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methylobacterium sp  (ATCC)


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    Structured Review

    ATCC methylobacterium sp
    Methylobacterium Sp, supplied by ATCC, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 86 stars, based on 1 article reviews
    methylobacterium sp - by Bioz Stars, 2025-02
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    Image Search Results


    Antibiotics and concentrations tested during the antibiotic susceptibility assay of  Methylobacterium sp.  K003 and Methylobacterium radiotolerans JCM 2831.

    Journal: Engineering Microbiology

    Article Title: Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

    doi: 10.1016/j.engmic.2024.100163

    Figure Lengend Snippet: Antibiotics and concentrations tested during the antibiotic susceptibility assay of Methylobacterium sp. K003 and Methylobacterium radiotolerans JCM 2831.

    Article Snippet: Genomic sequencing of Methylobacterium sp. K003 was conducted using a dual approach, which consisted of (i) short-read paired-end technology on the Illumina NextSeq 500 platform (Macrogen, South Korea) and (ii) long-read sequencing technology on the Oxford Nanopore Technologies platform (Oxford Nanopore Technologies, United Kingdom).

    Techniques: Drug Susceptibility Assay, Concentration Assay

    Identification of the bacterial strains isolated from cultures supplemented with the supernatant of P. elgii after 16S rRNA genes sequencing.

    Journal: Engineering Microbiology

    Article Title: Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

    doi: 10.1016/j.engmic.2024.100163

    Figure Lengend Snippet: Identification of the bacterial strains isolated from cultures supplemented with the supernatant of P. elgii after 16S rRNA genes sequencing.

    Article Snippet: Genomic sequencing of Methylobacterium sp. K003 was conducted using a dual approach, which consisted of (i) short-read paired-end technology on the Illumina NextSeq 500 platform (Macrogen, South Korea) and (ii) long-read sequencing technology on the Oxford Nanopore Technologies platform (Oxford Nanopore Technologies, United Kingdom).

    Techniques: Isolation, Sequencing

    Similarity cladogram of 16S rRNA genes of Methylobacterium sp. K003 and other valid Methylobacterium strains. The evolutionary position of Methylobacterium sp. K003 was assessed using the Maximum-Likelihood (ML) method with 1000 sampling repetitions (Bootstrap).

    Journal: Engineering Microbiology

    Article Title: Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

    doi: 10.1016/j.engmic.2024.100163

    Figure Lengend Snippet: Similarity cladogram of 16S rRNA genes of Methylobacterium sp. K003 and other valid Methylobacterium strains. The evolutionary position of Methylobacterium sp. K003 was assessed using the Maximum-Likelihood (ML) method with 1000 sampling repetitions (Bootstrap).

    Article Snippet: Genomic sequencing of Methylobacterium sp. K003 was conducted using a dual approach, which consisted of (i) short-read paired-end technology on the Illumina NextSeq 500 platform (Macrogen, South Korea) and (ii) long-read sequencing technology on the Oxford Nanopore Technologies platform (Oxford Nanopore Technologies, United Kingdom).

    Techniques: Sampling

    Genomic assembly of  Methylobacterium sp.  K003 performed using long- and short-read sequencing.

    Journal: Engineering Microbiology

    Article Title: Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

    doi: 10.1016/j.engmic.2024.100163

    Figure Lengend Snippet: Genomic assembly of Methylobacterium sp. K003 performed using long- and short-read sequencing.

    Article Snippet: Genomic sequencing of Methylobacterium sp. K003 was conducted using a dual approach, which consisted of (i) short-read paired-end technology on the Illumina NextSeq 500 platform (Macrogen, South Korea) and (ii) long-read sequencing technology on the Oxford Nanopore Technologies platform (Oxford Nanopore Technologies, United Kingdom).

    Techniques: Sequencing

    Circular map of the genome assembly of Methylobacterium sp. K003, showing the coding regions and the GG content. Outside to center: forward CDS (dark blue), reverse CDS (red), GC content, and GC slope (dark gray and light gray).

    Journal: Engineering Microbiology

    Article Title: Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

    doi: 10.1016/j.engmic.2024.100163

    Figure Lengend Snippet: Circular map of the genome assembly of Methylobacterium sp. K003, showing the coding regions and the GG content. Outside to center: forward CDS (dark blue), reverse CDS (red), GC content, and GC slope (dark gray and light gray).

