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Human Gut Metagenomic Analysis Uncovers Nearly 2,000 New Uncultured Bacterial Species

NEW YORK (GenomeWeb) – Researchers have identified about 2,000 previously unknown uncultured bacterial species in the human gut.

A team led by investigators from the European Molecular Biology Laboratory's European Bioinformatics Institute reconstructed about 92,000 bacterial genomes from almost 12,000 human gut metagenomic datasets, corresponding to 1,952 uncultured candidate bacterial species. This, they reported in a study published in Nature yesterday, represents a 281 percent increase in phylogenetic diversity.

"Using metagenomics to reconstruct bacterial genomes is a bit like reconstructing hundreds of puzzles after mixing all the pieces together, without knowing what the final image is meant to look like, and after completely removing a few pieces from the mix just to make it that bit harder," senior author Robert Finn, a group leader at EMBL-EBI, said in a statement. "Researchers are now at a stage where they can use a range of computational tools to complement and sometimes guide lab work, in order to uncover new insights into the human gut."

He and his colleagues collected 13,133 human gut metagenomic datasets from 75 different studies. The vast majority of these samples, 88 percent, were collected from North American or European populations.

Using the genome assembler SPAdes, the researchers assembled these metagenomes, and 11,850 produced contigs that they could bin using the software tool MetaBAT. After quality assessment with the CheckM tool, the researchers reported generating 40,029 metagenome-assembled genomes (MAGs) with more than 90 percent completeness and less than 5 percent contamination. They generated another 65,671 medium-quality MAGs. In all, they generated 92,143 MAGs, including those high-quality and medium-quality MAGs that reached a certain quality score cutoff. 

The researchers were able to assign nearly 27,000 of these MAGs to samples present in a human-specific reference (HR) database containing genomes from the Human Microbiome Project and Human Gastrointestinal Bacteria Genome Project datasets and assigned nearly 13,000 MAGs to bacterial genomes within RefSeq.

But 30 percent of these MAGs couldn't be assigned. Of the metagenomic species they found, 2,068 were absent from those references.

Using a phylogenetic tool that's part of CheckM and the UniProtKB protein sequence database, the researchers attempted to assign these unknown metagenomic species to taxonomic lineages. They were unable to assign 94 percent of these species to any isolate within UniProtKB, suggesting that 1,952 of these unknown metagenomic species represented uncultured candidate species.

Most could be assigned at the phylum or class level, though. At the family level, they were most commonly Coriobacteriaceae, Ruminococcaceae, and Peptostreptococcaceae, and at the genus level, Collinsella, Clostridium, and Prevotella. The researchers noted that some of these samples represent unknown diversity from within clades known to colonize the gut.

They further estimated that the new uncultured candidate species expand the diversity of the human gut bacterial lineages by 281 percent

These additional species also improved their ability to assign reads from samples originating from Africa and South America, the researchers said, noting a 215 percent and 278 percent boost, respectively. This, they added, underscores the need for diversity in sampling to get a fuller view of the makeup of the human gut microbiome.

By applying the genome-mining antiSMASH tool, the researchers scoured these human gut species for gene clusters encoding secondary metabolic biosynthetic pathways. Eighty-five percent of the gene clusters they found were novel, they reported, suggesting there could be many undiscovered natural compounds produced by gut microflora.

A number of these gene clusters also hinted at why these bacteria might be so hard to grow in culture: some appear to encode few genes associated with antioxidant and redox functions, while others encode genes involved in iron-sulfur and ion binding, meaning they might be better adapted to parts of the gut with low oxygen or iron levels.