Audrey M. Neyrinck

1. The human gastrointestinal tract harbors a complex and dynamic microbial ecosystem—known as the gut microbiota—which profoundly influences host physiology and health. 1 Importantly, the gut micr...

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. Abstract Figure: Graphical Bacteria-dependent metabolites that are decreased upon cancer cachexia in mice mitigate muscle atrophy in vitro.: 7 metabolites were identified as depleted in cachectic condition and microbiota-dependent, among which 2 of them, namely 2-phenylpropanoic acid (2PPA) and 3-(3,4-dihydroxyphenyl)propanoic acid (3,4OHPP), counteracted C2C12 myotube atrophy induced by dexamethasone. Created with BioRender.com.

Introduction. Acute myeloid leukemia (AML) is a hematological malignancy associated with muscle wasting. As the relative abundance of Lachnospira eligens was reduced in patients with AML compared to healthy individuals and correlated positively with muscle strength, we hypothesized that L. eligens positively impacts the muscle through the production of small metabolites reaching the systemic circulation. Methods. L. eligens levels were analyzed in two additional independent cohorts. Six L. eligens isolates were characterized through whole-genome sequencing to select clinically relevant strains. The composition of their culture supernatant was analyzed by metabolomics. The impact of L. eligens supernatant on dexamethasone- and interleukin-6-atrophied murine myotubes was assessed. Bioactive metabolites and their production mechanism were identified using among others bioactivity-guided fractionation. The underlying mechanism was also explored on the host side through myotubes′ transcriptome analysis and metabolic flux analysis. The relevance of bioactive metabolites and their production mechanism was evaluated through clinical data and samples analyses and in a mouse model of leukemia. Results. The levels of L. eligens are reduced in independent cohorts of patients with AML and its supernatant counteracts myotube atrophy. This anti-atrophic effect, conserved between strains of the same species, depends on the occurrence of mixed acid fermentation (MAF) in anoxic culture conditions and the presence of its acid end-products acetate, formate and D-lactate. Consistent with those results, blood levels of acetate are decreased and the relative abundance of fecal bacteria capable of performing aerobic respiration is increased in patients with AML. However, bacterial supernatant failed to prevent muscle atrophy and weakness in leukemic mice, likely due to insufficient sustained elevation of acid end-products in the blood. Conclusion. This work reveals the anti-atrophic effect of MAF end-products on myotubes and suggests the importance of considering gut electron acceptor levels (e.g. O ₂ ) in disorders affecting muscle health.

Obesity is associated with alterations in the gut microbiome that may contribute to metabolic and mental health disturbances. Fecal microbiota transplantation (FMT) from humans to mice is a model proposed to study human microbiota-associated disorders. In this study, we investigated whether gut microbiota from human donors with obesity could affect behavior and metabolomic profiles of mice. Stools from donors with obesity and from lean donors were inoculated to antibiotic-pretreated mice fed a standard low-fat diet throughout the experiment. Obese-recipient mice exhibited a lower bacterial alpha-diversity and limited changes in specific taxa (e.g., an increase in Eubacterium) but were similar to lean-recipient mice in terms of dietary intake, body weight, fat mass, anxiety/depression-like behavior and glucose homeostasis. Non-targeted LC–MS metabolomic analysis revealed no change in the portal and cava serum samples. However, 1-methylnicotinamide, indole-3-acetic acid (I3A) and methyllysine were increased in the cecal content of obese-recipient compared to lean-recipient mice. Microbial metabolites derived from amino acids were positively correlated with Eubacterium. These results indicate that FMT from donors with obesity to mice fed chow diet (low in lipids) leads to minor but persistent change in intestinal microbial-derived metabolites, without recapitulating the metabolic and behavioral alterations of obesity.