    Article Snippet: Genomic sequencing of Methylobacterium sp. K003 was conducted using a dual approach, which consisted of (i) short-read paired-end technology on the Illumina NextSeq 500 platform (Macrogen, South Korea) and (ii) long-read sequencing technology on the Oxford Nanopore Technologies platform (Oxford Nanopore Technologies, United Kingdom).

    Techniques:

    Genomic alignment of Methylobacterium sp. K003 (red) and Methylobacterium radiotolerans JCM 2831 (blue), showing regions with a minimum of 1000 nucleotides and 90 % identity. The outer band represents the size scale of the contigs, whereas blue bands with a two-layer depth indicate overlapping sequences present in both strains.

    Journal: Engineering Microbiology

    Article Title: Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

    doi: 10.1016/j.engmic.2024.100163

    Figure Lengend Snippet: Genomic alignment of Methylobacterium sp. K003 (red) and Methylobacterium radiotolerans JCM 2831 (blue), showing regions with a minimum of 1000 nucleotides and 90 % identity. The outer band represents the size scale of the contigs, whereas blue bands with a two-layer depth indicate overlapping sequences present in both strains.

    Article Snippet: Genomic sequencing of Methylobacterium sp. K003 was conducted using a dual approach, which consisted of (i) short-read paired-end technology on the Illumina NextSeq 500 platform (Macrogen, South Korea) and (ii) long-read sequencing technology on the Oxford Nanopore Technologies platform (Oxford Nanopore Technologies, United Kingdom).

    Techniques:

    Maximum-likelihood phylogenetic tree of Methylobacterium strains based on 233 core orthologous genes concatenated from genomic sequences. The dataset included 12 Methylobacterium strains, including Methylobacterium sp. K003 and its closely related strains, with Enterovirga rhinocerotis YIM 100770 as the outgroup.

    Journal: Engineering Microbiology

    Article Title: Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

    doi: 10.1016/j.engmic.2024.100163

    Figure Lengend Snippet: Maximum-likelihood phylogenetic tree of Methylobacterium strains based on 233 core orthologous genes concatenated from genomic sequences. The dataset included 12 Methylobacterium strains, including Methylobacterium sp. K003 and its closely related strains, with Enterovirga rhinocerotis YIM 100770 as the outgroup.

    Article Snippet: Genomic sequencing of Methylobacterium sp. K003 was conducted using a dual approach, which consisted of (i) short-read paired-end technology on the Illumina NextSeq 500 platform (Macrogen, South Korea) and (ii) long-read sequencing technology on the Oxford Nanopore Technologies platform (Oxford Nanopore Technologies, United Kingdom).

    Techniques: Genomic Sequencing

    Pangenomic and phylogenetic analysis of Methylobacterium sp. K003. (A) Pangenome distribution illustrating three gene categories across genomes: core genes (present in 99 % to 100 % of the genomes), shell genes (present in 15 % to 95 % of the genomes), and cloud genes (present in 0 % to 15 % of the genomes). (B) Venn diagram showing the number of genes common between Methylobacterium sp. K003 and its closest strain Methylobacterium radiotolerans JCM 2831. (C) Maximum-likelihood phylogenetic tree based on the presence and absence of genes from Methylobacterium sp. K003 pangenome. Blue bar represents the pangenome, with each line corresponding to a strain and each column indicating gene variation. Gene presence is depicted in a descending frequency, with empty spaces representing gene absence. Genome comparison includes Methylobacterium sp. K003 and its closest genomes, using a minimum blastp identity of 80 % for grouping genes into the core genomes.

    Journal: Engineering Microbiology

    Article Title: Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

    doi: 10.1016/j.engmic.2024.100163

    Figure Lengend Snippet: Pangenomic and phylogenetic analysis of Methylobacterium sp. K003. (A) Pangenome distribution illustrating three gene categories across genomes: core genes (present in 99 % to 100 % of the genomes), shell genes (present in 15 % to 95 % of the genomes), and cloud genes (present in 0 % to 15 % of the genomes). (B) Venn diagram showing the number of genes common between Methylobacterium sp. K003 and its closest strain Methylobacterium radiotolerans JCM 2831. (C) Maximum-likelihood phylogenetic tree based on the presence and absence of genes from Methylobacterium sp. K003 pangenome. Blue bar represents the pangenome, with each line corresponding to a strain and each column indicating gene variation. Gene presence is depicted in a descending frequency, with empty spaces representing gene absence. Genome comparison includes Methylobacterium sp. K003 and its closest genomes, using a minimum blastp identity of 80 % for grouping genes into the core genomes.

