Journal: Scientific Data

Article Title: Benchmarking second and third-generation sequencing platforms for microbial metagenomics

doi: 10.1038/s41597-022-01762-z

Figure Lengend Snippet: Overview of the main sequencing platform characteristics used in this study.

Article Snippet: We performed five short read sequencing (Ion Proton P1, Ion S5, Illumina HiSeq 3000, DNBSEQ G400, DNBSEQ T7) and two long read sequencing technologies (ONT MinION and PacBio Sequel II), making this study the one covering the widest diversity of sequencing technologies (Table ).

Techniques: Sequencing, Amplification

Journal: Scientific Data

Article Title: Benchmarking second and third-generation sequencing platforms for microbial metagenomics

doi: 10.1038/s41597-022-01762-z

Figure Lengend Snippet: Mapping summary per mock and sequencing technology.

Article Snippet: We performed five short read sequencing (Ion Proton P1, Ion S5, Illumina HiSeq 3000, DNBSEQ G400, DNBSEQ T7) and two long read sequencing technologies (ONT MinION and PacBio Sequel II), making this study the one covering the widest diversity of sequencing technologies (Table ).

Techniques: Sequencing

Journal: Scientific Data

Article Title: Benchmarking second and third-generation sequencing platforms for microbial metagenomics

doi: 10.1038/s41597-022-01762-z

Figure Lengend Snippet: Overall comparison between observed and excepted mock compositions per technology. After read mapping to the mock reference genome, a subsampling was performed 3 times at multiple sequencing depth from 10,000 to 1 million reads, except for ONT MinION and PacBio for which maximum depth was 500k. Spearman rank correlations were calculated between observed genomes abundances normalized by genome size (expressed in %) and the expected mock composition (%). Means ± SD are reported based on the 3 iterations performed per depth. PacBio sequencing was not performed on mock3 and mock2, DNBSEQ-T7 and DNBSEQ-G400 were not performed on mock3.

Article Snippet: We performed five short read sequencing (Ion Proton P1, Ion S5, Illumina HiSeq 3000, DNBSEQ G400, DNBSEQ T7) and two long read sequencing technologies (ONT MinION and PacBio Sequel II), making this study the one covering the widest diversity of sequencing technologies (Table ).

Techniques: Comparison, Sequencing, PacBio Sequencing

Journal: Scientific Data

Article Title: Benchmarking second and third-generation sequencing platforms for microbial metagenomics

doi: 10.1038/s41597-022-01762-z

Figure Lengend Snippet: Differential plot between observed and excepted species abundances in mock1. Abundances (%) for each genome were calculated at 500k depth for each sequencing platform and normalized by genome size. Differential abundance was determined by subtracting the excepted abundances (%) to the observed normalized abundances (%). Positive values, genomes are over-estimated; Negative values, under-estimated. Genomes colored in red indicate draft genomes. Genome size and GC percent are reported for each species.

Article Snippet: We performed five short read sequencing (Ion Proton P1, Ion S5, Illumina HiSeq 3000, DNBSEQ G400, DNBSEQ T7) and two long read sequencing technologies (ONT MinION and PacBio Sequel II), making this study the one covering the widest diversity of sequencing technologies (Table ).

Techniques: Sequencing

Journal: Scientific Data

Article Title: Benchmarking second and third-generation sequencing platforms for microbial metagenomics

doi: 10.1038/s41597-022-01762-z

Figure Lengend Snippet:

Article Snippet: We performed five short read sequencing (Ion Proton P1, Ion S5, Illumina HiSeq 3000, DNBSEQ G400, DNBSEQ T7) and two long read sequencing technologies (ONT MinION and PacBio Sequel II), making this study the one covering the widest diversity of sequencing technologies (Table ).

Techniques: Nanopore Sequencing, Bacteria

Journal: iScience

Article Title: Myeloid TLR4 signaling promotes post-injury withdrawal resolution of murine liver fibrosis

doi: 10.1016/j.isci.2023.106220

Figure Lengend Snippet: Metagenomic analysis during liver fibrosis resolution (A) High-throughput sequencing of 16S rRNA during fecal bacterial DNA analysis at specific timepoints illustrated in Figure S1 A. (B) Principal coordinate analysis (PCoA) based on the unweighted UniFrac analysis of the bacterial community structures. (C) The quantification of UniFrac distance in panel A, presented as dissimilarity values. (D) The diversity of observed operational taxonomic units (OTUs) (left); α-diversity presented as Shannon indices (right). (E) Linear discrimination analysis effect size (LEfSe) at the Family level showing significantly different gut microbiota taxonomies (linear discriminant analysis [LDA] score >3.6). (F) The observed OTUs of Family Erysipelotrichaceae. (G) Accumulated percentage of relative abundance of functional categories of KEGG Orthology Level 1 pathways significantly enriched or depleted in WT-96 h mice compared to those in WT-24 h mice, assessed by PICRUSt with LEfSE (p < 0.05; LDA >2). Data show the mean ± SD. ∗p < 0.05, unless otherwise specified. See also Table S1 and Figure S5 .

Article Snippet: The sequencing library of Erysipelotrichaceae bacterium was sequenced on GridION X5 (Oxford Nanopore Technologies) and DNBSEQ-G400 (MGI TECH CO., LTD) using paired 200-bp reads.

Techniques: Next-Generation Sequencing, Functional Assay

Journal: iScience

Article Title: Myeloid TLR4 signaling promotes post-injury withdrawal resolution of murine liver fibrosis

doi: 10.1016/j.isci.2023.106220

Figure Lengend Snippet: Metagenomic analysis during liver fibrosis resolution (A) High-throughput sequencing of 16S rRNA during fecal bacterial DNA analysis at specific timepoints illustrated in Figure S1 A. (B) Principal coordinate analysis (PCoA) based on the unweighted UniFrac analysis of the bacterial community structures. (C) The quantification of UniFrac distance in panel A, presented as dissimilarity values. (D) The diversity of observed operational taxonomic units (OTUs) (left); α-diversity presented as Shannon indices (right). (E) Linear discrimination analysis effect size (LEfSe) at the Family level showing significantly different gut microbiota taxonomies (linear discriminant analysis [LDA] score >3.6). (F) The observed OTUs of Family Erysipelotrichaceae. (G) Accumulated percentage of relative abundance of functional categories of KEGG Orthology Level 1 pathways significantly enriched or depleted in WT-96 h mice compared to those in WT-24 h mice, assessed by PICRUSt with LEfSE (p < 0.05; LDA >2). Data show the mean ± SD. ∗p < 0.05, unless otherwise specified. See also Table S1 and Figure S5 .

Article Snippet: The sequencing library of Erysipelotrichaceae bacterium was sequenced on GridION X5 (Oxford Nanopore Technologies) and DNBSEQ-G400 (MGI TECH CO., LTD) using paired 200-bp reads.

Techniques: Next-Generation Sequencing, Functional Assay