TY - JOUR T1 - The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics JF - GigaScience Y1 - 2023 A1 - Luc Cornet A1 - Benoit Durieu A1 - F. Baert A1 - Elizabet D'hooge A1 - David Colignon A1 - Loic Meunier A1 - Valérian Lupo A1 - Ilse Cleenwerck A1 - Heide-Marie Daniel A1 - Rigouts, Leen A1 - Damien Sirjacobs A1 - Stéphane Declerck A1 - Vandamme, Peter A1 - Annick Wilmotte A1 - Denis Baurain A1 - Pierre Becker KW - culture collections KW - Cyanobacteria KW - Genomics KW - Gloeobacterales KW - Metagenomics KW - nextflow KW - phylogenomics KW - Phylogeny KW - Singularity containers KW - Workflow AB -

Background: Microbial culture collections play a key role in taxonomy by studying the diversity of their strains and providing wellcharacterized biological material to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms were studied, resulting in the GEN-ERA toolbox. The latter is a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (e.g., yeasts). Findings: This public toolbox allows researchers without a specific training in bioinformatics to perform robust phylogenomic analyses. Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling. Technical details: Nextflow workflows are launched by a single command and are available on the GEN-ERA GitHub repository (https: //github.com/Lcornet/GENERA). All the workflows are based on Singularity containers to increase reproducibility. Testing: The toolbox was developed for a diversity of microorganisms, including bacteria and fungi. It was further tested on an empirical dataset of 18 (meta)genomes of early branching Cyanobacteria, providing the most up-to-date phylogenomic analysis of the Gloeobacterales order, the first group to diverge in the evolutionary tree of Cyanobacteria. Conclusion: The GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be used by all researchers interested in microbial taxonomy, as exemplified by our case study on Gloeobacterales.

VL - 12 M3 - 10.1093/gigascience/giad022 ER - TY - JOUR T1 - Reducing the number of accepted species in Aspergillus series Nigri JF - Studies in Mycology Y1 - 2022 A1 - C. Bian ED - Y. Kusuya ED - T. Yaguchi ED - S. Ban ED - V. Hubka KW - ASPERGILLUS LUCHUENSIS KW - ASPERGILLUS NIGER KW - ASPERGILLUS TUBINGENSIS KW - CLINICAL FUNGI KW - INDOOR FUNGI KW - INFRASPECIFIC VARIABILITY KW - MULTIGENE PHYLOGENY KW - MULTISPECIES COALESCENCE MODEL KW - Ochratoxin A KW - SPECIES DELIMITATION VL - 102 M3 - https://doi.org/10.3114/sim.2022.102.03 ER - TY - JOUR T1 - A Polyphasic Approach to Classification and Identification of Species within the Trichophyton benhamiae Complex JF - Journal of Fungi Y1 - 2021 A1 - F. Baert ED - Paulien Lefevere ED - Elizabet D'hooge ED - Dirk Stubbe ED - Ann Packeu VL - 7 CP - 8 M3 - 10.3390/jof7080602 ER - TY - JOUR T1 - The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach JF - Microbial Genomics Y1 - 2021 A1 - Luc Cornet A1 - Elizabet D'hooge A1 - Nicolas Magain A1 - Dirk Stubbe A1 - Ann Packeu A1 - Denis Baurain A1 - Pierre Becker KW - Dermatophytes KW - Fungi KW - Genomics KW - Phylogeny KW - Taxonomy VL - 7 CP - 11 M3 - 10.1099/mgen.0.000707 ER - TY - JOUR T1 - Updating the Taxonomy of Dermatophytes of the BCCM/IHEM Collection According to the New Standard: A Phylogenetic Approach. JF - Mycopathologia Y1 - 2019 A1 - F. Baert A1 - Dirk Stubbe A1 - Elizabet D'hooge A1 - Ann Packeu A1 - Marijke Hendrickx KW - Arthrodermataceae KW - BCCM/IHEM KW - Dermatophyten KW - Dermatophytes KW - ITS KW - phylogenetics KW - Phylogeny KW - Taxonomy KW - Tubulin AB -

Recent taxonomical revisions based on multilocus gene sequencing have provided some clarifications to dermatophyte (Arthrodermataceae) family tree. These changes promoted us to investigate the impact of the changed nomenclature of the dermatophyte strains in the BCCM/IHEM fungal collection, which contains strains of all dermatophyte genera except for Ctenomyces. For 688 strains from this collection, both internal transcribed spacer region (ITS) and partial β-tubulin (BT) sequences were aligned and a multilocus phylogenetic tree was constructed. The ITS + BT phylogentic tree was able to distinguish the genera Arthroderma, Lophophyton, Microsporum, Paraphyton, Nannizzia and Trichophyton with high certainty. Epidermophyton, which is widely considered as a well-defined genus with E. floccosum as the only representative, fell within the Nannizzia clade, whereas the phylogenetic analysis, based on the ITS region alone, differentiates Epidermophyton from Nannizzia as a separate genus. Re-identification and reclassification of many strains in the collection have had a profound impact on the composition of the BCCM/IHEM dermatophyte collection. The biggest change is the decline of prevalence of Arthroderma strains; starting with 103 strains, only 22 strains remain in the genus after reassessment. Most Arthroderma strains were reclassified into Trichophyton, with A. benhamiae and A. vanbreuseghemii leaving the genus. The amount of Microsporum strains also dropped significantly with most of these strains being reclassified into the genera Paraphyton and Nannizzia.

M3 - 10.1007/s11046-019-00338-7 ER - TY - JOUR T1 - Black aspergilli: A remaining challenge in fungal taxonomy? JF - Med Mycol Y1 - 2018 A1 - Elizabet D'hooge A1 - Pierre Becker A1 - Dirk Stubbe A1 - Normand, Anne-Cécile A1 - Piarroux, Renaud A1 - Marijke Hendrickx KW - antifungal susceptibility KW - Aspergillus sect. Nigri KW - MALDI-TOF MS KW - Phylogeny AB -

Aspergillus section Nigri is a taxonomically difficult but medically and economically important group. In this study, an update of the taxonomy of A. section Nigri strains within the BCCM/IHEM collection has been conducted. The identification accuracy of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was tested and the antifungal susceptibilities of clinical isolates were evaluated. A total of 175 strains were molecularly analyzed. Three regions were amplified (ITS, benA, and caM) and a multi-locus phylogeny of the combined loci was created by using maximum likelihood analysis. The in-house MALDI-TOF MS reference database was extended and an identification data set of 135 strains was run against a reference data set. Antifungal susceptibility was tested for voriconazole, itraconazole, and amphotericin B, using the EUCAST method. Phylogenetic analysis revealed 18 species in our data set. MALDI-TOF MS was able to distinguish between A. brasiliensis, A. brunneoviolaceus, A. neoniger, A. niger, A. tubingensis, and A. welwitschiae of A. sect. Nigri. In the routine clinical lab, isolates of A. sect. Nigri are often identified as A. niger. However, in the clinical isolates of our data set, A. tubingensis (n = 35) and A. welwitschiae (n = 34) are more common than A. niger (n = 9). Decreased antifungal susceptibility to azoles was observed in clinical isolates of the /tubingensis clade. This emphasizes the importance of identification up to species level or at least up to clade level in the clinical lab. Our results indicate that MALDI-TOF MS can be a powerful tool to replace classical morphology.

M3 - 10.1093/mmy/myy124 ER -