TY - GEN A1 - Friedrich, Ines A1 - Hollensteiner, Jacqueline A1 - Scherf, Janna A1 - Weyergraf, Judith A1 - Klassen, Anna A1 - Poehlein, Anja A1 - Hertel, Robert A1 - Daniel, Rolf T1 - Complete Genome Sequence of Stenotrophomonas indicatrix DAIF1 T2 - Microbiology Resource Announcements N2 - We present the complete genome of Stenotrophomonas indicatrix DAIF1, which was isolated from an oligotrophic pond in a water protection area. Whole-genome alignments indicated that strain DAIF1 belongs to the species Stenotrophomonas indicatrix. The whole genome (4,639,375 bp) harbors 4,108 protein-encoding genes, including 3,029 genes with assigned functions. Y1 - 2021 UR - https://mra.asm.org/content/10/6/e01484-20 U6 - https://doi.org/10.1128/MRA.01484-20 SN - 2576-098X VL - 10 IS - 6 SP - 1 EP - 3 ER - TY - GEN A1 - Hollensteiner, Jacqueline A1 - Friedrich, Ines A1 - Hollstein, Lucas A1 - Lamping, Jan-Philipp A1 - Wolf, Kalina A1 - Liesegang, Heiko A1 - Poehlein, Anja A1 - Hertel, Robert A1 - Daniel, Rolf T1 - Complete Genome Sequence of Kinneretia sp. Strain DAIF2, Isolated from a Freshwater Pond T2 - Microbiology Resource Announcements N2 - Kinneretia sp. strain DAIF2 was isolated from a eutrophic freshwater pond. The genome consists of a single chromosome (6,010,585 bp) with a GC content of 69.3%. The whole-genome-based phylogeny of DAIF2 revealed a closest relation to the genus Kinneretia. Y1 - 2021 UR - https://mra.asm.org/content/10/8/e00003-21 U6 - https://doi.org/10.1128/MRA.00003-21 SN - 2576-098X VL - 10 IS - 8 SP - 1 EP - 3 ER - TY - GEN A1 - Friedrich, Ines A1 - Hollensteiner, Jacqueline A1 - Schneider, Dominik A1 - Poehlein, Anja A1 - Hertel, Robert A1 - Daniel, Rolf T1 - First Complete Genome Sequences of Janthinobacterium lividum EIF1 and EIF2 and their Comparative Genome Analysis T2 - Genome Biology and Evolution N2 - We present the first two complete genomes of the Janthinobacterium lividum species, namely strains EIF1 and EIF2, which both possess the ability to synthesize violacein. The violet pigment violacein is a secondary metabolite with antibacterial, antifungal, antiviral, and antitumoral properties. Both strains were isolated from environmental oligotrophic water ponds in Göttingen. The strains were phylogenetically classified by ANI analysis and showed a species assignment to Janthinobacterium lividum with 97.72% (EIF1) and 97.66% (EIF2) identity. These are the first complete genome sequences of strains belonging to the species Janthinobacterium lividum. The genome of strain EIF1 consists of one circular chromosome (6,373,589 bp) with a GC-content of 61.98%. The genome contains 5,551 coding sequences, 122 rRNAs, 93 tRNAs, and 1 tm-RNA. The genome of EIF2 comprises one circular chromosome (6,399,352 bp) with a GC-content of 61.63% and a circular plasmid p356839 (356,839 bp) with a GC-content of 57.21%. The chromosome encodes 5,691 coding sequences, 122 rRNAs, 93 tRNAs, and 1 tm-RNA and the plasmid harbors 245 coding sequences. In addition to the highly conserved chromosomally encoded violacein operon, the plasmid comprises a non-ribosomal peptide synthetase cluster (NRPS) with similarity to xenoamicin, which is a bioactive compound effective against protozoan parasites. Y1 - 2020 UR - https://academic.oup.com/gbe/article/doi/10.1093/gbe/evaa148/5870831 U6 - https://doi.org/10.1093/gbe/evaa148 SN - 1759-6653 VL - 12 IS - 10 SP - 1782 EP - 1788 ER - TY - GEN A1 - Richts, Björn A1 - Hertel, Robert A1 - Potot, Sébastien A1 - Poehlein, Anja A1 - Daniel, Rolf A1 - Schyns, Ghislain A1 - Prágai, Zoltán A1 - Commichau, Fabian M. T1 - Complete Genome Sequence of the Prototrophic Bacillus subtilis subsp. subtilis Strain SP1 T2 - Microbiology Resource Announcements N2 - Here, we present the complete genome sequence of the Bacillus subtilis strain SP1. This strain is a descendant of the