Researchers use genome sequencing to unravel microbial ‘dark matter’

Originally published on September 12, 2016 for The Daily Californian

While scientists have known about the existence of microbes since the 1600s, for years bacteria and archaea, two branches of the tree of life, remained vastly unexplored due to limited methods of cultivation.

Traditional methods used by scientists to grow samples of bacteria have lacked the precision required to study microbes, in some cases fractions of a micron in size. However, in the past decade, emerging DNA and RNA sequencing technology has allowed scientists, including those at UC Berkeley, to probe further than was previously possible into the “dark matter” of microbiology — the multitude of microbial species yet to be discovered.

Two new processes used to study microorganisms, metagenomics and single-cell sequencing, have enabled this specificity, according to Tanja Woyke, Microbial Genomics Program Lead at the Joint Genome Institute.

One widely-used method, metagenomics, sequences the entire genome of all organisms in an environment sample and returns mixed DNA and RNA for scientists to piece together. Woyke’s team uses single-cell sequencing, which although more expensive, takes individual cells and sequences amplified genomes for more precision.

“It is exciting to see any genomic information from these big branches in the tree of life that nobody has been able to see before,” Woyke said. “All the research at UC Berkeley is really at the forefront.”

According to Woyke, the concept of “dark matter” originated from research in 2007 that used single-cell sequencing to determine genomic information from microbes. Using this method, her study found that one genetic sequence in a microbe’s DNA produced an unexpected response, different than in many other forms of life — a discovery that Woyke said challenges the previously accepted rules of genetics.

“To me, the implication is really that the biological rules that we apply to systems and organisms are a lot more flexible that we thought,” Woyke said.

According to Steven Lindow, a campus professor of plant pathology, future research into these microorganisms’ interactions has the potential for advances in human health by reducing the likelihood of genetic diseases. This discovery of microbiomes — a particular environment, such as the human body, that is home to microorganisms  — suggests that animals and plants are influenced by the DNA and behavior of the microorganisms living in and on them.

UC Berkeley researchers focus their research primarily on the fundamentals of microbiology, as opposed to immediate applications, according to Michi Taga, a campus associate professor of plant and microbial biology.

“If we’re able to understand (microorganisms’) functions, we can use their genes for any types of technology, whether it is as a drug or to break down a toxin,” Taga said. “If you know the diversity of genes that are out there, then you can develop new applications.”

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