Publications

@article{nokey_82,

title = {Accurately assembling nanopore sequencing data of highly pathogenic bacteria},

author = {Christine Thomas and Hanka Brangsch and Valentina Galeone and Martin Hölzer and Manja Marz and Jörg Linde},

doi = {10.1186/s12864-025-11793-6},

year  = {2025},

date = {2025-08-28},

journal = {BMC Genomics},

volume = {26},

abstract = {Background: Bacterial genome exploration and outbreak analysis rely heavily on robust whole-genome sequencing and bioinformatics analysis. Widely-used genomic methods, such as genotyping and detection of genetic markers demand high sequencing accuracy and precise genome assembly for reliable results.

Methods: To assess the utility of nanopore sequencing for genotyping highly pathogenic bacteria with low mutation rates, we sequenced six reference strains using Oxford Nanopore Technologies (ONT) R10.4.1 chemistry and Illumina and evaluated different assembly strategies. The publicly available RefSeq assemblies were chosen as the ground truth. Publicly available sequencing data from key foodborne and public-health-related bacterial pathogens were examined to provide a broader context for the analysis.

Results: While for Bacillus (Ba.) anthracis an almost perfect assembly was achieved, results varied for other species. For Brucella (Br.) spp., the final assemblies comprised five to 46 different nucleotides in comparison to Sanger-sequenced references. For some key foodborne and public-health-related bacterial pathogens (Klebsiella (K.) variicola, Listeria spp., Mycobacterium (M.) tuberculosis, Staphylococcus (Sta.) aureus, and Streptococcus (Str.) pyogenes) perfect genomes were obtained. Enhanced basecalling models have generally improved assembly accuracy, however, for certain species such as Br. abortus, older models have produced higher accuracy. While long-read polishing mainly improves assembly quality with only one round needed, our results indicate that this process may also degrade assembly quality. Overall, 81% of the observed errors in ONT assemblies were located within coding sequences (CDS). Furthermore, we found that methylation caused 6.5% of the errors, and the bacterial methylation-aware medaka polishing model reduced the number of errors linked to methylation. Core-genome Multilocus Sequence Typing (cgMLST) analysis revealed allele differences in Ba. anthracis, Br. abortus, and Francisella (F.) tularensis for some assemblers, although with fewer than five allele differences. In the case of Br. melitensis, some assemblies included five allele differences, whereas for Br. suis the correct cgMLST alleles were observed.

Conclusions: Assembling nanopore data from pathogenic bacteria vary in quality across different species and methods. However, errors persist in the final assemblies, including within cgMLST loci, influencing the reliability of outbreak predictions. Nevertheless, specific combinations of existing tools can generate perfect genome assemblies from bacterial ONT sequencing data for outbreak analysis without short-read polishing.},

keywords = {assembly, bacteria, DNA / genomics, nanopore},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_78,

title = {Identification and functional genomic analyses of Bartonella isolates from honey bees, and reassessment of the taxonomy of the genus Bartonella},

author = {Juliana Botero and Nikolas Basler and Margo Cnockaert and Charlotte Peeters and Maria Schreiber and Manja Marz and Dirk C. {de Graaf} and Jelle Matthijnssens and Peter Vandamme},

doi = {10.1016/j.syapm.2025.126625},

isbn = {0723-2020},

year  = {2025},

date = {2025-06-06},

journal = {Systematic and Applied Microbiology},

volume = {48},

abstract = {We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and whole-genome sequence analyses to identify 90 Bartonella isolates from honey bee gut samples in Belgium. While the identification of 62 isolates as Bartonella apihabitans and three as Bartonella choladocola was straightforward, the identification of 25 Bartonella apis-like isolates was challenging. A taxonomic and functional analysis of four B. apis-like genomes and of publicly available B. apis genomes demonstrated that neither OrthoANIu and digital DNA-DNA hybridization analyses, nor functional annotation supported a clear separation of B. apis and B. apis-like genomes. Different phylogenomic analyses showed that B. apis and B. apis-like strains formed a monophyletic clade with an inconsistent internal structure. We therefore considered the remaining 25 isolates identified as B. apis. We subsequently re-addressed an earlier phylogenetic and functional divergence between three major clades of Bartonella species which differed not only in phylogenomic position and ecology, but also in genome size and genomic percentage G + C content, and in many metabolic capabilities. We propose to reclassify the single species of the Bartonella tamiae clade into the novel genus Attibartonella gen. nov., with Attibartonella tamiae comb. nov. as the type species. Similarly, we propose to reclassify species of the honey bee-associated Bartonella clade into the novel genus Ditibartonella gen. nov., with Ditibartonella apis comb. nov. as the type species. The phylogenomic analyses of publicly available genome and metagenome sequences revealed additional Ditibartonella species in honey bee samples, highlighted an evolutionary adaptation of Ditibartonella bacteria to bee hosts and suggested shared transmission routes.},

keywords = {bacteria, classification, DNA / genomics, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_76,

title = {Immunity and bacterial recruitment in plant leaves are parallel processes that together shape sensitivity to temperature stress},

author = {Jisna Jose and Erik Teutloff and Teresa Mayer and Simrat Naseem and Emanuel Barth and Rayko Halitschke and Manja Marz and Matthew T. Agler},

doi = {10.1101/2024.06.10.598336},

year  = {2025},

date = {2025-04-25},

journal = {bioRxiv},

abstract = {Rising global temperatures necessitate developing resilient crops with better adaptability to changing climates. Under elevated temperatures, plant immunity is downregulated, increasing risk of foliar pathogen attack. Manipulating plant defense hormones is one way to mitigate this detrimental effect. However, it is unclear how plant immunity interacts with plant microbiome assembly and how temperature will thus affect overall plant health and stability. In this study, we compared two Arabidopsis thaliana genotypes that feature divergent strategies for recruitment of commensal bacteria from natural soil. NG2, an A. thaliana ecotype we collected from Jena, Germany, was grown in its native soil and compared to CLLF, a genotype that recruits higher bacterial loads and higher bacterial diversity but without any dysbiotic phenotype. CLLF hyperaccumulates salicylic acid (SA) and jasmonates, has constitutively upregulated innate defenses, and shows increased resistance to necrotrophic fungal and hemi-biotrophic bacterial pathogens, indicating that pathogen immunity and non-pathogen recruitment function in parallel. Some of its leaf bacteria can utlize SA as a carbon source, suggesting that immunity and recruitment may even be linked by chemical hormones. CLLF exhibits high tolerance to heat stress in comparison to the NG2, with SA-associated defense processes remaining active under heat. Synthetic community (SynCom) experiments revealed that when the taxonomic diversity of bacteria available to CLLF is artificially reduced, resilience to heat stress is compromised, leading to dysbiosis. However, this dysbiosis does not occur in CLLF with a full SynCom or in the NG2 with any SynCom. These findings suggest that the downregulation of defenses in response to heat may contribute to the avoidance of dysbiosis caused by certain leaf bacteria, while full bacteriome taxonomic diversity can help maintain balance.Competing Interest StatementThe authors have declared no competing interest.},

keywords = {bacteria, evolution, fungi, metagenomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_95,

title = {Multiplex Real-Time Polymerase Chain Reaction and Recombinase Polymerase Amplification: Methods for Quick and Cost-Effective Detection of Vancomycin-Resistant Enterococci (VRE)},

author = {Ibukun Elizabeth Osadare and Abdinasir Abdilahi and Martin Reinicke and Celia Diezel and Maximilian Collatz and Annett Reissig and Stefan Monecke and Ralf Ehricht},

doi = {10.3390/antibiotics14030295},

year  = {2025},

date = {2025-03-12},

journal = {Antibiotics},

volume = {14},

abstract = {Background/Objectives: Vancomycin-resistant enterococci (VRE) are one of the leading causes of antibiotic-resistant infections in the hospital setting worldwide, and this has become a major issue, because most patients infected with this strain are difficult to treat. Multiplex real-time polymerase chain reaction (RT PCR) is an advantageous technique that can amplify multiple targets in a single reaction, and can be used to quickly detect specific targets in VRE within two hours, starting from suspected colonies of bacterial cultures, without sample preparation. Methods: In this study, we selected the glycopeptide/vancomycin resistance genes that are most common in clinical settings, vanA and vanB, in combination with the species markers ddl_faecium and ddl_faecalis for the most common VRE species—Enterococcus faecium and Enterococcus faecalis. Results: DNA from forty clinical VRE strains was prepared using a fast and economic heat lysis method, and a multiplex real-time PCR assay was optimized and carried out subsequently. The results were in concordance with the results from recombinase polymerase amplification (RPA) of the same VRE samples. Conclusions: Multiplex RT PCR and RPA for VRE detection proffers a second method for the confirmation of vancomycin resistance, and it can be developed as a fast screening assay for patients before admission into high-risk settings.},

keywords = {bacteria, DNA / genomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_80,

title = {Exploring the genomic landscape of Chlamydiifrater species: novel features include multiple truncated major outer membrane proteins, unique genes and chlamydial plasticity zone orthologs},

author = {Martin Hölzer and Charlotte Reuschel and Fabien Vorimore and Karine Laroucau and Konrad Sachse},

doi = {10.1099/acmi.0.000936.v3},

year  = {2025},

date = {2025-02-03},

urldate = {2025-02-03},

journal = {Access Microbiology},

volume = {7},

abstract = {Recently discovered obligate intracellular bacteria belonging to the genus Chlamydiifrater with the species of Chlamydiifrater phoenicopteri and Chlamydiifrater volucris were studied to explore the composition of their genomes and their relatedness to Chlamydia, the other genus of the family Chlamydiaceae. We investigated 4 isolates of Cf. volucris, 2 of them newly sequenced, and one of Cf. phoenicopteri alongside 12 representatives of the Chlamydia species. Our study uncovers previously unrecognized genomic structures within Chlamydiifrater using a hybrid sequencing approach and advanced annotation pipelines, providing insights into species-specific adaptations and evolutionary dynamics. The integration of long-read sequencing data, comprehensive re-annotation strategies and pan-genomics enabled the localization of the unique plasticity zone and the identification of novel gene clusters in Chlamydiifrater strains, which improves our understanding of chlamydial genome architecture and plasticity in the family Chlamydiaceae. Our analysis revealed that 761 CDS (~80%) are shared among members of both genera. We further identified 158 unique genes of Chlamydiifrater species, but their annotation remains challenging because of the absence of functionally annotated orthologs in public databases. A full-length ompA gene encoding the major outer membrane porin was seen in all Chlamydiifrater strains. We also describe the localization and structure of multiple truncated CDS of ompA family members, representing one of this study’s most interesting findings. While genome analysis of Chlamydiifrater spp. confirmed numerous common features shared with representatives of the genus Chlamydia, many unique genomic elements were identified that underpin the distinct phenotype and separate genetic position of these new microorganisms.},

keywords = {annotation, bacteria, DNA / genomics, evolution, pregnancy},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_75,

title = {\textit{Trichosporon asahii}: A Potential Growth Promoter for \textit{C. gallinacea}? Implications for Chlamydial Infections and Cell Culture},

author = {Erika Ornelas-Eusebio and Fabien Vorimore and Rachid Aaziz and Maria-Lucia Mandola and Francesca Rizzo and Monica Marchino and Chiara Nogarol and Veronica Risco-Castillo and Gina Zanella and Christiane Schnee and Konrad Sachse and Karine Laroucau},

