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Reconstruction of Nearly 8,000 Microbial Genomes Expands Phylogenetic Diversity

NEW YORK (GenomeWeb) – Australian researchers have reconstructed nearly 8,000 bacterial and archaeal genomes from publicly availably metagenomic data.

Researchers are increasingly piecing together microbial genomes from metagenomic samples, rather than from cultures, allowing them to expand the diversity of sequenced samples.

As they reported today in Nature Microbiology, the University of Queensland's Gene Tyson and his colleagues said that their study has boosted the diversity of bacterial and archaeal phylogenetic trees by more than 30 percent. Additionally, their set of metagenome-assembled genomes includes the first representatives of some bacterial and archaeal lineages.

"The number and diversity of genomes presented in this study, and the many similar studies we anticipate will follow, move us closer to a comprehensive genomic representation of the microbial world," the authors wrote in their paper.

The researchers sifted through more than 1,500 metagenomic samples that had been submitted to the Sequence Read Archive before the end of December 2015. As they were hoping to bolster sequences from under-sampled microbial lineages, they focused on samples that were environmental in origin or were from the guts of non-human organisms.

From these, they teased out more than 64,295 metagenome-assembled genomes, though only 7,903 — 7,280 from bacteria and 623 from archaea — met their quality standards. They dubbed these the Uncultivated Bacteria and Archaea dataset. More than 93 percent of this set had an average coverage of greater than 10X and more than 95 percent had greater than 5X coverage spanning at least 90 percent of bases, the researchers reported.

A portion of genomes reached near completeness — Tyson and his colleagues estimated that 3,225 bacterial and 213 archaeal genomes in their set were more than 90 percent complete and, of those, 93.1 percent met the Human Microbiome Project criteria for high-quality draft genomes. However, the researchers noted that while their manuscript was being finalized, a new standard for metagenome-assembled genomes, called MIMAG, was announced. Under the new MIMAG standard, their near-complete sequences don't meet the high-quality draft requirements.

Using three different protein sets, the researchers examined where their metagenome-assembled genomes fell on archaeal and bacterial phylogenetic trees. While some of the new metagenome-assembled genomes belonged to major bacterial and archaeal phyla, others were the first genomic representatives of 17 bacterial and three archaeal phyla.

For instance, the phyla they dubbed Uncultured Bacterial Phylum 9 included the first genomic representatives of the Terra bacteria candidate phylum SHA-109. Those genomes had been isolated from baboon feces, palm oil effluent, a toluene-degrading community, and a dechlorination bioreactor.

On the archaeal side, the Uncultured Archaeal Phylum 2 includes the first representative from the Marin Hydrothermal Vent Group, and is home to three genomes collected by the Tara Oceans Expedition and one genome from the Beebe hydrothermal vent.

This set of genomes also improves phylogenetic diversity of sequenced bacteria and archaea, the researchers said. The addition of their set expanded the phylogenetic diversity of underrepresented phyla like Aminicenantes, Gemmatimonadetes, and Lentisphaerae, among others by some 75 percent, as well as of the better-covered Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria by 14 percent to 47 percent.

With these sequences and ones like them, the researchers said a better representation and view of the microbial world is beginning to emerge. "Detailed examination of such genomes will further our understanding of microbial evolution and metabolic diversity, and provide important insights into the role of microorganisms in both natural and industrial processes," they wrote.