Understanding Horizontal Gene Transfer network in human gut microbiota

Abstract

Background Horizontal Gene Transfer (HGT) is the process of transferring genetic materials between species. Through sharing genetic materials, microorganisms in the human microbiota form a network. The network can provide insights into understanding the microbiota. Here, we constructed the HGT networks from the gut microbiota sequencing data and performed network analysis to characterize the HGT networks of gut microbiota. Results We constructed the HGT network and perform the network analysis to two typical gut microbiota datasets, a 283-sample dataset of Mother-to-Child and a 148-sample dataset of longitudinal inflammatory bowel disease (IBD) metagenome. The results indicated that (1) the HGT networks are scale-free. (2) The networks expand their complexities, sizes, and edge numbers, accompanying the early stage of lives; and microbiota established in children shared high similarity as their mother (p-value = 0.0138), supporting the transmission of microbiota from mother to child. (3) Groups harbor group-specific network edges, and network communities, which can potentially serve as biomarkers. For instances, IBD patient group harbors highly abundant communities of Proteobacteria (p-value = 0.0194) and Actinobacteria (p-value = 0.0316); children host highly abundant communities of Proteobacteria (p-value = 2.8785 ) and Actinobacteria (p-value = 0.0015), and the mothers host highly abundant communities of Firmicutes (p-value = 8.0091 ). IBD patient networks contain more HGT edges in pathogenic genus, including Mycobacterium , Sutterella , and Pseudomonas . Children’s networks contain more edges from Bifidobacterium and Escherichia . Conclusion Hence, we proposed the HGT network constructions from the gut microbiota sequencing data. The HGT networks capture the host state and the response of microbiota to the environmental and host changes, and they are essential to understand the human microbiota.

Metagenomic analysis revealed a wide distribution of antibiotic resistance genes and biosynthesis of antibiotics in the gut of giant pandas

“…Efflux pumps are a part of bacteria’s intrinsic resistance mechanism and decrease different antibiotic concentrations within the cell wall [ 55 ]. Since efflux pumps can be transferred horizontally [ 56 ], the presence of acrB in adults and geriatrics could be involved in horizontal gene transfer events [ 57 ].…”

Leveraging Experimental Strategies to Capture Different Dimensions of Microbial Interactions

“…The transfer of genetic material between organisms can occur indirectly via transformation or transduction and directly via conjugation. Notable, a network of horizontal gene transfer was reported for the human gut microbiota ( Li et al, 2020 ). These examples illustrate that mapping contact-dependent interactions in general will help account for a wider diversity of relationships and may help uncover new mechanisms of interaction.…”

The impact of antibiotic exposure on antibiotic resistance gene dynamics in the gut microbiota of inflammatory bowel disease patients

“…The enrichment of mobile ARGs in certain bacterial phyla ( Hu et al, 2016 ) and the primary dissemination of resistance within the same genus or between different phyla ( De Abreu et al, 2021 ) through genetic exchanges are notable findings. Particularly, a large number of horizontal gene transfer (HGT) phenomena were observed in IBD patients ( Li et al, 2020 ), affecting the microbiome composition. Current research, however, lacks comprehensive understanding of ARGs transmission within the human gut microbiota before and after antibiotic use, making it crucial to characterize the resistome in this environment for developing personalized antimicrobial management strategies.…”

“…This study aims to investigate the impact of antibiotic treatment on the distribution and transfer of ARGs within the human gut microbiota. Mobile antibiotic resistance genes are particularly prevalent among patients with IBD ( Li et al, 2020 ). Individuals with IBD are often administered antibiotic therapy ( Nitzan et al, 2016 ) which can induce the horizontal transfer of ARGs within the intestinal microbiota.…”