In children, the microbiota of the nasopharynx and bronchoalveolar lavage fluid are both similar and different

Concordance between upper and lower airway microbiota in infants with cystic fibrosis

(2017) Sabine M.P.J. Prevaes et al.   EUROPEAN RESPIRATORY JOURNAL

The microbiota in bronchoalveolar lavage from young children with chronic lung disease includes taxa present in both the oropharynx and nasopharynx

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Official American Thoracic Society Technical Standards: Flexible Airway Endoscopy in Children

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Analysis of the Upper Respiratory Tract Microbiotas as the Source of the Lung and Gastric Microbiotas in Healthy Individuals

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Swarm v2: highly-scalable and high-resolution amplicon clustering

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Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

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Swarm: robust and fast clustering method for amplicon-based studies

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Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers

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Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

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Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

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UCHIME improves sensitivity and speed of chimera detection

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QIIME allows analysis of high-throughput community sequencing data

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FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

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PyNAST: a flexible tool for aligning sequences to a template alignment

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