For example, the exact composition of the microbial life in any given sample surely contains mixed populations, but the exact species and the relative abundance of them are unknown. When standard metagenomic analysis is applied (shotgun sequencing), there is disruption of the sequencing data and grouping by species can be very difficult. Newer techniques are permitting more accurate analysis through chromatin level probability maps so that the individual genomes of microbial species can be accurately reconstructed within a mixed sample.
The validity of some of the short cut techniques employed by metagenomic assemblers is typically assessed against published references of current metagenomic data. One problem is that the full complement of microbial life for any sample, for example, the human gut is still not fully understood. Metagenomics is only in its initial phases and surprises are revealed routinely in the analysis of tissue and environmental samples.
For example, very recent evaluation of the human gut metagenome revealed a previously unknown gut virus, which has been linked to human chronic disease. Researchers indicate that this virus, called Assphage, lives in the gut of more than half of the world’s population and infects a common gut bacteria, Bacteroidetes. This particular virus was identified through a computer program and had not been previously identified. Yet it is ubiquitous and is currently believed to have a major role in diabetes and obesity. So at this moment, exciting new technologies are deepening our understanding of ourselves as the complex linkages of co-dependent ecologies outlined in The Microcosm Within. Metagenomic assembly is one tool to assess that partnership. Yet, there will be many surprises along the path to our fuller understanding of the power of those associations.