Thousands of new microbial species making up the human microbiome have been identified from metagenome samples collected around the world. By reconstructing the microbial genomes found in over 9000 metagenome datasets, the microbial genomes of the unnamed species extend the knowledge of the human microbiome and should aid in development of future metagenomics technologies.
The work of identifying these new species was carried out by a team of researchers from Europe, New Zealand and the US, and included Harvard’s Dr. Curtis Huttenhower (a Microbiome Insights scientific advisory board member). The group used a scalable bioinformatics methodology to reconstruct the genomes of unknown bacteria found within the metagenome assemblies. Here the metagenome samples were site-specific human body samples (oral cavity, skin, vagina, and stool) from multiple people living all over the world. The diverse set included individuals of all ages, living varied lifestyles from 32 countries.
A wealth of information is contained in these samples, as they represent the whole-body microbiome of humans from different geographic locations that experience different climates and circumstances. Seven of the datasets also came from non-Westernized environments, further expanding the range of conditions the microbes are sampled from. Using these metagenomes as the starting point the researchers were able to apply their large-scale single-sample metagenomics assembly and identified 4930 species-level clades, 77% of which had no previous whole-genome level information.
Their method of assembly was optimized to maximize the quality of the microbial genomes being found in the metagenome sample, rather than the quantity. Despite this strict method, 154 723 new microbial genomes were identified, which more than doubles the current publicly available set of roughly 150 000 microbial genomes. With this investigation having doubled the catalogue of known microbial genomes, future studies attempting identify the contents of a metagenomics sample now have a more comprehensive reference set from which they can map out their samples. The metagenomics assembly strategies used in this work can also be applied to non-human associated metagenomes and will be applicable for new sequencing technologies such as synthetic or single molecule long read sequencing.
A large fraction of the previously unidentified species were seen in the non-Westernized samples; however, examples of the new species were prevalent throughout all samples. Roughly 2.5 million genes were also found within the known species-level clades, many of which were associated with conditions including infant development and Westernization. Several taxa of bacteria were found to be prevalent in this analysis despite not being observed in previous well-profiled populations. Still more taxa from underrepresented phyla, such as Saccharibacteria and Elusimicrobia, were found in oral and gut microbiomes.
According to the study authors, “the resulting genome set can thus serve as the basis for future strain-specific comparative genomics to associate variants in the human microbiome with environmental exposures and health outcomes across the globe.”
Pasolli E, Asnicar F, Manara S, et al. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell. 2019; 176: 649-662.