Gunka, Katrin

[["dc.bibliographiccitation.firstpage","1"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC Genomics"],["dc.bibliographiccitation.lastpage","14"],["dc.bibliographiccitation.volume","19"],["dc.contributor.author","Groß, Uwe"],["dc.contributor.author","Brzuszkiewicz, Elzbieta B."],["dc.contributor.author","Gunka, Katrin"],["dc.contributor.author","Starke, Jessica"],["dc.contributor.author","Riedel, Thomas"],["dc.contributor.author","Bunk, Boyke"],["dc.contributor.author","Spröer, Cathrin"],["dc.contributor.author","Wetzel, Daniela"],["dc.contributor.author","Poehlein, Anja"],["dc.contributor.author","Chibani, Cynthia"],["dc.contributor.author","Bohne, Wolfgang"],["dc.contributor.author","Overmann, Jörg"],["dc.contributor.author","Zimmermann, Ortrud"],["dc.contributor.author","Daniel, Rolf"],["dc.contributor.author","Liesegang, Heiko"],["dc.date.accessioned","2019-07-09T11:45:11Z"],["dc.date.available","2019-07-09T11:45:11Z"],["dc.date.issued","2018"],["dc.description.abstract","BACKGROUND: Clostridioides difficile infections (CDI) have emerged over the past decade causing symptoms that range from mild, antibiotic-associated diarrhea (AAD) to life-threatening toxic megacolon. In this study, we describe a multiple and isochronal (mixed) CDI caused by the isolates DSM 27638, DSM 27639 and DSM 27640 that already initially showed different morphotypes on solid media. RESULTS: The three isolates belonging to the ribotypes (RT) 012 (DSM 27639) and 027 (DSM 27638 and DSM 27640) were phenotypically characterized and high quality closed genome sequences were generated. The genomes were compared with seven reference strains including three strains of the RT 027, two of the RT 017, and one of the RT 078 as well as a multi-resistant RT 012 strain. The analysis of horizontal gene transfer events revealed gene acquisition incidents that sort the strains within the time line of the spread of their RTs within Germany. We could show as well that horizontal gene transfer between the members of different RTs occurred within this multiple infection. In addition, acquisition and exchange of virulence-related features including antibiotic resistance genes were observed. Analysis of the two genomes assigned to RT 027 revealed three single nucleotide polymorphisms (SNPs) and apparently a regional genome modification within the flagellar switch that regulates the fli operon. CONCLUSION: Our findings show that (i) evolutionary events based on horizontal gene transfer occur within an ongoing CDI and contribute to the adaptation of the species by the introduction of new genes into the genomes, (ii) within a multiple infection of a single patient the exchange of genetic material was responsible for a much higher genome variation than the observed SNPs."],["dc.description.sponsorship","Open-Access-Publikationsfonds 2018"],["dc.identifier.doi","10.1186/s12864-017-4368-0"],["dc.identifier.pmid","29291715"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/15054"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/59178"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.notes.intern","In goescholar not merged with http://resolver.sub.uni-goettingen.de/purl?gs-1/15123 but duplicate"],["dc.notes.status","final"],["dc.relation.issn","1471-2164"],["dc.rights","CC BY 4.0"],["dc.rights.access","openAccess"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.subject.ddc","570"],["dc.title","Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","1843"],["dc.bibliographiccitation.journal","Frontiers in Microbiology"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Seugendo, Mwanaisha"],["dc.contributor.author","Janssen, Iryna"],["dc.contributor.author","Lang, Vanessa"],["dc.contributor.author","Hasibuan, Irene"],["dc.contributor.author","Bohne, Wolfgang"],["dc.contributor.author","Cooper, Paul"],["dc.contributor.author","Daniel, Rolf"],["dc.contributor.author","Gunka, Katrin"],["dc.contributor.author","Kusumawati, R. L."],["dc.contributor.author","Mshana, Stephen E."],["dc.contributor.author","von Müller, Lutz"],["dc.contributor.author","Okamo, Benard"],["dc.contributor.author","Ortlepp, Jan R."],["dc.contributor.author","Overmann, Jörg"],["dc.contributor.author","Riedel, Thomas"],["dc.contributor.author","Rupnik, Maja"],["dc.contributor.author","Zimmermann, Ortrud"],["dc.contributor.author","Groß, Uwe"],["dc.date.accessioned","2019-07-09T11:45:47Z"],["dc.date.available","2019-07-09T11:45:47Z"],["dc.date.issued","2018"],["dc.description.abstract","Clostridioides (Clostridium) difficile infections (CDI) are considered worldwide as emerging health threat. Uptake of C. difficile spores may result in asymptomatic carrier status or lead to CDI that could range from mild diarrhea, eventually developing into pseudomembranous colitis up to a toxic megacolon that often results in high mortality. Most epidemiological studies to date have been performed in middle- and high income countries. Beside others, the use of antibiotics and the composition of the microbiome have been identified as major risk factors for the development of CDI. We therefore postulate that prevalence rates of CDI and the distribution of C. difficile strains differ between geographical regions depending on the regional use of antibiotics and food habits. A total of 593 healthy control individuals and 608 patients suffering from diarrhea