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lung microbiome

Aran Singanayagam, Andrew I Ritchie, Sebastian L Johnston
PURPOSE OF REVIEW: The emergence of next-generation 16S rRNA sequencing techniques has facilitated a more detailed study of the body's microbiota and led to renewed interest in the association between microbial exposure and asthma inception. In this review, we evaluate the evidence that the respiratory tract and intestinal microbiota contribute to asthma pathogenesis and progression. RECENT FINDINGS: Human studies have revealed associations between the presence of potentially pathogenic bacteria in the respiratory tract in early life and subsequent risk of allergic sensitization and asthma...
October 15, 2016: Current Opinion in Pulmonary Medicine
Xiaozhou Fan, Alexander V Alekseyenko, Jing Wu, Brandilyn A Peters, Eric J Jacobs, Susan M Gapstur, Mark P Purdue, Christian C Abnet, Rachael Stolzenberg-Solomon, George Miller, Jacques Ravel, Richard B Hayes, Jiyoung Ahn
OBJECTIVE: A history of periodontal disease and the presence of circulating antibodies to selected oral pathogens have been associated with increased risk of pancreatic cancer; however, direct relationships of oral microbes with pancreatic cancer have not been evaluated in prospective studies. We examine the relationship of oral microbiota with subsequent risk of pancreatic cancer in a large nested case-control study. DESIGN: We selected 361 incident adenocarcinoma of pancreas and 371 matched controls from two prospective cohort studies, the American Cancer Society Cancer Prevention Study II and the National Cancer Institute Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial...
October 14, 2016: Gut
Tsuyoshi Hamada, NaNa Keum, Reiko Nishihara, Shuji Ogino
Molecular pathological epidemiology (MPE) is an integrative field that utilizes molecular pathology to incorporate interpersonal heterogeneity of a disease process into epidemiology. In each individual, the development and progression of a disease are determined by a unique combination of exogenous and endogenous factors, resulting in different molecular and pathological subtypes of the disease. Based on "the unique disease principle," the primary aim of MPE is to uncover an interactive relationship between a specific environmental exposure and disease subtypes in determining disease incidence and mortality...
October 13, 2016: Journal of Gastroenterology
Patricia Moran Losada, Philippe Chouvarine, Marie Dorda, Silke Hedtfeld, Samira Mielke, Angela Schulz, Lutz Wiehlmann, Burkhard Tümmler
Chronic airway infections determine most morbidity in people with cystic fibrosis (CF). Herein, we present unbiased quantitative data about the frequency and abundance of DNA viruses, archaea, bacteria, moulds and fungi in CF lower airways. Induced sputa were collected on several occasions from children, adolescents and adults with CF. Deep sputum metagenome sequencing identified, on average, approximately 10 DNA viruses or fungi and several hundred bacterial taxa. The metagenome of a CF patient was typically found to be made up of an individual signature of multiple, lowly abundant species superimposed by few disease-associated pathogens, such as Pseudomonas aeruginosa and Staphylococcus aureus, as major components...
April 2016: ERJ Open Research
Laura Tipton, Elodie Ghedin, Alison Morris
The fungi that reside in the human lungs represent an understudied, but medically relevant comm-unity. From the few studies published on the lung mycobiome, we find that there are fungi in both the healthy and diseased respiratory tract, that these fungi vary widely between individuals, and that there is a trend toward lower fungal diversity among individuals with disease. This review discusses the few studies of the lung mycobiome and details the challenges that accompany lung mycobiome studies. These challenges include sample collection and processing, sequence amplification and processing, and a history of multiple names for species...
September 29, 2016: Virulence
Inge Kepert, Juliano Fonseca, Constanze Müller, Katrin Milger, Kerstin Hochwind, Matea Kostric, Maria Fedoseeva, Caspar Ohnmacht, Stefan Dehmel, Petra Nathan, Sabine Bartel, Oliver Eickelberg, Michael Schloter, Anton Hartmann, Philippe Schmitt-Kopplin, Susanne Krauss-Etschmann
BACKGROUND: Chronic immune diseases (CIDs), such as asthma, are highly prevalent. Currently available pharmaceuticals improve symptoms, but cannot cure the disease. This prompted demands for alternatives to pharmaceuticals such as probiotics for prevention of allergic disease. However, clinical trials have given inconsistent results. This is at least partly explained by the highly complex crosstalk among probiotic bacteria, the host´s microbiota, and immune cells. The identification of a bioactive substance from probiotic bacteria could circumvent this difficulty...
