draft genome sequencing and sequence data  (Biotechnology Information)

Journal: Frontiers in Microbiology

Article Title: Thiamine-Mediated Cooperation Between Auxotrophic Rhodococcus ruber ZM07 and Escherichia coli K12 Drives Efficient Tetrahydrofuran Degradation

doi: 10.3389/fmicb.2020.594052

Figure Lengend Snippet: Strains and plasmids used in this study.

Article Snippet: The draft genome sequence data of strain ZM07 have been included in the National Center for Biotechnology Information (NCBI), accession number JACVXT000000000 , and strain K12 genome sequence data can also be found in NCBI (GenBank accession number NC_000913.3 ).

Techniques: Mutagenesis, Plasmid Preparation, Expressing

Journal: Frontiers in Microbiology

Article Title: Thiamine-Mediated Cooperation Between Auxotrophic Rhodococcus ruber ZM07 and Escherichia coli K12 Drives Efficient Tetrahydrofuran Degradation

doi: 10.3389/fmicb.2020.594052

Figure Lengend Snippet: THF degradation and growth curves of strain ZM07 monocultured (A) and cocultured with strain K12 (B) in the first, second and third transfers. The solid lines represent THF concentration curves; the dotted lines represent growth curves (OD 600 ); the circles represent the first transfer; the squares represent the second transfer; and the triangles represent the third transfer. Error bars: SD from three independent replicates, which may be smaller than the marker.

Article Snippet: The draft genome sequence data of strain ZM07 have been included in the National Center for Biotechnology Information (NCBI), accession number JACVXT000000000 , and strain K12 genome sequence data can also be found in NCBI (GenBank accession number NC_000913.3 ).

Techniques: Concentration Assay, Marker

Journal: Frontiers in Microbiology

Article Title: Thiamine-Mediated Cooperation Between Auxotrophic Rhodococcus ruber ZM07 and Escherichia coli K12 Drives Efficient Tetrahydrofuran Degradation

doi: 10.3389/fmicb.2020.594052

Figure Lengend Snippet: Comparison of the KEGG metabolic pathways reconstructed from the complete genomes of ZM07 and K12. Here, thiamine metabolism (map00730) is shown. The ZM07-specific pathways are colored in green; the K12-specific pathways are colored in blue; shared pathways are colored in brown; and pathways present in neither ZM07 nor K12 are colored in white. The genes for thiF (No. 2.7.7.73), thiH (No. 4.1.99.19), and thiI (No. 2.8.1.4) are highlighted by purple boxes, and the gene for thiE (No. 2.5.1.3) is highlighted by red boxes.

Article Snippet: The draft genome sequence data of strain ZM07 have been included in the National Center for Biotechnology Information (NCBI), accession number JACVXT000000000 , and strain K12 genome sequence data can also be found in NCBI (GenBank accession number NC_000913.3 ).

Techniques: Comparison

Journal: Frontiers in Microbiology

Article Title: Thiamine-Mediated Cooperation Between Auxotrophic Rhodococcus ruber ZM07 and Escherichia coli K12 Drives Efficient Tetrahydrofuran Degradation

doi: 10.3389/fmicb.2020.594052

Figure Lengend Snippet: (A) Growth curves of strain ZM07 monocultured (pink line) and cocultured with K12 under the non-contact condition (blue line) in two-phase reactors and the growth curve of the two strains cocultured under the contact condition (yellow line). (B) THF degradation curves of strain ZM07 in the three cases described above. (C) Growth curve of strain K12 cocultured with ZM07 under the non-contact condition in a two-phase reactor. (D) Two-phase reactor used to separate the cultured strains in this study. The P -value indicates a significant difference between monocultured strain ZM07 and strain ZM07 cocultured with K12 in two-phase reactors and was determined using Student’s t -test ( n = 3, ∗∗∗ p < 0.001). Error bars: SD from three independent replicates, which may be smaller than the marker.