    Article Snippet: Genomic sequencing of Methylobacterium sp. K003 was conducted using a dual approach, which consisted of (i) short-read paired-end technology on the Illumina NextSeq 500 platform (Macrogen, South Korea) and (ii) long-read sequencing technology on the Oxford Nanopore Technologies platform (Oxford Nanopore Technologies, United Kingdom).

    Techniques: Comparison

    Distribution of encoded proteins in the genome of Methylobacterium sp. K003 across their respective COG categories.

    Journal: Engineering Microbiology

    Article Title: Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

    doi: 10.1016/j.engmic.2024.100163

    Figure Lengend Snippet: Distribution of encoded proteins in the genome of Methylobacterium sp. K003 across their respective COG categories.

    Article Snippet: Genomic sequencing of Methylobacterium sp. K003 was conducted using a dual approach, which consisted of (i) short-read paired-end technology on the Illumina NextSeq 500 platform (Macrogen, South Korea) and (ii) long-read sequencing technology on the Oxford Nanopore Technologies platform (Oxford Nanopore Technologies, United Kingdom).

    Techniques:

    Biosynthetic gene clusters of secondary metabolites from the genome of  Methylobacterium sp.  K003 compared to its reference strain Methylobacterium radiotolerans JCM 2831.

    Journal: Engineering Microbiology

    Article Title: Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

    doi: 10.1016/j.engmic.2024.100163

    Figure Lengend Snippet: Biosynthetic gene clusters of secondary metabolites from the genome of Methylobacterium sp. K003 compared to its reference strain Methylobacterium radiotolerans JCM 2831.

    Article Snippet: Genomic sequencing of Methylobacterium sp. K003 was conducted using a dual approach, which consisted of (i) short-read paired-end technology on the Illumina NextSeq 500 platform (Macrogen, South Korea) and (ii) long-read sequencing technology on the Oxford Nanopore Technologies platform (Oxford Nanopore Technologies, United Kingdom).

    Techniques:

    Peptide distribution and functional prediction in the genomes of Methylobacterium sp. K003 and Methylobacterium radiotolerans JCM 2831. (A) Total number of peptides with fewer than 100 residues and their predicted biological function in each strain (BAP). (B) Predicted biological functions of biologically active peptides (BAP) in each strain, with a focus on anti-inflammatory (AntiAngioPred), anticancer (AntiCP), and antifungal (AntiFP) activities.

    Journal: Engineering Microbiology

    Article Title: Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

    doi: 10.1016/j.engmic.2024.100163

    Figure Lengend Snippet: Peptide distribution and functional prediction in the genomes of Methylobacterium sp. K003 and Methylobacterium radiotolerans JCM 2831. (A) Total number of peptides with fewer than 100 residues and their predicted biological function in each strain (BAP). (B) Predicted biological functions of biologically active peptides (BAP) in each strain, with a focus on anti-inflammatory (AntiAngioPred), anticancer (AntiCP), and antifungal (AntiFP) activities.

    Article Snippet: Genomic sequencing of Methylobacterium sp. K003 was conducted using a dual approach, which consisted of (i) short-read paired-end technology on the Illumina NextSeq 500 platform (Macrogen, South Korea) and (ii) long-read sequencing technology on the Oxford Nanopore Technologies platform (Oxford Nanopore Technologies, United Kingdom).

    Techniques: Functional Assay

    Graphical representation of the similarity between biosynthetic gene cluster (BCG) families from Methylobacterium sp. K003 and Methylobacterium radiotolerans JCM 2831. Each link represents similar gene clusters between the analyzed strains. Singletons, presented in isolated form, are specific clusters unique to each strain, indicating no similarities between the strains.

    Journal: Engineering Microbiology

    Article Title: Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

    doi: 10.1016/j.engmic.2024.100163

    Figure Lengend Snippet: Graphical representation of the similarity between biosynthetic gene cluster (BCG) families from Methylobacterium sp. K003 and Methylobacterium radiotolerans JCM 2831. Each link represents similar gene clusters between the analyzed strains. Singletons, presented in isolated form, are specific clusters unique to each strain, indicating no similarities between the strains.

    Article Snippet: Genomic sequencing of Methylobacterium sp. K003 was conducted using a dual approach, which consisted of (i) short-read paired-end technology on the Illumina NextSeq 500 platform (Macrogen, South Korea) and (ii) long-read sequencing technology on the Oxford Nanopore Technologies platform (Oxford Nanopore Technologies, United Kingdom).

