMID: 28464950 PMCID: PMC5414144 DOI: 10.1186/s12917-017-1035-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 04/21/2017] [Indexed: 11/16/2022] Open
Abstract
Background Bovine respiratory disease (BRD) is caused by growth of single or multiple species of pathogenic bacteria in lung tissue following stress and/or viral infection. Next generation sequencing of 16S ribosomal RNA gene PCR amplicons (NGS 16S amplicon analysis) is a powerful culture-independent open reference method that has recently been used to increase understanding of BRD-associated bacteria in the upper respiratory tract of BRD cattle. However, it has not yet been used to examine the microbiome of the bovine lower respiratory tract. The objective of this study was to use NGS 16S amplicon analysis to identify bacteria in post-mortem lung and lymph node tissue samples harvested from fatal BRD cases and clinically healthy animals. Cranial lobe and corresponding mediastinal lymph node post-mortem tissue samples were collected from calves diagnosed as BRD cases by veterinary laboratory pathologists and from clinically healthy calves. NGS 16S amplicon libraries, targeting the V3-V4 region of the bacterial 16S rRNA gene were prepared and sequenced on an Illumina MiSeq. Quantitative insights into microbial ecology (QIIME) was used to determine operational taxonomic units (OTUs) which corresponded to the 16S rRNA gene sequences. Results Leptotrichiaceae, Mycoplasma, Pasteurellaceae, and Fusobacterium were the most abundant OTUs identified in the lungs and lymph nodes of the calves which died from BRD. Leptotrichiaceae, Fusobacterium, Mycoplasma, Trueperella and Bacteroides had greater relative abundances in post-mortem lung samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Leptotrichiaceae, Mycoplasma and Pasteurellaceae showed higher relative abundances in post-mortem lymph node samples collected from fatal cases of BRD in dairy calves, compared with clinically healthy calves without lung lesions. Two Leptotrichiaceae sequence contigs were subsequently assembled from bacterial DNA-enriched shotgun sequences. Conclusions The microbiomes of the cranial lung lobe and mediastinal lymph node from calves which died from BRD and from clinically healthy H-F calves have been characterised. Contigs corresponding to the abundant Leptotrichiaceae OTU were sequenced and found not to be identical to any known bacterial genus. This suggests that we have identified a novel bacterial species associated with BRD. Electronic supplementary material The online version of this article (doi:10.1186/s12917-017-1035-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dayle Johnston
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc Grange, Dunsany, Co. Meath, Ireland.,School of Agriculture Food Science and Veterinary Medicine, University College Dublin, Dublin, Belfield, Dublin 4, Ireland
| | - Bernadette Earley
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc Grange, Dunsany, Co. Meath, Ireland
| | - Paul Cormican
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc Grange, Dunsany, Co. Meath, Ireland
| | - Gerard Murray
- Department of Agriculture, Food and the Marine, Regional Veterinary Laboratory, Sligo, Co. Sligo, Ireland
| | - David Anthony Kenny
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc Grange, Dunsany, Co. Meath, Ireland
| | - Sinead Mary Waters
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc Grange, Dunsany, Co. Meath, Ireland
| | - Mark McGee
- Livestock Systems Research Department, Animal & Grassland Research and Innovation Centre, Teagasc Grange, Dunsany, Co. Meath, Ireland
| | - Alan Kieran Kelly
- School of Agriculture Food Science and Veterinary Medicine, University College Dublin, Dublin, Belfield, Dublin 4, Ireland
| | - Matthew Sean McCabe
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc Grange, Dunsany, Co. Meath, Ireland.
