Alcohol-induced changes in the gut microbiome and metabolome of rhesus macaques

Abstract

Rationale: Increasing evidence has demonstrated that changes in the gut microbiome, including those associated with dietary influences, are associated with alterations in many physiological processes. Alcohol consumption is common across human cultures and is likely to have a major effect on the gut microbiome, but there remains a paucity of information on its effects in primates.

Objectives: The effects of chronic alcohol consumption on the primate gut microbiome and metabolome were studied in rhesus macaques that were freely drinking alcohol. The objectives of the study were to determine what changes occurred in the gut microbiome following long-term exposure to alcohol and if these changes were reversible following a period of abstinence.

Methods: Animals consuming alcohol were compared to age-matched controls without access to alcohol and were studied before and after a period of abstinence. Fecal samples from rhesus macaques were used for 16S rRNA sequencing to profile the gut microbiome and for metabolomic profiling using mass spectrometry.

Results: Alcohol consumption resulted in a loss of alpha-diversity in rhesus macaques, though this was partially ameliorated by a period of abstinence. Higher levels of Firmicutes were observed in alcohol-drinking animals at the expense of a number of other microbial taxa, again normalizing in part with a period of abstinence. Metabolomic changes were primarily associated with differences in glycolysis when animals were consuming alcohol and differences in fatty acids when alcohol-drinking animals became abstinent.

Conclusions: The consumption of alcohol has specific effects on the microbiome and metabolome of rhesus macaques independent of secondary influences. Many of these changes are reversed by a relatively short period of abstinence.

Keywords: Alcohol; Metabolome; Microbiome; Rhesus macaque.

Figure 1.

Influence of alcohol on the gut microbiome in rhesus macaques. (A) Family-level relative abundance of intestinal microbiota in the stool of rhesus macaques without exposure to alcohol (left), with long-term free access to alcohol (right), and following a period of abstinence from alcohol (middle). (B) Alpha diversity from fecal samples collected from control rhesus macaques and animals with chronic access to alcohol before and after abstinence using the Chao1 measure (control vs. alcohol abstinent: two-tailed Mann-Whitney p = 0.0076; control vs. alcohol drinking: two-tailed Mann-Whitney p = 0.0003; alcohol drinking vs. alcohol abstinent: two-tailed Wilcoxon 0.2983). (C) Alpha diversity using the Shannon measure (control vs. alcohol abstinent: two-tailed Mann-Whitney p = 0.0414; control vs. alcohol drinking: two-tailed Mann-Whitney p = 0.0047; alcohol drinking vs. alcohol abstinent: two-tailed Wilcoxon 0.0969).

Figure 2.

Influence of alcohol on gut taxa in rhesus macaques at the Phylum level. For each phylum, a box-and-whisker plot is shown of the log-transformed abundance observed in control (left), alcohol-abstinent (center), and alcohol-drinking (right) rhesus macaques. Animals from the Yasuda et al. study are shown in gray, animals from the older cohort in solid black, and animals from the younger cohort in white with black outline. Significance was determined using LEfSe (Segata et al. 2011) and is shown in Table 2.

Figure 3.

Influence of alcohol on gut taxa in rhesus macaques at the Family level. For each family, a box-and-whisker plot is shown of the log-transformed abundance observed in control (left), alcohol-abstinent (center), and alcohol-drinking (right) rhesus macaques. Animals from the Yasuda et al. study are shown in gray, animals from the older cohort in solid black, and animals from the younger cohort in white with black outline. Significance was determined using LEfSe (Segata et al. 2011) and is shown in Table 2.

Figure 4.

Influence of alcohol on fecal metabolites in rhesus macaques. A box-and-whisker plot of scaled abundance is show in alcohol-drinking (left), and alcohol-abstinent (right) rhesus macaques. Animals from the older cohort in solid black and animals from the younger cohort in white with black outline. Significant main-effect of alcohol exposure was calculated a paired t-test with Benjamini-Hochberg correction for multiple test comparisons and is shown in Table 3.