streptomyces ambofaciens atcc 23877  (ATCC)

Journal: Frontiers in Microbiology

Article Title: Streptomyces tagetis sp. nov., a chromomycin producing bacteria isolated from the roots of Tagetes patula

doi: 10.3389/fmicb.2024.1361583

Figure Lengend Snippet: ANI, dDDH, and AAI among strain RG38 T and other closely related Streptomyces members.

Article Snippet: Streptomyces ambofaciens ATCC 23877 T , CP012382 , 84.7 , 29 , 81.6.

Techniques:

Journal: bioRxiv

Article Title: Phage-mediated dispersal of multicellular bacteria

doi: 10.1101/2023.07.22.549817

Figure Lengend Snippet: A. Pairwise comparison of S. ambofaciens ATCC 23877 and DSM 40697 chromosomes. The grey line indicates the position of genes whose order is perfectly conserved between strains. The blue dots indicate areas of synteny break. The red circles correspond to genomic islands containing at least 20 CDS in one of the strains. The blue arrows indicate the position of xSAM1-pSAM2 integrated elements as well as the genomic island of interest harboring Samy prophage, detailed in the panels B and C. The central compartment (delimitated by the distal rrn operons) , the arms (defined as terminal regions devoid of core genes), the terminal inverted repeats (TIRs) and the position of the origin of replication ( oriC ) in S. ambofaciens ATCC 23877 chromosome are indicated. The level of gene order conservation between both strains as well as the GC percent content calculated in a window of 50 kb are indicated below the dot-blot. B. Schematic representation of the genomic island containing the Samy prophage. The regions in which gene order is perfectly conserved in S. ambofaciens ATCC 23877 and DSM 40697 chromosomes are defined as the left and right synteny blocks (grey). The coordinates of the genomic island borders in S. ambofaciens ATCC 23877 strain are indicated in blue. The genomic island is composed of two regions: a remnant integrative element and the Samy prophage. These regions are separated by a short intergenic region (represented by an asterisk; 305 bp located from 6,589,473 to 6,589,777 bp) present in both strains. Two serine integrase coding sequences (red) have been predicted. The prophage also contains four tRNA encoding genes (pink). C. Comparison of the Samy and PhiC31 phage genomes. Gene functions are color-coded as detailed in the legend. The annotation of PhiC31 genes was previously reported in and (for the recombination directionality factor, RDF). Black vertical lines indicate the nine Samy genes identified as overexpressed compared to the entire Samy phage genome across all non or poorly-induced conditions (Supplementary Table S6 ). The genome comparison was performed using Easyfig software (e-value <10 -3 ). The percentage identity between DNA homologous sequences in Samy and PhiC31 is shown in shades of gray. Other abbreviations: DNK (Deoxynucleoside monophosphate kinase), MCP (major capsid protein), MTP (Major tail protein), TSS (Terminal small subunit), TLS (Terminal large subunit), TMP (Tape measure protein).

Article Snippet: Supplementary Fig. S1 : GC content (A) and size (B) of a panel of 330 Streptomyces phages Supplementary Fig. S2 : Multidimensional analyses of the transcriptomes of S. ambofaciens ATCC 23877 grown under various conditions Supplementary Fig. S3 : Heatmaps of pSAM1 (A) and pSAM2 (B) transcriptomes in different growth conditions Supplementary Fig. S4: Samy expression profile under the different conditions studied Supplementary Fig. S5: Samy phage morphology and infection assays Supplementary Fig. S6: Results of high-throughput sequencing of the double-stranded DNA virome of Streptomyces ambofaciens ATCC 23877 grown 4 days in BM medium Supplementary Fig. S7: Morphology of S. ambofaciens and S. coelicolor after 4 days growth in BM medium Supplementary Fig. S8: Counting colony-forming units after 4 days of growth in BM medium of S. ambofaciens ATCC 23877 reference strain and its isogenic ΔSamy #clone 3 mutant supplemented with conditioned supernatants Supplementary Table S1 : Strains used in this study Supplementary Table S2 : Primers used in this study Supplementary Table S3 : Media used in this study Supplementary Table S4 : List and characteristics of 330 Streptomyces phages referenced in Actinophage Database, NCBI and/or ICTV.

Techniques: Dot Blot, Software

Journal: bioRxiv

Article Title: Phage-mediated dispersal of multicellular bacteria

doi: 10.1101/2023.07.22.549817

Figure Lengend Snippet: The supernatants of S. ambofaciens ATCC 23877 grown in different media (Supplementary Table S3 ) were harvested after 4 days and 0.2 µm-filtered. Phage titer was determined by qPCR after DNAse treatment. The pH of the medium and the antibacterial activity against Micrococcus luteus of the supernatant after 4 days of growth are indicated on the top. All media had an initial pH of 7.3 (± 0.1), except MP5 and MP5 devoid of MOPS which had a pH of 7.5 (± 0.1). All the boxplots represent the first quartile, median and third quartile. The upper whisker extends from the hinge to the largest value no further than 1.5 * the inter-quartile range (IQR, i.e . distance between the first and third quartiles). The lower whisker extends from the hinge to the smallest value at most 1.5 * IQR of the hinge. Each dot represents an independent experiment. The p values of two-sided Wilcoxon rank sum tests with continuity correction is indicated for each comparison to the viral titer observed in HT condition.

