Is the lung microbiome alive? Lessons from Antarctic soil

The “microbiome” is the operative term to refer to a collection of all taxa constituting microbial communities, such as bacteria, archaea, fungi and protists (originally microbiota). The microbiome consists of the indigenous microbial communities and of the host environment that they inhabit. Actually, it has been shown that there is a close relationship between the microbiome and human health and disease condition. Although, initially, the lung was considered sterile, actually, the existence of a healthy lung microbiome is usually accepted. Lung microbiome changes are reported in Chronic Obstructive Pulmonary Disease (COPD) and in its exacerbation. Viral and bacterial infections of the respiratory system are a major cause of COPD exacerbations (AECOPD) leading to increased local and systemic inflammation. Detection rates of virus in AECOPD are variable between 25-62% according to the detection method. The study of human airway and lung disease virome is quite recent and still very limited. The purpose of this review is to summarize recent findings on the lung microbiome composition with a special emphasis on virome in COPD and in AECOPD. Some drugs of natural origins active against resistant bacteria and virus are described.

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The Gut/Lung Microbiome Axis in Obesity, Asthma, and Bariatric Surgery: A Literature Review

Obesity ◽

10.1002/oby.23107 ◽

2021 ◽

Vol 29 (4) ◽

pp. 636-644

Author(s):

Yeon Ji Kim ◽

Jack T. Womble ◽

Claudia K. Gunsch ◽

Jennifer L. Ingram

Keyword(s):

Bariatric Surgery ◽

Literature Review ◽

Lung Microbiome

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Lung microbiome composition and bronchial epithelial gene expression in patients with COPD versus healthy individuals: a bacterial 16S rRNA gene sequencing and host transcriptomic analysis

The Lancet Microbe ◽

10.1016/s2666-5247(21)00035-5 ◽

2021 ◽

Author(s):

Mohammadali Yavari Ramsheh ◽

Koirobi Haldar ◽

Anna Esteve-Codina ◽

Lillie F Purser ◽

Matthew Richardson ◽

...

Keyword(s):

Gene Expression ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Healthy Individuals ◽

Bronchial Epithelial ◽

Microbiome Composition ◽

Lung Microbiome ◽

Rrna Gene Sequencing ◽

Bacterial 16S Rrna Gene

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The lower respiratory tract microbiome of critically ill patients with COVID-19

Scientific Reports ◽

10.1038/s41598-021-89516-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Paolo Gaibani ◽

Elisa Viciani ◽

Michele Bartoletti ◽

Russell E. Lewis ◽

Tommaso Tonetti ◽

...

Keyword(s):

Respiratory Tract ◽

Critically Ill ◽

Critically Ill Patients ◽

Lower Respiratory Tract ◽

Multidrug Resistant ◽

Carbapenem Resistant ◽

Lung Microbiome ◽

Bacterial Microbiome ◽

Unweighted Unifrac ◽

Bacterial Superinfection

AbstractCOVID-19 infection may predispose to secondary bacterial infection which is associated with poor clinical outcome especially among critically ill patients. We aimed to characterize the lower respiratory tract bacterial microbiome of COVID-19 critically ill patients in comparison to COVID-19-negative patients. We performed a 16S rRNA profiling on bronchoalveolar lavage (BAL) samples collected between April and May 2020 from 24 COVID-19 critically ill subjects and 24 patients with non-COVID-19 pneumonia. Lung microbiome of critically ill patients with COVID-19 was characterized by a different bacterial diversity (PERMANOVA on weighted and unweighted UniFrac Pr(> F) = 0.001) compared to COVID-19-negative patients with pneumonia. Pseudomonas alcaligenes, Clostridium hiranonis, Acinetobacter schindleri, Sphingobacterium spp., Acinetobacter spp. and Enterobacteriaceae, characterized lung microbiome of COVID-19 critically ill patients (LDA score > 2), while COVID-19-negative patients showed a higher abundance of lung commensal bacteria (Haemophilus influenzae, Veillonella dispar, Granulicatella spp., Porphyromonas spp., and Streptococcus spp.). The incidence rate (IR) of infections during COVID-19 pandemic showed a significant increase of carbapenem-resistant Acinetobacter baumannii (CR-Ab) infection. In conclusion, SARS-CoV-2 infection and antibiotic pressure may predispose critically ill patients to bacterial superinfection due to opportunistic multidrug resistant pathogens.

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Phosphorus stress induces the synthesis of novel glycolipids in Pseudomonas aeruginosa that confer protection against a last-resort antibiotic

The ISME Journal ◽

10.1038/s41396-021-01008-7 ◽

2021 ◽

Author(s):

Rebekah A. Jones ◽

Holly Shropshire ◽

Caimeng Zhao ◽

Andrew Murphy ◽

Ian Lidbury ◽

...

Keyword(s):

Cystic Fibrosis ◽

Pseudomonas Aeruginosa ◽

Antibiotic Sensitivity ◽

Polymyxin B ◽

Growth Conditions ◽

Membrane Lipid ◽

Comparative Genomic ◽

P Limitation ◽

Lung Microbiome ◽

Glycolipid Synthesis

AbstractPseudomonas aeruginosa is a nosocomial pathogen with a prevalence in immunocompromised individuals and is particularly abundant in the lung microbiome of cystic fibrosis patients. A clinically important adaptation for bacterial pathogens during infection is their ability to survive and proliferate under phosphorus-limited growth conditions. Here, we demonstrate that P. aeruginosa adapts to P-limitation by substituting membrane glycerophospholipids with sugar-containing glycolipids through a lipid renovation pathway involving a phospholipase and two glycosyltransferases. Combining bacterial genetics and multi-omics (proteomics, lipidomics and metatranscriptomic analyses), we show that the surrogate glycolipids monoglucosyldiacylglycerol and glucuronic acid-diacylglycerol are synthesised through the action of a new phospholipase (PA3219) and two glycosyltransferases (PA3218 and PA0842). Comparative genomic analyses revealed that this pathway is strictly conserved in all P. aeruginosa strains isolated from a range of clinical and environmental settings and actively expressed in the metatranscriptome of cystic fibrosis patients. Importantly, this phospholipid-to-glycolipid transition comes with significant ecophysiological consequence in terms of antibiotic sensitivity. Mutants defective in glycolipid synthesis survive poorly when challenged with polymyxin B, a last-resort antibiotic for treating multi-drug resistant P. aeruginosa. Thus, we demonstrate an intriguing link between adaptation to environmental stress (nutrient availability) and antibiotic resistance, mediated through membrane lipid renovation that is an important new facet in our understanding of the ecophysiology of this bacterium in the lung microbiome of cystic fibrosis patients.

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Laboratory diagnosis of pneumonia in the molecular age

European Respiratory Journal ◽

10.1183/13993003.01144-2016 ◽

2016 ◽

Vol 48 (6) ◽

pp. 1764-1778 ◽

Cited By ~ 47

Author(s):

Antoni Torres ◽

Nelson Lee ◽

Catia Cilloniz ◽

Jordi Vila ◽

Menno Van der Eerden

Keyword(s):

Laboratory Diagnosis ◽

High Rate ◽

Microbial Pathogens ◽

Molecular Diagnostic ◽

Respiratory Pathogens ◽

Major Advance ◽

Lung Microbiome ◽

Microbiological Methods ◽

New Knowledge ◽

Diagnostic Technology

Pneumonia remains a worldwide health problem with a high rate of morbidity and mortality. Identification of microbial pathogens which cause pneumonia is an important area for optimum clinical management of pneumonia patients and is a big challenge for conventional microbiological methods. The development and implementation of molecular diagnostic tests for pneumonia has been a major advance in the microbiological diagnosis of respiratory pathogens in recent years. However, with new knowledge regarding the microbiome, together with the recognition that the lungs are a dynamic microbiological ecosystem, our current concept of pneumonia is not totally realistic as this new concept of pneumonia involves a dysbiosis or alteration of the lung microbiome. A new challenge for microbiologists and clinicians has therefore arisen. There is much to learn regarding the information provided by this new diagnostic technology, which will lead to improvements in the time to antibiotic therapy, targeted antibiotic selection and more effective de-escalation and improved stewardship for pneumonia patients. This article provides an overview of current methods of laboratory diagnosis of pneumonia in the molecular age.

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