Fungi in the Wound Microbiome

Abstract

Significance: Culture-independent methods have revealed the diverse and dynamic bacterial communities that colonize chronic wounds. Only recently have studies begun to examine fungal colonization and interactions with the bacterial component of the microbiome, their relationship with the host, and influence on wound outcomes. Recent Advances: Studies using culture-independent sequencing methods reveal that fungi often go undetected in wounds. Candida spp. and Cladosporidium spp. are the most commonly identified fungi in wounds. The wound environment may promote multispecies biofilm formation between bacteria and fungi in wounds, with implications for pathogenicity, treatment, and outcomes. Critical Issues: Identifying microorganisms that are problematic for healing will require a comprehensive understanding of all members of the polymicrobial wound community, including fungi and bacteria. Improved reference databases and bioinformatics tools for studying fungal communities will stimulate further research into the fungal microbiome. Future Directions: Continued study of polymicrobial wound communities using culture-independent methods will further our understanding of the relationships between microbial bioburden, the host response, and impact on healing, complications, and patient outcomes. Future studies should encompass all types of microbiota, including fungi, and focus on potential multi-kingdom interactions that contribute to pathogenicity, biofilm formation, and poor outcomes.

Keywords: biofilm; chronic wounds; fungi; microbiome.

Lindsay Kalan, PhD

Figure 1.

(A) Schematic of the fungal rRNA operon highlighting the ITS region and primer binding sites. (B) Bioinformatics workflow to process and analyze ITS amplicons from microbiome specimens. After polymerase chain reaction amplification, OTUs can be clustered with standardized pipelines and classified against fungal reference databases. The fungal ITS1 region can vary in size between different species, unlike amplification of hypervariable regions of the bacterial 16S rRNA gene that result in the same size amplicon. *PIPITS is a fungal-specific software pipeline. ITS, internal transcribed spacer; OTU, operational taxonomic units; QIIME, Quantitative Insights into Microbial Ecology; rRNA, ribosomal RNA.

Figure 2.

The microbiome of DFU contains many species of both bacteria and fungi that are not always detected by culture-dependent techniques. Molecular-based approaches have primarily focused on bacteria as evidenced by the number of articles published since 2008. In comparison, only two studies have profiled fungi in chronic wound microbiomes with molecular approaches. DFU, diabetic foot ulcers.

Figure 3.

Number of observed fungal species detected in DFU. Individual subjects are labeled across the x-axis and the observed species along the y-axis for multiple time points per subject. Box plots are colored by healing time (<12 weeks, blue; >12 weeks, pink). Each point represents a single sample and the fill corresponds to the ratio of allergenic to pathogenic fungi (green, high allergens; purple, high pathogens; gray, equal allergens/pathogens).

Figure 4.

Inter-kingdom biofilms formed between fungi and bacteria isolated from the same DFU specimen. The fungi (yellow) form a three-dimensional structure that bacteria (purple) attach to. Candida albicans + Citrobacter fruendii (top) and Trichosporon asahii + Staphylococcus simulans (bottom).