Anaerobic fungi (Neocallimastigomycota) are common inhabitants of the digestive tract of large mammalian herbivores, where they make an important contribution to plant biomass degradation. The internal transcribed spacer 1 (ITS1) region is currently the DNA molecular marker of choice for anaerobic fungal community analysis, despite its known size polymorphism and variation potentially influencing its accuracy. Therefore, in our study we assessed the accuracy of the ITS1 region for anaerobic fungal community analysis using DNA sequencing of pure anaerobic fungal cultures and mock communities derived from them.
We found that taxonomic annotation of DNA sequences obtained from individual pure cultures was not always consistent, irrespective of whether sequence data was generated from clone libraries or high-throughput sequencing. The detection limit of the high-throughput sequencing method also appeared to be influenced by factors other than the parameters used during processing of the sequence data. Furthermore, the accuracy of the method was found to be influenced by sample community composition. As such, there is a need to develop an alternative DNA molecular marker for anaerobic fungi.