in communities in Germany, Ghana, Tanzania and Indonesia were selected for a comparative multi-center cross-sectional study. The study populations were screened for the presence of C. difficile in stool samples. Cultured C. difficile strains (n = 84) were further subtyped and characterized using PCR-ribotyping, determination of toxin production, and antibiotic susceptibility testing. Prevalence rates of C. difficile varied widely between the countries. Whereas high prevalence rates were observed in symptomatic patients living in Germany and Indonesia (24.0 and 14.7%), patients from Ghana and Tanzania showed low detection rates (4.5 and 6.4%). Differences were also obvious for ribotype distribution and toxin repertoires. Toxin A+/B+ ribotypes 001/072 and 078 predominated in Germany, whereas most strains isolated from Indonesian patients belonged to toxin A+/B+ ribotype SLO160 and toxin A-/B+ ribotype 017. With 42.9-73.3%, non-toxigenic strains were most abundant in Africa, but were also found in Indonesia at a rate of 18.2%. All isolates were susceptible to vancomycin and metronidazole. Mirroring the antibiotic use, however, moxifloxacin resistance was absent in African C. difficile isolates but present in Indonesian (24.2%) and German ones (65.5%). This study showed that CDI is a global health threat with geographically different prevalence rates which might reflect distinct use of antibiotics. Significant differences for distributions of ribotypes, toxin production, and antibiotic susceptibilities were observed."],["dc.identifier.doi","10.3389/fmicb.2018.01843"],["dc.identifier.pmid","30131799"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/15318"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/59311"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","1664-302X"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.subject.ddc","610"],["dc.title","Prevalence and Strain Characterization of Clostridioides (Clostridium) difficile in Representative Regions of Germany, Ghana, Tanzania and Indonesia - A Comparative Multi-Center Cross-Sectional Study"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","170152"],["dc.bibliographiccitation.journal","Scientific data"],["dc.bibliographiccitation.volume","4"],["dc.contributor.author","Schneider, Dominik"],["dc.contributor.author","Thürmer, Andrea"],["dc.contributor.author","Gollnow, Kathleen"],["dc.contributor.author","Lugert, Raimond"],["dc.contributor.author","Gunka, Katrin"],["dc.contributor.author","Groß, Uwe"],["dc.contributor.author","Daniel, Rolf"],["dc.date.accessioned","2019-07-09T11:44:31Z"],["dc.date.available","2019-07-09T11:44:31Z"],["dc.date.issued","2017-10-17"],["dc.description.abstract","We present bacterial 16S rRNA gene datasets derived from stool samples of 44 patients with diarrhea indicative of a Clostridioides difficile infection. For 20 of these patients, C. difficile infection was confirmed by clinical evidence. Stool samples from patients originating from Germany, Ghana, and Indonesia were taken and subjected to DNA isolation. DNA isolations of stool samples from 35 asymptomatic control individuals were performed. The bacterial community structure was assessed by 16S rRNA gene analysis (V3-V4 region). Metadata from patients and control individuals include gender, age, country, presence of diarrhea, concomitant diseases, and results of microbiological tests to diagnose C. difficile presence. We provide initial data analysis and a dataset overview. After processing of paired-end sequencing data, reads were merged, quality-filtered, primer sequences removed, reads truncated to 400 bp and dereplicated. Singletons were removed and sequences were sorted by cluster size, clustered at 97% sequence similarity and chimeric sequences were discarded. Taxonomy to each operational taxonomic unit was assigned by BLASTn searches against Silva database 123.1 and a table was constructed."],["dc.identifier.doi","10.1038/sdata.2017.152"],["dc.identifier.pmid","29039846"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/14810"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/59030"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.relation.issn","2052-4463"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.subject.ddc","610"],["dc.title","Gut bacterial communities of diarrheic patients with indications of Clostridioides difficile infection."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","eaal3011"],["dc.bibliographiccitation.issue","475"],["dc.bibliographiccitation.journal","Science Signaling"],["dc.bibliographiccitation.volume","10"],["dc.contributor.author","Gundlach, Jan"],["dc.contributor.author","Herzberg, Christina"],["dc.contributor.author","Kaever, Volkhard"],["dc.contributor.author","Gunka, Katrin"],["dc.contributor.author","Hoffmann, Tamara"],["dc.contributor.author","Weiss, Martin"],["dc.contributor.author","Gibhardt, Johannes"],["dc.contributor.author","Thuermer, Andrea"],["dc.contributor.author","Hertel, Dietrich"],["dc.contributor.author","Daniel, Rolf"],["dc.contributor.author","Bremer, Erhard"],["dc.contributor.author","Commichau, Fabian M."],["dc.contributor.author","Stulke, Joerg"],["dc.date.accessioned","2018-11-07T10:24:56Z"],["dc.date.available","2018-11-07T10:24:56Z"],["dc.date.issued","2017"],["dc.description.abstract","The second messenger cyclic di-adenosine monophosphate (c-di-AMP) is