doi = {10.3390/microorganisms13020288},

year  = {2025},

date = {2025-01-27},

urldate = {2025-01-27},

journal = {Microorganisms},

volume = {13},

number = {2},

abstract = {The cultivation of Chlamydia gallinacea, a recently identified species, is challenging due to the lack of an optimized protocol. In this study, several infection protocols were tested, including different cell lines, incubation temperatures, centrifugation methods and culture media. However, none were successful in field samples. The only exception was a chance co-culture with Trichosporon asahii, a microorganism commonly found in the chicken gut. This suggests that current in vitro methods may not be optimized for this species and that host-associated microorganisms may influence the in vivo growth of C. gallinacea, which is typically found in the chicken gut. These findings raise new questions and highlight the need for further investigation of microbial interactions within the host, particularly to understand their role in the proliferation of chlamydial species.},

keywords = {bacteria, fungi, metagenomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Algal Growth and Morphogenesis-Promoting Factors Released by Cold-Adapted Bacteria Contribute to the Resilience and Morphogenesis of the Seaweed Ulva (Chlorophyta) in Antarctica (Potter Cove)},

author = {Fatemeh Ghaderiardakani and Johann F. Ulrich and Emanuel Barth and Maria Liliana Quartino and Thomas Wichard},

doi = {10.1007/s00344-024-11507-4},

year  = {2024},

date = {2024-10-14},

journal = {Journal of Plant Growth Regulation},

abstract = {Macroalgae are found in a variety of marine vegetation ecosystems around the world, contributing significantly to global net primary production. In particular, the sea lettuce species, i.e., members of the genus Ulva (Chlorophyta), are located in many ecological niches and are characterized by excellent adaptability to environmental changes but depend on essential associated bacteria, which release algal growth and morphogenesis-promoting-factors (AGMPFs). Our work investigated the hypothesis that bacteria need to be stress-adapted to provide sufficient amounts of AGMPFs for the growth and morphogenesis of Ulva throughout its life cycle, even under severe environmental conditions. Our study thus aimed to understand which bacteria contribute to overcoming a variety of stressors in polar regions. Green macroalgae were collected from Potter Cove, King George Island (Isla 25 de Mayo), Antarctica, to study the associated microbiome and, subsequently, to identify AGMPFs releasing bacteria. Therefore, microbiome analysis was combined with morphogenetic bioassays and chemical analysis, identifying bacteria essential for algal growth under Antarctic conditions. Hereby, axenic cultures of Ulva compressa (cultivar Ulva mutabilis, Ria Formosa, Portugal), previously developed as a model system for bacteria-induced algal growth and morphogenesis, were inoculated with freshly isolated and cultivable Antarctic bacteria to determine their morphogenetic activity. The exploratory microbiome investigation identified numerous cold-adapted AGMPF-producing bacteria. Unlike the temperate-adapted bacterial strains originally isolated from the U. mutabilis holobiont, the cold-adapted isolates Maribacter sp. BPC-D8 and Sulfitobacter sp. BPC-C4 released sufficient amounts of AGMPFs, such as thallusin and still unknown compounds, necessary for the morphogenesis of the Antarctic Ulva even at 2 °C. Our results illustrate the role of chemical mediators provided by bacteria in cross-kingdom interactions under cold conditions within aquatic systems. The newly isolated bacteria will enable further functional studies to understand the resilience of the holobiont Ulva and might be applied in algal aquaculture even under adverse conditions. The study highlights the importance of eco-physiological assays in microbiome analysis.},

keywords = {algae, bacteria},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_94,

title = {Fast and Economic Microarray-Based Detection of Species-, Resistance-, and Virulence-Associated Genes in Clinical Strains of Vancomycin-Resistant Enterococci (VRE)},

author = {Ibukun Elizabeth Osadare and Stefan Monecke and Abdinasir Abdilahi and Elke Müller and Maximilian Collatz and Sascha Braun and Annett Reissig and Wulf Schneider-Brachert and Bärbel Kieninger and Anja Eichner and Anca Rath and Jürgen Fritsch and Dominik Gary and Katrin Frankenfeld and Thomas Wellhöfer and Ralf Ehricht},

doi = {10.3390/s24196476},

year  = {2024},

date = {2024-10-08},

journal = {Sensors},

volume = {24},

abstract = {Today, there is a continuous worldwide battle against antimicrobial resistance (AMR) and that includes vancomycin-resistant enterococci (VRE). Methods that can adequately and quickly detect transmission chains in outbreaks are needed to trace and manage this problem fast and cost-effectively. In this study, DNA-microarray-based technology was developed for this purpose. It commenced with the bioinformatic design of specific oligonucleotide sequences to obtain amplification primers and hybridization probes. Microarrays were manufactured using these synthesized oligonucleotides. A highly parallel and stringent labeling and hybridization protocol was developed and employed using isolated genomic DNA from previously sequenced (referenced) clinical VRE strains for optimal sensitivity and specificity. Microarray results showed the detection of virulence, resistance, and species-specific genes in the VRE strains. Theoretical predictions of the microarray results were also derived from the sequences of the same VRE strain and were compared to array results while optimizing protocols until the microarray result and theoretical predictions were a match. The study concludes that DNA microarray technology can be used to quickly, accurately, and economically detect specifically and massively parallel target genes in enterococci.},

keywords = {bacteria, classification, DNA / genomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_74,

title = {Nanopore sequencing enables novel detection of deuterium incorporation in DNA},

author = {Christian {Höner zu Siederdissen} and Jannes Spangenberg and Kevin Bisdorf and Sebastian Krautwurst and Akash Srivastava and Manja Marz and Martin Taubert},

doi = {10.1016/j.csbj.2024.09.027},

year  = {2024},

date = {2024-10-03},

urldate = {2024-10-03},

journal = {Computational and Structural Biotechnology Journal},

volume = {23},

abstract = {Identifying active microbes is crucial to understand their role in ecosystem functions. Metabolic labeling with heavy, non-radioactive isotopes, i.e., stable isotope probing (SIP), can track active microbes by detecting heavy isotope incorporation in biomolecules such as DNA. However, the detection of heavy isotope-labeled nucleotides directly during sequencing has, to date, not been achieved. In this study, Oxford nanopore sequencing was utilized to detect heavy isotopes incorporation in DNA molecules. Two isotopes widely used in SIP experiments were employed to label a bacterial isolate: deuterium (D, as D2O) and carbon-13 (13C, as glucose). We hypothesize that labeled DNA is distinguishable from unlabeled DNA by changes in the nanopore signal. To verify this distinction, we employed a Bayesian classifier trained on signal distributions of short oligonucleotides (k-mers) from labeled and unlabeled sequencing reads. Our results show a clear distinction between D-labeled and unlabeled reads, based on changes in median and median absolute deviation (MAD) of the nanopore signals for different k-mers. In contrast, 13C-labeled DNA cannot be distinguished from unlabeled DNA. For D, the model employed correctly predicted more than 85% of the reads. Even when metabolic labeling was conducted with only 30% D2O, 80% of the obtained reads were correctly classified with a 5% false discovery rate. Our work demonstrates the feasibility of direct detection of deuterium incorporation in DNA molecules during Oxford nanopore sequencing. This finding represents a first step in establishing the combined use of nanopore sequencing and SIP for tracking active organisms in microbial ecology.},

keywords = {bacteria, DNA / genomics, machine learning, metagenomics, nanopore, nucleic acid modifications},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_63,

title = {RIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level},

author = {Kevin Lamkiewicz and Lisa-Marie Barf and Konrad Sachse and Martin Hölzer},

doi = {10.1186/s13059-024-03312-9},

year  = {2024},

date = {2024-07-01},

journal = {Genome Biology},

volume = {25},

issue = {1},

abstract = {Microbial pangenome analysis identifies present or absent genes in prokaryotic genomes. However, current tools are limited when analyzing species with higher sequence diversity or higher taxonomic orders such as genera or families. The Roary ILP Bacterial core Annotation Pipeline (RIBAP) uses an integer linear programming approach to refine gene clusters predicted by Roary for identifying core genes. RIBAP successfully handles the complexity and diversity of Chlamydia, Klebsiella, Brucella, and Enterococcus genomes, outperforming other established and recent pangenome tools for identifying all-encompassing core genes at the genus level. RIBAP is a freely available Nextflow pipeline at github.com/hoelzer-lab/ribap and zenodo.org/doi/10.5281/zenodo.10890871.},

keywords = {annotation, bacteria, DNA / genomics, evolution, software},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Immunity and bacterial recruitment in plant leaves are parallel processes whose link shapes sensitivity to temperature stress},

author = {Jisna Jose and Erik Teutloff and Simrat Naseem and Emanuel Barth and Rayko Halitschke and Manja Marz and Matthew T. Agler},

doi = {10.1101/2024.06.10.598336},

year  = {2024},

date = {2024-06-10},

journal = {bioRxiv},

abstract = {Rising global temperatures necessitate developing climate-resilient crops with better adaptability to changing climates. Under elevated temperatures, plant immunity is downregulated, putting them at risk of foliar pathogen attack. Manipulating plant defense hormones is one way to mitigate this detrimental effect. However, it is unclear how plant immunity interacts with plant microbiome assembly and how temperature will thus affect overall plant health and stability. We used chemical mutagenesis to identify a phenotypically healthy genotype of A. thaliana, “CLLF”, that compared to the wild type naturally recruits an altered leaf bacteriome, including unusually high bacteria loads. Simultaneously, CLLF hyperaccumulates salicylic acid (SA) and jasmonates, has constitutively upregulated systemic and innate defenses, and has increased resistance to necrotrophic fungal and hemi-biotrophic bacterial pathogens, indicating that pathogen immunity and non-pathogen recruitment function in parallel. Growth of specific non-pathogenic leaf bacteria on SA as a carbon source suggests the same hormones may even link the two processes. CLLF also showed high tolerance to heat stress in comparison to the wild type, but SA-associated defense processes are not downregulated under heat. Synthetic community (SynCom) experiments showed that when the taxonomic diversity of bacteria available to CLLF is artificially reduced, resilience to heat stress is compromised, leading to dysbiosis, but this does not occur with the full SynCom or in the wild type with any SynCom. Thus, the downregulation of defenses in response to heat may contribute to avoidance of dysbiosis caused by some leaf bacteria, but full bacteriome taxonomic diversity can restore balance.



Significance Statement Plants are living ecosystems colonized by diverse microorganisms who strongly shape host health. Understanding how balance arises in host-associated microbiomes is a key step to understanding how to preserve, manage and possibly optimize these complex ecosystems, especially in a changing climate. Using a random mutagenesis approach in a natural A. thaliana ecotype, we find that constitutively upregulated defenses are associated with both tolerance to (a)biotic threats and healthy recruitment of leaf bacteria, very likely in a direct manner. Thus, immunity and bacterial recruitment in leaves operate in parallel. Synthetic community experiments show further that this link plays important roles in shaping plant resilience to heat stress, an important consideration in developing plants more stable to climate change.},

keywords = {bacteria, evolution, fungi, RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_93,

title = {ConsensusPrime—A Bioinformatic Pipeline for Efficient Consensus Primer Design—Detection of Various Resistance and Virulence Factors in MRSA—A Case Study},

author = {Maximilian Collatz and Martin Reinicke and Celia Diezel and Sascha D. Braun and Stefan Monecke and Annett Reissig and Ralf Ehricht},

doi = {10.3390/biomedinformatics4020068},

year  = {2024},

date = {2024-05-10},

urldate = {2024-05-10},

journal = {BioMedInformatics},

volume = {4},

abstract = {Background: The effectiveness and reliability of diagnostic tests that detect DNA sequences largely hinge on the quality of the used primers and probes. This importance is especially evident when considering the specific sample being analyzed, as it affects the molecular background and potential for cross-reactivity, ultimately determining the test’s performance.

