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Gut Microbe Studies Expand Bacterial Culture Collections, Reference Genomes

NEW YORK (GenomeWeb) – Two independent research teams have cultured and characterized thousands of bacterial strains from fecal samples of healthy humans, generating reference genomes for hundreds of organisms not sequenced in the past.

For the first study, appearing online today in Nature Biotechnology, researchers from BGI-Shenzhen, the South China University of Technology, and elsewhere isolated almost 6,500 bacterial representatives from fecal samples donated by 155 healthy individuals, using 11 types of growth media to culture the gut bacteria under anaerobic conditions in the lab.

From there, the investigators turned to 16S ribosomal RNA sequencing, as well as whole-genome sequencing for almost 1,800 isolates, to produce 1,520 high-quality draft genomes for bacteria from 388 species clusters spread across the bacterial phylogenetic tree, including 264 new reference genomes in 134 species clusters. The most prominent phylum was Firmicutes, which was represented by 796 genomes, though they also generated genomes for hundreds of genomes for Bacteroidetes, Actinobacteria, and other phyla.

The authors noted that the strains are now part of the China National GeneBank, "and may be useful for studies that aim to alter microbiota functions, as novel probiotics, or for verification of disease-associated bacterial markers."

In follow-up experiments, the team demonstrated that this new resource — dubbed the Culturable Genome Reference (CGR) collection — significantly increased the number of gut microbial community members that could be identified with fecal metagenomic sequencing. It also relied on the CGR for functional analyses of the bacterial species clusters present and reported on results from a pan-genome analysis that spanned more than three dozen gut microbial species.

"Our cultivation methods can be applied to expand the CGR until it is saturated with the genomes of culturable gut bacteria," the authors wrote. "After that, single-cell sequencing can be used to investigate genomes of unculturable bacteria, with an overall aim of defining a saturated set of reference genomes of gut microbiota to underpin a better understanding of gut microbiome biology." 

For a related Nature Biotechnology study, researchers from the Wellcome Sanger Institute, Australia's Hudson Institute of Medical Research, and elsewhere established the "Human Gastrointestinal Bacteria Culture Collection" (HBC), a set of 737 newly cultured and sequenced bacterial strains selected from thousands of microbial isolates in fecal samples from eight volunteers in the UK and a dozen North American individuals.

"Culturing, genome sequencing, and isolate archiving, as reported here, will underpin substantially improved microbiome-based analysis of the human gastrointestinal tract, and potentially other sites," the authors wrote, adding that "[t]raditional microbiology methods can continue to enable access to the bacterial isolates that are sorely needed to perform experimental characterization and validation, and improving our understanding of important human-associated microbial communities."

The team's HBC spanned 273 bacterial species and 31 families from the Firmicutes, Bacteroidetes, and other phyla, and included 173 reference genomes representing 105 new species. By bringing the HBC genomes together with another 617 publicly available gut microbe genome sequences, the group went on to produce the "Human Gastrointestinal Bacteria Genome Collection," or HGG.

As part of their follow-up work, the researchers used the HGG set — a collection of 1,354 new and previously sequenced bacterial genomes representing 530 species — to classify microbes in nearly 13,500 samples assessed by shotgun metagenomic sequencing, showing that it could boost bacterial classification compared to analyses done with data from the Human Microbiome Project.

"For researchers trying to find out which species of bacteria are present in a person's microbiome, the database of reference genomes from pure isolates of gut bacteria is crucial," co-author Robert Finn, a researcher at the European Bioinformatics Institute's European Molecular Biology Laboratory, said in a statement. "Then if they want to test a hypothesis, for example that a particular species is enriched in a certain disease, they can get the isolate itself from the collection and physically test in the laboratory if this species seems to be important."