essential in the Gram-positive model organism Bacillus subtilis and in related pathogenic bacteria. It controls the activity of the conserved ydaO riboswitch and of several proteins involved in potassium (K+) uptake. We found that the YdaO protein was conserved among several different bacteria and provide evidence that YdaO functions as a K+ transporter. Thus, we renamed the gene and protein KimA (K+ importer A). Reporter activity assays indicated that expression beyond the c-di-AMP-responsive riboswitch of the kimA upstream regulatory region occurred only in bacteria grown in medium containing low K+ concentrations. Furthermore, mass spectrometry analysis indicated that c-di-AMP accumulated in bacteria grown in the presence of high K+ concentrations but not in low concentrations. A bacterial strain lacking all genes encoding c-di-AMP-synthesizing enzymes was viable when grown in medium containing low K+ concentrations, but not at higher K+ concentrations unless it acquired suppressor mutations in the gene encoding the cation exporter NhaK. Thus, our results indicated that the control of potassium homeostasis is an essential function of c-di-AMP."],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft [SPP1879]"],["dc.identifier.doi","10.1126/scisignal.aal3011"],["dc.identifier.isi","000400128400003"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/42751"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Amer Assoc Advancement Science"],["dc.relation.issn","1937-9145"],["dc.relation.issn","1945-0877"],["dc.title","Control of potassium homeostasis is an essential function of the second messenger cyclic di-AMP in Bacillus subtilis"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","7088"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","7102"],["dc.bibliographiccitation.volume","49"],["dc.contributor.author","Benda, Martin"],["dc.contributor.author","Woelfel, Simon"],["dc.contributor.author","Faßhauer, Patrick"],["dc.contributor.author","Gunka, Katrin"],["dc.contributor.author","Klumpp, Stefan"],["dc.contributor.author","Poehlein, Anja"],["dc.contributor.author","Kálalová, Debora"],["dc.contributor.author","Šanderová, Hana"],["dc.contributor.author","Daniel, Rolf"],["dc.contributor.author","Krásný, Libor"],["dc.contributor.author","Stülke, Jörg"],["dc.date.accessioned","2021-09-01T06:42:09Z"],["dc.date.available","2021-09-01T06:42:09Z"],["dc.date.issued","2021"],["dc.description.abstract","Abstract RNA turnover is essential in all domains of life. The endonuclease RNase Y (rny) is one of the key components involved in RNA metabolism of the model organism Bacillus subtilis. Essentiality of RNase Y has been a matter of discussion, since deletion of the rny gene is possible, but leads to severe phenotypic effects. In this work, we demonstrate that the rny mutant strain rapidly evolves suppressor mutations to at least partially alleviate these defects. All suppressor mutants had acquired a duplication of an about 60 kb long genomic region encompassing genes for all three core subunits of the RNA polymerase—α, β, β′. When the duplication of the RNA polymerase genes was prevented by relocation of the rpoA gene in the B. subtilis genome, all suppressor mutants carried distinct single point mutations in evolutionary conserved regions of genes coding either for the β or β’ subunits of the RNA polymerase that were not tolerated by wild type bacteria. In vitro transcription assays with the mutated polymerase variants showed a severe decrease in transcription efficiency. Altogether, our results suggest a tight cooperation between RNase Y and the RNA polymerase to establish an optimal RNA homeostasis in B. subtilis cells."],["dc.description.abstract","Abstract RNA turnover is essential in all domains of life. The endonuclease RNase Y (rny) is one of the key components involved in RNA metabolism of the model organism Bacillus subtilis. Essentiality of RNase Y has been a matter of discussion, since deletion of the rny gene is possible, but leads to severe phenotypic effects. In this work, we demonstrate that the rny mutant strain rapidly evolves suppressor mutations to at least partially alleviate these defects. All suppressor mutants had acquired a duplication of an about 60 kb long genomic region encompassing genes for all three core subunits of the RNA polymerase—α, β, β′. When the duplication of the RNA polymerase genes was prevented by relocation of the rpoA gene in the B. subtilis genome, all suppressor mutants carried distinct single point mutations in evolutionary conserved regions of genes coding either for the β or β’ subunits of the RNA polymerase that were not tolerated by wild type bacteria. In vitro transcription assays with the mutated polymerase variants showed a severe decrease in transcription efficiency. Altogether, our results suggest a tight cooperation between RNase Y and the RNA polymerase to establish an optimal RNA homeostasis in B. subtilis cells."],["dc.identifier.doi","10.1093/nar/gkab528"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/88991"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-455"],["dc.relation.eissn","1362-4962"],["dc.relation.issn","0305-1048"],["dc.title","Quasi-essentiality of RNase Y in Bacillus subtilis is caused by its critical role in the control of mRNA homeostasis"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]