    Techniques: Isolation

    Similarities between biosynthetic gene clusters (BCGs) found in Methylobacterium sp. K003 and Paenibacillus elgii AC13. (A) The total number of Pfam domains per BCG shared between the analyzed strains. (B) Graphical representation of similar BCGs between K003 and AC13 strains.

    Journal: Engineering Microbiology

    Article Title: Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

    doi: 10.1016/j.engmic.2024.100163

    Figure Lengend Snippet: Similarities between biosynthetic gene clusters (BCGs) found in Methylobacterium sp. K003 and Paenibacillus elgii AC13. (A) The total number of Pfam domains per BCG shared between the analyzed strains. (B) Graphical representation of similar BCGs between K003 and AC13 strains.

    Article Snippet: Genomic sequencing of Methylobacterium sp. K003 was conducted using a dual approach, which consisted of (i) short-read paired-end technology on the Illumina NextSeq 500 platform (Macrogen, South Korea) and (ii) long-read sequencing technology on the Oxford Nanopore Technologies platform (Oxford Nanopore Technologies, United Kingdom).

    Techniques:

    Comparative analysis of phenotypic predictions from the genome assembly of Methylobacterium sp. K003. The comparison includes genomes of the closest strains according to dDDH, as available in the NCBI database. Scoring system: a value of zero indicates a negative phenotype, whereas values of 1 and 2 correspond to positive phenotypes in the phypat and phypat+PGL predictors, respectively. A value of 3 indicates a positive phenotype in both predictors.

    Journal: Engineering Microbiology

    Article Title: Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

    doi: 10.1016/j.engmic.2024.100163

    Figure Lengend Snippet: Comparative analysis of phenotypic predictions from the genome assembly of Methylobacterium sp. K003. The comparison includes genomes of the closest strains according to dDDH, as available in the NCBI database. Scoring system: a value of zero indicates a negative phenotype, whereas values of 1 and 2 correspond to positive phenotypes in the phypat and phypat+PGL predictors, respectively. A value of 3 indicates a positive phenotype in both predictors.

    Article Snippet: Genomic sequencing of Methylobacterium sp. K003 was conducted using a dual approach, which consisted of (i) short-read paired-end technology on the Illumina NextSeq 500 platform (Macrogen, South Korea) and (ii) long-read sequencing technology on the Oxford Nanopore Technologies platform (Oxford Nanopore Technologies, United Kingdom).

    Techniques: Comparison

    Comparative analysis between the phenotypes of  Methylobacterium sp.  K003 and Methylobacterium radiotolerans JCM 2831 strain, where (+) represents the presence and (–) the absence.

    Journal: Engineering Microbiology

    Article Title: Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

    doi: 10.1016/j.engmic.2024.100163

    Figure Lengend Snippet: Comparative analysis between the phenotypes of Methylobacterium sp. K003 and Methylobacterium radiotolerans JCM 2831 strain, where (+) represents the presence and (–) the absence.

    Article Snippet: Genomic sequencing of Methylobacterium sp. K003 was conducted using a dual approach, which consisted of (i) short-read paired-end technology on the Illumina NextSeq 500 platform (Macrogen, South Korea) and (ii) long-read sequencing technology on the Oxford Nanopore Technologies platform (Oxford Nanopore Technologies, United Kingdom).

    Techniques:

    Fatty acids profile (%) of  Methylobacterium sp.  K003 compared to its reference strain Methylobacterium radiotolerans JCM 2831. Peaks with imperfect separation were collectively reported as

    Journal: Engineering Microbiology

    Article Title: Impact of Paenibacillus elgii supernatant on screening bacterial strains with potential for biotechnological applications

    doi: 10.1016/j.engmic.2024.100163

    Figure Lengend Snippet: Fatty acids profile (%) of Methylobacterium sp. K003 compared to its reference strain Methylobacterium radiotolerans JCM 2831. Peaks with imperfect separation were collectively reported as "Summed Features" with specific components identified: Summed Feature 2 (putative 12:0 aldehyde), Summed Feature 3 (C16:1 ω6c and/or C16:1 ω7c), and Summed Feature 8 (C18:1 ω7c and/or C18:1 ω6c). Absence of a particular fatty acid is denoted by (−).

    Article Snippet: Genomic sequencing of Methylobacterium sp. K003 was conducted using a dual approach, which consisted of (i) short-read paired-end technology on the Illumina NextSeq 500 platform (Macrogen, South Korea) and (ii) long-read sequencing technology on the Oxford Nanopore Technologies platform (Oxford Nanopore Technologies, United Kingdom).

    Techniques: