Inferring Species Compositions of Complex Fungal Communities from Long- and Short-Read Sequence Data
Yiheng Hu, László Irinyi, Minh Thuy Vi Hoang, Tavish Eenjes, Abigail Graetz, Eric A. Stone, Wieland Meyer, Benjamin Schwessinger, John P. Rathjen
Abstract
Our study is unique in that it provides an in-depth comparative study of a real-life complex fungal community analyzed with multiple long- and short-read sequencing approaches. These technologies and their application are currently of great interest to diverse biologists as they seek to characterize the community compositions of microbiomes. Although great progress has been made on bacterial community compositions, microbial eukaryotes such as fungi clearly lag behind. Our study provides a detailed breakdown of strategies to improve species identification with immediate relevance to real-world studies. We find that real-life data sets do not always behave as expected, distinct from reports based on simulated data sets.