Pipleine-Specific Detection of Indoor Mycobiomes Using Short-Read and Long-Read ITS Sequencing Approaches
Fungi in indoor environments can affect human health, particularly when pathogenic species are present. Reliable detection and identification of these fungi are essential for risk assessment and environmental monitoring. This study provides one of the first direct comparisons between short-read ITS2 and long-read full-length ITS sequencing for profiling fungal communities in built environments. We demonstrate that full-length ITS sequencing offers enhanced species-level resolution, critical for identifying clinically important taxa, while ITS2 sequencing remains effective for community-wide analysis. Despite differences in sequencing targets and resolution, the two pipelines showed strong correlation in detecting core fungal genera. Importantly, pipeline-specific biases affected the detection of important taxa and varied by sample type and environment. These findings highlight the importance of method selection in indoor mycobiome studies and suggest that combining short- and long-read sequencing approaches may provide a more complete picture of fungal diversity, improving our ability to monitor indoor air quality and occupant health risks.