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143
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Baharom F, Rankin G, Blomberg A, Smed-Sörensen A. Human Lung Mononuclear Phagocytes in Health and Disease. Front Immunol 2017; 8:499. [PMID: 28507549 PMCID: PMC5410584 DOI: 10.3389/fimmu.2017.00499] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/11/2017] [Indexed: 12/17/2022] Open
Abstract
The lungs are vulnerable to attack by respiratory insults such as toxins, allergens, and pathogens, given their continuous exposure to the air we breathe. Our immune system has evolved to provide protection against an array of potential threats without causing collateral damage to the lung tissue. In order to swiftly detect invading pathogens, monocytes, macrophages, and dendritic cells (DCs)-together termed mononuclear phagocytes (MNPs)-line the respiratory tract with the key task of surveying the lung microenvironment in order to discriminate between harmless and harmful antigens and initiate immune responses when necessary. Each cell type excels at specific tasks: monocytes produce large amounts of cytokines, macrophages are highly phagocytic, whereas DCs excel at activating naïve T cells. Extensive studies in murine models have established a division of labor between the different populations of MNPs at steady state and during infection or inflammation. However, a translation of important findings in mice is only beginning to be explored in humans, given the challenge of working with rare cells in inaccessible human tissues. Important progress has been made in recent years on the phenotype and function of human lung MNPs. In addition to a substantial population of alveolar macrophages, three subsets of DCs have been identified in the human airways at steady state. More recently, monocyte-derived cells have also been described in healthy human lungs. Depending on the source of samples, such as lung tissue resections or bronchoalveolar lavage, the specific subsets of MNPs recovered may differ. This review provides an update on existing studies investigating human respiratory MNP populations during health and disease. Often, inflammatory MNPs are found to accumulate in the lungs of patients with pulmonary conditions. In respiratory infections or inflammatory diseases, this may contribute to disease severity, but in cancer patients this may improve clinical outcomes. By expanding on this knowledge, specific lung MNPs may be targeted or modulated in order to attain favorable responses that can improve preventive or treatment strategies against respiratory infections, lung cancer, or lung inflammatory diseases.
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Affiliation(s)
- Faezzah Baharom
- Immunology and Allergy Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Gregory Rankin
- Department of Public Health and Clinical Medicine, Division of Medicine, Umeå University, Umeå, Sweden
| | - Anders Blomberg
- Department of Public Health and Clinical Medicine, Division of Medicine, Umeå University, Umeå, Sweden
| | - Anna Smed-Sörensen
- Immunology and Allergy Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
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Respiratory Microbiome of Endangered Southern Resident Killer Whales and Microbiota of Surrounding Sea Surface Microlayer in the Eastern North Pacific. Sci Rep 2017; 7:394. [PMID: 28341851 PMCID: PMC5428453 DOI: 10.1038/s41598-017-00457-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/27/2017] [Indexed: 01/01/2023] Open
Abstract
In the Salish Sea, the endangered Southern Resident Killer Whale (SRKW) is a high trophic indicator of ecosystem health. Three major threats have been identified for this population: reduced prey availability, anthropogenic contaminants, and marine vessel disturbances. These perturbations can culminate in significant morbidity and mortality, usually associated with secondary infections that have a predilection to the respiratory system. To characterize the composition of the respiratory microbiota and identify recognized pathogens of SRKW, exhaled breath samples were collected between 2006–2009 and analyzed for bacteria, fungi and viruses using (1) culture-dependent, targeted PCR-based methodologies and (2) taxonomically broad, non-culture dependent PCR-based methodologies. Results were compared with sea surface microlayer (SML) samples to characterize the respective microbial constituents. An array of bacteria and fungi in breath and SML samples were identified, as well as microorganisms that exhibited resistance to multiple antimicrobial agents. The SML microbes and respiratory microbiota carry a pathogenic risk which we propose as an additional, fourth putative stressor (pathogens), which may adversely impact the endangered SRKW population.
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145
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Garg N, Luzzatto-Knaan T, Melnik AV, Caraballo-Rodríguez AM, Floros DJ, Petras D, Gregor R, Dorrestein PC, Phelan VV. Natural products as mediators of disease. Nat Prod Rep 2017; 34:194-219. [PMID: 27874907 PMCID: PMC5299058 DOI: 10.1039/c6np00063k] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: up to 2016Humans are walking microbial ecosystems, each harboring a complex microbiome with the genetic potential to produce a vast array of natural products. Recent sequencing data suggest that our microbial inhabitants are critical for maintaining overall health. Shifts in microbial communities have been correlated to a number of diseases including infections, inflammation, cancer, and neurological disorders. Some of these clinically and diagnostically relevant phenotypes are a result of the presence of small molecules, yet we know remarkably little about their contributions to the health of individuals. Here, we review microbe-derived natural products as mediators of human disease.
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Affiliation(s)
- Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Alexey V. Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | | | - Dimitrios J. Floros
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Rachel Gregor
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Vanessa V. Phelan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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Ishifuji T, Sando E, Kaneko N, Suzuki M, Kilgore PE, Ariyoshi K, Morimoto K, Hosokawa N, Yaegashi M, Aoshima M. Recurrent pneumonia among Japanese adults: disease burden and risk factors. BMC Pulm Med 2017; 17:12. [PMID: 28077107 PMCID: PMC5225545 DOI: 10.1186/s12890-016-0359-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/23/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND In Japan and other societies with rapidly aging populations, recurrent pneumonia (RP) is a major clinical problem yet only limited information exists regarding the burden of this disease. METHODS A prospective study of adult pneumonia was conducted to investigate the incidence of RP and potential risk factors. From February 1, 2012 to January 31, 2013, patients aged ≥ 15 years who were diagnosed with pneumonia were prospectively enrolled in a representative community hospital located in central Japan. Patients were followed for one-year to evaluate the recurrence of pneumonia and characteristics associated with RP. Cox proportional hazards models were constructed to compute adjusted hazard ratios (aHR) and ascertain risk factors significantly associated with RP. RESULTS In total, 841 patients with a median age of 73 years (range 15-101 years) were enrolled totaling 1,048 person-years of observation with a median follow-up time of 475 days. A total of 137 patients had at least one recurrent episode with an incidence rate of 13.1 per 100 person-years (95% confidence interval: 11.1-15.5). In multivariate analysis, a past history of pneumonia (aHR 1.95, 95% CI: 1.35-2.8), chronic pulmonary disease (aHR 1.86, 1.24-2.78) and inhaled corticosteroid usage (aHR 1.78, 1.12-2.84) and hypnotic/sedative medication usage (aHR 2.06, 1.28-3.31) were identified as independent risk factors for recurrent pneumonia, whereas angiotensin converting enzyme-inhibitors usage was associated with a reduction of the risk of RP (aHR 0.22, 0.05-0.91). The detection of P. aeruginosa was significantly associated with RP even after adjusting for chronic pulmonary diseases (aHR = 2.37). CONCLUSIONS Recurrent pneumonia constitutes a considerable proportion of the pneumonia burden in Japan. A past history of pneumonia, chronic pulmonary disease, inhaled corticosteroid and hypnotic/sedative medication usage and detection of P. aeruginosa were identified as independent risk factors for recurrent pneumonia and special attention regarding the use of medications in this vulnerable population is needed to reduce the impact of this disease in aging populations.
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Affiliation(s)
- Tomoko Ishifuji
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Sakamoto 1-12-4, Nagasaki, 852–8523, Japan
- Department of Clinical Tropical Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Eiichiro Sando
- Department of Clinical Tropical Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
- Department of General Internal Medicine, Kameda Medical Center, Kamogawa, Chiba Japan
| | - Norihiro Kaneko
- Department of Pulmonology, Kameda Medical Center, Kamogawa, Chiba Japan
| | - Motoi Suzuki
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Sakamoto 1-12-4, Nagasaki, 852–8523, Japan
| | - Paul E. Kilgore
- Department of Family Medicine and Public Health Sciences, School of Medicine, Wayne State University, Michigan, USA
| | - Koya Ariyoshi
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Sakamoto 1-12-4, Nagasaki, 852–8523, Japan
- Department of Clinical Tropical Medicine, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Konosuke Morimoto
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Sakamoto 1-12-4, Nagasaki, 852–8523, Japan
| | - Naoto Hosokawa
- Department of Infectious Diseases, Kameda Medical Center, Kamogawa, Japan
| | - Makito Yaegashi
- Department of General Internal Medicine, Kameda Medical Center, Kamogawa, Chiba Japan
| | - Masahiro Aoshima
- Department of Pulmonology, Kameda Medical Center, Kamogawa, Chiba Japan
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147
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Bacteria isolated from lung modulate asthma susceptibility in mice. ISME JOURNAL 2017; 11:1061-1074. [PMID: 28045458 PMCID: PMC5437918 DOI: 10.1038/ismej.2016.181] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 11/03/2016] [Accepted: 11/11/2016] [Indexed: 12/12/2022]
Abstract
Asthma is a chronic, non-curable, multifactorial disease with increasing incidence in industrial countries. This study evaluates the direct contribution of lung microbial components in allergic asthma in mice. Germ-Free and Specific-Pathogen-Free mice display similar susceptibilities to House Dust Mice-induced allergic asthma, indicating that the absence of bacteria confers no protection or increased risk to aeroallergens. In early life, allergic asthma changes the pattern of lung microbiota, and lung bacteria reciprocally modulate aeroallergen responsiveness. Primo-colonizing cultivable strains were screened for their immunoregulatory properties following their isolation from neonatal lungs. Intranasal inoculation of lung bacteria influenced the outcome of allergic asthma development: the strain CNCM I 4970 exacerbated some asthma features whereas the pro-Th1 strain CNCM I 4969 had protective effects. Thus, we confirm that appropriate bacterial lung stimuli during early life are critical for susceptibility to allergic asthma in young adults.
