Biology subjects

Harbig, T. A.

Publications and source records attributed to Harbig, T. A..

4 recordsLinked to original sources

bioRxiv2025

Genetic modification of intractable staphylococcal clones by heat-shock facilitated phage transduction

Increasing recognition of commensal bacteria as a requirement for microbiome integrity and pathogen exclusion puts urgency to the molecular characterization of commensal interactions. However, many commensals cannot be transformed with available methodology because of potent restriction barriers. We developed a new method for the introduction of plasmid DNA into otherwise intractable non-Staphylococcus aureus (NAS) staphylococci, important commensal members of human nose and skin microbiomes, by phage transduction. We demonstrate that a precise pulse of recipient bacteria with elevated temperatures prior to exposure to transducing phages renders NAS isolates effectively and transiently amenable to transduction. Transduction of NAS mutants lacking restriction-modification (RM) systems did not profit from a heat shock indicating that it is the transient deactivation of RM enzymes that permit transduction. Our method also facilitated the transduction of other Bacillota from the genera Bacillus and Listeria indicating that it will support research on different bacterial groups from diverse ecosystems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/647181v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@233348org.highwire.dtl.DTLVardef@fbf57corg.highwire.dtl.DTLVardef@1b1abadorg.highwire.dtl.DTLVardef@17e283f_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2022

Technical report on best practices for hybrid and long read de novo assembly of bacterial genomes utilizing Illumina and Oxford Nanopore Technologies reads

The emergence of commercial long read sequencing technologies in the 2010s and the concomitant development of new bioinformatics tools bears the potential of de novo genome assemblies of unprecedented contiguity and quality. However, until today these novel technologies suffer from high rates of sequencing errors. These may be overcome by using long and short reads in combination, in so called hybrid approaches, or by increasing the through-put and thereby the coverage of sequencing runs. In particular the latter will thereby increase the cost of the assembly inevitably. Herein, to-date long read and hybrid assemblers were tested on real whole genome sequencing Illumina and Oxford Nanopore Technologies read data sets and sub samples of these in order to elaborate a best practice for de novo assembly. The findings suggest that although long reads alone can be used to reconstruct complete and contiguous genomes, in particular the single-nucleotide and indel error rate remains high compared to hybrid approaches and that this can impact downstream applications such as variation discovery and gene prediction negatively.

bioinformatics↗

bioRxiv2022

Horizontal transfer of bacteriocin biosynthesis genes requires metabolic adaptation to improve compound production and cellular fitness

Biosynthetic gene clusters (BGCs) encoding the production of bacteriocins are widespread amongst bacterial isolates and are important genetic determinants of competitive fitness within a given habitat. Staphylococci produce a tremendous diversity of compounds and the corresponding BGCs are frequently associated with mobile genetic elements, suggesting gain and loss of biosynthetic capacity. Pharmaceutical biology has shown that compound production in heterologous hosts is often challenging and many BGC recipients produce initially low compound amounts or show reduced growth rates. To assess whether transfer of BGCs between closely related S. aureus strains can be instantly effective or requires elaborate metabolic adaptation, we investigated the intra species transfer of a BGC encoding the ribosomally synthesized and post-translationally modified peptide (RiPP) micrococcin P1 (MP1). We found that acquisition of the BGC by S. aureus RN4220 enabled immediate MP1 production but also imposed a metabolic burden, which was relieved after prolonged cultivation by adaptive mutation. We used a multiomics approach to study this phenomenon and found adaptive evolution to select for strains with increased activity of the tricarboxylic acid cycle (TCA), which enhanced metabolic fitness and levels of compound production. Metabolome analysis revealed increases of central metabolites including citrate and -ketoglutarate in the adapted strain, suggesting metabolic adaptation to overcome the BGC-associated growth defects. Our results indicate that BCG acquisition requires genetic and metabolic predispositions allowing the integration of bacteriocin production into the cellular metabolism. Inappropriate metabolic characteristics of recipients can entail physiological burdens, negatively impacting the competitive fitness of recipients within natural bacterial communities. ImportanceHuman microbiomes are critically associated with human health and disease. Importantly, pathogenic bacteria can hide in human associated communities and can cause disease when the composition of the community becomes dysbalanced. Bacteriocin producing commensals are able to displace pathogens from microbial communities, suggesting that their targeted introduction in human microbiomes might prevent pathogen colonisation and infection. However, in view of future probiotic approaches, strains are needed that produce high levels of bioactive compounds and retain cellular fitness within mixed bacterial communities. Our work offers insights into the metabolic burdens associated with the production of the bacteriocin micrococcin P1 and highlights evolutionary strategies that increase cellular fitness in the context of production. Most likely metabolic adaptations are broadly relevant for bacteriocin producers and need to be considered for the future development of effective microbiome editing strategies.

microbiology↗

bioRxiv2021

OmicsTIDE: Interactive Exploration of Trends in Multi-Omics Data

MotivationThe increasing amount of data produced by omics technologies has significantly improved the understanding of how biological information is transferred across different omics layers and to which extent it is involved in the manifestation of a given phenotype. Besides data-driven analysis strategies, interactive visualization tools have been developed to make the analysis in the multi-omics field more transparent. However, most state-of-the-art tools do not reconstruct the impact of a given omics layer on the final integration result. In general, the amount of omics data analyses strategies and the fields of applications lack a clearer classification of the different approaches. ResultsWe developed a classification for omics data focusing on different aspects of multi-omics data sets, such as data type and experimental design. Based on this classification we developed the Omics Trend-comparing Interactive Data Explorer (OmicsTIDE), an interactive visualization tool developed to address the limitations of current visualization approaches in the multi-omics field. The tool consists of an automated part that clusters omics data to determine trends and an interactive visualization. The trends are visualized as profile plots and are connected by a Sankey diagram that allows an interactive pairwise trend comparison to discover concordant and discordant trends. Moreover, large-scale omics data sets are broken down into small subsets of concordant and discordant regulatory trends within few analysis steps. We demonstrate the interactive analysis using OmicsTIDE with two case studies focusing on different types of experimental designs. AvailabilityOmicsTIDE is a web tool and available via http://tuevis.informatik.uni-tuebingen.de/ Contactkay.nieselt@uni-tuebingen.de

bioinformatics↗