Recovery and microbial host assignment of mobile genetic elements in complex microbiomes: insights from a spiked gut sample.
Bloemen B, Delvoye M, Hoffman S, Marchal K, Vanneste K
Summary
0.0/10This study develops techniques to identify which bacteria in microbiomes carry mobile genetic elements—genes that jump between microbes and spread traits like antibiotic resistance. The combined approach helps researchers track how antibiotic resistance spreads through bacterial populations.
Key Findings
Combined nanopore adaptive sampling, DNA methylation detection, and Hi-C sequencing can effectively identify bacterial hosts of mobile genetic elements in complex microbiomes
These methods require careful experimental design, interpretation, and validation despite their technical power
Validation using spiked samples with known bacteria demonstrated the approach's capability to track mobile element distribution
Original Abstract
Mobile genetic elements (MGEs) are major drivers of horizontal gene transfer, including the spread of antimicrobial resistance (AMR) genes. However, determining the microbial host of an MGE in complex microbiomes remains challenging. Here, we spike a niche-aspecific Mobile genetic elements are important contributors to horizontal gene transfer, including of antimicrobial resistance genes. Understanding which microbes carry these mobile elements is vital to assess the spread of resistance. Here, we use a nanopore adaptive sampling approach to increase detection of low-abundance bacteria and mobile elements and use DNA methylation detection and Hi-C sequencing to determine mobile element hosts. By introducing a known bacterium and isolating a native strain, we could evaluate the performance of these methods, indicating that although powerful, they require careful experimental design, interpretation, and validation. However, when combined, these approaches enable a comprehensive investigation of mobile elements and gene transfer dynamics in complex environments.