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lung microbiome

Georgios D Kitsios
Severe bacterial pneumonia is a major global cause of morbidity and mortality, yet current diagnostic approaches rely on identification of causative pathogens by cultures, which require extended incubation periods and often fail to detect relevant pathogens. Consequently, patients are prescribed broad-spectrum antibiotics in a "one-size-fits-all" manner, which may be inappropriate for their individual needs and promote antibiotic resistance. My research focuses on leveraging next-generation sequencing of microbial DNA directly from patient samples for the development of new, culture-independent definitions of pneumonia...
March 2018: MSystems
Hong Wang, Xiao-Bin Ji, Bei Mao, Cheng-Wei Li, Hai-Wen Lu, Jin-Fu Xu
OBJECTIVES: Pseudomonas aeruginosa (P. aeruginosa) occupies an important niche in the pathogenic microbiome of bronchiectasis. The objective of this study is to evaluate the clinical characteristics and prognostic value of P. aeruginosa in Chinese adult patients with bronchiectasis. METHODS: This retrospective and follow-up study enrolled 1188 patients diagnosed with bronchiectasis at Shanghai Pulmonary Hospital between January 2011 and December 2012. The patients' clinical data including anthropometry, clinical symptoms, serum biomarkers, radiographic manifestations and lung function indices were reviewed...
March 14, 2018: BMJ Open
Robert P Dickson, John R Erb-Downward, Nicole R Falkowski, Ellen M Hunter, Shanna L Ashley, Gary B Huffnagle
RATIONALE: The "gut-lung axis" is commonly invoked to explain the microbiome's influence on lung inflammation. Yet the lungs harbor their own microbiome which is altered in respiratory disease. The relative influence of gut and lung bacteria on lung inflammation is unknown. OBJECTIVES: To determine if baseline lung immune tone reflects local (lung-lung) or remote (gut-lung) microbe-host interactions. METHODS: We compared lung, tongue, and cecal bacteria in forty healthy, genetically-identical 10-week old mice using 16S rRNA gene quantification and sequencing...
March 13, 2018: American Journal of Respiratory and Critical Care Medicine
Rohita Sinha, Lisa A Weissenburger-Moser, Jennifer L Clarke, Lynette M Smith, Art J Heires, Debra J Romberger, Tricia D LeVan
Chronic obstructive pulmonary disease (COPD) is an inflammatory disorder characterized by incompletely reversible airflow obstruction. The complexity of the lung microbial community in COPD patients has been highlighted in recent years. Evidence suggests that transplantation, medications, age, and disease severity influence microbial community membership. However, the dynamics of the lung microbiome in stable COPD patients remain poorly understood. In this study, we completed a longitudinal 16S ribosomal RNA survey of the lung microbiome on replicate sputum samples collected from 4 former smokers with COPD (Stage 2) within a 2-day time period...
2018: PloS One
Wendy Fonseca, Nicholas W Lukacs, Catherine Ptaschinski
Respiratory syncytial virus (RSV) is a common pathogen that infects virtually all children by 2 years of age and is the leading cause of hospitalization of infants worldwide. While most children experience mild symptoms, some children progress to severe lower respiratory tract infection. Those children with severe disease have a much higher risk of developing childhood wheezing later in life. Many risk factors are known to result in exacerbated disease, including premature birth and early age of RSV infection, when the immune system is relatively immature...
2018: Frontiers in Immunology
Charitharth Vivek Lal, Nelida Olave, Colm Travers, Gabriel Rezonzew, Kalsang Dolma, Alexandra Simpson, Brian Halloran, Zubair Aghai, Pragnya Das, Nirmal Sharma, Xin Xu, Kristopher Genschmer, Derek Russell, Tomasz Szul, Nengjun Yi, J Edwin Blalock, Amit Gaggar, Vineet Bhandari, Namasivayam Ambalavanan
Premature infants are at high risk for developing bronchopulmonary dysplasia (BPD), characterized by chronic inflammation and inhibition of lung development, which we have recently identified as being modulated by microRNAs (miRNAs) and alterations in the airway microbiome. Exosomes and exosomal miRNAs may regulate cell differentiation and tissue and organ development. We discovered that tracheal aspirates from infants with severe BPD had increased numbers of, but smaller, exosomes compared with term controls...
March 8, 2018: JCI Insight
Youhei Takahashi, Atsushi Saito, Hirofumi Chiba, Koji Kuronuma, Kimiyuki Ikeda, Tomofumi Kobayashi, Shigeru Ariki, Motoko Takahashi, Yasushi Sasaki, Hiroki Takahashi
BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is the most frequent and severe form of idiopathic interstitial pneumonias. Although IPF has not been thought to be associated with bacterial communities, recent papers reported the possible role of microbiome composition in IPF. The roles of microbiomes in respiratory functions and as clinical biomarkers for IPF remain unknown. In this study, we aim to identify the relationship between the microbial environment in the lung and clinical findings...
