Airway microbial communities, smoking and asthma in a general population sample
Elena M. Turek,Michael J. Cox,Michael Hunter,Jennie Hui,Phillip James,Saffron A.G. Willis-Owen,Leah Cuthbertson,Alan L. James,A. William Musk,Miriam F. Moffatt,William O.C.M. Cookson +10 more
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TLDR
This article investigated airway bacterial communities in a general population sample of 529 Australian adults and found that the healthy airway microbiota in this population were contained within a highly structured ecosystem, suggesting balanced relationships between the microbiome and human host factors.About:
This article is published in EBioMedicine.The article was published on 2021-09-01 and is currently open access. It has received 14 citations till now. The article focuses on the topics: Population & Microbiome.read more
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A Pandemic Lesson for Global Lung Diseases: Exacerbations Are Preventable
TL;DR: In this paper , a global reduction in the incidence of common seasonal respiratory viral infections has resulted from measures to limit the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the pandemic.
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Gut–lung Microbiota Interactions in Chronic Obstructive Pulmonary Disease (COPD): Potential Mechanisms Driving Progression to COPD and Epidemiological Data
TL;DR: There is a need for further clinical studies to characterize the pulmonary microbiota and to obtain new information about the pathogenesis of lung disease to improve knowledge and treatment strategies and identify new therapeutic targets.
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The respiratory tract microbiome: moving from correlation to causation
TL;DR: Insight is provided into a previously unrecognised role for the airway commensal Rothia mucilaginosa in attenuating proinflammatory responses to P. aeruginosa, an effect demonstrated consistently across a range of experimental models.
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Respiratory dysbiosis in cats with spontaneous allergic asthma
TL;DR: A significant difference in airway microbiota composition was documented between spontaneously asthmatic pet cats and healthy research cats mirroring the finding of dysbiosis in asthitic humans.
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A clinicians’ review of the respiratory microbiome
TL;DR: This review aims to outline how the microbiome is investigated, the healthy respiratory microbiome and its role in respiratory disease, and to describe future directions for microbiome research.
References
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Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more
TL;DR: In this paper, a different approach to problems of multiple significance testing is presented, which calls for controlling the expected proportion of falsely rejected hypotheses -the false discovery rate, which is equivalent to the FWER when all hypotheses are true but is smaller otherwise.
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast,Elmar Pruesse,Pelin Yilmaz,Jan Gerken,Timmy Schweer,Pablo Yarza,Jörg Peplies,Frank Oliver Glöckner +7 more
TL;DR: The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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WGCNA: an R package for weighted correlation network analysis.
Peter Langfelder,Steve Horvath +1 more
TL;DR: The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis that includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software.
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Enterotypes of the human gut microbiome
Manimozhiyan Arumugam,Jeroen Raes,Eric Pelletier,Denis Le Paslier,Takuji Yamada,Daniel R. Mende,Gabriel Fernandes,Julien Tap,Thomas Brüls,Jean-Michel Batto,Marcelo Bertalan,Natalia Borruel,Francesc Casellas,Leyden Fernández,Laurent Gautier,Torben Hansen,Masahira Hattori,Tetsuya Hayashi,Michiel Kleerebezem,Ken Kurokawa,Marion Leclerc,Florence Levenez,Chaysavanh Manichanh,H. Bjørn Nielsen,Trine Nielsen,Nicolas Pons,Julie Poulain,Junjie Qin,Thomas Sicheritz-Pontén,Sebastian Tims,David Torrents,Edgardo Ugarte,Erwin G. Zoetendal,Jun Wang,Francisco Guarner,Oluf Pedersen,Willem M. de Vos,Søren Brunak,Joël Doré,Jean Weissenbach,S. Dusko Ehrlich,Peer Bork +41 more
TL;DR: Three robust clusters (referred to as enterotypes hereafter) are identified that are not nation or continent specific and confirmed in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous.