Multi-Omics Reveals that Lead Exposure Disturbs Gut Microbiome Development, Key Metabolites, and Metabolic Pathways

Abstract

Lead exposure remains a global public health issue, and the recent Flint water crisis has renewed public concern about lead toxicity. The toxicity of lead has been well established in a variety of systems and organs. The gut microbiome has been shown to be highly involved in many critical physiological processes, including food digestion, immune system development, and metabolic homeostasis. However, despite the key role of the gut microbiome in human health, the functional impact of lead exposure on the gut microbiome has not been studied. The aim of this study is to define gut microbiome toxicity induced by lead exposure in C57BL/6 mice using multiomics approaches, including 16S rRNA sequencing, whole genome metagenomics sequencing, and gas chromatography-mass spectrometry (GC-MS) metabolomics. 16S rRNA sequencing revealed that lead exposure altered the gut microbiome trajectory and phylogenetic diversity. Metagenomics sequencing and metabolomics profiling showed that numerous metabolic pathways, including vitamin E, bile acids, nitrogen metabolism, energy metabolism, oxidative stress, and the defense/detoxification mechanism, were significantly disturbed by lead exposure. These perturbed molecules and pathways may have important implications for lead toxicity in the host. Taken together, these results demonstrated that lead exposure not only altered the gut microbiome community structures/diversity but also greatly affected metabolic functions, leading to gut microbiome toxicity.

Figure 1

Lead exposure disturbed the trajectories of gut microbiome development as assessed by beta diversity metrics (A). Lead exposure also reduced/inhibited the phylogenetic diversity of the gut bacteria as examined using alpha diversity metrics (B). Here, 16S rRNA gene sequencing was performed, followed by bacterial taxonomic assignment via QIIME. Beta diversity evaluated the diversity in the microbial community between samples, whereas alpha diversity reflected the species richness.

Figure 2

The fold changes of selected significantly changed gut bacterial genera between the controls and lead-treated mice (A. 4 weeks post-lead exposure; B. 13 weeks post-lead exposure). The fold changes were calculated using the group means for each bacterial genus.

Figure 3

The abundance of key metabolites was measured by GC-MS to examine the impact of lead exposure on the metabolic functions of the gut microbiome. Vitamin E, bile acids and cholesterol and its derivative were significantly reduced in mice after exposure to lead for 13 weeks (A. α-tocopherol, B. γ-tocopherol, C. cholic acid, D. deoxycholic acid, E. ursodeoxycholic acid; F. cholesterol; and G. coprostanol).

Figure 4

Metagenomics and metabolomics analyses showing that lead exposure significantly alters the nitrogen metabolism of the gut bacteria, as evidenced by the perturbed key genes and metabolites (A. urease accessory protein UreE; B. creatinine amidohydrolase; C. urea; D. hydroxylamine; E. nitrite reductase [NAD(P)H]; and F. copper-containing nitrite reductase). N.D.: non-detectable.

Figure 5

Energy metabolism, which is a key metabolic function of the gut microbiome, was disturbed by lead exposure, as demonstrated by the altered abundance of a number of bacterial genes and the key metabolite glycerol-3-phosphate. N.D.: non-detectable. Note: the relative abundance reflects only the gene levels and not the protein levels.

Figure 6

Alterations in key genes and metabolites involved in oxidative stress and the defense response indicate that lead exposure activates cellular defense genes (A and B), DNA repair systems (C, D and E), and detoxification pathways (F, G and H).