Additional file 2 of The Staphylococcus aureus-antagonizing human nasal commensal Staphylococcus lugdunensis depends on siderophore piracy
Creators: name: Rosenstein, Ralf
name: Torres Salazar, Benjamin O.
name: Sauer, Claudia
name: Heilbronner, Simon
name: Krismer, Bernhard
name: Peschel, Andreas
Publisher: name: figshare
Year: 2024
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Biotechnology
subject: Ecology
subject: Science Policy
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Supplementary Material 2: Supplementary Figure S1. Microbiome profiles within the genus Staphylococcus at the species level. Relative proportions of staphylococcal species present in the nasal microbiomes at time points 18 months and 23 months are presented by stacked bar charts. The different bacterial species are indicated by colours as shown in the legend on the right. The presence of S. lugdunensis reads in the metagenomes is indicated (Slu). The microbiome profiles that could be assigned to the CSTs published by Liu et al. [11] are labelled accordingly. Profiles not fitting to one of these types are designated “nd”. Supplementary Figure S2. Microbiome profiles within the genus Corynebacterium at the species level. Corynebacterium species profiles determined in metagenome analyses at time points 18 and 23 months. Relative proportions of Corynebacterium species present in the nasal microbiomes are presented by stacked bar charts. The different Corynebacterium species are indicated by colours as listed in the legend on the right. For C. accolens, C. pseudodiphteriticum, and C. tuberculostearicum, different strains (“KPL strains”) were determined but labeled with the same colours according to a strain assignment by the Lemon lab [45]. The presence of S. lugdunensis reads in the metagenomes is indicated (Slu). The microbiome profiles that could be assigned to the CSTs published by [11] are labelled accordingly. Profiles not fitting to one of these types are designated “nd”. Supplementary Figure S3. Correlation of S. aureus with other microbiome species. Correlation coefficients were inferred based on a centered log-ratio-transformed abundance table of species reads by correlation network analyses using the Namap/Pearson algorithm of MetagenoNets [20] with thresholds for prevalence and occurrence of 0.1% and 20%, respectively. Based on these parameters, we obtained correlation measures for 28 species throughout all 24 samples. Shown are the associations of S. aureus with other microbiome species (shown at the x-axis). Positive associations are indicated by green bars, negative associations by red bars. The corresponding Pearson correlation coefficients are indicated at the x-axis. Supplementary Figure S4. Nasal bacterial species producing siderophores have the capacity to support growth of S. lugdunensis. (A) Siderophore concentration in spent media from nasal bacteria after three days of incubation detected via SideroTec AssayTM kit. Siderophores could be detected in spent media from staphylococcal species and E. coli; siderophore detection was not assessable for C. kroppenstedtii due to the essential presence of Tween 80 in growth medium that interacts with the reaction solutions provided by the SideroTec AssayTM kit. (B) Occurrence and sizes (diameter in mm) of growth zones of S. lugdunensis promoted by siderophore-containing spent media from nasal bacteria. Staphylococcal species and E. coli support S. lugdunensis growth under iron-restricted conditions. Data points represent average values of three independent biological replicates, and vertical red lines show means of each species. Supplementary Figure S5. Representative pictures of lugdunin susceptibility determination of nasal bacteria and S. lugdunensis growth promotion by siderophore-containing spent media from nasal bacteria. (A) Lugdunin susceptibility determination by the example of S. aureus USA300. 2 μl containing different amounts of lugdunin (0 to 100 ng) were spotted onto lawns of bacteria on sheep blood agar plates, resulting in zones of inhibition for lugdunin-susceptible bacteria. The spot with the lowest amount of lugdunin showing a clear inhibition was used to determine lugdunin susceptibility. (B) Growth promotion of S. lugdunensis HKU09-01 by siderophore-containing spent media of nasal bacteria. Iron-restricted BHI agar supplemented with 10% horse serum (as transferrin source) were inoculated with a lawn of S. lugdunensis. Spent media of different bacteria were spotted onto S. lugdunensis lawns resulting in zones of enhanced growth when siderophores were present. Diameters were measured and noted. Supplementary Figure S6. Lugdunin susceptibility of nasal bacterial species. Different amounts of lugdunin (0 to 100 ng in 2 μl) were spotted onto lawns of nasal bacteria, resulting in zones of inhibition. Data points represent average values of three independent experiments, and vertical red lines show medians of each group.