Fig 1.
Extracts from the 16S rRNA phylogenies of Streptomyces (full figure in S1 Fig and https://itol.embl.de/shared/1MX60mtB0Ohk3) inferred using iqtree2 and the GTR+F+R5 model showing the placement of isolates (green dots) with related rRNA sequences from the ezBioCloud 16S rRNA database (blue), soil isolates from Sudan (yellow dots [48]) and isolates collected by Sengupta, Goodfellow and Hamid (NCBI accessions EU544231.1 to EU544241.1 from human actinomycetoma (purple) and from donkey withers (lilac).
A red dot on branches indicates ultrafast bootstrap support >95. Triangles are used to represent collapsed clades.
Fig 2.
The 16S rRNA phylogeny of Actinomadura showing the placement of isolates (green) with related rRNA sequences from the ezBioCloud database (blue; pink for known pathogens). Inferred using iqtree2 and the GTR+F+R4 model. A black dot on branches indicates ultrafast bootstrap support >95. All isolates form a clade with Actinomadura madurae and Actinomadura darangshiensis, though support for this grouping is low.
Table 1.
Summarising the pairwise ANI, AAI and estimated DDH values of the S. somaliensis and S. sudanensis type strain genomes compared to genomes in GTDB.
Species thresholds are usually defined by ANI >95%, AAI >95% and DDH >70%. Values that fall below these thresholds are highlighted in grey. Results indicate that GTDB GCF_000258695 (annotated as S. somaliensis) is most closely related to S. sudanensis, though it is a different species.
Fig 3.
Tree of single copy orthologs belonging to the GTDB bac120 dataset, from the genomes of Streptomyces related isolates from the Mycetoma Research Centre (green), their relatives according to ANI in GTDB (with the closest relatives indicated in blue) and genomes from type strains of species typically associated with actinomycetoma (black). A red dot on branches indicates ultrafast bootstrap support >95. Triangles are used to represent collapsed clades. The tree was inferred in iqtree2 using the C20 model. The full figure is available at https://itol.embl.de/shared/1MX60mtB0Ohk3.
Fig 4.
Pairwise comparison of Average Nucleotide Identity between the genomes of Isolates from the Mycetoma Research Centre (red) and their closest relatives in GTDB (all genomes from GTDB with an ANI >90 with any single isolate genome or the genome of type strains). The heatmap is ordered based on hierarchical clustering (Ward, Euclidean distance). Black lines delineate species boundaries based on ANI > 95%. The genomes of the reference species are from type strains.
Table 2.
Summarising the pairwise ANI, AAI and estimated DDH values between isolates and their nearest relatives with sequenced genomes.
S. somaliensis and S. sundanensis type strain genomes are compared to genomes in GTDB. Values that fall below defined thresholds for assigning strains to the same species are highlighted in grey.
Fig 5.
Tree of single copy orthologs that belong to the GTDB bac120 dataset from the genomes of Actinomadura related isolates from the Mycetoma Research Centre (green), their relatives according to ANI in GTDB (with the closest relatives indicated in blue) and genomes from type strains of species typically associated with actinomycetoma (black). Additionally, the type strain genome of any organism previously isolated from mycetoma patients and present in the GTDB is highlighted (pink). A red dot on branches indicates ultrafast bootstrap support >95. The tree was inferred in iqtree2 using the C20 model.
Fig 6.
The distribution of genome sizes (in Mb) of all species within the Streptomyces genus (as defined by GTDB) for which a high quality genome is available (see materials and methods).
The mean genome size for the genus is 8.45Mb. The genomes of all S. sudanensis and S. somaliensis related isolates are amongst the smallest genomes in the genus.
Table 3.
Assembly statistics for all isolate genomes sequenced in this project.
The genomes from these assemblies are available under NCBI Bioproject PRJNA782605.
Table 4.
Initial clinical classification of isolates compared to the molecular taxonomic assignments.
Fig 7.
Comparative antibiotic susceptibility profiles of actinomycetoma isolates based on a disk diffusion assay.
Halo size was recorded in cm. Yellow low IC. Blue high IC. The isolates were grouped using hierarchical clustering based on their IC profiles using the default parameters of heatmap2 in R.