Journal: Movement Disorders

Article Title: The nasal and gut microbiome in Parkinson's disease and idiopathic rapid eye movement sleep behavior disorder

doi: 10.1002/mds.27105

Figure Lengend Snippet: Overviews of genomic reconstructions of two novel microbial populations depleted in patients with PD. (A) OTU_171, classified as Melainabacterium, (B) OTU_469, classified as alpha‐proteobacterium. 1) Contiguous sequences with lengths, 2) metagenomic depth of coverage, 3) % similarity to MelB1, 4 and 5) predicted proteins colored according to functional categories, 6 and 7) tRNA and rRNA loci, and E) endoglucanase with synuclein‐like domain; pink spokes highlight unique essential genes, golden spokes highlight phylogenetic marker genes. kb = kilobase; tRNA, transfer RNA.

Article Snippet: Metagenomic sequencing was conducted at GATC Biotech AG (Konstanz, Germany).

Techniques: Functional Assay, Marker

Journal: Scientific Reports

Article Title: An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities

doi: 10.1038/s41598-021-89881-2

Figure Lengend Snippet: The precision of MCM2α reported as percentage coefficient of variation (%CV) from triplicate technical repeats of each of the family of organisms reported by the 13 different laboratories for the 16S rRNA sequencing approach of MCM2α V12 (A), MCM2α V4–6 (B), MCM2β V1–2 (C), MCM2β V4–6 (D), and of the shotgun metagenomic sequencing approach for MCM2α (E) and MCM2β (F).

Article Snippet: Shotgun metagenomic sequencing was performed by LGC Genomics GmbH (Berlin, Germany).

Techniques: Sequencing

Journal: Frontiers in Medicine

Article Title: Multi-omic approach to decipher the impact of skincare products with pre/postbiotics on skin microbiome and metabolome

doi: 10.3389/fmed.2023.1165980

Figure Lengend Snippet: Relative abundance of select bacterial species or strains identified as significantly differentially abundant between time points and product groups, identified by (A) 16S rRNA gene sequencing and (B) shotgun metagenomics. Select species shown here and in were significantly differentiated per ANCOM-BC. Results of post hoc pairwise testing by Wilcoxon rank sum test provided to show differences per each time and within treatment groups. Significance represented as follows: ‘*’ = 0.01 < p < 0.05; ‘**’ = 0.001 < p < 0.01; ‘***’ = 0.0001 < p < 0.001; and ‘****’ = p < 0.0001. BW, body wash; BL, body lotion.

Article Snippet: Shotgun metagenomic sequencing was conducted by CosmosID (Germantown, Maryland).

Techniques: Sequencing

Journal: Frontiers in Medicine

Article Title: Multi-omic approach to decipher the impact of skincare products with pre/postbiotics on skin microbiome and metabolome

doi: 10.3389/fmed.2023.1165980

Figure Lengend Snippet: Functional characterization of skin microbiome by shotgun metagenomics. Differentially abundant bacterial MetaCyc pathways between baseline and after product application in Prebiotic Body wash (BW)/Body lotion (BL) group (A) , Control group (B) and between Prebiotic BW/BL and control group at 6 weeks (C) identified by Linear Discriminant Analysis Effect Size analysis (LEFSe). LEfSe is calculated with a Kruskal–Wallis alpha value of 0.05, a Wilcoxon alpha value of 0.05, and a logarithmic LDA score threshold of 1.0. Red bars to the left convey that the pathways in that group are more abundant in the “red” group than the other. Blue bars to the right convey that the pathways are more abundant in the “blue” group.

Article Snippet: Shotgun metagenomic sequencing was conducted by CosmosID (Germantown, Maryland).

Techniques: Functional Assay, Control

Journal: Frontiers in Medicine

Article Title: Multi-omic approach to decipher the impact of skincare products with pre/postbiotics on skin microbiome and metabolome

doi: 10.3389/fmed.2023.1165980

Figure Lengend Snippet: Pearson’s correlation between discriminant bacteria identified from 16S rRNA gene sequencing (A–C) and shotgun metagenomics (D–I) and Skin Hydration in all treatment groups using the R package ggpubr v.0.6.0 and 95% confidence level with linear regression.

Article Snippet: Shotgun metagenomic sequencing was conducted by CosmosID (Germantown, Maryland).

Techniques: Bacteria, Sequencing

Journal: Metabolites

Article Title: What Has Longitudinal ‘Omics’ Studies Taught Us about Irritable Bowel Syndrome? A Systematic Review

doi: 10.3390/metabo13040484

Figure Lengend Snippet: The characteristics and key findings of the studies reviewed (arranged alphabetically by the first author’s last name).

Article Snippet: Ankersen, 2021 [ ] , Denmark , 34 IBS patients (either IBS-D or IBS-M) randomised to receive either web-based low FODMAP diet intervention or probiotic; Rome III criteria for diagnosis , Stool sample , CeGaT GmbH culture-independent, whole-genome, shotgun metagenomic, next-generation sequencing of genomic DNA , Four time points, during the course of 1 year , - web-based low FODMAP diet intervention and probiotic intervention were both efficacious in managing IBS symptoms - in both cases, treatment response could not be predicted or explained by the composition of host gut microbiota.

Techniques: Biomarker Discovery, Microarray, Real-time Polymerase Chain Reaction, Functional Assay, Expressing, Next-Generation Sequencing, Bacteria, Gene Expression, Genome Wide, Probiotics, Isolation, Amplification, Sequencing, Starch, Fluorescence, FACS, Concentration Assay, Control, Clinical Proteomics, RNA Sequencing, Modification