Journal: mSystems

Article Title: Cobamide Sharing Is Predicted in the Human Skin Microbiome

doi: 10.1128/msystems.00677-22

Figure Lengend Snippet: Cobalamin riboswitch regulation varies across skin taxa. (A) The taxonomic abundance of hits for cobalamin riboswitches (Rfam clan CL00101) are shown, with an expanded view of low abundance hits to the right. Total cobalamin riboswitch hits within each microenvironment are indicated. (B to G) Cobalamin riboswitch-containing reads identified from INFERNAL analysis were aligned to Cutibacterium acnes KPA171202 (B), Veillonella parvula DSM 2008 (C), Pseudomonas putida KT2440 (D), Corynebacterium kroppenstedtii DSM 44385 (E), Corynebacterium amycolatum FDAARGOS 1107 (F), and Streptococcus sanguinis SK36 (G) genomes. Dark gray lines along the light gray genome track indicate the position of mapped INFERNAL hits within the genome. Genes upstream and downstream of the riboswitches are colored by their general functional annotation. White (other function) indicates genes not currently known to be associated with cobamides. Gray (hypothetical) indicates a hypothetical protein that has no functional annotation. Right-facing gene arrows and upright dark gray riboswitch icons indicate forward strand orientation, and left-facing gene arrows and inverted riboswitch icons indicate reverse strand orientation. Genomic regions are not to scale.

Article Snippet: Seventy-one Corynebacterium isolate genomes were acquired either from the National Center for Biotechnology Information (NCBI) in August 2020 as complete assemblies or from human skin isolates as draft assemblies.

Techniques: Functional Assay

Journal: mSystems

Article Title: Cobamide Sharing Is Predicted in the Human Skin Microbiome

doi: 10.1128/msystems.00677-22

Figure Lengend Snippet: Corynebacterium amycolatum produces cobamides and constitutively expresses cobamide biosynthesis genes. (A) E. coli ATCC 14169 was used as a microbiological indicator for the detection of cobamide concentration in Corynebacterium amycolatum LK19 cell extracts. Growth of E. coli was measured in minimal media with cyanocobalamin standards between 0.1 and 1.5 ng/ml to generate a standard curve. (B) E. coli growth with cyanocobalamin standards or different dilutions of C. amycolatum LK19 cell extract diluted between 10,000- and 50,000-fold. OD 600 values from 6 biological replicates and at least 3 technical replicates are shown. (C) The expression levels of cobB , cobH , and cobT were measured after 48 h of C. amycolatum LK19 culture in minimal media with cyanocobalamin supplementation (0, 250, and 2,500 ng/ml). Each culture/condition was grown in triplicate. Bars represent the mean gene expression ratio, calculated using the Pfaffl method, and error bars represent standard deviation. Cob gene expression was normalized to the 16S rRNA gene. Significance testing between cyanocobalamin concentrations was performed for each cob gene using the Kruskal-Wallis test, with significance defined as P < 0.05.

Article Snippet: Seventy-one Corynebacterium isolate genomes were acquired either from the National Center for Biotechnology Information (NCBI) in August 2020 as complete assemblies or from human skin isolates as draft assemblies.

Techniques: Concentration Assay, Expressing, Gene Expression, Standard Deviation

Journal: mSystems

Article Title: Cobamide Sharing Is Predicted in the Human Skin Microbiome

doi: 10.1128/msystems.00677-22

Figure Lengend Snippet: Cobamide-producing Corynebacterium abundance is associated with microbiome diversity and atopic dermatitis disease state. Within each metagenome, the cumulative relative abundance of cobamide-producing corynebacteria (CPC) was calculated. (A) NMDS plots based on Bray-Curtis indices for healthy adult samples within each skin microenvironment are shown. Points are colored by Corynebacterium cobamide producer relative abundance and sized by alpha diversity (Shannon). (B) The relative abundance of CPC in pediatric atopic dermatitis patient samples at baseline, flare, and postflare time points or in healthy control subjects. A Kruskal-Wallis test was performed followed by Dunn’s test with Bonferroni correction to determine statistical significance between groups (*, P < 0.05; **, P < 0.01). The sample size for each group are as follows: baseline n = 70, flare n = 144, postflare n = 144, control n = 57. (C) The relative abundance of CPC in each individual skin site sampled. Black lines connect time points for a given patient. Certain sites were sampled from both sides of the body, therefore each point represents the average abundance of for each individual at the specified skin site.

Article Snippet: Seventy-one Corynebacterium isolate genomes were acquired either from the National Center for Biotechnology Information (NCBI) in August 2020 as complete assemblies or from human skin isolates as draft assemblies.