laboratory strain 168. The strain is suit- able for biotechnological applications because the prototrophy for tryptophan has been restored. Due to laboratory cultivation, the strain has acquired 24 additional sequence variations. Y1 - 2020 UR - https://mra.asm.org/content/9/32/e00825-20 U6 - https://doi.org/10.1128/MRA.00825-20 SN - 2576-098X VL - 9 IS - 32 ER - TY - GEN A1 - Hertel, Robert A1 - Schöne, Kerstin A1 - Mittelstädt, Carolin A1 - Meißner, Janek A1 - Zschoche, Nick A1 - Collignon, Madeline A1 - Kohler, Christian A1 - Friedrich, Ines A1 - Schneider, Dominik A1 - Hoppert, Michael A1 - Kuhn, Ramona A1 - Schwedt, Inge A1 - Scholz, Patricia A1 - Poehlein, Anja A1 - Martienssen, Marion A1 - Ischebeck, Till A1 - Daniel, Rolf A1 - Commichau, Fabian M. T1 - Characterization of glyphosate-resistant Burkholderia anthina and Burkholderia cenocepacia isolates from a commercial Roundup® solution T2 - Environmental Microbiology Reports N2 - Roundup® is the brand name for herbicide solutions containing glyphosate, which specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase of the shikimate pathway. The inhibition of the EPSP synthase causes plant death because EPSP is required for biosynthesis of aromatic amino acids. Glyphosate also inhibits the growth of archaea, bacteria, Apicomplexa, algae and fungi possessing an EPSP synthase. Here, we have characterized two glyphosate-resistant bacteria from a Roundup solution. Taxonomic classification revealed that the isolates 1CH1 and 2CH1 are Burkholderia anthina and Burkholderia cenocepacia strains respectively. Both isolates cannot utilize glyphosate as a source of phosphorus and synthesize glyphosate-sensitive EPSP synthase variants. Burkholderia. anthina 1CH1 and B. cenocepacia 2CH1 tolerate high levels of glyphosate because the herbicide is not taken up by the bacteria. Previously, it has been observed that the exposure of soil bacteria to herbicides like glyphosate promotes the development of antibiotic resistances. Antibiotic sensitivity testing revealed that the only the B. cenocepacia 2CH1 isolate showed increased resistance to a variety of antibiotics. Thus, the adaptation of B. anthina 1CH1 and B. cenocepacia 2CH1 to glyphosate did not generally increase the antibiotic resistance of both bacteria. However, our study confirms the genomic adaptability of bacteria belonging to the genus Burkholderia. Y1 - 2022 U6 - https://doi.org/10.1111/1758-2229.13022 SN - 1758-2229 VL - 14 IS - 1 SP - 70 EP - 84 ER - TY - GEN A1 - Richts, Björn A1 - Lentes, Sabine A1 - Poehlein, Anja A1 - Daniel, Rolf A1 - Commichau, Fabian M. T1 - A Bacillus subtilis ΔpdxT mutant suppresses vitamin B6 limitation by acquiring mutations enhancing pdxS gene dosage and ammonium assimilation T2 - Environmental Microbiology Reports N2 - Pyridoxal‐5’‐phosphate (PLP), the biologically active form of vitamin B6, serves as a cofactor for many enzymes. The Gram‐positive model bacterium Bacillus subtilis synthesizes PLP via the PdxST enzyme complex, consisting of the PdxT glutaminase and the PdxS PLP synthase subunits, respectively. PdxT converts glutamine to glutamate and ammonia of which the latter is channelled to PdxS. At high extracellular ammonium concentrations, the PdxS PLP synthase subunit does not depend on PdxT. Here, we assessed the potential of a B. subtilis ΔpdxT mutant to adapt to PLP limitation at the genome level. The majority of ΔpdxT suppressors had amplified a genomic region containing the pdxS gene. We also identified mutants having acquired as yet undescribed mutations in ammonium assimilation genes, indicating that the overproduction of PdxS and the NrgA ammonium transporter partially relieve vitamin B6 limitation in a ΔpdxT mutant when extracellular ammonium is scarce. Furthermore, we found that PdxS positively affects complex colony formation in B. subtilis. The catalytic mechanism of the PdxS PLP synthase subunit could be the reason for the limited evolution of the enzyme and why we could not identify a PdxS variant producing PLP independently of PdxT at low ammonium concentrations. Y1 - 2021 UR - https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1758-2229.12936 U6 - https://doi.org/10.1111/1758-2229.12936 SN - 1758-2229 VL - 13 IS - 2 SP - 218 EP - 233 ER - TY - GEN A1 - Kohm, Katharina A1 - Floccari, Valentina A1 - Lutz, Veronika A1 - Nordmann, Birthe A1 - Mittelstädt, Carolin A1 - Poehlein, Anja A1 - Dragos, Anna A1 - Commichau, Fabian M. A1 - Hertel, Robert T1 - The Bacillus phage SPβ and its relatives: A temperate phage model system reveals new strains, species, prophage integration loci, conserved proteins and lysogeny management components T2 - bioRxiv beta N2 - The Bacillus phage SPβ has been known for about 50 years, but only a few strains are avalible. We isolated four new wild type strains of the SPbeta species. Phage vB_BsuS-Goe14 introduces its prophage into the spoVK locus, previously not observed to be used by SPβ-like phages. We could also reveal the SPβ-like phage genome replication strategy, the genome packaging mode, and the phage genome opening point. We extracted 55 SPβ-like prophages from public Bacillus genomes, thereby discovering three more integration loci and one additional type of integrase. The identified prophages resembled four new species clusters and three species orphans in the genus Spbetavirus. The determined core proteome of all SPβ-like prophages consists of 38 proteins. The integration cassette proved to be not conserved even though present in all strains. It consists of distinct integrases. Analysis of SPβ transcriptomes revealed three conserved genes, yopQ, yopR, and yokI, to be transcribed from a dormant prophage. While yopQ and yokI could be deleted from the prophage without activating the prophage, damaging of yopR led to a clear-plaque phenotype. Under the applied laboratory conditions, the yokI mutant showed an elevated virion release implying the YokI protein being a component of the arbitrium system. Y1 - 2021 UR - https://www.biorxiv.org/content/10.1101/2021.11.22.469490v1 U6 - https://doi.org/10.1101/2021.11.22.469490 ER - TY - GEN A1 - Michalik, Stephan A1 - Reder, Alexander A1 - Richts, Björn A1 - Faßhauer, Patrick A1 - Mäder, Ulrike A1 - Pedreira, Tiago A1 - Poehlein, Anja A1 - Heel, Auke van A1 - Tilburg, Amanda van A1 - Altenbuchner, Josef A1 - Klewing, Anika A1 - Reuß, Daniel A1 - Daniel, Rolf A1 - Commichau, Fabian M. A1 - Kuipers, Oscar A1 - Hamoen, Leendert A1 - Völker, Uwe A1 - Stülke, Jörg T1 - The Bacillus subtilis Minimal Genome Compendium T2 - ACS Synthetic Biology N2 - To better understand cellular life, it is essential to decipher the contribution of individual components and their interactions. Minimal genomes are an important tool to investigate these interactions. Here, we provide a database of 105 fully annotated genomes of a series of strains with sequential deletion steps of the industrially relevant model bacterium Bacillus subtilis starting with the laboratory wild type strain B. subtilis 168 and ending with B. subtilis PG38, which lacks approximately 40% of the original genome. The annotation is supported by sequencing of key intermediate strains as well as integration of literature knowledge for the annotation of the deletion scars and their potential effects. The strain compendium presented here represents a comprehensive genome library of the entire MiniBacillus project. This resource will facilitate the more effective application of the different strains in basic science as well as in biotechnology. Y1 - 2021 UR - https://pubs.acs.org/doi/10.1021/acssynbio.1c00339 U6 - https://doi.org/10.1021/acssynbio.1c00339 SN - 2161-5063 VL - 10 IS - 10 SP - 2767 EP - 2771 ER -