Hohenheim Center for Livestock Microbiome Research (HoLMiR)

Permanent URI for this collectionhttps://hohpublica.uni-hohenheim.de/handle/123456789/17567

Browse

Browsing Hohenheim Center for Livestock Microbiome Research (HoLMiR) by Classification "570"

Type the first few letters and click on the Browse button
Now showing 1 - 2 of 2
  • Thumbnail Image
    Publication
    Functionality of the Na+-translocating NADH:quinone oxidoreductase and quinol:fumarate reductase from Prevotella bryantii inferred from homology modeling
    (2024) Hau, Jann-Louis; Schleicher, Lena; Herdan, Sebastian; Simon, Jörg; Seifert, Jana; Fritz, Günter; Steuber, Julia
    Members of the family Prevotellaceae are Gram-negative, obligate anaerobic bacteria found in animal and human microbiota. In Prevotella bryantii , the Na + -translocating NADH:quinone oxidoreductase (NQR) and quinol:fumarate reductase (QFR) interact using menaquinone as electron carrier, catalyzing NADH:fumarate oxidoreduction. P. bryantii NQR establishes a sodium-motive force, whereas P. bryantii QFR does not contribute to membrane energization. To elucidate the possible mode of function, we present 3D structural models of NQR and QFR from P. bryantii to predict cofactor-binding sites, electron transfer routes and interaction with substrates. Molecular docking reveals the proposed mode of menaquinone binding to the quinone site of subunit NqrB of P. bryantii NQR. A comparison of the 3D model of P. bryantii QFR with experimentally determined structures suggests alternative pathways for transmembrane proton transport in this type of QFR . Our findings are relevant for NADH-dependent succinate formation in anaerobic bacteria which operate both NQR and QFR.
  • Thumbnail Image
    Publication
    NaMeco - Nanopore full-length 16S rRNA gene reads clustering and annotation
    (2026) Yergaliyev, Timur; Rios-Galicia, Bibiana; Camarinha-Silva, Amélia; Yergaliyev, Timur; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Rios-Galicia, Bibiana; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany; Camarinha-Silva, Amélia; Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
    Background: Nanopore sequencing is currently one of the leading third-generation sequencing technologies on the market and is gaining popularity among researchers. Due to its long-read capabilities, full-length 16S rRNA gene metabarcoding using Oxford Nanopore Technologies (ONT) offers great potential for metataxonomic studies. However, the relatively high error rate poses a significant challenge for bioinformatic processing, often limiting taxonomy resolution to the genus level despite the longer read length. Results: This study presents NaMeco, a novel tool specifically developed to efficiently process long 16S rRNA gene reads sequenced using Oxford Nanopore Technologies, requiring minimal user input. Our tool performs read quality control, primer-specific extraction of sequences and their clustering, followed by taxonomic annotation with percent identity thresholds that minimize the amount of false-positive annotations. It produces several outputs: a table of cluster counts, taxonomic annotations of clusters, their representative sequences in fasta format and taxa counts at each taxonomy rank. Output files are compatible with the Qiime2 pipeline and can be imported into the required format for downstream analyses. Conclusions: NaMeco, in combination with the full SSU GTDB database, outperforms existing tools such as NanoCLUST and EPI2ME, while delivering taxonomy accuracy and detection rates comparable to Emu.