Techniques: Control

Journal: mSystems

Article Title: Cobamide Sharing Is Predicted in the Human Skin Microbiome

doi: 10.1128/msystems.00677-22

Figure Lengend Snippet: De novo cobamide biosynthesis is host-associated within the Corynebacterium genus. (A and B) Genome length (A) and number of gene clusters (B) for 71 Corynebacterium genomes from host- or environment-associated species were determined using anvi’o. (C and D) Significantly enriched COG functions in environment-associated (C) or host-associated (D) genomes were identified with anvi’o function “anvi-get-enriched-functions-per-pan-group.” The top 20 significantly enriched COG functions (q < 0.05) are shown, ordered by ascending significance. (E) A Corynebacterium phylogenetic tree based on comparison of 71 conserved single-copy genes was generated using FastTree within the anvi’o environment. The tree is rooted with Tsukamurella paurometabola , and bootstrapping values are indicated (*, 100% bootstrap support). Species are colored by host or environment association, and by genome length. KOfamScan was used to identify the presence (dark pink) or absence (light pink) of cobamide biosynthesis genes within each genome. Cobamide biosynthesis subsections are indicated and are differentially colored based on those found in Fig. 1A . Blue, host-associated; orange, environment-associated. *, P < 0.0001 as calculated by a two-sided Mann-Whitney U test.

Article Snippet: Seventy-one Corynebacterium isolate genomes were acquired either from the National Center for Biotechnology Information (NCBI) in August 2020 as complete assemblies or from human skin isolates as draft assemblies.

Techniques: Comparison, Generated, MANN-WHITNEY

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: GEDpm-cg: Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum

doi: 10.3389/fbioe.2021.768289

Figure Lengend Snippet: Schematic diagram of GEDpm-cg and the point mutation editing technique based on uploaded sequences. GEDpm-cg is a web-based computer-aided design tool for the construction of genomic point mutations in C. glutamicum . When input files containing information of point mutations, vector and targeted genome are uploaded, GEDpm-cg is able to provide precise and high-throughput in-silico designed results for in vitro editing vector DNA assembly and in vivo point mutation editing in C. glutamicum . The design of point mutations by GEDpm-cg can be divided into the overlap-based vector DNA assembly and the suicide plasmid-mediated counter-selection point mutation genome editing. For vector DNA assembly, design tools such as j5 or Raven are able to assist the design of vector DNA assembly for biologists, while no tool is available for the design of suicide plasmid-mediated counter-selection point mutation genome editing. UHA, upstream homologous arm; DHA, downstream homologous arm; green band, homologous end between UHA and vector; yellow band, homologous end between DHA and vector, blue diamond, base before point mutation; red diamond, base after point mutation. Underlined names indicate the easily-neglected verification primers.

Article Snippet: In this study, to reduce the effort and time needed for point mutation editing design and provide a comprehensive packaged result for laboratory biologists, we developed a user-friendly online tool , named the Genome Editing automated Design platform for point mutation construction in Corynebacterium glutamicum (GEDpm-cg, https://gedpm-cg.biodesign.ac.cn/ ).

Techniques: Mutagenesis, Plasmid Preparation, High Throughput Screening Assay, In Silico, In Vitro, In Vivo, Selection

Journal: Standards in Genomic Sciences

Article Title: Genomic analysis of four strains of Corynebacterium pseudotuberculosis bv. Equi isolated from horses showing distinct signs of infection

doi: 10.1186/s40793-017-0234-6

Figure Lengend Snippet: Classification and general features of the species strain designation T [cite MIGS reference]

Article Snippet: As of February 2016, thirty-three genomes of the species Corynebacterium pseudotuberculosis had been deposited into the National Center for Biotechnology Information database.

Techniques: Bacteria, Staining

Journal: Standards in Genomic Sciences

Article Title: Genomic analysis of four strains of Corynebacterium pseudotuberculosis bv. Equi isolated from horses showing distinct signs of infection

doi: 10.1186/s40793-017-0234-6

Figure Lengend Snippet: Optical map of Corynebacterium pseudotuberculosis MB11. The figure shows the alignment of the KpnI sites observed in the optical map ( bottom scale bar ) with those predicted by the in silico assembly ( top scale bar ). Vertical lines connect identical restriction sites observed in the optical map and those predicted by the assembly, demonstrating that the genome was assembled in the correct order

Article Snippet: As of February 2016, thirty-three genomes of the species Corynebacterium pseudotuberculosis had been deposited into the National Center for Biotechnology Information database.

Techniques: In Silico

Journal: Standards in Genomic Sciences

Article Title: Genomic analysis of four strains of Corynebacterium pseudotuberculosis bv. Equi isolated from horses showing distinct signs of infection

doi: 10.1186/s40793-017-0234-6

Figure Lengend Snippet: Circular map of the genome for the sequenced Corynebacterium pseudotuberculosis strains. The outermost ring in blue shows the features extracted from the MB11 genome using a .gbk file. The next ring shows the CDSs predicted on the forward strand of MB11 in red , followed by the CDSs on the reverse strand with their features in blue . The other three rings in red , green , and blue show proteins predicted by blastx for the MB14, MB30, and MB66 genomes, respectively, compared to the MB11 genome. The two innermost rings show the GC content and GC skew, followed by the size of the genome in base pairs

Article Snippet: As of February 2016, thirty-three genomes of the species Corynebacterium pseudotuberculosis had been deposited into the National Center for Biotechnology Information database.

Techniques: