Abstract
BackgroundModern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. The bioinformatics tools available are mainly devoted to profiling the bacterial and viral fractions and only a few software packages consider fungi. As the human fungal microbiome (human mycobiome) can play an important role in the onset and progression of diseases, a comprehensive description of host-microbiota interactions cannot ignore this component.ResultsHumanMycobiomeScan is a bioinformatics tool for the taxonomic profiling of the mycobiome directly from raw data of next-generation sequencing. The tool uses hierarchical databases of fungi in order to unambiguously assign reads to fungal species more accurately and > 10,000 times faster than other comparable approaches. HumanMycobiomeScan was validated using in silico generated synthetic communities and then applied to metagenomic data, to characterize the intestinal fungal components in subjects adhering to different subsistence strategies.ConclusionsAlthough blind to unknown species, HumanMycobiomeScan allows the characterization of the fungal fraction of complex microbial ecosystems with good performance in terms of sample denoising from reads belonging to other microorganisms. HumanMycobiomeScan is most appropriate for well-studied microbiomes, for which most of the fungal species have been fully sequenced. This released version is functionally implemented to work with human-associated microbiota samples. In combination with other microbial profiling tools, HumanMycobiomeScan is a frugal and efficient tool for comprehensive characterization of microbial ecosystems through shotgun metagenomics sequencing.
Highlights
Modern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition
In an attempt to bridge this gap, here we present HumanMycobiomeScan, a new bioinformatics tool that taxonomically profiles the mycobiome within the original microbiome, requiring only a few minutes to process thousands of metagenomics reads
HumanMycobiomeScan was more accurate in profiling the mycobiome of synthetic metagenomes than other existing methods, with blastN showing the closest performance but being considerably slower (Fig. 2c)
Summary
Modern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. Culture-dependent techniques, which generally combine methods such as microscopy [10], biochemical assays [11] and growth on selective media [12], represent a classical approach for the profiling of complex microbial ecosystems, and have the great advantage of allowing the determination of the viable fraction of the mycobiome. No gold standard approach for culture-independent mycobiome analysis has yet been developed, as highlighted by the variety of genomic regions and techniques used in different studies [2, 5, 21,22,23] In this context, a pipeline devoted to the characterization of the mycobiome based on metagenomic reads from whole genome sequencing of microbial communities is completely missing. HumanMycobiomeScan is available at the website: http://sourceforge.net/projects/hmscan
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