Journal: bioRxiv

Article Title: MetaGut: Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing

doi: 10.1101/2023.03.10.531901

Figure Lengend Snippet: The Figure shows a) the positions of pre-Tx and control samples, displayed as colored dots, in the joint PCoA space of all samples, as well as the positions of pre-Tx Cluster 1, Cluster 2, and Cluster 3 in PCoA space (shaded areas), b) bar plots visualizing the microbiome compositions of healthy control and pre-Tx alloHSCT samples, stratified by pre-Tx cluster membership, and c) the rate of reads that carry an ARG element, separately for control and pre-Tx alloHSCT samples and stratified by pre-Tx cluster membership. The bar plots show the 20 genera that attained the highest aggregated sum of frequency across all time points, and, of these, within each sample, only the genera that 1.) were assigned at least 20 reads to and 2.) passed the mapping-based taxon validation step of MetaGut were depicted. The combined abundances of genera with fewer than 20 reads is shown in the category “not enough reads”; the category “not validated” shows the combined abundances of genera with more than 20 Kraken2-assigned reads that did not pass the mapping-based taxon validation step of MetaGut. Sample labels below the bar plots specify patient or control sample ID, followed, for alloHSCT samples, by the day of sampling relative to the stem cell transplantation time point.

Article Snippet: Theoretical composition of the “Zymo Gut Microbiome Standard” as well as abundances based on Kraken2 mappings to our comprehensive database as well as Minimap2 based mapping to the references provided by Zymo (using one estimate based on read counts and a second estimate based on nucleotide counts).

Techniques: Sampling, Transplantation Assay

Journal: bioRxiv

Article Title: MetaGut: Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing

doi: 10.1101/2023.03.10.531901

Figure Lengend Snippet: Shown are, for each sample, bar plots that visualize the respective compositions of the bacterial, fungal, archaeal, DNA-viral, and non-fungal eukaryotic components of the sample microbiome. Normalization was applied independently to each bar plot. The bar plots only show the 20 (for bacteria, fungi and DNA viruses), 4 (for archaea), and 2 (for non-fungal eukaryotes) genera that attained the highest mean relative frequency within the considered taxonomic category across all timepoints, and, of these, within each sample, only the genera that a) were assigned at least 20 reads by Kraken2, and b) passed the mapping-based taxon validation step of MetaGut. The combined abundance of genera within each taxonomic category with fewer than 20 reads is shown in the category “not enough reads”; the category “not validated” shows the combined abundance of genera with more than 20 reads that did not pass the mapping-based validation step. Sample labels below the bar plots specify healthy control ID or the patient ID, followed by the day of sampling relative to the transplantation event.

Article Snippet: Theoretical composition of the “Zymo Gut Microbiome Standard” as well as abundances based on Kraken2 mappings to our comprehensive database as well as Minimap2 based mapping to the references provided by Zymo (using one estimate based on read counts and a second estimate based on nucleotide counts).

Techniques: Sampling, Transplantation Assay

Journal: bioRxiv

Article Title: MetaGut: Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing

doi: 10.1101/2023.03.10.531901

Figure Lengend Snippet: The Figure shows, for alloHSCT samples collected during the leukopenic period, a) sample positions in the joint PCoA space of all samples, b) bar plots visualizing sample microbiome compositions, and c) rates of reads carrying an ARG element. All visualizations are stratified by pre-Tx cluster membership of the corresponding patients; in the top panel, pre-Tx cluster membership is indicated by dot color. The bar plots show the 20 genera that attained the highest mean frequency across all time points, and, of these, within each sample, only the genera that 1.) were assigned at least 20 reads and 2.) passed the mapping-based taxon validation step of MetaGut were depicted. The combined abundance of genera with fewer than 20 reads is shown in the category “not enough reads”; the category “not validated” shows the combined abundance of genera with more than 20 Kraken2-assigned reads that did not pass the mapping-based validation step. Sample labels below the bar plots specify patient ID, followed by the day of sampling relative to the stem cell transplantation time point.

Article Snippet: Theoretical composition of the “Zymo Gut Microbiome Standard” as well as abundances based on Kraken2 mappings to our comprehensive database as well as Minimap2 based mapping to the references provided by Zymo (using one estimate based on read counts and a second estimate based on nucleotide counts).

Techniques: Sampling, Transplantation Assay

Journal: bioRxiv

Article Title: MetaGut: Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing

doi: 10.1101/2023.03.10.531901

Figure Lengend Snippet: The figure shows, for alloHSCT samples collected during the reconstitution period, a) sample positions in the joint PCoA space of all samples, b) bar plots visualizing sample microbiome compositions, and c) rates of reads carrying an ARG element. All visualizations are stratified by pre-Tx cluster membership of the corresponding patients; in the top panel, pre-Tx cluster membership is indicated by dot color. The bar plots show the 20 genera that attained the highest mean frequency across all time points, and, of these, within each sample, only the genera that 1.) were assigned at least 20 reads and 2.) passed the mapping-based taxon validation step of MetaGut were depicted. The combined abundance of genera with fewer than 20 reads is shown in the category “not enough reads”; the category “not validated” shows the combined abundance of genera with more than 20 Kraken2-assigned reads that did not pass the mapping-based validation step. Sample labels below the bar plots specify patient ID, followed by the day of sampling relative to the stem cell transplantation time point.

Article Snippet: Theoretical composition of the “Zymo Gut Microbiome Standard” as well as abundances based on Kraken2 mappings to our comprehensive database as well as Minimap2 based mapping to the references provided by Zymo (using one estimate based on read counts and a second estimate based on nucleotide counts).

Techniques: Sampling, Transplantation Assay