The microbiome modulating activity of bile acids

Abstract

Bile acids are potent antibacterial compounds and play an important role in shaping the microbial ecology of the gut. Here, we combined flow cytometry, growth rate measurements (OD₆₀₀), and NMR- and mass spectrometry-based metabolomics to systematically profile the impact of bile acids on the microbiome using in vitro and in vivo models. This study confirmed that (1) unconjugated bile acids possess more potent antibacterial activity than conjugated bile acids; (2) Gram-positive bacteria are more sensitive to bile acids than Gram-negative bacteria; (3) some probiotic bacteria such as Lactobacillus and Bifidobacterium and 7α-dehydroxylating bacteria such as Clostridium scindens show bile acid resistance that is associated with activation of glycolysis. Moreover, we demonstrated that (4) as one of most hydrophobic bile acids, lithocholic acid (LCA) shows reduced toxicity to bacteria in the cecal microbiome in both in vivo and in vitro models; (5) bile acids directly and rapidly affect bacterial global metabolism including membrane damage, disrupted amino acid, nucleotide, and carbohydrate metabolism; and (6) in vivo, short-term exposure to bile acids significantly affected host metabolism via alterations of the bacterial community structure. This study systematically profiled interactions between bile acids and gut bacteria providing validation of previous observation and new insights into the interaction of bile acids with the microbiome and mechanisms related to bile acid tolerance.

Keywords: Bile acid; bile acid resistance; flow cytometry; growth rate measurements; gut bacteria; mass spectrometry; metabolomics; nmr.

Figure 1.

Scheme for determining the antibacterial activity of bile acids in vivo and vitro.

Figure 2.

The growth rate and physiological response of Bacteriodes fragilis and Ruminococcus bromii to bile acid exposure in vitro.

Figure 3.

UPLC-MS/MS-based metabolomics analysis of Ruminococcus bromii in response to bile acid exposure in vitro.

Figure 4.

The growth rate and UPLC-MS/MS-based metabolomics analysis of Bifidobacterium longum in response to bile acid exposure in vitro.

Figure 5.

The growth rate and physiological response of Clostridium scindens to bile acid exposure in vitro.

Figure 6.

The bacterial community and physiological response of isolated cecal bacteria to bile acid exposure in vitro.

Figure 7.

¹H NMR-based metabolomics analysis of isolated cecal bacteria in response to bile acid exposure in vitro.

Figure 8.

UPLC-MS/MS-based metabolomics analysis of isolated cecal bacteria in response to bile acid exposure in vitro.

Figure 9.

The response of cecal bacteria to bile acid exposure in vivo.