Purpose Inulin-type fructans (ITF) are fermentable dietary fibres (DF) that can confer beneficial metabolic health effects through changes in the gut microbiota. Many papers suggest that complex food rich in DF could be more relevant than purified DF in terms of health effect. We compared the prebiotic effect of natural source of inulin (scorzonera) versus native inulin extracted from chicory root in a model of obesity. Methods Mice were fed during 6 weeks a low-fat (LF), high-fat (HF) or high-fat diet enriched with either purified inulin from chicory root (Inu) or lyophilized scorzonera (Sco), with the same amount of ITF intake (10%) versus a non-fermentable fibre (cellulose). Metabolic parameters were correlated with the gut microbiome composition (16S rRNA gene sequencing). Results Both inulin sources reduced food intake without significantly modifying body weight gain or adiposity compared to HF. Purified inulin and lyophilized scorzonera differentially modulate the gut physiology and microbiota. Both inulin and scorzonera shifted global gut microbial composition from HF group, decreased members of Desulfovibrionaceae and boosted bifidobacteria level. Some effects were specific to Sco group, such as the increase of Akkermansia and the decrease of Bacteroides, that correlated to biological outcomes. Inu improved hepatic steatosis whereas scorzonera boosted intestinal immunity markers and antimicrobial peptides expression, and increased intestinal crypt depth. Conclusion Differences occur between natural edible versus isolated sources of ITF. Both sources of inulin shifted the gut microbiota, but differently affected intestinal and lipid homeostasis. This study highlights the importance of food matrix and origins of fructans for their use in the context of metabolic disorders.

Alterations in bile acid profile and pathways contribute to hepatic inflammation in cancer cachexia, a syndrome worsening the prognosis of cancer patients. As the gut microbiota impinges on host metabolism through bile acids, the current study aimed to explore the functional contribution of gut microbial dysbiosis to bile acid dysmetabolism and associated disorders in cancer cachexia. Using three mouse models of cancer cachexia (the C26, MC38 and HCT116 models), we evidenced a reduction in the hepatic levels of several secondary bile acids, mainly taurodeoxycholic (TDCA). This reduction in hepatic TDCA occurred before the appearance of cachexia. Longitudinal analysis of the gut microbiota pinpointed an ASV, identified as Xylanibacter rodentium, as a bacterium potentially involved in the reduced production of TDCA. Coherently, stable isotope-based experiments highlighted a robust decrease in the microbial 7α-dehydroxylation (7α-DH) activity with no changes in the bile salt hydrolase (BSH) activity in cachectic mice. This approach also highlighted a reduced microbial 7α-hydroxysteroid dehydrogenase (7α-HSDH) and 12α-hydroxysteroid dehydrogenase (12α-HSDH) activities in these mice. The contribution of the lower production of TDCA to cancer cachexia was explored in vitro and in vivo. In vitro, TDCA prevented myotube atrophy, whereas in vivo hepatic whole transcriptome analysis revealed that TDCA administration to cachectic mice improved the unfolded protein response and cholesterol homeostasis pathways. Coherently, TDCA administration reversed hepatic cholesterol accumulation in these mice. Altogether, this work highlights the contribution of the gut microbiota to bile acid dysmetabolism and the therapeutic interest of the secondary bile acid TDCA for hepatic cholesterol homeostasis in the context of cancer cachexia. Such discovery may prove instrumental in the understanding of other metabolic diseases characterized by microbial dysbiosis. More broadly, our work demonstrates the interest and relevance of microbial activity measurements using stable isotopes, an approach currently underused in the microbiome field.

