Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks

Abstract

Objective Despite widespread use of antibiotics for the treatment of life-threatening infections and for research on the role of commensal microbiota, our understanding of their effects on the host is still very limited. Design Using a popular mouse model of microbiota depletion by a cocktail of antibiotics, we analysed the effects of antibiotics by combining intestinal transcriptome together with metagenomic analysis of the gut microbiota. In order to identify specific microbes and microbial genes that influence the host phenotype in antibiotic-treated mice, we developed and applied analysis of the transkingdom network. Results We found that most antibiotic-induced alterations in the gut can be explained by three factors: depletion of the microbiota; direct effects of antibiotics on host tissues and the effects of remaining antibiotic-resistant microbes. Normal microbiota depletion mostly led to downregulation of different aspects of immunity. The two other factors (antibiotic direct effects on host tissues and antibiotic-resistant microbes) primarily inhibited mitochondrial gene expression and amounts of active mitochondria, increasing epithelial cell death. By reconstructing and analysing the transkingdom network, we discovered that these toxic effects were mediated by virulence/quorum sensing in antibiotic-resistant bacteria, a finding further validated using in vitro experiments. Conclusions In addition to revealing mechanisms of antibiotic-induced alterations, this study also describes a new bioinformatics approach that predicts microbial components that regulate host functions and establishes a comprehensive resource on what, why and how antibiotics affect the gut in a widely used mouse model of microbiota depletion by antibiotics.

Investigating a holobiont: Microbiota perturbations and transkingdom networks

“…1 Indeed, we have faced the common problem that there is evidence of a microbiota effect on a host phenotype, but it was unclear which microbe was responsible. Building on our previous experience with gene networks, 25,48,50 we developed a new approach that models host-microbiota interaction that we called transkingdom network.…”

“…36,37 One approach to identify the taxonomic profile of a microbial community is with 16S rRNA amplicon sequencing, in which highly variable regions of 16S ribosomal rRNA from all microbes in a sample are amplified by PCR and subject to high throughput sequencing 38 or hybridization to probes on a special microarray chip called Phylochip. 1,39 In the case of sequencing, relative abundances of taxa are calculated from copy number of amplicons from the corresponding taxa. Abundance profiles for different taxonomic ranks are commonly generated (i.e., strain, species, genus, family etc.)…”

“…Interestingly, antibiotics had much more pronounced effect on T cell numbers than on IgA-producing cells. 1 This may be one of the reasons for the discrepancy between germfree and antibiotic-treated BcKO mice (Fig. 2) as their phenotype was IgA-dependent.…”

“…Surprisingly, we found that only about one third of gene expression changes in the gut of antibiotic-treated mice could be attributed to the depletion of normal microbiota verified by comparison to germfree mice. 1 This effect was primarily manifested by decreased expression of genes related to many aspects of innate and adaptive immunity. Interestingly, antibiotics had much more pronounced effect on T cell numbers than on IgA-producing cells.…”

“…The results of our study that evaluated global intestinal transcriptome after treatment with antibiotics cocktail can aid in these decisions by providing a thorough characterization of changes in host gene expression that can be specifically attributed to 3 factors, namely, the lack of microbiota, the effect of antibiotics-resistant microbes, and direct effects of antibiotics. 1 …”