Fig. 1: Schematic representation of the optimized experimental pipeline and overview of the multi-center LRT microbiome study. | Nature Communications

Fig. 1: Schematic representation of the optimized experimental pipeline and overview of the multi-center LRT microbiome study.

From: Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness

Fig. 1

a General schematic representation of the study design and experimental pipeline. The workflow included sample liquefying, human DNA removal, ultrasonic beating to improve microbial cell lysis, DNA extraction using Chelex 100, DNA and protein precipitation, and the final steps of library preparation and sequencing. See the methods for detailed information. The plot was created with BioRender.com (citation: https://biorender.com/j76b222). b Venn diagram showing the total number of species detected in each hospital. c Percentage of detected samples for the top 10 prevalent microbial species present in the LRT microbiome from Hospital A (red), Hospital B (yellow), and Hospital C (blue), respectively. d Phylogenetic tree of 289 annotated metagenome-assembled genomes (MAGs). Bacterial species names are colored according to their phylum: The stars, circles, and squares indicate the collection sites. The bars in the outermost circle indicate the fraction of the query genome that aligns with the reference genome (up to 100%). Prevalent species with more than 3 MAGs are highlighted by colored arcs and labels. e Bar plot indicating the demographic and clinical factors significantly associated with the variation of the LRT microbiome profiles. Source data are provided as a Source Data file. Abbreviation: ARG, antibiotic resistance gene.

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