Methods: Predicting primers based on the consensus sequence of the target has multiple advantages, including high specificity, diagnostic reliability, broad applicability, and long-term validity. Automated curation of the input sequences ensures high-quality primers and probes.

Results: Here, we present a use case for developing a set of consensus primers and probes to identify antibiotic resistance and virulence genes in Staphylococcus (S.) aureus using the ConsensusPrime pipeline. Extensive qPCR experiments with several S. aureus strains confirm the exceptional quality of the primers designed using the pipeline.

Conclusions: By improving the quality of the input sequences and using the consensus sequence as a basis, the ConsensusPrime pipeline pipeline ensures high-quality primers and probes, which should be the basis of molecular assays.},

keywords = {bacteria, DNA / genomics, software},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_60,

title = {Detection of a novel genotype of \textit{Chlamydia buteonis} in falcons from the Emirates},

author = {F. Vorimore and R. Aaziz and L. {Al Qaysi} and U. Wernery and N. Borel and Konrad Sachse and K. Laroucau},

doi = {10.1016/j.vetmic.2024.110027},

year  = {2024},

date = {2024-02-16},

journal = {Veterinary Microbiology},

volume = {291},

pages = {110027},

abstract = {Chlamydiaceae are a family of obligate intracellular bacterial pathogens that affect both humans and animals. Recently, a new species named Chlamydia (C.) buteonis was isolated from hawks. In this study, we aimed to investigate the prevalence of Chlamydiaceae in 60 falcons that underwent a routine health check at a specialized clinic in Dubai, United Arab Emirates. Using real-time PCR, we analyzed cloacal and tracheal swabs from these birds and found that 39 of them tested positive for Chlamydiaceae. Subsequent real-time PCR assays specific for C. psittaci, C. abortus, C. avium, and C. gallinacea yielded negative results, while testing positive for C. buteonis. Analysis of ompA and MLST sequences indicated a highly conserved group of strains within this set of samples, but with sequences distinct from the C. buteonis RSHA reference strains and other C. buteonis strains isolated from hawks in the United States. Two strains were further isolated by cell culture and sequenced using whole-genome sequencing, confirming the clustering of these falcon strains within the C. buteonis species, but in a separate clade from the previously identified hawk strains. We also developed a SNP-based PCR-HRM assay to distinguish between these different genotypes. Overall, our findings suggest a high prevalence of C. buteonis in falcons in Dubai and highlight the importance of monitoring this pathogen in birds of prey.},

keywords = {bacteria, DNA / genomics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_44,

title = {\textit{De novo} genome assembly resolving repetitive structures enables genomic analysis of 35 European \textit{Mycoplasmopsis bovis} strains},

author = {Sandra Triebel and Konrad Sachse and Michael Weber and Martin Heller and Celia Diezel and Martin Hölzer and Christiane Schnee and Manja Marz },

doi = {10.1186/s12864-023-09618-5},

isbn = {1471-2164},

year  = {2023},

date = {2023-09-16},

urldate = {2023-09-16},

journal = {BMC Genomics},

volume = {24},

number = {548},

issue = {1},

abstract = {Mycoplasmopsis (M.) bovis, the agent of mastitis, pneumonia, and arthritis in cattle, harbors a small genome of approximately 1 Mbp. Combining data from Illumina and Nanopore technologies, we sequenced and assembled the genomes of 35 European strains and isolate DL422_88 from Cuba. While the high proportion of repetitive structures in M. bovis genomes represent a particular challenge, implementation of our own pipeline Mycovista (available on GitHub www.github.com/sandraTriebel/mycovista ) in a hybrid approach enabled contiguous assembly of the genomes and, consequently, improved annotation rates considerably. To put our European strain panel in a global context, we analyzed the new genome sequences together with 175 genome assemblies from public databases. Construction of a phylogenetic tree based on core genes of these 219 strains revealed a clustering pattern according to geographical origin, with European isolates positioned on clades 4 and 5. Genomic data allowing assignment of strains to tissue specificity or certain disease manifestations could not be identified. Seven strains isolated from cattle with systemic circular condition (SCC), still a largely unknown manifestation of M. bovis disease, were located on both clades 4 and 5. Pairwise association analysis revealed 108 genomic elements associated with a particular clade of the phylogenetic tree. Further analyzing these hits, 25 genes are functionally annotated and could be linked to a M. bovis protein, e.g. various proteases and nucleases, as well as ten variable surface lipoproteins (Vsps) and other surface proteins. These clade-specific genes could serve as useful markers in epidemiological and clinical surveys.},

keywords = {assembly, bacteria, DNA / genomics, nanopore, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {NFDI4Microbiota – national research data infrastructure for microbiota research},

author = {Konrad U. Förstner and Anke Becker and Jochen Blom and Peer Bork and Thomas Clavel and Marius Dieckmann and Alexander Goesmann and Barbara Götz and Thomas Gübitz and Franziska Hufsky and Sebastian Jünemann and Marie-Louise Körner and Manja Marz and Ulisses Nunes Da Rocha and Jörg Overmann and Alfred Pühler and Dietrich Rebholz-Schuhmann and Alexander Sczyrba and Jens Stoye and Justine Vandendorpe and Thea Van Rossum and Alice McHardy},

doi = {10.3897/rio.9.e110501},

year  = {2023},

date = {2023-08-24},

journal = {Research Ideas and Outcomes},

volume = {9},

pages = {e110501},

abstract = {Microbes – bacteria, archaea, unicellular eukaryotes, and viruses – play an important role in human and environmental health. Growing awareness of this fact has led to a huge increase in microbiological research and applications in a variety of fields. Driven by technological advances that allow high-throughput molecular characterization of microbial species and communities, microbiological research now offers unparalleled opportunities to address current and emerging needs. As well as helping to address global health threats such as antimicrobial resistance and viral pandemics, it also has a key role to play in areas such as agriculture, waste management, water treatment, ecosystems remediation, and the diagnosis, treatment and prevention of various diseases. Reflecting this broad potential, billions of euros have been invested in microbiota research programs worldwide. Though run independently, many of these projects are closely related. However, Germany currently has no infrastructure to connect such projects or even compare their results. Thus, the potential synergy of data and expertise is being squandered. The goal of the NFDI4Microbiota consortium is to serve and connect this broad and heterogeneous research community by elevating the availability and quality of research results through dedicated training, and by facilitating the generation, management, interpretation, sharing, and reuse of microbial data. In doing so, we will also foster interdisciplinary interactions between researchers. NFDI4Microbiota will achieve this by creating a German microbial research network through training and community-building activities, and by creating a cloud-based system that will make the storage, integration and analysis of microbial data, especially omics data, consistent, reproducible, and accessible across all areas of life sciences. In addition to increasing the quality of microbial research in Germany, our training program will support widespread and proper usage of these services. Through this dual emphasis on education and services, NFDI4Microbiota will ensure that microbial research in Germany is synergistic and efficient, and thus excellent. By creating a central resource for German microbial research, NDFDI4Microbiota will establish a connecting hub for all NFDI consortia that work with microbiological data, including GHGA, NFDI4Biodiversity, NFDI4Agri and several others. NFDI4Microbiota will provide non-microbial specialists from these consortia with direct and easy access to the necessary expertise and infrastructure in microbial research in order to facilitate their daily work and enhance their research. The links forged through NFDI4Microbiota will not only increase the synergy between NFDI consortia, but also elevate the overall quality and relevance of microbial research in Germany.},

keywords = {bacteria, fungi, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_41,

title = {\textit{Streptomyces marispadix} sp. nov., isolated from marine beach sediment},

author = {José Diogo Neves Dos Santos and Inês Rosado Vitorino and Nicolai Kallscheuer and Akash Srivastava and Sebastian Krautwurst and Manja Marz and Christian Jogler and Alexandre Lobo-da-Cunha and José Catita and Hugo Gonçalves and Ignacio González and Fernando Reyes and Olga Maria Lage},

doi = {10.1099/ijsem.0.005956},

isbn = {1466-5034},

year  = {2023},

date = {2023-07-25},

urldate = {2023-07-25},

journal = {International Journal of Systematic and Evolutionary Microbiology},

volume = {73},

number = {7},

abstract = {A novel actinomycetal strain, designated M600PL45_2T, was isolated from marine sediments obtained from Ingleses beach, Porto, on the Northern Coast of Portugal and was subjected to a polyphasic taxonomic characterisation study. The here described Gram-reaction-positive strain is characterised by the production of a brown pigment in both solid and liquid medium and forms typical helical hyphae that differentiate into smooth spores. The results of a phylogenetic analysis based on the 16S rRNA gene sequence indicated that M600PL45_2T has a high similarity to two members of the genus Streptomyces , Streptomyces bathyalis ASO4wetT (98.51 %) and Streptomyces daqingensis NEAU ZJC8T (98.44 %). The genome of M600PL45_2T has a size of 6 695 159 bp, a DNA G+C content of 70.71 mol% and 5538 coding sequences. M600PL45_2T grows at 15–37 °C and with a maximal growth rate between 25 °C and 30 °C. Growth at pH 6.0 to 9.0 with the optimal range between 6.0 and 7.5 was observed. M600PL45_2T showed a high salinity tolerance, growing with 0–10 % (w/v) NaCl, with best growth with 1–3% (w/v) NaCl. Major cellular fatty acids are iso-C15:0 (25.03 %), anteiso-C15:0 (17.70) and iso-C16:0 (26.90 %). The novel isolate was able to grow in media containing a variety of nitrogen and carbon sources. An antimicrobial activity screening indicated that an extract of M600PL45_2T has inhibitory activity against Staphylococcus aureus . On the basis of the polyphasic data, M600PL45_2T (= CECT 30365T = DSM 114036T) is introduced as the type strain of a novel species, that we named Streptomyces marispadix sp. nov.},

keywords = {bacteria, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_40,

title = {Oxford nanopore technologies-a valuable tool to generate whole-genome sequencing data for \textit{in silico} serotyping and the detection of genetic markers in \textit{Salmonella}},

author = {Christine Thomas and Ulrich Methner and Manja Marz and Jörg Linde},

doi = {10.3389/fvets.2023.1178922},

isbn = {2297-1769},

year  = {2023},

date = {2023-06-01},

urldate = {2023-06-01},

journal = {Frontiers in Veterinary Science},

volume = {10},

abstract = {Bacteria of the genus Salmonella pose a major risk to livestock, the food economy, and public health. Salmonella infections are one of the leading causes of food poisoning. The identification of serovars of Salmonella achieved by their diverse surface antigens is essential to gain information on their epidemiological context. Traditionally, slide agglutination has been used for serotyping. In recent years, whole-genome sequencing (WGS) followed by in silico serotyping has been established as an alternative method for serotyping and the detection of genetic markers for Salmonella. Until now, WGS data generated with Illumina sequencing are used to validate in silico serotyping methods. Oxford Nanopore Technologies (ONT) opens the possibility to sequence ultra-long reads and has frequently been used for bacterial sequencing. In this study, ONT sequencing data of 28 Salmonella strains of different serovars with epidemiological relevance in humans, food, and animals were taken to investigate the performance of the in silico serotyping tools SISTR and SeqSero2 compared to traditional slide agglutination tests. Moreover, the detection of genetic markers for resistance against antimicrobial agents, virulence, and plasmids was studied by comparing WGS data based on ONT with WGS data based on Illumina. Based on the ONT data from flow cell version R9.4.1, in silico serotyping achieved an accuracy of 96.4 and 92% for the tools SISTR and SeqSero2, respectively. Highly similar sets of genetic markers comparing both sequencing technologies were identified. Taking the ongoing improvement of basecalling and flow cells into account, ONT data can be used for Salmonella in silico serotyping and genetic marker detection.},

keywords = {bacteria, nanopore},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_35,

title = {Genomic analysis of 61 \textit{Chlamydia psittaci} strains reveals extensive divergence associated with host preference},

author = {Konrad Sachse and Martin Hölzer and Fabien Vorimore and Lisa-Marie Barf and Carsten Sachse and Karine Laroucau and Manja Marz and Kevin Lamkiewicz },

doi = {10.1186/s12864-023-09370-w},

isbn = {1471-2164},

year  = {2023},

date = {2023-05-29},

urldate = {2023-05-29},

journal = {BMC Genomics},

volume = {24},

issue = {1},

pages = {288},

abstract = {Background

Chlamydia (C.) psittaci, the causative agent of avian chlamydiosis and human psittacosis, is a genetically heterogeneous species. Its broad host range includes parrots and many other birds, but occasionally also humans (via zoonotic transmission), ruminants, horses, swine and rodents. To assess whether there are genetic markers associated with host tropism we comparatively analyzed whole-genome sequences of 61 C. psittaci strains, 47 of which carrying a 7.6-kbp plasmid.



Results

Following clean-up, reassembly and polishing of poorly assembled genomes from public databases, phylogenetic analyses using C. psittaci whole-genome sequence alignment revealed four major clades within this species. Clade 1 represents the most recent lineage comprising 40/61 strains and contains 9/10 of the psittacine strains, including type strain 6BC, and 10/13 of human isolates. Strains from different non-psittacine hosts clustered in Clades 2– 4. We found that clade membership correlates with typing schemes based on SNP types, ompA genotypes, multilocus sequence types as well as plasticity zone (PZ) structure and host preference. Genome analysis also revealed that i) sequence variation in the major outer membrane porin MOMP can result in 3D structural changes of immunogenic domains, ii) past host change of Clade 3 and 4 strains could be associated with loss of MAC/perforin in the PZ, rather than the large cytotoxin, iii) the distinct phylogeny of atypical strains (Clades 3 and 4) is also reflected in their repertoire of inclusion proteins (Inc family) and polymorphic membrane proteins (Pmps).



Conclusions

Our study identified a number of genomic features that can be correlated with the phylogeny and host preference of C. psittaci strains. Our data show that intra-species genomic divergence is associated with past host change and includes deletions in the plasticity zone, structural variations in immunogenic domains and distinct repertoires of virulence factors.},

keywords = {alignment, assembly, bacteria, DNA / genomics, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{Fuesslin2022,

title = {Prediction of Antibiotic Susceptibility Profiles of \textit{Vibrio cholerae} Isolates From Whole Genome Illumina and Nanopore Sequencing Data: CholerAegon},

author = {Valeria Fuesslin and Sebastian Krautwurst and Akash Srivastava and Doris Winter and Britta Liedigk and Thorsten Thye and Silvia Herrera-León and Shirlee Wohl and Jürgen May and Julius N. Fobil and Daniel Eibach and Manja Marz and Kathrin Schuldt},

url = {https://github.com/RaverJay/CholerAegon },

doi = {10.3389/fmicb.2022.909692},

year  = {2022},

date = {2022-06-22},

journal = {Front Microbiol},

volume = {13},

pages = {909692},

abstract = {During the last decades, antimicrobial resistance (AMR) has become a global public health concern. Nowadays multi-drug resistance is commonly observed in strains of Vibrio cholerae, the etiological agent of cholera. In order to limit the spread of pathogenic drug-resistant bacteria and to maintain treatment options the analysis of clinical samples and their AMR profiles are essential. Particularly, in low-resource settings a timely analysis of AMR profiles is often impaired due to lengthy culturing procedures for antibiotic susceptibility testing or lack of laboratory capacity. In this study, we explore the applicability of whole genome sequencing for the prediction of AMR profiles of V. cholerae. We developed the pipeline CholerAegon for the in silico prediction of AMR profiles of 82 V. cholerae genomes assembled from long and short sequencing reads. By correlating the predicted profiles with results from phenotypic antibiotic susceptibility testing we show that the prediction can replace in vitro susceptibility testing for five of seven antibiotics. Because of the relatively low costs, possibility for real-time data analyses, and portability, the Oxford Nanopore Technologies MinION sequencing platform—especially in light of an upcoming less error-prone technology for the platform—appears to be well suited for pathogen genomic analyses such as the one described here. Together with CholerAegon, it can leverage pathogen genomics to improve disease surveillance and to control further spread of antimicrobial resistance.},

keywords = {bacteria, DNA / genomics, nanopore},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_90,

title = {Description of Staphylococcal Strains from Straw-Coloured Fruit Bat (Eidolon helvum) and Diamond Firetail (Stagonopleura guttata) and a Review of their Phylogenetic Relationships to Other Staphylococci},

author = {Stefan Monecke and Frieder Schaumburg and Adebayo O. Shittu and Stefan Schwarz and Kristin Mühldorfer and Christian Brandt and Sascha D. Braun and Maximilian Collatz and Celia Diezel and Darius Gawlik and Dennis Hanke and Helmut Hotzel and Elke Müller and Martin Reinicke and Andrea T. Feßler and Ralf Ehricht},

doi = {10.3389/fcimb.2022.878137},

year  = {2022},

date = {2022-05-11},

urldate = {2022-05-11},

journal = {Frontiers in Cellular and Infection Microbiology},

volume = {12},

abstract = {The phylogenetic tree of the Staphylococcus aureus complex consists of several distinct clades and the majority of human and veterinary S. aureus isolates form one large clade. In addition, two divergent clades have recently been described as separate species. One was named Staphylococcus argenteus, due to the lack of the “golden” pigment staphyloxanthin. The second one is S. schweitzeri, found in humans and animals from Central and West Africa. In late 2021, two additional species, S. roterodami and S. singaporensis, have been described from clinical samples from Southeast Asia.

In the present study, isolates and their genome sequences from wild Straw-coloured fruit bats (Eidolon helvum) and a Diamond firetail (Stagonopleura guttata, an estrildid finch) kept in a German aviary are described. The isolates possessed staphyloxanthin genes and were closer related to S. argenteus and S. schweitzeri than to S. aureus. Phylogenetic analysis revealed that they were nearly identical to both, S. roterodami and S. singaporensis.

We propose considering the study isolates, the recently described S. roterodami and S. singaporensis as well as some Chinese strains with MLST profiles stored in the PubMLST database as different clonal complexes within one new species. According to the principle of priority we propose it should be named S. roterodami. 

This species is more widespread than previously believed, being observed in Western Africa, Southeast Asia and Southern China. It has a zoonotic connection to bats and has been shown to be capable of causing skin and soft tissue infections in humans. It is positive for staphyloxanthin, and it could be mis-identified as S. aureus (or S. argenteus) using routine procedures. However, it can be identified based on distinct MLST alleles, and “S. aureus” sequence types ST2470, ST3135, ST3952, ST3960, ST3961, ST3963, ST3965, ST3980, ST4014, ST4075, ST4076, ST4185, ST4326, ST4569, ST6105, ST6106, ST6107, ST6108, ST6109, ST6999 and ST7342 belong to this species.},

keywords = {bacteria, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_96,

title = {Characterisation and Molecular Analysis of an Unusual Chimeric Methicillin Resistant Staphylococcus Aureus Strain and its Bacteriophages},

author = {Sindy Burgold-Voigt and Stefan Monecke and Alexandra Simbeck and Thomas Holzmann and Bärbel Kieninger and Elisabeth M. Liebler-Tenorio and Sascha D. Braun and Maximilian Collatz and Celia Diezel and Elke Müller and Wulf Schneider-Brachert and Ralf Ehricht},

doi = {10.3389/fgene.2021.723958},

year  = {2021},

date = {2021-11-18},

journal = {Frontiers in Genetics},

volume = {12},

abstract = {In the context of microarray-based epidemiological typing of the clonal organism Staphylococcus aureus/MRSA, a strain was identified that did not belong to known clonal complexes. The molecular analysis by microarray-based typing yielded signals suggesting that it was a mosaic or hybrid strain of two lineages. To verify this result, the isolate was sequenced with both, short-read Illumina and long-read Nanopore technologies and analysed in detail. This supported the hypothesis that the genome of this strain, ST6610-MRSA-IVg comprised of segments originating from two different clonal complexes (CC).

While the backbone of the strain´s genome, i.e., roughly 2 megabases, belongs to CC8, a continuous insert of 894 kb (approx. 30% of the genome) originated from CC140. Beside core genomic markers in the normal succession and orientation, this insert also included the mecA gene, coding for PbP2a and causing methicillin resistance , localised on an SCCmec IVg element. This particular SCCmec type was also previously observed in CC140 MRSA from African countries. A second conspicuous observation was the presence of the trimethoprim resistance gene dfrG within on a prophage that occupied an attachment site normally used by Panton-Valentine Leucocidin (PVL) phages. 

This observation could indicate a role of large-scale chromosomal recombination in the evolution of S. aureus as well as a role of phages in the dissemination of antibiotic resistance genes.},

keywords = {bacteria, DNA / genomics, evolution},

pubstate = {published},

tppubtype = {article}

}

@article{Yates:21,

title = {The evolution and changing ecology of the African hominid oral microbiome},

author = {James A. Fellows Yates and Irina M. Velsko and Franziska Aron and Cosimo Posth and Courtney A. Hofman and Rita M. Austin and Cody E. Parker and Allison E. Mann and Kathrin Nägele and Kathryn Weedman Arthur and John W. Arthur and Catherine C. Bauer and Isabelle Crevecoeur and Christophe Cupillard and Matthew C. Curtis and Love Dalén and Marta Díaz-Zorita Bonilla and J. Carlos Díez Fernández-Lomana and Dorothée G. Drucker and Elena Escribano Escrivá and Michael Francken and Victoria E. Gibbon and Manuel R. González Morales and Ana Grande Mateu and Katerina Harvati and Amanda G. Henry and Louise Humphrey and Mario Menéndez and Dušan Mihailović and Marco Peresani and Sofía Rodríguez Moroder and Mirjana Roksandic and Hélène Rougier and Sandra Sázelová and Jay T. Stock and Lawrence Guy Straus and Jiří Svoboda and Barbara Teßmann and Michael J. Walker and Robert C. Power and Cecil M. Lewis and Krithivasan Sankaranarayanan and Katerina Guschanski and Richard W. Wrangham and Floyd E. Dewhirst and Domingo C. Salazar-García and Johannes Krause and Alexander Herbig and Christina Warinner},

doi = {10.1073/pnas.2021655118},

year  = {2021},

date = {2021-05-18},

urldate = {2021-05-18},

journal = {Proc Natl Acad Sci},

volume = {118},

number = {20},

pages = {e2021655118},

publisher = {Proceedings of the National Academy of Sciences},

abstract = {The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine–platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.},

keywords = {ancient DNA, bacteria, evolution, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{Kalvari:21,

title = {Rfam 14: expanded coverage of metagenomic, viral and microRNA families},

author = {Ioanna Kalvari and Eric P Nawrocki and Nancy Ontiveros-Palacios and Joanna Argasinska and Kevin Lamkiewicz and Manja Marz and Sam Griffiths-Jones and Claire Toffano-Nioche and Daniel Gautheret and Zasha Weinberg and Elena Rivas and Sean R Eddy and Robert D Finn and Alex Bateman and Anton I Petrov},

url = {https://rfam.org/},

doi = {10.1093/nar/gkaa1047},

year  = {2020},

date = {2020-11-19},

urldate = {2020-11-19},

journal = {Nucleic Acids Res},

volume = {49},

number = {D1},

pages = {D192--D200},

publisher = {Oxford University Press (OUP)},

abstract = {Rfam is a database of RNA families where each of the 3444 families is represented by a multiple sequence alignment of known RNA sequences and a covariance model that can be used to search for additional members of the family. Recent developments have involved expert collaborations to improve the quality and coverage of Rfam data, focusing on microRNAs, viral and bacterial RNAs. We have completed the first phase of synchronising microRNA families in Rfam and miRBase, creating 356 new Rfam families and updating 40. We established a procedure for comprehensive annotation of viral RNA families starting with Flavivirus and Coronaviridae RNAs. We have also increased the coverage of bacterial and metagenome-based RNA families from the ZWD database. These developments have enabled a significant growth of the database, with the addition of 759 new families in Rfam 14. To facilitate further community contribution to Rfam, expert users are now able to build and submit new families using the newly developed Rfam Cloud family curation system. New Rfam website features include a new sequence similarity search powered by RNAcentral, as well as search and visualisation of families with pseudoknots. Rfam is freely available at https://rfam.org.},

keywords = {alignment, annotation, bacteria, coronavirus, database, metagenomics, ncRNAs, RNA / transcriptomics, software, viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Flores:20,

title = {A marine Chlamydomonas sp. emerging as an algal model},

author = {David Carrasco Flores and Markus Fricke and Valentin Wesp and Daniel Desirò and Anja Kniewasser and Martin Hölzer and Manja Marz and Maria Mittag},

doi = {10.1111/jpy.13083},

year  = {2020},

date = {2020-10-11},

urldate = {2020-10-11},

journal = {J Phycol},

volume = {57},

number = {1},

pages = {54--69},

publisher = {Wiley},

abstract = {The freshwater microalga Chlamydomonas reinhardtii, which lives in wet soil, has served for decades as a model for numerous biological processes, and many tools have been introduced for this organism. Here, we have established a stable nuclear transformation for its marine counterpart, Chlamydomonas sp. SAG25.89, by fusing specific cis-acting elements from its Actin gene with the gene providing hygromycin resistance and using an elaborated electroporation protocol. Like C. reinhardtii, Chlamydomonas sp. has a high GC content, allowing reporter genes and selection markers to be applicable in both organisms. Chlamydomonas sp. grows purely photoautotrophically and requires ammonia as a nitrogen source because its nuclear genome lacks some of the genes required for nitrogen metabolism. Interestingly, it can grow well under both low and very high salinities (up to 50 g · L-1) rendering it as a model for osmotolerance. We further show that Chlamydomonas sp. grows well from 15 to 28°C, but halts its growth at 32°C. The genome of Chlamydomonas sp. contains some gene homologs the expression of which is regulated according to the ambient temperatures and/or confer thermal acclimation in C. reinhardtii. Thus, knowledge of temperature acclimation can now be compared to the marine species. Furthermore, Chlamydomonas sp. can serve as a model for studying marine microbial interactions and for comparing mechanisms in freshwater and marine environments. Chlamydomonas sp. was previously shown to be immobilized rapidly by a cyclic lipopeptide secreted from the antagonistic bacterium Pseudomonas protegens PF-5, which deflagellates C. reinhardtii.},

keywords = {algae, bacteria, DNA / genomics, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{Hölzer:20,

title = {Comparative Genome Analysis of 33 \textit{Chlamydia} Strains Reveals Characteristic Features of \textit{Chlamydia Psittaci} and Closely Related Species},

author = {Martin Hölzer and Lisa-Marie Barf and Kevin Lamkiewicz and Fabien Vorimore and Marie Lataretu and Alison Favaroni and Christiane Schnee and Karine Laroucau and Manja Marz and Konrad Sachse},

url = {github.com/hoelzer-lab/ribap},

doi = {10.3390/pathogens9110899},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Pathogens},

volume = {9},

number = {11},

pages = {899},

publisher = {MDPI AG},

abstract = {To identify genome-based features characteristic of the avian and human pathogen Chlamydia (C.) psittaci and related chlamydiae, we analyzed whole-genome sequences of 33 strains belonging to 12 species. Using a novel genome analysis tool termed Roary ILP Bacterial Annotation Pipeline (RIBAP), this panel of strains was shown to share a large core genome comprising 784 genes and representing approximately 80% of individual genomes. Analyzing the most variable genomic sites, we identified a set of features of C. psittaci that in its entirety is characteristic of this species: (i) a relatively short plasticity zone of less than 30,000 nt without a tryptophan operon (also in C. abortus, C. avium, C. gallinacea, C. pneumoniae), (ii) a characteristic set of of Inc proteins comprising IncA, B, C, V, X, Y (with homologs in C. abortus, C. caviae and C. felis as closest relatives), (iii) a 502-aa SinC protein, the largest among Chlamydia spp., and (iv) an elevated number of Pmp proteins of subtype G (14 in C. psittaci, 14 in Cand. C. ibidis). In combination with future functional studies, the common and distinctive criteria revealed in this study provide important clues for understanding the complexity of host-specific behavior of individual Chlamydia spp.},

keywords = {annotation, bacteria, DNA / genomics, software},

pubstate = {published},

tppubtype = {article}

}

@article{Liebler-Tenorio:20,

title = {Regeneration of Pulmonary Tissue in a Calf Model of Fibrinonecrotic Bronchopneumonia Induced by Experimental Infection with Chlamydia psittaci},

author = {Elisabeth M. Liebler-Tenorio and Jacqueline Lambertz and Carola Ostermann and Konrad Sachse and Petra Reinhold},

doi = {10.3390/ijms21082817},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {Int J Mol Sci},

volume = {21},

number = {8},

pages = {2817},

publisher = {MDPI AG},

abstract = {Pneumonia is a cause of high morbidity and mortality in humans. Animal models are indispensable to investigate the complex cellular interactions during lung injury and repair in vivo. The time sequence of lesion development and regeneration is described after endobronchial inoculation of calves with Chlamydia psittaci. Calves were necropsied 2–37 days after inoculation (dpi). Lesions and presence of Chlamydia psittaci were investigated using histology and immunohistochemistry. Calves developed bronchopneumonia at the sites of inoculation. Initially, Chlamydia psittaci replicated in type 1 alveolar epithelial cells followed by an influx of neutrophils, vascular leakage, fibrinous exudation, thrombosis and lobular pulmonary necrosis. Lesions were most extensive at 4 dpi. Beginning at 7 dpi, the number of chlamydial inclusions declined and proliferation of cuboidal alveolar epithelial cells and sprouting of capillaries were seen at the periphery of necrotic tissue. At 14 dpi, most of the necrosis had been replaced with alveoli lined with cuboidal epithelial cells resembling type 2 alveolar epithelial cells and mild fibrosis, and hyperplasia of organized lymphoid tissue were observed. At 37 dpi, regeneration of pulmonary tissue was nearly complete and only small foci of remodeling remained. The well-defined time course of development and regeneration of necrotizing pneumonia allows correlation of morphological findings with clinical data or treatment regimen.

},

keywords = {bacteria},

pubstate = {published},

tppubtype = {article}

}

@article{Wegner:19,

title = {Biogeochemical regimes in shallow aquifers reflect the metabolic coupling of elements of nitrogen, sulfur and carbon.},

author = {Carl-Eric Wegner and Michael Gaspar and Patricia Geesink and Martina Herrmann and Manja Marz and Kirsten Küsel},

doi = {10.1128/AEM.02346-18},

year  = {2019},

date = {2019-02-20},

urldate = {2019-01-01},

journal = {Appl Environ Microbiol},

volume = {85},

number = {5},

pages = {e02346-18},

abstract = {Near-surface groundwaters are prone to receive (in)organic matter input from their recharge areas and are known to harbour autotrophic microbial communities linked to nitrogen and sulfur metabolism. Here, we use multi-"omic" profiling to gain holistic insights into the turnover of inorganic nitrogen compounds, carbon fixation processes and organic matter processing in groundwater. We sampled microbial biomass from two superimposed aquifers via monitoring wells that follow groundwater flow from its recharge area through differences in hydrogeochemical settings and land use. Functional profiling revealed that groundwater microbiomes are mainly driven by nitrogen (nitrification, denitrification, anammox) and to a lesser extent sulfur cycling (sulfur oxidation and sulfate reduction), dependent on local hydrochemical differences. Surprisingly, the differentiation potential of the groundwater microbiome surpasses that of hydrochemistry for individual monitoring wells. Dominated by few phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Thaumarchaeota), the taxonomic profiling of groundwater metagenomes and metatranscriptomes revealed pronounced differences between merely present microbiome members and those actively participating in community gene expression and biogeochemical cycling. Unexpectedly, we observed a constitutive expression of carbohydrate-active enzymes, encoded by different microbiome members, along with the groundwater flow path. The turnover of organic carbon apparently complements for lithoautotrophic carbon assimilation pathways mainly used by the groundwater microbiome dependent on the availability of oxygen and inorganic electron donors like ammonium. Groundwater is a key resource for drinking water production and irrigation. The interplay between geological setting, hydrochemistry, carbon storage and groundwater microbiome ecosystem functioning is crucial for our understanding of these important ecosystem services. We targeted the encoded and expressed metabolic potential of groundwater microbiomes along an aquifer transect that diversifies in terms of hydrochemistry and land use. Our results showed that the groundwater microbiome has a higher spatial differentiation potential than hydrochemistry.},

keywords = {bacteria, groundwater, metagenomics},

pubstate = {published},

tppubtype = {article}

}

@article{Moebius:17,

title = {Complete Genome Sequence of JII-1961, a Bovine \textit{Mycobacterium avium} subsp. \textit{paratuberculosis} Field Isolate from Germany},

author = {Petra Möbius and Gabriele Nordsiek and Martin Hölzer and Michael Jarek and Manja Marz and Heike Köhler},

doi = {10.1128/genomeA.00870-17},

year  = {2017},

date = {2017-08-24},

urldate = {2017-01-01},

journal = {Genome Announc},

volume = {5},

number = {34},

abstract = {Mycobacterium avium subsp. paratuberculosis causes Johne’s disease in ruminants and was also detected in nonruminant species, including human beings, and in milk products. We announce here the 4.829-Mb complete genome sequence of the cattle-type strain JII-1961 from Germany, which is very similar to cattle-type strains recovered from different continents.

},

keywords = {assembly, bacteria, DNA / genomics},

pubstate = {published},

tppubtype = {article}

}

@article{Riege:17,

title = {Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D},

author = {Konstantin Riege and Martin Hölzer and Tilman E Klassert and Emanuel Barth and Julia Bräuer and Maximilian Collatz and Franziska Hufsky and Nelly F. Mostajo and Magdalena Stock and Bertram Vogel and Hortense Slevogt and Manja Marz},

doi = {10.1038/srep40598},

year  = {2017},

date = {2017-01-17},

urldate = {2017-01-17},

journal = {Sci Rep},

volume = {7},

pages = {40598},

abstract = {Mycoses induced by C.albicans or A.fumigatus can cause important host damage either by deficient or exaggerated immune response. Regulation of chemokine and cytokine signaling plays a crucial role for an adequate inflammation, which can be modulated by vitamins A and D. Non-coding RNAs (ncRNAs) as transcription factors or cis-acting antisense RNAs are known to be involved in gene regulation. However, the processes during fungal infections and treatment with vitamins in terms of therapeutic impact are unknown. We show that in monocytes both vitamins regulate ncRNAs involved in amino acid metabolism and immune system processes using comprehensive RNA-Seq analyses. Compared to protein-coding genes, fungi and bacteria induced an expression change in relatively few ncRNAs, but with massive fold changes of up to 4000. We defined the landscape of long-ncRNAs (lncRNAs) in response to pathogens and observed variation in the isoforms composition for several lncRNA following infection and vitamin treatment. Most of the involved antisense RNAs are regulated and positively correlated with their sense protein-coding genes. We investigated lncRNAs with stimulus specific immunomodulatory activity as potential marker genes: LINC00595, SBF2-AS1 (A.fumigatus) and RP11-588G21.2, RP11-394l13.1 (C.albicans) might be detectable in the early phase of infection and serve as therapeutic targets in the future.},

keywords = {bacteria, differential expression analysis, fungi, ncRNAs, RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{Klassert:17,

title = {Differential Effects of Vitamins A and D on the Transcriptional Landscape of Human Monocytes during Infection},

author = {Tilman E Klassert and Julia Bräuer and Martin Hölzer and Magdalena Stock and Konstantin Riege and Cristina Zubiría-Barrera and Mario M Müller and Silke Rummler and Christine Skerka and Manja Marz and Hortense Slevogt},

doi = {10.1038/srep40599},

year  = {2017},

date = {2017-01-17},

urldate = {2017-01-17},

journal = {Sci Rep},

volume = {7},

pages = {40599},

abstract = {Vitamin A and vitamin D are essential nutrients with a wide range of pleiotropic effects in humans. Beyond their well-documented roles in cellular differentiation, embryogenesis, tissue maintenance and bone/calcium homeostasis, both vitamins have attracted considerable attention due to their association with-immunological traits. Nevertheless, our knowledge of their immunomodulatory potential during infection is restricted to single gene-centric studies, which do not reflect the complexity of immune processes. In the present study, we performed a comprehensive RNA-seq-based approach to define the whole immunomodulatory role of vitamins A and D during infection. Using human monocytes as host cells, we characterized the differential role of both vitamins upon infection with three different pathogens: Aspergillus fumigatus, Candida albicans and Escherichia coli. Both vitamins showed an unexpected ability to counteract the pathogen-induced transcriptional responses. Upon infection, we identified 346 and 176 immune-relevant genes that were regulated by atRA and vitD, respectively. This immunomodulatory activity was dependent on the inflammatory stimulus, allowing us to distinguish regulatory patterns which were specific for each stimulatory setting. Moreover, we explored possible direct and indirect mechanisms of vitamin-mediated regulation of the immune response. Our findings highlight the importance of vitamin-monitoring in critically ill patients. Moreover, our results underpin the potential of atRA and vitD as therapeutic options for anti-inflammatory treatment.},

keywords = {bacteria, differential expression analysis, fungi, RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{Starke:17,

title = {Candidate Brocadiales dominates C, N and S cycling in anoxic groundwater of a pristine limestone-fracture aquifer},

author = {Robert Starke and Martina Müller and Michael Gaspar and Manja Marz and Kirsten Küsel and Kai Uwe Totsche and Martin Bergen and Nico Jehmlich},

doi = {10.1016/j.jprot.2016.11.003},

year  = {2016},

date = {2016-11-10},

urldate = {2016-11-10},

journal = {J Proteomics},

volume = {152},

pages = {153--160},

abstract = {Groundwater-associated microorganisms are known to play an important role in the biogeochemical C, N and S cycling. Metaproteomics was applied to characterize the diversity and the activity of microbes to identify key species in major biogeochemical processes in the anoxic groundwater of a pristine karstic aquifer located in Hainich, central Germany. Sampling was achieved by pumping 1000L water from two sites of the upper aquifer assemblage and filtration on 0.3μm glass filters. In total, 3808 protein groups were identified. Interestingly, the two wells (H4/2 and H5/2) differed not only in microbial density but also in the prevalence of different C, N and S cycling pathways. The well H5/2 was dominated by the anaerobic ammonia-oxidizing (anammox) candidate Brocadiales (31%) while other orders such as Burkholderiales (2%) or Nitrospirales (3%) were less abundant. Otherwise, the well H4/2 featured only low biomass and remarkably fewer proteins (391 to 3631 at H5/2). Candidate Brocadiales was affiliated to all major carbon fixation strategies, and to the cycling of N and S implying a major role in biogeochemical processes of groundwater aquifers. The findings of our study support functions which can be linked to the ecosystem services provided by the microbial communities present in aquifers. Subsurface environments especially the groundwater ecosystems represent a large habitat for microbial activity. Microbes are responsible for energy and nutrient cycling and are massively involved in the planet's sustainability. Microbial diversity is tremendous and the central question in current microbial ecology is "Who eats what, where and when?". In this study, we characterize a natural aquifer inhabiting microbial community to obtain evidence for the phylogenetic diversity and the metabolic activity by protein abundance and we highlight important biogeochemical cycling processes. The aquifer was dominated by Candidatus Brocadiales while other phylotypes such as Burkholderiales, Caulobacterales and Nitrospirales were less abundant. The candidate comprised all major carbon fixation strategies, ammonification, anammox and denitrification as well as assimilatory sulfate reduction. Our findings have broad implications for the understanding of microbial activities in this aquifer and consequently specific functions can be linked to the ecosystem services provided by the microbial communities present in aquifers.},

keywords = {bacteria, groundwater, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{Winter:16,

title = {Finding approximate gene clusters with Gecko 3},

author = {Sascha Winter and Katharina Jahn and Stefanie Wehner and Leon Kuchenbecker and Manja Marz and Jens Stoye and Sebastian Böcker},

url = {http://bio.informatik.uni-jena.de/software/gecko3/},

doi = {10.1093/nar/gkw843},

year  = {2016},

date = {2016-09-26},

urldate = {2016-09-26},

journal = {Nucleic Acids Res},

volume = {44},

pages = {9600--9610},

abstract = {Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding gene clusters in hundreds of genomes. Existing tools are often restricted to few (in many cases, only two) genomes, and often make restrictive assumptions such as short perfect conservation, conserved gene order or monophyletic gene clusters. We present Gecko 3, an open-source software for finding gene clusters in hundreds of bacterial genomes, that comes with an easy-to-use graphical user interface. The underlying gene cluster model is intuitive, can cope with low degrees of conservation as well as misannotations and is complemented by a sound statistical evaluation. To evaluate the biological benefit of Gecko 3 and to exemplify our method, we search for gene clusters in a dataset of 678 bacterial genomes using Synechocystis sp. PCC 6803 as a reference. We confirm detected gene clusters reviewing the literature and comparing them to a database of operons; we detect two novel clusters, which were confirmed by publicly available experimental RNA-Seq data. The computational analysis is carried out on a laptop computer in <40 min.},

keywords = {bacteria, DNA / genomics, evolution, software},

pubstate = {published},

tppubtype = {article}

}

@article{Hoelzer:16a,

title = {Whole-Genome Sequence of \textit{Chlamydia gallinacea} Type Strain 08-1274/3},

author = {Martin Hölzer and Karine Laroucau and Heather Huot Creasy and Sandra Ott and Fabien Vorimore and Patrik M. Bavoil and Manja Marz and Konrad Sachse},

doi = {10.1128/genomeA.00708-16},

year  = {2016},

date = {2016-07-21},

urldate = {2016-07-21},

journal = {Genome Announc},

volume = {4},

number = {4},

abstract = {The recently introduced bacterial species Chlamydia gallinacea is known to occur in domestic poultry and other birds. Its potential as an avian pathogen and zoonotic agent is under investigation. The whole-genome sequence of its type strain, 08-1274/3, consists of a 1,059,583-bp chromosome with 914 protein-coding sequences (CDSs) and a plasmid (p1274) comprising 7,619 bp with 9 CDSs.},

keywords = {assembly, bacteria, DNA / genomics},

pubstate = {published},

tppubtype = {article}

}

@article{Barth:16,

title = {The Evolution of COP9 Signalosome in Unicellular and Multicellular Organisms},

author = {Emanuel Barth and Ron Hübler and Aria Baniahmad and Manja Marz},

doi = {10.1093/gbe/evw073},

year  = {2016},

date = {2016-01-01},

urldate = {2016-01-01},

journal = {Genome Biol Evol},

volume = {8},

number = {4},

pages = {1279--1289},

abstract = {The COP9 signalosome (CSN) is a highly conserved protein complex, recently being crystallized for human. In mammals and plants the COP9 complex consists of nine subunits, CSN 1-8 and CSNAP. The CSN regulates the activity of culling ring E3 ubiquitin and plays central roles in pleiotropy, cell cycle, and defense of pathogens. Despite the interesting and essential functions, a thorough analysis of the CSN subunits in evolutionary comparative perspective is missing. Here we compared 61 eukaryotic genomes including plants, animals, and yeasts genomes and show that the most conserved subunits of eukaryotes among the nine subunits are CSN2 and CSN5. This may indicate a strong evolutionary selection for these two subunits. Despite the strong conservation of the protein sequence, the genomic structures of the intron/exon boundaries indicate no conservation at genomic level. This suggests that the gene structure is exposed to a much less selection compared with the protein sequence. We also show the conservation of important active domains, such as PCI (proteasome lid-CSN-initiation factor) and MPN (MPR1/PAD1 amino-terminal). We identified novel exons and alternative splicing variants for all CSN subunits. This indicates another level of complexity of the CSN. Notably, most COP9-subunits were identified in all multicellular and unicellular eukaryotic organisms analyzed, but not in prokaryotes or archaeas. Thus, genes encoding CSN subunits present in all analyzed eukaryotes indicate the invention of the signalosome at the root of eukaryotes. The identification of alternative splice variants indicates possible "mini-complexes" or COP9 complexes with independent subunits containing potentially novel and not yet identified functions.},

keywords = {bacteria, evolution, fungi, splicing},

pubstate = {published},

tppubtype = {article}

}

@article{Moebius:15,

title = {Comprehensive insights in the \textit{Mycobacterium avium} subsp. \textit{paratuberculosis} genome using new WGS data of sheep strain JIII-386 from Germany},

author = {Petra Möbius and Martin Hölzer and Marius Felder and Gabriele Nordsiek and Marco Groth and Heike Köhler and Kathrin Reichwald and Matthias Platzer and Manja Marz},

doi = {10.1093/gbe/evv154},

year  = {2015},

date = {2015-09-17},

urldate = {2015-09-17},

journal = {Genome Biol Evol},

volume = {7},

number = {9},

pages = {2585--2601},

abstract = {Mycobacterium avium (M. a.) subsp. paratuberculosis (MAP) - the etiologic agent of Johne's disease - affects cattle, sheep and other ruminants worldwide. To decipher phenotypic differences among sheep and cattle strains (belonging to MAP-S [Type-I/III] respectively MAP-C [Type-II]) comparative genome analysis needs data from diverse isolates originating from different geographic regions of the world. The current study presents the so far best assembled genome of a MAP-S-strain: sheep isolate JIII-386 from Germany. One newly sequenced cattle isolate (JII-1961, Germany), four published MAP strains of MAP-C and MAP-S from U.S. and Australia and M. a. subsp. hominissuis (MAH) strain 104 were used for assembly improvement and comparisons. All genomes were annotated by BacProt and results compared with NCBI annotation. Corresponding protein-coding sequences (CDSs) were detected, but also CDSs that were exclusively determined either by NCBI or BacProt. A new Shine-Dalgarno sequence motif (5'AGCTGG3') was extracted. Novel CDSs including PE-PGRS family protein genes and about 80 non-coding RNAs exhibiting high sequence conservation are presented. Previously found genetic differences between MAP-types are partially revised. Four out of ten assumed MAP-S-specific large sequence polymorphism regions (LSP s) are still present in MAP-C strains; new LSP s were identified. Independently of the regional origin of the strains, the number of individual CDSs and single nucleotide variants confirm the strong similarity of MAP-C strains and show higher diversity among MAP-S strains. This study gives ambiguous results regarding the hypothesis that MAP-S is the evolutionary intermediate between MAH and MAP-C, but it clearly shows a higher similarity of MAP to MAH than to M. intracellulare.},

keywords = {annotation, assembly, bacteria, DNA / genomics},

pubstate = {published},

tppubtype = {article}

}

@article{Bauer:14,

title = {Transcriptomic immune response of the cotton stainer \textit{Dysdercus fasciatus} to experimental elimination of vitamin-supplementing intestinal symbionts},

author = {Eugen Bauer and Hassan Salem and Manja Marz and Heiko Vogel and Martin Kaltenpoth},

url = {http://www.ebi.ac.uk/ena/data/view/PRJEB6171},

doi = {10.1371/journal.pone.0114865},

year  = {2014},

date = {2014-12-09},

urldate = {2014-12-09},

journal = {PLoS One},

volume = {9},

pages = {e114865},

abstract = {The acquisition and vertical transmission of bacterial symbionts plays an important role in insect evolution and ecology. However, the molecular mechanisms underlying the stable maintenance and control of mutualistic bacteria remain poorly understood. The cotton stainer Dysdercus fasciatus harbours the actinobacterial symbionts Coriobacterium glomerans and Gordonibacter sp. in its midgut. The symbionts supplement limiting B vitamins and thereby significantly contribute to the host's fitness. In this study, we experimentally disrupted the symbionts' vertical transmission route and performed comparative transcriptomic analyses of genes expressed in the gut of aposymbiotic (symbiont-free) and control individuals to study the host immune response in presence and absence of the mutualists. Annotation of assembled cDNA reads identified a considerable number of genes involved in the innate immune system, including different protein isoforms of several immune effector proteins (specifically i-type lysozyme, defensin, hemiptericin, and pyrrhocoricin), suggesting the possibility for a highly differentiated response towards the complex resident microbial community. Gene expression analyses revealed a constitutive expression of transcripts involved in signal transduction of the main insect immune pathways, but differential expression of certain antimicrobial peptide genes. Specifically, qPCRs confirmed the significant down-regulation of c-type lysozyme and up-regulation of hemiptericin in aposymbiotic individuals. The high expression of c-type lysozyme in symbiont-containing bugs may serve to lyse symbiont cells and thereby harvest B-vitamins that are necessary for subsistence on the deficient diet of Malvales seeds. Our findings suggest a sophisticated host response to perturbation of the symbiotic gut microbiota, indicating that the innate immune system not only plays an important role in combating pathogens, but also serves as a communication interface between host and symbionts.},

keywords = {annotation, assembly, bacteria, differential expression analysis, insects, RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{Salem:14,

title = {Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host},

author = {Hassan Salem and Eugen Bauer and Anja S Strauss and Heiko Vogel and Manja Marz and Martin Kaltenpoth},

doi = {10.1098/rspb.2014.1838},

year  = {2014},

date = {2014-12-07},

urldate = {2014-12-07},

journal = {Proc Biol Sci},

volume = {281},

pages = {20141838},

abstract = {Despite the demonstrated functional importance of gut microbes, our understanding of how animals regulate their metabolism in response to nutritionally beneficial symbionts remains limited. Here, we elucidate the functional importance of the African cotton stainer's (Dysdercus fasciatus) association with two actinobacterial gut symbionts and subsequently examine the insect's transcriptional response following symbiont elimination. In line with bioassays demonstrating the symbionts' contribution towards host fitness through the supplementation of B vitamins, comparative transcriptomic analyses of genes involved in import and processing of B vitamins revealed an upregulation of gene expression in aposymbiotic (symbiont-free) compared with symbiotic individuals; an expression pattern that is indicative of B vitamin deficiency in animals. Normal expression levels of these genes, however, can be restored by either artificial supplementation of B vitamins into the insect's diet or reinfection with the actinobacterial symbionts. Furthermore, the functional characterization of the differentially expressed thiamine transporter 2 through heterologous expression in Xenopus laevis oocytes confirms its role in cellular uptake of vitamin B1. These findings demonstrate that despite an extracellular localization, beneficial gut microbes can be integral to the host's metabolic homeostasis, reminiscent of bacteriome-localized intracellular mutualists.},

keywords = {bacteria, differential expression analysis, insects, RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{Wehner:14,

title = {Dissemination of 6S RNA among bacteria},

author = {Stefanie Wehner and Katrin Damm and Roland K Hartmann and Manja Marz},

doi = {10.4161/rna.29894},

year  = {2014},

date = {2014-10-31},

urldate = {2014-10-31},

journal = {RNA Biol},

volume = {11},

pages = {1467--1478},

abstract = {6S RNA is a highly abundant small non-coding RNA widely spread among diverse bacterial groups. By competing with DNA promoters for binding to RNA polymerase (RNAP), the RNA regulates transcription on a global scale. RNAP produces small product RNAs derived from 6S RNA as template, which rearranges the 6S RNA structure leading to dissociation of 6S RNA:RNAP complexes. Although 6S RNA has been experimentally analysed in detail for some species, such as Escherichia coli and Bacillus subtilis, and was computationally predicted in many diverse bacteria, a complete and up-to-date overview of the distribution among all bacteria is missing. In this study we searched with new methods for 6S RNA genes in all currently available bacterial genomes. We ended up with a set of 1,750 6S RNA genes, of which 1,367 are novel and bona fide, distributed among 1,610 bacteria, and had a few tentative candidates among the remaining 510 assembled bacterial genomes accessible. We were able to confirm two tentative candidates by Northern blot analysis. We extended 6S RNA genes of the Flavobacteriia significantly in length compared to the present Rfam entry. We describe multiple homologs of 6S RNAs (including split 6S RNA genes) and performed a detailed synteny analysis.},

keywords = {assembly, bacteria, ncRNAs, RNA / transcriptomics, RNA structure},

pubstate = {published},

tppubtype = {article}

}

@article{Wehner:14a,

title = {Detection of very long antisense transcripts by whole transcriptome RNA-Seq analysis of \textit{Listeria monocytogenes} by semiconductor sequencing technology},

author = {Stefanie Wehner and Gopala K Mannala and Xiaoxing Qing and Ramakanth Madhugiri and Trinad Chakraborty and Mobarak A Mraheil and Torsten Hain and Manja Marz},

doi = {10.1371/journal.pone.0108639},

year  = {2014},

date = {2014-10-06},

urldate = {2014-01-01},

journal = {PLoS One},

volume = {9},

pages = {e108639},

abstract = {The Gram-positive bacterium Listeria monocytogenes is the causative agent of listeriosis, a severe food-borne infection characterised by abortion, septicaemia, or meningoencephalitis. L. monocytogenes causes outbreaks of febrile gastroenteritis and accounts for community-acquired bacterial meningitis in humans. Listeriosis has one of the highest mortality rates (up to 30%) of all food-borne infections. This human pathogenic bacterium is an important model organism for biomedical research to investigate cell-mediated immunity. L. monocytogenes is also one of the best characterised bacterial systems for the molecular analysis of intracellular parasitism. Recently several transcriptomic studies have also made the ubiquitous distributed bacterium as a model to understand mechanisms of gene regulation from the environment to the infected host on the level of mRNA and non-coding RNAs (ncRNAs). We have used semiconductor sequencing technology for RNA-seq to investigate the repertoire of listerial ncRNAs under extra- and intracellular growth conditions. Furthermore, we applied a new bioinformatic analysis pipeline for detection, comparative genomics and structural conservation to identify ncRNAs. With this work, in total, 741 ncRNA locations of potential ncRNA candidates are now known for L. monocytogenes, of which 611 ncRNA candidates were identified by RNA-seq. 441 transcribed ncRNAs have never been described before. Among these, we identified novel long non-coding antisense RNAs with a length of up to 5,400 nt e.g. opposite to genes coding for internalins, methylases or a high-affinity potassium uptake system, namely the kdpABC operon, which were confirmed by qRT-PCR analysis. RNA-seq, comparative genomics and structural conservation of L. monocytogenes ncRNAs illustrate that this human pathogen uses a large number and repertoire of ncRNA including novel long antisense RNAs, which could be important for intracellular survival within the infected eukaryotic host.},

keywords = {bacteria, ncRNAs, RNA / transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{Lechner:14,

title = {Genomewide comparison and novel ncRNAs of Aquificales},

author = {Marcus Lechner and Astrid I. Nickel and Stefanie Wehner and Konstantin Riege and Nicolas Wieseke and Benedikt M. Beckmann and Roland K. Hartmann and Manja Marz},

doi = {10.1186/1471-2164-15-522},

year  = {2014},

date = {2014-06-25},

urldate = {2014-06-25},

journal = {BMC Genomics},

volume = {15},

pages = {522},

abstract = {The Aquificales are a diverse group of thermophilic bacteria that thrive in terrestrial and marine hydrothermal environments. They can be divided into the families Aquificaceae, Desulfurobacteriaceae and Hydrogenothermaceae. Although eleven fully sequenced and assembled genomes are available, only little is known about this taxonomic order in terms of RNA metabolism. In this work, we compare the available genomes, extend their protein annotation, identify regulatory sequences, annotate non-coding RNAs (ncRNAs) of known function, predict novel ncRNA candidates, show idiosyncrasies of the genetic decoding machinery, present two different types of transfer-messenger RNAs and variations of the CRISPR systems. Furthermore, we performed a phylogenetic analysis of the Aquificales based on entire genome sequences, and extended this by a classification among all bacteria using 16S rRNA sequences and a set of orthologous proteins.Combining several in silico features (e.g. conserved and stable secondary structures, GC-content, comparison based on multiple genome alignments) with an in vivo dRNA-seq transcriptome analysis of Aquifex aeolicus, we predict roughly 100 novel ncRNA candidates in this bacterium. We have here re-analyzed the Aquificales, a group of bacteria thriving in extreme environments, sharing the feature of a small, compact genome with a reduced number of protein and ncRNA genes. We present several classical ncRNAs and riboswitch candidates. By combining in silico analysis with dRNA-seq data of A. aeolicus we predict nearly 100 novel ncRNA candidates.},

keywords = {alignment, annotation, assembly, bacteria, classification, ncRNAs, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{Sachse:14,

title = {Evidence for the existence of two new members of the family Chlamydiaceae and proposal of \textit{Chlamydia avium} sp. nov. and \textit{Chlamydia gallinacea} sp. nov.},

author = {Konrad Sachse and Karine Laroucau and Konstantin Riege and Stefanie Wehner and Meik Dilcher and Heather Huot Creasy and Manfred Weidmann and Garry Myers and Fabien Vorimore and Nadia Vicari and Simone Magnino and Elisabeth Liebler-Tenorio and Anke Ruettger and Patrik M. Bavoil and Frank T. Hufert and Ramon Rosselló-Móra and Manja Marz},

doi = {10.1016/j.syapm.2013.12.004},

year  = {2014},

date = {2014-01-22},

urldate = {2014-01-22},

journal = {Syst Appl Microbiol},

volume = {37},

pages = {79--88},

abstract = {The family Chlamydiaceae with the recombined single genus Chlamydia currently comprises nine species, all of which are obligate intracellular organisms distinguished by a unique biphasic developmental cycle. Anecdotal evidence from epidemiological surveys in flocks of poultry, pigeons and psittacine birds have indicated the presence of non-classified chlamydial strains, some of which may act as pathogens. In the present study, phylogenetic analysis of ribosomal RNA and ompA genes, as well as multi-locus sequence analysis of 11 field isolates were conducted. All independent analyses assigned the strains into two different clades of monophyletic origin corresponding to pigeon and psittacine strains or poultry isolates, respectively. Comparative genome analysis involving the type strains of currently accepted Chlamydiaceae species and the designated type strains representing the two new clades confirmed that the latter could be classified into two different species as their average nucleotide identity (ANI) values were always below 94%, both with the closest relative species and between themselves. In view of the evidence obtained from the analyses, we propose the addition of two new species to the current classification: Chlamydia avium sp. nov. comprising strains from pigeons and psittacine birds (type strain 10DC88(T); DSMZ: DSM27005(T), CSUR: P3508(T)) and Chlamydia gallinacea sp. nov. comprising strains from poultry (type strain 08-1274/3(T); DSMZ: DSM27451(T), CSUR: P3509(T)).},

keywords = {bacteria, classification, phylogenetics},

pubstate = {published},

tppubtype = {article}

}

@article{Gimpel:12,

title = {SR1 - a small RNA with two remarkably conserved functions},

author = {Matthias Gimpel and Heike Preis and Emanuel Barth and Lydia Gramzow and Sabine Brantl},

doi = {10.1093/nar/gks895},

year  = {2012},

date = {2012-10-02},

urldate = {2012-01-01},

journal = {Nucleic Acids Res},

volume = {40},

pages = {11659--11672},

abstract = {SR1 is a dual-function sRNA that acts as a base-pairing regulatory RNA on the ahrC mRNA and as a peptide-encoding mRNA on the gapA operon. The SR1-encoded peptide SR1P binds GapA thereby stabilizing gapA mRNA. Under glycolytic conditions, SR1 transcription is repressed by CcpN and CcpA. A computer-based search identified 23 SR1 homologues in Bacillus, Geobacillus, Anoxybacillus and Brevibacillus species. All homologues share a high structural identity with Bacillus subtilis SR1, and the encoded SR1P peptides are highly similar. In the Bacillus cereus group, the sr1p region is present in triplicate or duplicate resulting in longer SR1 species. In all cases, sr1 expression is under control of CcpN, and transcriptional lacZ fusions of nine examined SR1 homologues were sensitive to glucose. Two homologues showed an additional glucose-independent repression by CcpN and an unknown factor. A total of 10 out of 11 tested SR1P homologues complemented a B. subtilis Δsr1 strain in their ability to stabilize gapA mRNA, but only five of them bound GapA tightly. In vitro binding assays with six SR1/ahrC pairs suggest that-despite divergent primary sequences-the base-pairing function is also preserved. In summary, SR1 is an sRNA with two functions that have been conserved over ≈1 billion years.},

keywords = {bacteria, ncRNAs},

pubstate = {published},

tppubtype = {article}

}

@article{Beckmann:12,

title = {A pRNA-induced structural rearrangement triggers 6S-1 RNA release from RNA polymerase in \textit{Bacillus subtilis}},

author = {Benedikt M. Beckmann and Philipp G. Hoch and Manja Marz and Dagmar K. Willkomm and Margarita Salas and Roland K. Hartmann},

doi = {10.1038/emboj.2012.23},

year  = {2012},

date = {2012-01-01},

urldate = {2012-01-01},

journal = {EMBO J},

volume = {31},

pages = {1727--1738},

abstract = {Bacillus subtilis 6S-1 RNA binds to the housekeeping RNA polymerase (σ(A)-RNAP) and directs transcription of short 'product' RNAs (pRNAs). Here, we demonstrate that once newly synthesized pRNAs form a sufficiently stable duplex with 6S-1 RNA, a structural rearrangement is induced in cis, which involves base-pairing between sequences in the 5'-portion of the central bulge and nucleotides that become available as a result of pRNA invasion. The rearrangement decreases 6S-1 RNA affinity for σ(A)-RNAP. Among the pRNA length variants synthesized by σ(A)-RNAP (up to ∼14 nt), only the longer ones, such as 12-14-mers, form a duplex with 6S-1 RNA that is sufficiently long-lived to induce the rearrangement. Yet, an LNA (locked nucleic acid) 8-mer can induce the same rearrangement due to conferring increased duplex stability. We propose that an interplay of rate constants for polymerization (k(pol)), for pRNA:6S-1 RNA hybrid duplex dissociation (k(off)) and for the rearrangement (k(conf)) determines whether pRNAs dissociate or rearrange 6S-1 structure to trigger 6S-1 RNA release from σ(A)-RNAP. A bioinformatic screen suggests that essentially all bacterial 6S RNAs have the potential to undergo a pRNA-induced structural rearrangement.},

keywords = {bacteria, ncRNAs},

pubstate = {published},

tppubtype = {article}

}

@article{Lechner:11,

title = {Proteinortho: detection of (co-)orthologs in large-scale analysis},

author = {Marcus Lechner and Sven Findeiss and Lydia Steiner and Manja Marz and Peter F Stadler and Sonja J Prohaska},

url = {http://bioinf.pharmazie.uni-marburg.de/supplements/proteinortho/},

doi = {10.1186/1471-2105-12-124},

year  = {2011},

date = {2011-04-28},

urldate = {2011-04-28},

journal = {BMC Bioinf},

volume = {12},

pages = {124},

abstract = {Orthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood of sequence data, and hence the rapidly increasing number of genomes that can be compared simultaneously, calls for efficient software tools as brute-force approaches with quadratic memory requirements become infeasible in practise. The rapid pace at which new data become available, furthermore, makes it desirable to compute genome-wide orthology relations for a given dataset rather than relying on relations listed in databases. The program Proteinortho described here is a stand-alone tool that is geared towards large datasets and makes use of distributed computing techniques when run on multi-core hardware. It implements an extended version of the reciprocal best alignment heuristic. We apply Proteinortho to compute orthologous proteins in the complete set of all 717 eubacterial genomes available at NCBI at the beginning of 2009. We identified thirty proteins present in 99% of all bacterial proteomes. Proteinortho significantly reduces the required amount of memory for orthology analysis compared to existing tools, allowing such computations to be performed on off-the-shelf hardware.},

keywords = {alignment, bacteria, phylogenetics, proteins, software},

pubstate = {published},

tppubtype = {article}

}

@article{Yusuf:10,

title = {Bcheck: a wrapper tool for detecting RNase P RNA genes},

author = {Dilmurat Yusuf and Manja Marz and Peter F Stadler and Ivo L Hofacker},

url = {http://rna.tbi.univie.ac.at/bcheck},

doi = {10.1186/1471-2164-11-432},

year  = {2010},

date = {2010-07-13},

urldate = {2010-07-13},

journal = {BMC Genomics},

volume = {11},

pages = {432},

abstract = {Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present Bcheck, a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern matching and sensitivity of covariance models. The core of Bcheck is a library of subfamily specific descriptor models and covariance models. Scanning all microbial genomes in GenBank identifies RNase P RNA genes in 98% of 1024 microbial chromosomal sequences within just 4 hours on single CPU. Comparing to existing annotations found in 387 of the GenBank files, Bcheck predictions have more intact structure and are automatically classified by subfamily membership. For eukaryotic chromosomes Bcheck could identify the known RNase P RNA genes in 84 out of 85 metazoan genomes and 19 out of 21 fungi genomes. Bcheck predicted 37 novel eukaryotic RNase P RNA genes, 32 of which are from fungi. Gene duplication events are observed in at least 20 metazoan organisms. Scanning of meta-genomic data from the Global Ocean Sampling Expedition, comprising over 10 million sample sequences (18 Gigabases), predicted 2909 unique genes, 98% of which fall into ancestral bacteria A type of RNase P RNA and 66% of which have no close homolog to known prokaryotic RNase P RNA. The combination of efficient filtering by means of a descriptor-based search and subsequent construction of a high-quality gene model by means of a covariance model provides an efficient method for the detection of RNase P RNA genes in large-scale sequencing data. Bcheck is implemented as webserver and can also be downloaded for local use from http://rna.tbi.univie.ac.at/bcheck.},

keywords = {annotation, bacteria, classification, fungi, ncRNAs, RNA / transcriptomics, software},

pubstate = {published},

tppubtype = {article}

}

@article{nokey_92,

title = {Molecular Characterization of Chimeric Staphylococcus aureus Strains from Waterfowl},

author = { Stefan Monecke and Sascha D. Braun and Maximillian Collatz and Celia Diezel and Elke Müller and Martin Reinicke and Adriana Cabal Rosel and Andrea T. Feßler and Dennis Hanke and Igor Loncaric and Stefan Schwarz and Sonia Cortez de Jäckel and Werner Ruppitsch and Dolores Gavier Widen and Helmut Hotzel and Ralf Ehricht},

doi = {10.3390/microorganisms12010096},

journal = {Microorganisms},

volume = {12},

abstract = {Staphylococcus aureus is a versatile pathogen that does not only occur in humans but also in various wild and domestic animals, including several avian species. When characterizing S. aureus isolates from waterfowl, isolates were identified as atypical CC133 by DNA microarray analysis. They differed from previously sequenced CC133 strains in the presence of the collagen adhesin gene cna; some also showed a different capsule type and a deviant spa type. Thus, they were subjected to whole-genome sequencing. This revealed multiple insertions of large regions of DNA from other S. aureus lineages into a CC133-derived backbone genome. Three distinct strains were identified based on the size and extent of these inserts. One strain comprised two small inserts of foreign DNA up- and downstream of oriC; one of about 7000 nt or 0.25% originated from CC692 and the other, at ca. 38,000 nt or 1.3% slightly larger one was of CC522 provenance. The second strain carried a larger CC692 insert (nearly 257,000 nt or 10% of the strain’s genome), and its CC522-derived insert was also larger, at about 53,500 nt or 2% of the genome). The third strain carried an identical CC692-derived region (in which the same mutations were observed as in the second strain), but it had a considerably larger CC522-like insertion of about 167,000 nt or 5.9% of the genome. Both isolates of the first, and two out of four isolates of the second strain also harbored a hemolysin-beta-integrating prophage carrying “bird-specific” virulence factors, ornithine cyclodeaminase D0K6J8 and a putative protease D0K6J9. Furthermore, isolates had two different variants of SCC elements that lacked mecA/mecC genes. These findings highlight the role of horizontal gene transfer in the evolution of S. aureus facilitated by SCC elements, by phages, and by a yet undescribed mechanism for large-scale exchange of core genomic DNA.},

keywords = {bacteria, DNA / genomics, evolution},

pubstate = {published},

tppubtype = {article}

}