Article Snippet: Supplementary Fig. S1 : GC content (A) and size (B) of a panel of 330 Streptomyces phages Supplementary Fig. S2 : Multidimensional analyses of the transcriptomes of S. ambofaciens ATCC 23877 grown under various conditions Supplementary Fig. S3 : Heatmaps of pSAM1 (A) and pSAM2 (B) transcriptomes in different growth conditions Supplementary Fig. S4: Samy expression profile under the different conditions studied Supplementary Fig. S5: Samy phage morphology and infection assays Supplementary Fig. S6: Results of high-throughput sequencing of the double-stranded DNA virome of Streptomyces ambofaciens ATCC 23877 grown 4 days in BM medium Supplementary Fig. S7: Morphology of S. ambofaciens and S. coelicolor after 4 days growth in BM medium Supplementary Fig. S8: Counting colony-forming units after 4 days of growth in BM medium of S. ambofaciens ATCC 23877 reference strain and its isogenic ΔSamy #clone 3 mutant supplemented with conditioned supernatants Supplementary Table S1 : Strains used in this study Supplementary Table S2 : Primers used in this study Supplementary Table S3 : Media used in this study Supplementary Table S4 : List and characteristics of 330 Streptomyces phages referenced in Actinophage Database, NCBI and/or ICTV.

Techniques: Activity Assay, Whisker Assay

Journal: bioRxiv

Article Title: Phage-mediated dispersal of multicellular bacteria

doi: 10.1101/2023.07.22.549817

Figure Lengend Snippet: A. Kinetics of phage production. S. ambofaciens ATCC 23877 was grown in BM medium. The viral titer of supernatants filtered and DNAse-treated were determined by qPCR. Each color represents an independent experiment. The boxplot is plotted as described in the legend to . The p value of two-sided Wilcoxon rank sum tests with continuity correction is 0.0294 when comparing the viral titers at 24 h and 48h, and 1 (no difference) when comparing the evolution of the titer on the following days. B. Imaging of Samy phage produced by transmission electron microscopy. S. ambofaciens ATCC 23877 was grown during 4 days in BM medium. The supernatant was concentrated by CsCl-gradient ultracentrifugation. Viral particles were negatively stained with uranyl acetate. Scale bar: 100 nm.

Article Snippet: Supplementary Fig. S1 : GC content (A) and size (B) of a panel of 330 Streptomyces phages Supplementary Fig. S2 : Multidimensional analyses of the transcriptomes of S. ambofaciens ATCC 23877 grown under various conditions Supplementary Fig. S3 : Heatmaps of pSAM1 (A) and pSAM2 (B) transcriptomes in different growth conditions Supplementary Fig. S4: Samy expression profile under the different conditions studied Supplementary Fig. S5: Samy phage morphology and infection assays Supplementary Fig. S6: Results of high-throughput sequencing of the double-stranded DNA virome of Streptomyces ambofaciens ATCC 23877 grown 4 days in BM medium Supplementary Fig. S7: Morphology of S. ambofaciens and S. coelicolor after 4 days growth in BM medium Supplementary Fig. S8: Counting colony-forming units after 4 days of growth in BM medium of S. ambofaciens ATCC 23877 reference strain and its isogenic ΔSamy #clone 3 mutant supplemented with conditioned supernatants Supplementary Table S1 : Strains used in this study Supplementary Table S2 : Primers used in this study Supplementary Table S3 : Media used in this study Supplementary Table S4 : List and characteristics of 330 Streptomyces phages referenced in Actinophage Database, NCBI and/or ICTV.