Background: Alcohol use disorder (AUD) is a global health problem with limited therapeutic options. The biochemical mechanisms that lead to this disorder are not yet fully understood, and in this respect, metabolomics represents a promising approach to decipher metabolic events related to AUD. The plasma metabolome contains a plethora of bioactive molecules that reflects the functional changes in host metabolism but also the impact of the gut microbiome and nutritional habits.Methods: In this study, we investigated the impact of severe AUD (sAUD), and of a 3-week period of alcohol abstinence, on the blood metabolome (non-targeted LC-MS metabolomics analysis) in 96 sAUD patients hospitalized for alcohol withdrawal.Results: We found that the plasma levels of different lipids ((lyso)phosphatidylcholines, long-chain fatty acids), short-chain fatty acids (i.e. 3-hydroxyvaleric acid) and bile acids were altered in sAUD patients. In addition, several microbial metabolites, including indole-3-propionic acid, p-cresol sulfate, hippuric acid, pyrocatechol sulfate, and metabolites belonging to xanthine class (paraxanthine, theobromine and theophylline) were sensitive to alcohol exposure and alcohol withdrawal. 3-Hydroxyvaleric acid, caffeine metabolites (theobromine, paraxanthine, and theophylline) and microbial metabolites (hippuric acid and pyrocatechol sulfate) were correlated with anxiety, depression and alcohol craving. Metabolomics analysis in postmortem samples of frontal cortex and cerebrospinal fluid of those consuming a high level of alcohol revealed that those metabolites can be found also in brain tissue.Conclusions: Our data allow the identification of neuroactive metabolites, from interactions between food components and microbiota, which may represent new targets arising in the management of neuropsychiatric diseases such as sAUD.Funding: Gut2Behave project was initiated from ERA-NET NEURON network (Joint Transnational Call 2019) and was financed by Academy of Finland, French National Research Agency (ANR-19-NEUR-0003-03) and the Fonds de la Recherche Scientifique (FRS-FNRS; PINT-MULTI R.8013.19, Belgium). Metabolomics analysis of the TSDS samples was supported by grant from the Finnish Foundation for Alcohol Studies.

Dietary fibres constitute a heterogeneous class of nutrients that are key in the prevention of various chronic diseases. Most dietary fibres are fermented by the gut microbiome and may, thereby, modulate the gut microbial ecology and metabolism, impacting human health. Dietary fibres may influence the occurrence of specific bacterial taxa, with this effect varying between individuals. The effect of dietary fibres on microbial diversity is a matter of debate. Most intervention studies with dietary fibres in the context of obesity and related metabolic disorders reveal the need for an accurate assessment of the microbiome to better understand the variable response to dietary fibres. Epidemiological studies confirm that a high dietary fibre intake is strongly associated with a reduced occurrence of many types of cancer. However, there is a need to determine the impact of intervention with specific dietary fibres on cancer risk, therapy efficacy and toxicity, as well as in cancer cachexia. In this Review, we summarize the mechanisms by which the gut microbiome can mediate the physiological benefits of dietary fibres in the contexts of obesity, cardiometabolic diseases and cancer, their incidence being clearly linked to low dietary fibre intake.

Aims/hypothesis: We aimed to investigate the association between the abundance of Dysosmobacter welbionis, a commensal gut bacterium, and metabolic health in human participants with obesity and diabetes, and the influence of metformin treatment and prebiotic intervention. Methods: Metabolic variables were assessed and faecal samples were collected from 106 participants in a randomised controlled intervention with a prebiotic stratified by metformin treatment (Food4Gut trial). The abundance of D. welbionis was measured by quantitative PCR and correlated with metabolic markers. The in vitro effect of metformin on D. welbionis growth was evaluated and an in vivo study was performed in mice to investigate the effects of metformin and D. welbionis J115^T supplementation, either alone or in combination, on metabolic variables. Results: D. welbionis abundance was unaffected by prebiotic treatment but was significantly higher in metformin-treated participants. Responders to prebiotic treatment had higher baseline D. welbionis levels than non-responders. D. welbionis was negatively correlated with aspartate aminotransferase (AST) and alanine aminotransferase (ALT) levels and fasting blood glucose levels in humans with obesity and type 2 diabetes. In vitro, metformin had no direct effect on D. welbionis growth. In mice, D. welbionis J115^T treatment reduced body weight gain and liver weight, and improved glucose tolerance to a better level than metformin, but did not have synergistic effects with metformin. Conclusions/interpretation: D. welbionis abundance is influenced by metformin treatment and associated with prebiotic response, liver health and glucose metabolism in humans with obesity and diabetes. This study suggests that D. welbionis may play a role in metabolic health and warrants further investigation. Clinical trial: NCT03852069 Graphical