Analysis of the Pulmonary Microbiome Composition of Legionella pneumophila-Infected Patients
- 916 Downloads
The analysis of the lung microbiome composition is a field of research that recently emerged. It gained great interest in pulmonary diseases such as pneumonia since the microbiome seems to be involved in host immune responses, inflammation, and protection against pathogens. Thus, it is possible that the microbial communities living in the lungs play a role in the outcome and severity of lung infections such as Legionella-caused pneumonia and in the response to antibiotic therapy. In this chapter, all steps necessary for the characterization of the bacterial and fungal fraction of the lung microbiome using high-throughput sequencing approaches are explained, starting from the selection of clinical samples to the analysis of the taxonomic composition, diversity, and ecology of the microbiome.
Key wordsPulmonary microbiome Legionella pneumophila 16S rRNA gene ITS High-throughput sequencing Bioinformatics Microbial ecology
Work in the CB laboratory is financed by the Institut Pasteur and AECP was fianced by a fellowship from grant ANR-10-LABX-62-IBEID and grant ANR 15 CE17 0014 03.
- 2.Andrews S (2010) FastQC a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed 26 Apr 2010
- 3.Hannon Lab (2009) FASTX toolkit. http://hannonlab.cshl.edu/fastx_toolkit/index.html. Accessed 2 Feb 2010
- 5.Aronesty E (2011) ea-utils: “Command-line tools for processing biological sequencing data”. https://expressionanalysis.github.io/ea-utils/. Accessed 20 June 2017
- 17.R Core Team (2017) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. http://www.R-project.org/. Accessed 28 Sept 2017
- 19.Oksanen J, Guillaume F, Friendly M et al (2017) vegan: Community Ecology Package. R package version 2.4-4. http://CRAN.R-project.org/package=vegan. Accessed 24 Aug 2017
- 23.Oksanen J (2015) Multivariate analysis of ecological communities in R: vegan tutorial. http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf
- 29.Illumina (2013) 16S Metagenomic sequencing library preparation. https://support.illumina.com/documents/documentation/chemistry_documentation/16s/16s-metagenomic-library-prep-guide-15044223-b.pdf
- 30.Illumina (2017) 16S Metagenomics studies with the MiSeq system. https://www.illumina.com/content/dam/illumina-marketing/documents/products/appnotes/appnote_16s_sequencing.pdf