September 23, 2016: Journal of Allergy and Clinical Immunology
Robert P Dickson, Benjamin H Singer, Michael W Newstead, Nicole R Falkowski, John R Erb-Downward, Theodore J Standiford, Gary B Huffnagle
Sepsis and the acute respiratory distress syndrome (ARDS) are major causes of mortality without targeted therapies. Although many experimental and clinical observations have implicated gut microbiota in the pathogenesis of these diseases, culture-based studies have failed to demonstrate translocation of bacteria to the lungs in critically ill patients. Here, we report culture-independent evidence that the lung microbiome is enriched with gut bacteria both in a murine model of sepsis and in humans with established ARDS...
2016: Nature Microbiology
N Torow, B J Marsland, M W Hornef, E S Gollwitzer
Although largely deprived from exogenous stimuli in utero, the mucosal barriers of the neonate after birth are bombarded by environmental, nutritional, and microbial exposures. The microbiome is established concurrently with the developing immune system. The nature and timing of discrete interactions between these two factors underpins the long-term immune characteristics of these organs, and can set an individual on a trajectory towards or away from disease. Microbial exposures in the gastrointestinal and respiratory tracts are some of the key determinants of the overall immune tone at these mucosal barriers and represent a leading target for future intervention strategies...
September 21, 2016: Mucosal Immunology
James T Rosenbaum, Mark J Asquith
PURPOSE OF REVIEW: The microbiome is the term that describes the microbial ecosystem that cohabits an organism such as humans. The microbiome has been implicated in a long list of immune-mediated diseases which include rheumatoid arthritis, ankylosing spondylitis, and even gout. The mechanisms to account for this effect are multiple. The clinical implications from observations on the microbiome and disease are broad. RECENT FINDINGS: A growing number of microbiota constituents such as Prevotella copri, Porphyromonas gingivalis, and Collinsella have been correlated or causally related to rheumatic disease...
October 2016: Current Rheumatology Reports
Andrea Hahn, Amit Sanyal, Geovanny F Perez, Anamaris M Colberg-Poley, Joseph Campos, Mary C Rose, Marcos Pérez-Losada
BACKGROUND: Cystic fibrosis (CF) is an autosomal recessive disease characterized by recurrent lung infections. Studies of the lung microbiome have shown an association between decreasing diversity and progressive disease. 454 pyrosequencing has frequently been used to study the lung microbiome in CF, but will no longer be supported. We sought to identify the benefits and drawbacks of using two state-of-the-art next generation sequencing (NGS) platforms, MiSeq and PacBio RSII, to characterize the CF lung microbiome...
November 2016: Journal of Microbiological Methods
Bo-Young Hong, Nancy Paula Maulén, Alexander J Adami, Hector Granados, María Elvira Balcells, Jorge Cervantes
The critical role of commensal microbiota in the human body has been increasingly recognized, and our understanding of its implications in human health and disease has expanded rapidly. The lower respiratory tract contains diverse communities of microbes known as lung microbiota, which are present in healthy individuals and in individuals with respiratory diseases. The dysbiosis of the airway microbiota in pulmonary tuberculosis (TB) may play a role in the pathophysiological processes associated with TB disease...
October 2016: Clinical Microbiology Reviews
Magali Noval Rivas, Timothy R Crother, Moshe Arditi
PURPOSE OF REVIEW: Asthma is a complex and heterogeneous disease with strong genetic and environmental components that manifests within a variety of clinical features and diverse patterns of immune responses. Asthma prevalence has dramatically increased over the last decade in Westernized societies, thereby suggesting a key function of environmental factors in disease promotion and development. RECENT FINDINGS: 'Early-life' microbial exposure and bacterial colonization are crucial for the maturation and the education of the immune system...
September 13, 2016: Current Opinion in Pediatrics
Adam T Hill
Long-term macrolide therapy offers an evidence-based treatment to reduce frequent exacerbations in stable adult patients with bronchiectasis. There is limited evidence that they also attenuate the decline in lung function and improve health-related quality of life. The benefits and risks of long-term macrolides need to be clearly explored for individual patients. Further work is needed to understand the optimal drug, dose and regimen, the mechanisms behind these benefits, appropriate patient selection, sustainability of efficacy, potential long-term risk on the lung microbiome, and their placement with or without inhaled antibiotic treatment...
August 31, 2016: Chest
Lieuwe D Bos, Peter J Sterk, Stephen J Fowler
Exhaled breath contains thousands of volatile organic compounds that reflect the metabolic process occurring in the host both locally in the airways and systemically. They also arise from the environment and airway microbiome. Comprehensive analysis of breath volatile organic compounds (breathomics) provides opportunities for noninvasive biomarker discovery and novel mechanistic insights. Applications in patients with obstructive lung diseases, such as asthma and chronic obstructive pulmonary disease, include not only diagnostics (especially in children and other challenging diagnostic areas) but also identification of clinical treatable traits, such as airway eosinophilia and risk of infection/exacerbation, that are not specific to diagnostic labels...
October 2016: Journal of Allergy and Clinical Immunology
Joachim D Pleil
Exhaled breath has joined blood and urine as a valuable resource for sampling and analyzing biomarkers in human media for assessing exposure, uptake metabolism, and elimination of toxic chemicals. This article focuses current use of exhaled gas, aerosols, and vapor in human breath, the methods for collection, and ultimately the use of the resulting data. Some advantages of breath are the noninvasive and self-administered nature of collection, the essentially inexhaustible supply, and that breath sampling does not produce potentially infectious waste such as needles, wipes, bandages, and glassware...
November 2016: Archives of Toxicology
Emma M de Koff, Karin M de Winter – de Groot, Debby Bogaert
PURPOSE OF REVIEW: Progression of lung disease in cystic fibrosis (CF) is punctuated by Pseudomonas aeruginosa infection and recurrent pulmonary exacerbations, and is the major determinant of a patient's life expectancy. With the advent of novel deep-sequencing techniques, polymicrobial bacterial assemblages rather than single pathogens seem to be responsible for the deterioration of pulmonary function. This review summarizes recent insights into the development of the CF respiratory tract microbiome, with its determinants and its relations to clinical parameters...
November 2016: Current Opinion in Pulmonary Medicine
Leopoldo N Segal, Jose C Clemente, Jun-Chieh J Tsay, Sergei B Koralov, Brian C Keller, Benjamin G Wu, Yonghua Li, Nan Shen, Elodie Ghedin, Alison Morris, Phillip Diaz, Laurence Huang, William R Wikoff, Carles Ubeda, Alejandro Artacho, William N Rom, Daniel H Sterman, Ronald G Collman, Martin J Blaser, Michael D Weiden
Microaspiration is a common phenomenon in healthy subjects, but its frequency is increased in chronic inflammatory airway diseases, and its role in inflammatory and immune phenotypes is unclear. We have previously demonstrated that acellular bronchoalveolar lavage samples from half of the healthy people examined are enriched with oral taxa (here called pneumotypeSPT) and this finding is associated with increased numbers of lymphocytes and neutrophils in bronchoalveolar lavage. Here, we have characterized the inflammatory phenotype using a multi-omic approach...
2016: Nature Microbiology
Sushma K Cribbs, James M Beck
Significant advances in culture-independent methods have expanded our knowledge about the diversity of the lung microbial environment. Complex microorganisms and microbial communities can now be identified in the distal airways in a variety of respiratory diseases, including cystic fibrosis (CF) and the posttransplantation lung. Although there are significant methodologic concerns about sampling the lung microbiome, several studies have now shown that the microbiome of the lower respiratory tract is distinct from the upper airway...
August 4, 2016: Translational Research: the Journal of Laboratory and Clinical Medicine
Helene F Rosenberg, Joanne C Masterson, Glenn T Furuta
There is currently substantial interest in the therapeutic properties of probiotic microorganisms as recent research suggests that oral administration of specific bacterial strains may reduce inflammation and alter the nature of endogenous microflora in the gastrointestinal tract. Eosinophils are multifunctional tissue leukocytes, prominent among the resident cells of the gastrointestinal mucosa that promote local immunity. Recent studies with genetically altered mice indicate that eosinophils not only participate in maintaining gut homeostasis, but that the absence of eosinophils may have significant impact on the nature of the endogenous gut microflora and responses to gut pathogens, notably Clostridium difficile Furthermore, in human subjects, there is an intriguing relationship between eosinophils, allergic inflammation, and the nature of the lung microflora, notably a distinct association between eosinophil infiltration and detection of bacteria of the phylum Actinobacteria...
August 22, 2016: Journal of Leukocyte Biology
Jamie Rylance, Anstead Kankwatira, David E Nelson, Evelyn Toh, Richard B Day, Huaiying Lin, Xiang Gao, Qunfeng Dong, Erica Sodergren, George M Weinstock, Robert S Heyderman, Homer L Twigg, Stephen B Gordon
BACKGROUND: Domestic combustion of biomass fuels, such as wood, charcoal, crop residue and dung causes Household Air Pollution (HAP). These inhaled particulates affect more than half of the world's population, causing respiratory problems such as infection and inflammatory lung disease. We examined whether the presence of black carbon in alveolar macrophages was associated with alterations in the lung microbiome in a Malawi population. METHODS: Bronchoalveolar lavage samples from 44 healthy adults were sequenced using 16S rDNA amplification to assess microbial diversity, richness and relative taxa abundance...
2016: BMC Microbiology
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