Background: Lateral gene transfer (LGT), also known as horizontal gene transfer (HGT), is an important factor in the genomic diversification of microbial communities through which recipients may acquire advantageous traits to adapt and thrive in a given ecological niche. While host/selective pressures (e.g., exposure to antibiotics) are thought to create favorable conditions for LGT, including the exchange of cassettes related to antibiotic resistance, the degree to which this occurs and whether it differs by antibiotic regimen is not well understood.
Methods: We assessed this phenomenon using gnotobiotic mice colonized with a known/synthetic consortium of 12 bacteria (Münch et al., Cell Host Microbe 2023). Over 80 days, we collected 112 stool metagenomes from male oligo-mouse-microbiota (OMM) mice treated with vancomycin, tetracycline, and ciprofloxacin, respectively, in five-day pulses with weekly stool collections (n=5/group). We generated de novo assemblies using MEGAHIT from which LGT events were profiled using WAAFLE, our recently released culture-independent method for detecting and profiling novel LGT from shotgun metagenomic assemblies (Hsu & Nzabarushimana et al., Nature Microbiology 2024).
Results: Taxonomic profiling showed stable bacterial composition throughout the experiment (~9 to 10 consortia species/sample). When assessing simple LGT count, as expected, we observed that the number of events rose and fell in parallel with antibiotic-induced changes in overall bacterial density. However, after adjusting for bacterial load (i.e., by normalizing quantified LGT by gene count), we observed differential effects among our three treatment groups. While the rate of LGT tended to reliably recover after antibiotic treatment in the tetracycline and vancomycin groups, suggesting the emergence of selected mutants or more resilient bacteria, we observed a more delayed version of this phenomenon in the ciprofloxacin group, in which the LGT rate rebounded with treatment early in the study, but less so later. In terms of assessing this network of exchange, we observed that some members were preferentially exchanging with others while others did not participate in LGT at all—Enterococcus faecalis tended to most frequently exchange genes with Bacteroides caecimuris, while Blautia coccoides, Acutalibacter muris, and Bifidobacterium animalis did not have any observed LGT events. Work to elucidate the exact genes exchanged, their directionality (i.e., donor/recipient), and the presence of antibiotic-resistant haplotypes is ongoing.
Conclusion: Our results demonstrate the heterogeneous impact of different antibiotic regimes on the landscape of LGT. A deeper exploration of the interplay between microbial fitness, LGT fixation, and antibiotic resistance is underway.