New research opens up the future of high-resolution genomics in microbial ecology

One of the purposes of human beings wanting to better understand themselves is to understand the genetic makeup of microbes in their
environment.

The technique bypasses culture and extracts genomic information (DNA sequences) from environmental microbes, and scientists may be close to unlocking the secrets of
microbial diversity.

The main obstacle to reconstruction is the metagenome-assembled genome, however, this technique is capable of distinguishing between the genomes
of closely related microorganisms that coexist in the environment.

Now, a team of researchers led by Kyoto University has taken another step forward by developing a comprehensive approach
to detecting genomic diversity within a species, an uncultured bacterial DNA.

Lead author Yusuke Okazaki explains: "This enhanced MAG method is able to detect previously overlooked variants, allowing us to focus on DNA sequences and structural features of the genome to study genomic information
.
"

The microdiversity spectrum of the genome of environmental bacteria has been found to be wider
than expected.
While some species maintain cloning-like populations, others exhibit such a wide diversity that it poses a major challenge to the reconstruction of DNA sequences
.
To this end, identifying microbial diversity is critical
to understanding microbial ecology and evolution.

Okazaki added: "Because most microorganisms in the environment are difficult to cultivate, the identification of microbial diversity in environmental microorganisms is limited
.
"

To solve this problem, the team took a three-step approach, starting with a comprehensive metagenome sampling of an ecosystem that targeted two groups of bacterial plankton at a plankton station at a plankton station in Lake Biwa for 12 months
.

In subsequent steps, genomic microvariation was found to be an inconsistency between assembled genome sequences and pre-assembled DNA sequencing readings
.

"This study opens the future of high-resolution genomics in microbial ecology," the authors note, "to help us tease out what
looks the same but is actually different.
" ”

essay

Long-read-resolved, ecosystem-wide exploration of nucleotide and structural microdiversity of lake bacterioplankton genomes