Techniques: Imaging, Produced, Transmission Assay, Electron Microscopy, Staining

Journal: bioRxiv

Article Title: Phage-mediated dispersal of multicellular bacteria

doi: 10.1101/2023.07.22.549817

Figure Lengend Snippet: A. Growth and pH in BM and MP5 media. Each symbol represents an independent experiment. Due to the presence of large aggregates (see panel B), the pseudo-opacimetry (OD 600 nm ) was not exploitable for DSM 40697 strain after 48h of growth in BM medium. B. Dispersed versus aggregated growth of S. ambofaciens strains in BM media. The results are representative of the appearance of the most frequently observed cultures, as the quantity and size of cell clusters may vary from one experiment to the other. The S. ambofaciens ATCC 23877 Δ Samy strain corresponds to clone #3, deleted from at least the phage integrase by a CRIPSR-based approach (Supplementary Table S1 ). Scale bar: 1.5 cm. C. Microscopy of Streptomyces colonies after 4 days growth in BM medium . S. ambofaciens ATCC 23877 and its derivate CRISPR-deleted of Samy prophage (clone #3) were grown in BM medium and imaged using differential interference contrast microscopy (also see Supplementary Figure S7.A ). Scale bar: 10 µm. D. Colony forming units after 4 days of growth in BM medium . The S. ambofaciens ATCC 23877 ΔSamy strains correspond to three independent mutants (#1, #3 and #4) we obtained by a CRIPSR-based approach (Supplementary Table S1 ). The boxplot is plotted as described in the legend to . Each dot represents an independent experiment per condition. The p values of two-sided Wilcoxon rank sum tests with continuity correction are indicated for each comparison. Please note that this number is the result of both cell survival and mycelium dispersal (propensity to form separate colonies). E. Correlation between Samy phage production and colony forming units by diverse S. ambofaciens strains. S. ambofaciens strains obtained from distinct collections (Supplementary Table S1 ) were grown during 4 days in BM medium, before counting colony forming units and phage production in the supernatants. Even strains ATCC 23877 and DSM 40697 were cultured for this experiment from stocks produced by another laboratory. Each dot represents an independent experiment per strain. The correlation was analyzed by a Spearman’s rank correlation test. Results of two independent experiments. F. Bioassay performed with the supernatants of S. ambofaciens ATCC 23877 WT strain and its derivatives deleted in Samy regions (clones #1, #3 and #4 - Supplementary Table S1 ) cultures grown during 4 days in BM medium. The boxplot is plotted as described in the legend of . The p values of two-sided Wilcoxon rank sum tests with continuity correction are indicated.

Article Snippet: Supplementary Fig. S1 : GC content (A) and size (B) of a panel of 330 Streptomyces phages Supplementary Fig. S2 : Multidimensional analyses of the transcriptomes of S. ambofaciens ATCC 23877 grown under various conditions Supplementary Fig. S3 : Heatmaps of pSAM1 (A) and pSAM2 (B) transcriptomes in different growth conditions Supplementary Fig. S4: Samy expression profile under the different conditions studied Supplementary Fig. S5: Samy phage morphology and infection assays Supplementary Fig. S6: Results of high-throughput sequencing of the double-stranded DNA virome of Streptomyces ambofaciens ATCC 23877 grown 4 days in BM medium Supplementary Fig. S7: Morphology of S. ambofaciens and S. coelicolor after 4 days growth in BM medium Supplementary Fig. S8: Counting colony-forming units after 4 days of growth in BM medium of S. ambofaciens ATCC 23877 reference strain and its isogenic ΔSamy #clone 3 mutant supplemented with conditioned supernatants Supplementary Table S1 : Strains used in this study Supplementary Table S2 : Primers used in this study Supplementary Table S3 : Media used in this study Supplementary Table S4 : List and characteristics of 330 Streptomyces phages referenced in Actinophage Database, NCBI and/or ICTV.

Techniques: Microscopy, CRISPR, Cell Culture, Produced, Clone Assay

Journal: bioRxiv

Article Title: Phage-mediated dispersal of multicellular bacteria

doi: 10.1101/2023.07.22.549817

Figure Lengend Snippet: After germination of the spore, the multicellular bacteria form successively primary and secondary mycelia. In the absence of prophage, the S. ambofaciens DSM 40497 tends to form particularly large and dense pellets in response to metabolic stress encountered in BM medium (nitrogen unbalance, translation inhibition, basic pH). Under the same conditions, phage production by S. ambofaciens ATCC 23877 is correlated with dispersed growth in sparse clumps and filaments. We propose that phage-induced cell death within the secondary mycelium leads to a dislocation of multicellular aggregates. The subsequent increase in the number of small colonies promotes strain dispersal under stressful conditions.

Article Snippet: Supplementary Fig. S1 : GC content (A) and size (B) of a panel of 330 Streptomyces phages Supplementary Fig. S2 : Multidimensional analyses of the transcriptomes of S. ambofaciens ATCC 23877 grown under various conditions Supplementary Fig. S3 : Heatmaps of pSAM1 (A) and pSAM2 (B) transcriptomes in different growth conditions Supplementary Fig. S4: Samy expression profile under the different conditions studied Supplementary Fig. S5: Samy phage morphology and infection assays Supplementary Fig. S6: Results of high-throughput sequencing of the double-stranded DNA virome of Streptomyces ambofaciens ATCC 23877 grown 4 days in BM medium Supplementary Fig. S7: Morphology of S. ambofaciens and S. coelicolor after 4 days growth in BM medium Supplementary Fig. S8: Counting colony-forming units after 4 days of growth in BM medium of S. ambofaciens ATCC 23877 reference strain and its isogenic ΔSamy #clone 3 mutant supplemented with conditioned supernatants Supplementary Table S1 : Strains used in this study Supplementary Table S2 : Primers used in this study Supplementary Table S3 : Media used in this study Supplementary Table S4 : List and characteristics of 330 Streptomyces phages referenced in Actinophage Database, NCBI and/or ICTV.

Techniques: Inhibition