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148
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Ackerman AL, Underhill DM. The mycobiome of the human urinary tract: potential roles for fungi in urology. ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:31. [PMID: 28217696 DOI: 10.21037/atm.2016.12.69] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The mycobiome, defined as the fungal microbiota within a host environment, is an important but understudied component of the human microbial ecosystem. New culture-independent approaches to determine microbial diversity, such as next-generation sequencing methods, have discovered specific, characteristic, commensal fungal populations present in different body sites. These studies have also identified diverse patterns in fungal communities associated with various diseases. While alterations in urinary bacterial communities have been noted in disease states, a comprehensive description of the urinary mycobiome has been lacking. Early evidence suggests the urinary mycobiome is a diverse community with high intraindividual variability. In other disease systems, the mycobiome is thought to interact with other biomes and the host to play a role in organ homeostasis and pathology; further study will be needed to elucidate the role fungi play in bladder health and disease.
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Affiliation(s)
- A Lenore Ackerman
- Division of Urology, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - David M Underhill
- Department of Medicine and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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149
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Lee JT, Frank DN, Ramakrishnan V. Microbiome of the paranasal sinuses: Update and literature review. Am J Rhinol Allergy 2016; 30:3-16. [PMID: 26867525 DOI: 10.2500/ajra.2016.30.4255] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Our understanding of the resident microbiome of the paranasal sinuses has changed considerably in recent years. Once presumed to be sterile, healthy sinus cavities are now known to harbor a diverse assemblage of microorganisms, and, it is hypothesized that alterations in the kinds and quantities of these microbes may play a role in the pathogenesis of chronic rhinosinusitis (CRS). OBJECTIVES To review the current literature regarding the sinus microbiome and collate research findings from relevant studies published to date. METHODS A systematic literature review was performed on all molecular studies that investigated the microbial communities of the paranasal sinuses. Methods of detection, microbiome composition, and comparative profiling between patients with and without CRS were explored. RESULTS A complex consortium of microorganisms has been demonstrated in the sinuses of both patients with and without CRS. However, the latter generally have been characterized by reduced biodiversity compared with controls, with selective enrichment of particular microbes (e.g., Staphylococcus aureus). Such disruptions in the resident microbiome may contribute to disease pathogenesis by enhancing the virulence of potential pathogens and adversely modulating immune responses. CONCLUSION The advent of culture-independent molecular approaches has led to a greater appreciation of the intricate microbial ecology of the paranasal sinuses. Microbiota composition, distribution, and abundance impact mucosal health and influence pathogen growth and function. A deeper understanding of the host-microbiome relationship and its constituents may encourage development of new treatment paradigms for CRS, which target restoration of microbiome homeostasis and cultivation of optimal microbial communities.
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Affiliation(s)
- Jivianne T Lee
- Department of Otolaryngology-Head and Neck Surgery, Orange County Sinus Institute, Southern California Permanente Medical Group, Irvine, California, USA
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Sviriaeva EN, Korneev KV, Drutskaya MS, Kuprash DV. Mechanisms of Changes in Immune Response during Bacterial Coinfections of the Respiratory Tract. BIOCHEMISTRY (MOSCOW) 2016; 81:1340-1349. [PMID: 27914459 DOI: 10.1134/s0006297916110110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Acute diseases of the respiratory tract are often caused by viral pathogens and accompanying secondary bacterial infections. It is known that the development of such bacterial complications is caused mainly by a decreased infiltration with immune system cells and by suppressed inflammation in the lungs. There are significant advances in understanding the mechanisms of secondary infections, although many details remain unclear. This review summarizes current knowledge of the molecular and cellular changes in the host organism that can influence the course of bacterial coinfections in the respiratory tract.
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Affiliation(s)
- E N Sviriaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
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