Aberrant microbiomes are associated with increased antibiotic resistance gene load in hybrid mice

Abstract

Antibiotic resistance is a priority public health problem resulting from eco-evolutionary dynamics within microbial communities and their interaction at a mammalian host interface or geographical scale. The links between mammalian host genetics, bacterial gut community, and antimicrobial resistance gene (ARG) content must be better understood in natural populations inhabiting heterogeneous environments. Hybridization, the interbreeding of genetically divergent populations, influences different components of the gut microbial communities. However, its impact on bacterial traits such as antibiotic resistance is unknown. Here, we present that hybridization might shape bacterial communities and ARG occurrence. We used amplicon sequencing to study the gut microbiome and to predict ARG composition in natural populations of house mice (Mus musculus). We compared gastrointestinal bacterial and ARG diversity, composition, and abundance across a gradient of pure and hybrid genotypes in the European House Mouse Hybrid Zone. We observed an increased overall predicted richness of ARG in hybrid mice. We found bacteria-ARG interactions by their co-abundance and detected phenotypes of extreme abundances in hybrid mice at the level of specific bacterial taxa and ARGs, mainly multidrug resistance genes. Our work suggests that mammalian host genetic variation impacts the gut microbiome and chromosomal ARGs. However, it raises further questions on how the mammalian host genetics impact ARGs via microbiome dynamics or environmental covariates.

Keywords: antimicrobial resistance gene; hybridization; mice; microbiome.

Figure 1

Antibiotic resistance and regulatory genes associated with ARGs in house mouse microbiome; (A) geographical distribution of collected house mice included in this study; the colon content microbiome was assessed for 493 house mice collected from two different transects, in northeastern Germany close to Berlin (Brandenburg, N = 441) and southeastern Germany close to the Czech border (Bavaria, N = 52), both along the HMHZ (schematized by the purple line); the map on the right-side of the panel indicates the approximate location of both transects along the hybrid zone (purple); each point represents a mouse; the scale in the x-axis indicates the genotype of the mouse (hybrid index: HI), ranging from pure M. m. domesticus (HI = 0.0, N = 79) to pure M. m. musculus (HI = 1.0, N = 23); (B) hybrid effect on ARG richness is independent of the transect; ARG richness predictions were compared across a gradient of Mus musculus genotypes (HI), ranging from 0 (pure M. m. domesticus, in blue) to 1 (pure M. m. musculus, in red), to (i) test hybrid effect on alpha diversity and (ii) detect differences on alpha diversity between parental subspecies, transects or both; the richness of predicted ARGs increased towards the centre of the hybrid zone, supporting a hybrid (transgressive) effect on the richness of ARGs (Chao1 index, LL = −1757.22, α= 0.371, padj = .0015); ARG content in the parental subspecies M. m. domesticus was richer than M. m. musculus parental subspecies (G test: χ²(2, 493) = 4.74, padj = .007); (C) house mouse network analysis on the co-abundance of ARG and bacterial ASV abundance; nodes correspond to ASVs or ARGs, and colours correspond to the annotated family or target drug class category; node size was scaled based on Kleinberg’s hub scores (hub centrality scores); the metric increases with the number of links a node has to other nodes and with the relevance in the structure of the network (higher if a node is connecting different clusters of the network); high hub centrality scores reflect higher influence of a node on other taxa and ARGs; edges are predicted interactions, green edges are positive and purple are negative, and edge thickness reflects association strength; bacterial nodes are circles, and ARGs are squared; in bold, ASVs and ARGs with the highest hub scores.

Figure 2

Transgressive abundance patterns in central antimicrobial resistance genes and bacteria for community composition; ARGs and bacterial ASVs are listed in decreasing order based on Kleinberg’s hub centrality scores (gradient of hub centrality, left); the prevalence for ASVs and ARGs is represented in the x-axis; the hybrid effect on the abundance of bacteria, or ARGs (transgressiveness), is encoded in the size and colour, its direction in shape; most important (central) ARGs are transgressive, showing an increased abundance in hybrids and are multidrug resistance genes; P-values were adjusted for false discovery rate (FDR) employing the Benjamini–Hochberg procedure; FDR-values <0.001 = ***, <0.01 = **, <0.05 = *.