‘Smart tweezer’ can pluck out single bacterium target from microbiome

Researchers have developed a ‘smart tweezer’ that is able to pluck a particular bacterial strain from a microbiome of trillions and sequence its genome in a more cost- and resource-effective way than current methods allow. The versatile tool could enable precision microbiome research and breakthroughs in disease diagnosis and treatment.

The sequencing of bacterial genomes has significantly improved our understanding of the biology of many bacterial pathogens and identified novel antibiotic targets. When it comes to microbiomes, researchers often want to study one type of bacteria, not all of them. The problem is that a specific bacterium is just one part of a complex environment that includes other bacteria, viruses, fungi and host cells, each with their own equally complex DNA.

Currently, scientists need to isolate particular bacterial strains from a given sample using a culture media that selectively grows that strain. It’s a time- and resource-consuming process that doesn’t work for all bacteria. However, researchers from the Icahn School of Medicine at Mount Sinai in the US have unveiled an innovative method, mEnrich-seq, designed to substantially enhance microbiome research.

“Imagine you’re a scientist who needs to study one particular type of bacteria in a complex environment,” said Gang Fang, the study’s corresponding author. “It’s like trying to find a needle in a haystack; mEnrich-seq essentially gives researchers a ‘smart tweezer’ to pick up the needle they’re interested in.”

In developing mEnrich-seq, the researchers aimed to differentiate bacteria from each other before sequencing to enrich bacteria of interest and deplete background DNA. To do this, the tool exploits the naturally occurring bacterial DNA methylation motifs, the ‘secret codes’ written on bacterial DNA that they use to differentiate themselves as part of their native immune systems. Indeed, in the name “mEnrich-seq,” the ‘m’ stands for methylation and ‘seq’ for sequencing.

Once pulled out by the ‘smart tweezer,’ researchers can assemble the genome or genomes of the targeted bacteria, enabling it to be studied more precisely. The researchers demonstrated mEnrich-seq’s abilities by using it on urine samples from three patients with urinary tract infections (UTIs) to reconstruct E. coli genomes. They found that the tool covered more than 99.97% of the genomes across all three samples, enabling the comprehensive analysis of antibiotic-resistant genes in each genome. mEnrich-seq facilitated the culture-free study of E. coli genomes from urine microbiome with better sensitivity (lower relative abundance of bacteria) than standard methods.

They then turned their attention to Akkermansia muciniphila, a bacterium colonizing the intestinal tract and linked to diseases such as obesity and type 2 diabetes. It’s also known to be challenging to isolate from fecal samples. However, using mEnrich-seq, the researchers were able to do so, covering more than 99.7% of A. muciniphila genomes from three samples.

The researchers say that mEnrich-seq opens new horizons in various research areas by offering a more economical approach to microbiome research, which is particularly beneficial in large-scale studies with limited resources. They say it can focus on a wide range of bacteria, making it a versatile tool for research and clinical applications. And by enabling more targeted microbiome research, mEnrich-seq could accelerate the development of new diagnostic tools and treatments.

“One of the most exciting aspects of mEnrich-seq is its potential to uncover previously missed details, like antibiotic resistance genes that traditional sequencing methods couldn’t detect due to a lack of sensitivity,” Fang said. “This could be a significant step forward in combating the global issue of antibiotic resistance.”

The researchers plan to refine the tool to further improve its efficiency and expand its range of applications.

“We envision mEnrich-seq as a sensitive and versatile tool in the future of microbiome studies and clinical applications,” said Fang.

The study was published in the journal Nature Methods.

Source: Icahn School of Medicine at Mount Sinai via EurekAlert!

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