February 27, 2018: Respiratory Research
Jamil Jubrail, Nisha Kurian, Florence Niedergang
In the normal non-diseased lung, various macrophage populations maintain homeostasis and sterility by ingesting and clearing inhaled particulates, pathogens and apoptotic cells from the local environment. This process of phagocytosis leads to the degradation of the internalized material, coordinated induction of gene expression, antigen presentation and cytokine production, implicating phagocytosis as a central regulator of innate immunity. Phagocytosis is extremely efficient and any perturbation of this function is deleterious...
December 2017: Biomedical Journal
F Drakopanagiotakis, Lukasz Wujak, Malgorzata Wygrecka, P Markart
Idiopathic pulmonary fibrosis (IPF) is a chronic, debilitating, fibrotic lung disease leading to respiratory failure and ultimately to death. Being the prototype of interstitial lung diseases, IPF is characterized by marked heterogeneity regarding its clinical course. Despite significant progress in the understanding of its pathogenesis, we still cannot reliably predict the course of the disease and the response to treatment of an individual patient. Non-invasive biomarkers, in particular serum biomarkers, for the (early) diagnosis, differential diagnosis, prognosis and prediction of therapeutic response are urgently needed...
January 30, 2018: Matrix Biology: Journal of the International Society for Matrix Biology
Fernando J Martinez, MeiLan K Han, James P Allinson, R Graham Barr, Richard C Boucher, Peter Calverley, Bartolome R Celli, Stephanie A Christenson, Ronald G Crystal, Malin Fagerås, Christine M Freeman, Lars Groenke, Eric A Hoffman, Mehmet Kesimer, Konstantinos Kostikas, Robert Paine Iii, Shahin Rafii, Stephen I Rennard, Leopoldo N Segal, Renat Shaykhiev, Christopher Stevenson, Ruth Tal-Singer, Jørgen Vestbo, Prescott G Woodruff, Jeffrey L Curtis, Jadwiga A Wedzicha
Chronic obstructive pulmonary disease (COPD) is a heterogeneous disorder with varying presentations and progression, but limited disease-modifying therapies. Trajectories of lung function decline in COPD differ significantly between individuals, with differences detectable in young adulthood. "Early disease" (initial manifestations in young individuals) should be distinguished from "late mild disease" (disease of mild severity in older individuals potentially present for decades). For research purposes, we propose an operational definition of early COPD: ever-smokers (≥10 pack-years) younger than 50 years with any of these abnormalities: (1) FEV1/FVC< lower limit of normal; (2) compatible CT abnormalities (airway abnormality and/or emphysema); or (3) FEV1 decline (≥60 mL/year)...
February 6, 2018: American Journal of Respiratory and Critical Care Medicine
David Mayhew, Nathalie Devos, Christophe Lambert, James R Brown, Stuart C Clarke, Viktoriya L Kim, Michal Magid-Slav, Bruce E Miller, Kristoffer K Ostridge, Ruchi Patel, Ganesh Sathe, Daniel F Simola, Karl J Staples, Ruby Sung, Ruth Tal-Singer, Andrew C Tuck, Stephanie Van Horn, Vincent Weynants, Nicholas P Williams, Jeanne-Marie Devaster, Tom M A Wilkinson
BACKGROUND: Alterations in the composition of the lung microbiome associated with adverse clinical outcomes, known as dysbiosis, have been implicated with disease severity and exacerbations in COPD. OBJECTIVE: To characterise longitudinal changes in the lung microbiome in the AERIS study (Acute Exacerbation and Respiratory InfectionS in COPD) and their relationship with associated COPD outcomes. METHODS: We surveyed 584 sputum samples from 101 patients with COPD to analyse the lung microbiome at both stable and exacerbation time points over 1 year using high-throughput sequencing of the 16S ribosomal RNA gene...
January 31, 2018: Thorax
John E Pearl, Mrinal Das, Andrea M Cooper
Accurate prediction of which patient will progress from a sub-clinical Mycobacterium tuberculosis infection to active tuberculosis represents an elusive, yet critical, clinical research objective. From the individual perspective, progression can be considered to be the product of a series of unfortunate events or even a run of bad luck. Here, we identify the subtle physiological relationships that can influence the odds of progression to active TB and how this progression may reflect directed dysbiosis in a number of interrelated systems...
January 29, 2018: Cellular & Molecular Immunology
Maria José Rosa, Alison G Lee, Rosalind J Wright
PURPOSE OF REVIEW: The objective of this review is to provide an update on our evolving understanding of the effects of stress in pregnancy and during early development on the onset of asthma-related phenotypes across childhood, adolescence, and into early adulthood. RECENT FINDINGS: Accumulating evidence over the past 2 decades has established that prenatal and early-life psychological stress and stress correlates (e.g., maternal anxiety or depression) increase the risk for childhood respiratory disorders...
