Identifying Gene Sharing in Microbes with DNA Barcode Scans

Jim Crocker
8th March, 2024

Identifying Gene Sharing in Microbes with DNA Barcode Scans

Image Source: Natural Science News, 2024

Key Findings

  • Scientists developed a new method, MECOS, to track gene sharing in gut bacteria more accurately
  • MECOS revealed about 3,000 gene transfer events, including antibiotic resistance genes
  • The technique is over ten times more detailed than previous methods
Horizontal gene transfer (HGT) is akin to bacteria sharing survival manuals, allowing them to exchange genetic material and adapt to threats such as antibiotics. This process has profound implications for human health, particularly as antibiotic resistance becomes more widespread. While scientists have made strides in understanding HGT, traditional methods have limitations that make it difficult to capture the full picture of how genes are shared within microbial communities. Researchers from Capital Medical University have developed a new technique called metagenomics co-barcoding sequencing (MECOS) to better detect HGT events within the gut microbiomes of humans and mice[1]. MECOS addresses the shortcomings of previous methods by increasing the length of DNA fragments that can be analyzed, thereby providing a more detailed view of the genetic exchanges taking place. MECOS improves upon earlier techniques by extracting longer DNA fragments, which are then tagged using a special enzyme called a transposome. These tagged DNA fragments are hybridized to beads that contain unique barcodes, allowing for the precise tracking of genetic material. An integrated bioinformatic pipeline then processes this data, correcting for any potential errors and identifying true HGT events. The study's findings are significant, revealing approximately 3,000 blocks of HGT involving around 6,000 genes across 100 different taxonomic groups. This level of detail is over ten times greater than what was previously possible with short-read metagenomic sequencing (mNGS)[2]. Notably, many of the detected HGT events include genes that confer resistance to tetracycline, an antibiotic, through a mechanism known as ribosomal protection. This breakthrough builds on previous work, such as the development of Microbe-seq, which allowed scientists to sequence individual microbes from complex communities with single-cell resolution[3]. MECOS extends this capability by providing a high-throughput method to analyze HGT with greater accuracy and detail. The study also complements findings from the use of long-read sequencing techniques, which have shown promise in characterizing complete microbial genomes despite higher error rates[4]. MECOS leverages the advantages of long-read sequencing—such as improved contig length—while addressing its limitations through a novel barcoding system and error correction. Furthermore, the MECOS technique aligns with efforts to mitigate the spread of antibiotic resistance, as seen in research exploring the role of probiotic bacteria in preventing the transfer of resistance genes[5]. By providing a clearer understanding of how resistance genes are transferred between bacteria, MECOS could inform strategies to combat antibiotic resistance. In conclusion, MECOS represents a significant advancement in the study of HGT, with the potential to transform our understanding of microbial ecology and evolution. By offering a more comprehensive view of how genes are shared within microbial communities, this technique from Capital Medical University could lead to novel approaches for managing antibiotic resistance and preserving the efficacy of antibiotics for future generations.

BiotechGeneticsBiochem

References

Main Study

1) Detecting horizontal gene transfer with metagenomics co-barcoding sequencing.

Published 5th March, 2024

https://doi.org/10.1128/spectrum.03602-23

Related Studies

2) Examining horizontal gene transfer in microbial communities.

https://doi.org/10.1038/s41579-021-00534-7

3) High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome.

https://doi.org/10.1126/science.abm1483

4) Implications of Error-Prone Long-Read Whole-Genome Shotgun Sequencing on Characterizing Reference Microbiomes.

https://doi.org/10.1016/j.isci.2020.101223

5) Probiotic Bacillus Affects Enterococcus faecalis Antibiotic Resistance Transfer by Interfering with Pheromone Signaling Cascades.

https://doi.org/10.1128/AEM.00442-21


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