Article Snippet: The draft genome sequence data of strain ZM07 have been included in the National Center for Biotechnology Information (NCBI), accession number JACVXT000000000 , and strain K12 genome sequence data can also be found in NCBI (GenBank accession number NC_000913.3 ).

Techniques: Cell Culture, Marker

Journal: Frontiers in Microbiology

Article Title: Thiamine-Mediated Cooperation Between Auxotrophic Rhodococcus ruber ZM07 and Escherichia coli K12 Drives Efficient Tetrahydrofuran Degradation

doi: 10.3389/fmicb.2020.594052

Figure Lengend Snippet: Relative abundances of ZM07, K12, and K12Δ thiE in a two-strain system (ZM07 and K12) (A) and in a three-strain system (B) across different transfers without thiamine. Relative abundances of three strains in a two-strain system (ZM07 and trace amount of K12) (C) and in a three-strain system (ZM07, K12 and trace amount of K12Δ thiE ) (D) across different transfers. The plots within (B,D) show details of the relative abundance of K12Δ thiE in corresponding experiments. Three independent replicates were performed for each group. Error bars: SD from three independent replicates.

Article Snippet: The draft genome sequence data of strain ZM07 have been included in the National Center for Biotechnology Information (NCBI), accession number JACVXT000000000 , and strain K12 genome sequence data can also be found in NCBI (GenBank accession number NC_000913.3 ).

Techniques:

Journal: Frontiers in Microbiology

Article Title: Thiamine-Mediated Cooperation Between Auxotrophic Rhodococcus ruber ZM07 and Escherichia coli K12 Drives Efficient Tetrahydrofuran Degradation

doi: 10.3389/fmicb.2020.594052

Figure Lengend Snippet: Relative abundances of ZM07, K12, and K12Δ thiE in two-strain systems (ZM07 and K12) (A) , (ZM07 and K12Δ thiE ) (B) and a three-strain system (C) in different transfers with 0.01 mM thiamine. (D) Relative abundances of K12 and K12Δ thiE in the above experiments in two-strain systems (the relative abundance of strain K12 in a cocultured system of ZM07 and K12 in (A) and the relative abundance of strain K12Δ thiE in a cocultured system of ZM07 and K12Δ thiE in panel (B) in different transfers with 0.01 mM thiamine. (E) Relative abundances of K12 and K12Δ thiE in the above experiments in the three-strain system (ZM07, K12, and K12Δ thiE in (C) in different transfers with 0.01 mM thiamine. Three independent replicates were performed for each group. Error bars: SD from three independent replicates. The P value indicates statistical significance between K12 and K12Δ thiE determined using Student’s t -test ( n = 3, ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001).

Article Snippet: The draft genome sequence data of strain ZM07 have been included in the National Center for Biotechnology Information (NCBI), accession number JACVXT000000000 , and strain K12 genome sequence data can also be found in NCBI (GenBank accession number NC_000913.3 ).

Techniques:

Journal: Frontiers in Microbiology

Article Title: Thiamine-Mediated Cooperation Between Auxotrophic Rhodococcus ruber ZM07 and Escherichia coli K12 Drives Efficient Tetrahydrofuran Degradation

doi: 10.3389/fmicb.2020.594052

Figure Lengend Snippet: Proposed schematic depiction of the interaction mechanism among strains ZM07, K12, and K12Δ thiE during THF degradation. Strain K12 provides thiamine (red circles) to ZM07 and K12Δ thiE , and strain ZM07 might provide succinate or other downstream products (purple diamonds) to K12 and K12Δ thiE as a carbon source by degrading THF. In thiamine-free medium, ZM07 and K12 formed a stable symbiotic system, and K12Δ thiE disappeared during passaging; in thiamine-rich media, both K12 and K12Δ thiE represented only a small proportion of the coculture system.

Article Snippet: The draft genome sequence data of strain ZM07 have been included in the National Center for Biotechnology Information (NCBI), accession number JACVXT000000000 , and strain K12 genome sequence data can also be found in NCBI (GenBank accession number NC_000913.3 ).

Techniques: Passaging