Aging is the system-wide loss of homeostasis, eventually leading to death. There is growing evidence that the microbiome not only evolves with its aging host, but also directly affects aging via the modulation of metabolites involved in important cellular functions. The widely used model organism C. elegans exhibits high selectivity towards its native microbiome members which confer a range of differential phenotypes and possess varying functional capacities. The ability of one such native microbiome species, Chryseobacterium sp. CHNTR56 MYb120, to improve the lifespan of C. elegans and to promote the production of Vitamin B6 in the co-colonizing member Comamonas sp. 12022 MYb131 are some of its beneficial effects on the worm host. We hypothesize that studying its metabolic influence on the different life stages of the worm could provide further insights into mutualistic interactions. The present work applied LC-MS untargeted metabolomics and isotope labeling to study the impact of the native microbiome member Chryseobacterium sp. CHNTR56 MYb120 on the metabolism of C. elegans. In addition to the upregulation of biosynthesis and detoxification pathway intermediates, we found that Chryseobacterium sp. CHNTR56 MYb120 upregulates the glyoxylate shunt in mid-adult worms which is linked to the upregulation of trehalose, an important metabolite for desiccation tolerance in older worms.