This study demonstrates that the gut microbiome has a significant impact on mammalian blood metabolites. Using mass spectrometry-based metabolomics, researchers compared plasma samples from germ-free (GF) and conventional (conv) mice and found that the presence of gut bacteria greatly influences the levels of various metabolites. Over 10% of detected features showed significant changes in concentration between the two groups, with amino acid metabolites being particularly affected. For example, the production of bioactive indole-containing metabolites such as indoxyl sulfate and indole-3-propionic acid (IPA) was influenced by the gut microbiome. IPA, an antioxidant, was shown to be dependent on the presence of gut bacteria, specifically Clostridium sporogenes. Additionally, the microbiome was found to influence the host's phase II metabolic response, leading to the presence of various sulfated, glycine-conjugated, and glucuronide adducts in conv mice. The study also revealed that the microbiome affects the diversity of indole-containing compounds in serum. For instance, the plasma concentrations of tryptophan and N-acetyltryptophan were significantly lower in conv mice compared to GF mice. The microbiome was also found to influence the production of other metabolites, such as hippuric acid, which is formed through glycine conjugation. The presence of the microbiome significantly increased the levels of various metabolites, including those associated with phase II drug metabolism. The findings suggest a complex interplay between bacterial and mammalian metabolism, with the microbiome playing a crucial role in the host's metabolic processes. The study highlights the importance of the gut microbiome in human health and disease, as it influences the production of various metabolites that can have both harmful and beneficial effects on the host. The results also emphasize the potential of metabolomics-based studies in understanding the impact of the microbiome on mammalian biochemistry.This study demonstrates that the gut microbiome has a significant impact on mammalian blood metabolites. Using mass spectrometry-based metabolomics, researchers compared plasma samples from germ-free (GF) and conventional (conv) mice and found that the presence of gut bacteria greatly influences the levels of various metabolites. Over 10% of detected features showed significant changes in concentration between the two groups, with amino acid metabolites being particularly affected. For example, the production of bioactive indole-containing metabolites such as indoxyl sulfate and indole-3-propionic acid (IPA) was influenced by the gut microbiome. IPA, an antioxidant, was shown to be dependent on the presence of gut bacteria, specifically Clostridium sporogenes. Additionally, the microbiome was found to influence the host's phase II metabolic response, leading to the presence of various sulfated, glycine-conjugated, and glucuronide adducts in conv mice. The study also revealed that the microbiome affects the diversity of indole-containing compounds in serum. For instance, the plasma concentrations of tryptophan and N-acetyltryptophan were significantly lower in conv mice compared to GF mice. The microbiome was also found to influence the production of other metabolites, such as hippuric acid, which is formed through glycine conjugation. The presence of the microbiome significantly increased the levels of various metabolites, including those associated with phase II drug metabolism. The findings suggest a complex interplay between bacterial and mammalian metabolism, with the microbiome playing a crucial role in the host's metabolic processes. The study highlights the importance of the gut microbiome in human health and disease, as it influences the production of various metabolites that can have both harmful and beneficial effects on the host. The results also emphasize the potential of metabolomics-based studies in understanding the impact of the microbiome on mammalian biochemistry.