Microbially-catalyzed conjugation of GABA and tyramine to bile acids

Abstract

Bile acids (BAs) are cholesterol-derived molecules in the human gut that aid in digestion and nutrient absorption, regulate host metabolic processes, and influence gut microbiome composition. Both the host and its microbiome contribute to enzymatic modifications that shape the chemical diversity of BAs in the gut. Several bacterial species have been reported to conjugate standard amino acids to BAs, but it was not known if bacteria conjugate other classes of amines to BAs. We show thatBacteroides fragilisstrain P207, isolated from a bacterial bloom in the J-pouch of a patient with ulcerative colitis (UC) pouchitis, conjugates standard amino acids and the neuroactive amines γ-aminobutyric acid (GABA) and tyramine to deoxycholic acid. We extended our analysis to other human gut isolates and identified bacterial species that conjugate GABA and tyramine to primary and secondary BAs, and further identified diverse BA-GABA and -tyramine amides in human stool. A time-series metabolomic analysis of UC J-pouch contents revealed a lack of secondary bile acids and a shifting BA conjugate profile before, during and after onset of pouchitis, including temporal changes in several BA-GABA amides. Treatment of pouchitis with ciprofloxacin was associated with a marked reduction of nearly all BA amides in the J-pouch. Our study expands the known repertoire of conjugated bile acids produced by bacteria to include BA conjugates to the neuroactive amines GABA and tyramine, and demonstrates that these molecules are present in the human gut.ImportanceBile acids (BAs) are modified in multiple ways by host enzymes and the microbiota to produce a chemically diverse set of molecules that assist in the digestive process and impact many physiological functions. This study reports the discovery of bacterial species that conjugate the neuroactive molecules, GABA and tyramine, to primary and secondary BAs. We further present evidence that BA-GABA and BA-tyramine conjugates are present in the human gut, and document a shifting BA-GABA profile in a human pouchitis patient before, during and after inflammation and antibiotic treatment. GABA and tyramine are potent neuroactive molecules and common metabolic products of the gut microbiota. GABA- and tyramine-conjugated BAs may influence receptor-mediated regulatory mechanisms within the gastrointestinal tract and absorption of these molecules and their entry into the enterohepatic circulation may impact host physiology at distal tissue sites. This discovery defines new conjugated bile acids in the human gut.

The Underappreciated Diversity of Bile Acid Modifications

“…Inspecting plausible annotations of the delta masses by matching to multiple databases (see STAR Methods), revealed several candidates from the polyamine biosynthetic pathway (Figure 4A; Table S4). Consistent with our observations that polyamines and their biosynthetic precursors are conjugated to bile acids, while this paper was in review, the polyamine, g-aminobutyric acid (GABA), was shown in two preprints to be conjugated to deoxycholic acid by microbes belonging to species Bacteroides fragilis, Mediterraneibacter gnavus, Bifidobacterium longum, and Bacteroides ovatus isolated from the J-pouch of a patient suffering from ulcerative colitis pouchitis 74 and lithocholic GABA amidates and as ester when chenodeoxycholic acid or lithocholic acid were added to human stool, ex vivo. 75 Given that polyamines are involved in several cellular processes, including transcription, translation, stress protection, metabolism, growth, and aging, and that they are involved in many diseases, such as cancer and neurodegeneration, 76,77 we were interested in pursuing our investigation of these putative polyamine bile amidates.…”

Bile acid fitness determinants of a Bacteroides fragilis isolate from a human pouchitis patient

“…DC concentrations that attenuated growth of B. fragilis P207 in vitro are similar to those found in healthy individuals. DC was undetectable in the stool of patient 207 ( 74 ) when B. fragilis P207 bloomed to become the dominant species in the pouch ( 24 ). Thus, it is reasonable to conclude that the absence of deoxycholate contributed, at least in part, to the population expansion of B. fragilis in patient 207, though other factors relating to the overall metabolic versatility of B. fragilis ( 75 , 76 ) likely contributed to its bloom as well.…”