Metagenomic Analysis of Microbial Dark Matter in Healthy Human Gut Microbiome
Open AccessAs the most abundant life form on earth, microorganisms have a significant impact on the environment and human health. However, it is thought that more than 99% of these microorganisms have never been cultivated because of limitations of currently available technology and knowledge. The term “microbial dark matter” refers to the sequences that cannot be mapped to known organisms. Metagenomics, a study analyzing the sample by direct extraction and cloning all the sequences, provides insight into microbial dark matter. It can help us to understand the microbiome, the entire habitat including the microbes, their genome and the surrounding environmental condition. Here, two metagenomics pipelines were developed to analyze the microbiome. The first metagenomics pipeline applies to the creation of a reference database of a microbiome and the subsequent reporting on the abundance profile of microbiome data. Three healthy human gut microbiome metagenomics datasets were used to create a human gut reference database, GutFeelingKB. A clinical-style report template, FecalBiome report, was produced based on GutFeelingKB and the abundance profiles to display the state of a microbiome. The second metagenomics pipeline can be used to explore human gut microbial dark matter. Using this pipeline to analyze from GutFeelingKB and Men’s Lifestyle Validation Study (MLVS), we found four contigs that may be from uncultured organisms. We were also able to assemble complete plant virus genomes from the human fecal samples.
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