The Human Gut Resistome up to Extreme Longevity

Abstract

Antibiotic resistance (AR) is indisputably a major health threat which has drawn much attention in recent years. In particular, the gut microbiome has been shown to act as a pool of AR genes, potentially available to be transferred to opportunistic pathogens. Herein, we investigated for the first time changes in the human gut resistome during aging, up to extreme longevity, by analyzing shotgun metagenomics data of fecal samples from a geographically defined cohort of 62 urban individuals, stratified into four age groups: young adults, elderly, centenarians, and semisupercentenarians, i.e., individuals aged up to 109 years. According to our findings, some AR genes are similarly represented in all subjects regardless of age, potentially forming part of the core resistome. Interestingly, aging was found to be associated with a higher burden of some AR genes, including especially proteobacterial genes encoding multidrug efflux pumps. Our results warn of possible health implications and pave the way for further investigations aimed at containing AR accumulation, with the ultimate goal of promoting healthy aging. IMPORTANCE Antibiotic resistance is widespread among different ecosystems, and in humans it plays a key role in shaping the composition of the gut microbiota, enhancing the ecological fitness of certain bacterial populations when exposed to antibiotics. A considerable component of the definition of healthy aging and longevity is associated with the structure of the gut microbiota, and, in this regard, the presence of antibiotic-resistant bacteria is critical to many pathologies that come about with aging. However, the structure of the resistome has not yet been sufficiently elucidated. Here, we show distinct antibiotic resistance assets and specific microbial consortia characterizing the human gut resistome through aging.

Keywords: aging; antibiotic resistance; extreme longevity; metagenome; microbiome; resistome.

FIG 1

Age-related variation in the taxonomic composition of the human gut resistome. Principal-coordinate analysis of Bray-Curtis dissimilarities between the family (a) and genus-level (d) profiles of the gut resistome of young adults (Y), younger elderly individuals (E), centenarians (C), and semisupercentenarians (S). Significant separation was found at both phylogenetic levels (P = 0.0015 and 0.001, respectively; permutation test with pseudo-F ratios). Pie charts of the 25 most abundant families (b) and genera (e) for each group (Y, E, C, and S). Boxplots showing the relative abundance distribution of significantly differentially represented families (c) and genera (f) between age groups (Wilcoxon test, Bonferroni corrected P value). ***, P ≤ 0.0001; **, P ≤ 0.001; *, P ≤ 0.05.

FIG 2

The human gut resistome across aging. (a) Principal-coordinate analysis of Bray-Curtis dissimilarities between the gut resistome profiles of young adults (Y), younger elderly individuals (E), centenarians (C), and semisupercentenarians (S). A significant separation was found (P = 0.012, permutation test with pseudo-F ratios). (b) Hierarchical pie plot, with the external pie chart depicting the resistance mechanisms of the whole gut resistome data set, while the internal donut recalls the type of antibiotics for each mechanism, with annotation obtained from the Antibiotic Resistance Ontology. (c) The core human gut resistome consists of 8 antibiotic resistance determinants with mean relative abundance above 2% across all age groups.

FIG 3

Age group-specific antibiotic resistance determinants. (a) Heat map computed on the abundances of counts normalized by library size and log₂ scaled. The color code ranges from blue (low abundance) to red (high abundance). The samples are in columns, while the rows show the gene names of the antibiotic resistance determinants (ARDs) significantly associated with age, as identified by the three methods used (DESeq2, overdispersed Poisson generalized linear model, and Poisson regression model; Bonferroni corrected P value ≤ 0.05). Clustering was computed over Euclidean distances by the Ward linkage method. (b) Bar plots showing the normalized abundance (read counts per million normalized by sequencing depth) of age group-specific ARDs in the gut resistomes of young adults (group Y), younger elderly individuals (E), centenarians (C), and semisupercentenarians (S). Phylum-level assignments of ARD reads are also shown. ARDs are organized by drug to which resistance is conferred.

FIG 4

Co-occurrence network between age group-specific antibiotic resistance determinants and related bacterial species. Nodes identify ARDs (color coded by the antibiotic to which they confer resistance) or the bacterial species assigned to them. Only connected components with more than 2 nodes are depicted. The node size is proportional to the node degree (i.e., the number of edges connected to the node), and the links are Spearman correlations (see Materials and Methods).