Journal: Microbial Cell Factories

Article Title: Refining and illuminating acetogenic Eubacterium strains for reclassification and metabolic engineering

doi: 10.1186/s12934-024-02301-8

Figure Lengend Snippet: Eubacterium strains used in this study

Article Snippet: “Butyribacterium methylotrophicum” , Marburg , DSM 3468; ATCC 33266 , CP132155.1 CP132156.1 , 4,278,751 , 47.5 , 3,979 , 4,075 , 16; 61 , 93x , 99.75% , 331x , 99.53% , This study.

Techniques:

Journal: Microbial Cell Factories

Article Title: Refining and illuminating acetogenic Eubacterium strains for reclassification and metabolic engineering

doi: 10.1186/s12934-024-02301-8

Figure Lengend Snippet: MLSA maximum-likelihood phylogenetic tree of the analyzed Eubacterium strains. The alignment was created from 2341 orthologous groups present in all genomes. The tree was inferred with 500 bootstraps with RAxML. The lengths of the tree branches were scaled according to the number of substitutions per site

Article Snippet: “Butyribacterium methylotrophicum” , Marburg , DSM 3468; ATCC 33266 , CP132155.1 CP132156.1 , 4,278,751 , 47.5 , 3,979 , 4,075 , 16; 61 , 93x , 99.75% , 331x , 99.53% , This study.

Techniques:

Journal: Microbial Cell Factories

Article Title: Refining and illuminating acetogenic Eubacterium strains for reclassification and metabolic engineering

doi: 10.1186/s12934-024-02301-8

Figure Lengend Snippet: Phylogenetic, genomic, and physiological comparison of methanol-utilizing Eubacterium strains. A Pairwise digital DNA-DNA hybridization values and average amino acid identities of the eleven Eubacterium strains. Strains are separated into three distinct clades comprising E. limosum , E. callanderi , and E. maltosivorans . B Arrangement of the methyltransferase system genes in the analyzed Eubacterium strains. C Growth behavior of methanol-utilizing Eubacterium strains represented by at least one strain of each clade ( E. limosum clade; type strain DSM 20543 T , E. callanderi clade; type strain DSM3662. T , strain ‘Marburg’ DSM 3468, and ‘KIST612’, as well as the E. maltosivorans clade; ‘32’ DSM 20517). From left to right, optical density, methanol utilization, acetate-, butyrate-, and hexanoate production. Error bars indicate standard deviations. n = 3

Article Snippet: “Butyribacterium methylotrophicum” , Marburg , DSM 3468; ATCC 33266 , CP132155.1 CP132156.1 , 4,278,751 , 47.5 , 3,979 , 4,075 , 16; 61 , 93x , 99.75% , 331x , 99.53% , This study.

Techniques: Comparison, DNA-DNA Hybridization

Journal: PLoS ONE

Article Title: The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline

doi: 10.1371/journal.pone.0142334

Figure Lengend Snippet: Designed mock community.

Article Snippet: Genomic DNA from Acinetobacter johnsonii (NCIMB 8154), Aminobacter aminovorans (NCIMB 9039), Devosia riboflavin (NCIMB 8177), Eubacterium barkeri (NCIMB 10623), Geofilum rubicundum (NCIMB 14482), Paracoccus denitrificans (NCIMB 8944), Prosthecobacter fusiformis (NCIMB 12777) and Xanthomonas sp . (NCIMB 592) were obtained from NCIMB (Aberdeen, Scotland).

Techniques:

Journal: PLoS ONE

Article Title: The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline

doi: 10.1371/journal.pone.0142334

Figure Lengend Snippet: (a) Stacked bar charts showing the relative abundance of bacterial families obtained by sequencing of a serial dilution of the plasmid-based mock community (from 10 and 10 7 copies of 16S gene for each of the 14 bacterial strains) compared to the actual relative abundance (right stacked bar). (b) Generalized UniFrac distance based PCoA analysis of the sequencing of a serial dilution of the plasmid-based mock community shown in a compared with the negative control generated by sequencing molecular biology-grade water with the same pipeline (H 2 O). UniFrac weight parameter (Alpha) was set to 0.6 for this analysis. (c) Stacked bar charts showing the relative abundance of bacterial families obtained by sequencing 7 mixes with different ratios of two of the bacterial plasmids containing the 16S gene of Geofilum rubicundum (GR) and Eubacterium barkeri (EB). The sequencing was performed in triplicate for all the samples (starting from the extracted DNA); the means of the triplicates are shown in a and individual triplicates are shown in b and c .

Article Snippet: Genomic DNA from Acinetobacter johnsonii (NCIMB 8154), Aminobacter aminovorans (NCIMB 9039), Devosia riboflavin (NCIMB 8177), Eubacterium barkeri (NCIMB 10623), Geofilum rubicundum (NCIMB 14482), Paracoccus denitrificans (NCIMB 8944), Prosthecobacter fusiformis (NCIMB 12777) and Xanthomonas sp . (NCIMB 592) were obtained from NCIMB (Aberdeen, Scotland).

Techniques: Sequencing, Serial Dilution, Plasmid Preparation, Negative Control, Generated