Degraeve, A. L. | bioRxiv Science

bioRxiv2026

Gut microbiota-dependent phenylpropanoic acid derivatives reduced in cancer cachexia protect against myotube atrophy

Cancer cachexia is a debilitating disease characterized by muscle atrophy. Given the gut dysbiosis in cancer cachexia and the increasing evidence of a gut-muscle axis, we explored the potential beneficial effects of bacteria-dependent metabolites on myotube atrophy. Using both hypothesis-driven and hypothesis-free approaches, in-depth metabolomic analysis of blood samples from cachectic C26 tumor-bearing mice treated or not with antibiotics, as well as disease-free germ-free and conventionalized mice, identified 7 bacteria-dependent metabolites decreased under cachectic conditions. Such alterations were not mediated by reduced caloric intake. Among them, 2 metabolites, namely 2-phenylpropanoic acid (2PPA, also known as 2-phenylpropionic acid) and 3-(3,4-dihydroxyphenyl)propanoic acid (3,4OHPP, also known as 3,4-dihydroxyhydrocinnamic acid or dihydrocaffeic acid), demonstrated anti-atrophying effect, alone and in combination, on mouse C2C12 myotubes. Transcriptomics revealed that these 2 bacteria-dependent metabolites restored the amino acid homeostasis with an activation of ATF4 and the serine biosynthesis pathway. Pharmacological inhibition of the phosphoglycerate dehydrogenase (PHGDH), the rate-limiting enzyme of this pathway, prevented the anti-atrophying effects of 2PPA and 3,4OHPP, indicating a causal role for PHGDH in this effect. By identifying microbiota-dependent metabolites as potential therapeutic levers, the current work not only advances our understanding of microbiome-host crosstalk in disease but also opens avenues for innovative, targeted interventions to mitigate muscle atrophy.

microbiology↗

bioRxiv2025

The gut microbiome shapes pharmacology and treatment outcomes for a key anti-inflammatory therapy

The human gut microbiome encodes a formidable metabolic repertoire that harvests nutrients from the diet, but these same pathways may also metabolize medications. Indeed, large screens have revealed extensive microbial metabolism of drugs in vitro, but the pharmacologic and clinical repercussions of microbiota-mediated metabolism in vivo remain to be discerned. As a proof-of-concept, we investigate how human gut microbes contribute to in vivo pharmacology and efficacy of a key anti-inflammatory drug, methotrexate (MTX). Specifically, we demonstrate that the gut microbiome shapes drug pharmacology in vivo in mice, both by directly metabolizing the drug and by inducing host pathways that promote drug metabolism. Moreover, interindividual variation in the human gut microbiome contributes to variation in pharmacokinetic (PK) profiles. When we quantified metabolites produced by microbes, we unexpectedly identified novel MTX metabolites, one of which, p-methylaminobenzoyl-L-glutamic acid (pMABG), was a major byproduct of microbial metabolism both in vitro and in vivo. Further, we find that a large proportion of patient-associated microbes are capable of metabolizing MTX. Finally, we show that microbial metabolism of MTX is linked to PK profiles and disease outcomes in a mouse model of inflammatory arthritis. Taken together, these findings provide evidence that the human gut microbiome causally contributes to drug pharmacology in vivo for a key anti-inflammatory drug through known and novel mechanisms. Our studies provide a framework for elucidating the clinical relevance of drug microbial metabolism in the context of treatment response. These results are a first step towards understanding and manipulating the human gut microbiome in the treatment of autoimmunity and the advancement of precision medicine for millions of patients taking MTX for immune or inflammatory conditions. HighlightsO_LIThe gut microbiome impacts methotrexate (MTX) pharmacology in mice C_LIO_LIThe human gut microbiome contributes to interindividual variation in MTX pharmacology C_LIO_LIHuman gut microbes produce novel MTX metabolites, pMABG and 6-MPDA C_LIO_LIMicrobial metabolism of MTX is linked to treatment outcomes C_LI

pharmacology and toxicology↗