January 23, 2018: Current Opinion in Allergy and Clinical Immunology
Marianne S Muhlebach, Bryan T Zorn, Charles R Esther, Joseph E Hatch, Conor P Murray, Lidija Turkovic, Sarath C Ranganathan, Richard C Boucher, Stephen M Stick, Matthew C Wolfgang
The cystic fibrosis (CF) lung microbiome has been studied in children and adults; however, little is known about its relationship to early disease progression. To better understand the relationship between the lung microbiome and early respiratory disease, we characterized the lower airways microbiome using bronchoalveolar lavage (BAL) samples obtained from clinically stable CF infants and preschoolers who underwent bronchoscopy and chest computed tomography (CT). Cross-sectional samples suggested a progression of the lower airways microbiome with age, beginning with relatively sterile airways in infancy...
January 2018: PLoS Pathogens
Laura Tipton, Christian L Müller, Zachary D Kurtz, Laurence Huang, Eric Kleerup, Alison Morris, Richard Bonneau, Elodie Ghedin
BACKGROUND: No microbe exists in isolation, and few live in environments with only members of their own kingdom or domain. As microbiome studies become increasingly more interested in the interactions between microbes than in cataloging which microbes are present, the variety of microbes in the community should be considered. However, the majority of ecological interaction networks for microbiomes built to date have included only bacteria. Joint association inference across multiple domains of life, e...
January 15, 2018: Microbiome
Richard B Hayes, Jiyoung Ahn, Xiaozhou Fan, Brandilyn A Peters, Yingfei Ma, Liying Yang, Ilir Agalliu, Robert D Burk, Ian Ganly, Mark P Purdue, Neal D Freedman, Susan M Gapstur, Zhiheng Pei
Importance: Case-control studies show a possible relationship between oral bacteria and head and neck squamous cell cancer (HNSCC). Prospective studies are needed to examine the temporal relationship between oral microbiome and subsequent risk of HNSCC. Objective: To prospectively examine associations between the oral microbiome and incident HNSCC. Design, Setting, and Participants: This nested case-control study was carried out in 2 prospective cohort studies: the American Cancer Society Cancer Prevention Study II Nutrition Cohort (CPS-II) and the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO)...
January 11, 2018: JAMA Oncology
Milena Sokolowska, Remo Frei, Nonhlanhla Lunjani, Cezmi A Akdis, Liam O'Mahony
The mucosal immune system is in constant communication with the vast diversity of microbes present on body surfaces. The discovery of novel molecular mechanisms, which mediate host-microbe communication, have highlighted the important roles played by microbes in influencing mucosal immune responses. Dendritic cells, epithelial cells, ILCs, T regulatory cells, effector lymphocytes, NKT cells and B cells can all be influenced by the microbiome. Many of the mechanisms being described are bacterial strain- or metabolite-specific...
2018: Asthma research and practice
A Mitsuhashi, Y Okuma
Antibodies against immune checkpoint inhibitors such as anti-programmed cell death protein 1 (PD-1) and anti-programmed death ligand 1 (PD-L1) play a key role in the treatment of advanced lung cancer. To examine the clinical benefits of these agents, preclinical and clinical studies have been conducted to identify definitive biomarkers associated with cancer status. Analysis of the blood and feces of tumor patients has attracted attention in recent studies attempting to identify non-invasive biomarkers such as cytokines, soluble PD-L1, peripheral blood mononuclear cells, and gut microbiota...
January 8, 2018: Clinical & Translational Oncology
Carmen Gonzalez-Martinez, Katharina Kranzer, Grace McHugh, Elizabeth L Corbett, Hilda Mujuru, Mark P Nicol, Sarah Rowland-Jones, Andrea M Rehman, Tore J Gutteberg, Trond Flaegstad, Jon O Odland, Rashida A Ferrand
BACKGROUND: Human immunodeficiency virus (HIV)-related chronic lung disease (CLD) among children is associated with substantial morbidity, despite antiretroviral therapy. This may be a consequence of repeated respiratory tract infections and/or dysregulated immune activation that accompanies HIV infection. Macrolides have anti-inflammatory and antimicrobial properties, and we hypothesised that azithromycin would reduce decline in lung function and morbidity through preventing respiratory tract infections and controlling systemic inflammation...
December 28, 2017: Trials
Leah Cuthbertson, Vanessa Craven, Lynne Bingle, William O C M Cookson, Mark L Everard, Miriam F Moffatt
INTRODUCTION: Persistent bacterial bronchitis (PBB) is a leading cause of chronic wet cough in young children. This study aimed to characterise the respiratory bacterial microbiota of healthy children and to assess the impact of the changes associated with the development of PBB. Blind, protected brushings were obtained from 20 healthy controls and 24 children with PBB, with an additional directed sample obtained from PBB patients. DNA was extracted, quantified using a 16S rRNA gene quantitative PCR assay prior to microbial community analysis by 16S rRNA gene sequencing...
2017: PloS One
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