Identification of gut microbial bile acid metabolic enzymes via an AI-assisted pipeline

Cell

August 07, 2025

Yong Ding, Xi Luo, Jiasheng Guo, Baiying Xing, Haoyu Lin, Haohan Ma, Yicun Wang, Meng Li, Chuan Ye, Sen Yan, Kangjie Lin, Jinxin Zhang, Yingying Zhuo, Qixing Nie, Donghui Yang, Zhipeng Zhang, Yanli Pang, Kai Wang, Ming Ma, Luhua Lai, Changtao Jiang

https://doi.org/10.1016/j.cell.2025.07.017

ABSTRACT: The modifications of bile acids (BAs) are fundamental to their role in host physiology and pathology. Identifying their synthetases is crucial for uncovering the diversity of BAs and developing targeted interventions, yet it remains a significant challenge. To address this hurdle, we developed an artificial intelligence (AI)-assisted workflow, bile acid enzyme announcer unit tool (BEAUT), which predicted over 600,000 candidate BA metabolic enzymes that we compiled into the human generalized microbial BA metabolic enzyme (HGBME) database (https://beaut.bjmu.edu.cn). We identified a series of uncharacterized BA enzymes, including monoacid acylated BA hydrolase (MABH) and 3-acetoDCA synthetase (ADS). Notably, ADS can produce an unreported skeleton BA, 3-acetoDCA, with a carbon-carbon bond extension. After determining its bacterial source and catalytic mechanism, we found that 3-acetoDCA is widely distributed among populations and regulates the microbial interactions in the gut. In conclusion, our work offers alternative insights into the relationship between microbial BAs and the host from an enzymatic perspective.

摘要：膽汁酸 (BAs) 的修飾對其在宿主生理和病理學(xué)中的作用至關(guān)重要。鑒定其合成酶對于揭示BAs的多樣性和開發(fā)有針對性的干預(yù)措施至關(guān)重要，但這仍然是一項重大挑戰(zhàn)。為了解決這一難題，我們開發(fā)了一種人工智能 (AI) 輔助工作流程——膽汁酸酶播報單元工具 (BEAUT)。該工具預(yù)測了超過600,000種候選BA代謝酶，并將其匯編到人類通用微生物BA代謝酶 (HGBME) 數(shù)據(jù)庫 ( https://beaut.bjmu.edu.cn ) 中。我們鑒定了一系列未表征的BA酶，包括單酸?；疊A水解酶 (MABH) 和3-乙酰DCA合成酶(ADS)。值得注意的是，ADS可以生成一種未報道的骨架BA，即3-乙酰DCA，其具有碳碳鍵的延伸。在確定了其細(xì)菌來源和催化機(jī)制后，我們發(fā)現(xiàn)3-乙酰DCA在人群中分布廣泛，并調(diào)節(jié)腸道微生物的相互作用?？傊?，我們的研究從酶學(xué)角度為微生物BA與宿主之間的關(guān)系提供了新的見解。

Keywords: ADS; 3-acetoDCA; MABH; gut microbiota; bile acid; biosynthesis enzyme; artificial intelligence

關(guān)鍵詞：3-乙酰DCA合成酶；單酸酰化BA水解酶；腸道微生物群；膽汁酸；生物合成酶；人工智能

SUMMARY: Through functional validation, the study identified more than 40 previously unrecorded BA-metabolizing enzymes. Among these, monoacyl 3-acylated BA hydrolase (MABH)—derived from Hungatella hathewayi—is responsible for hydrolyzing monoacyl 3-acylcholic acids (such as 3-acetylcholic acid and 3-propionylcholic acid) but exhibits no activity toward 3-succinylcholic acid. Additionally, a novel class of thiamine pyrophosphate (ThDP)-dependent BA-metabolizing enzymes, namely 3-acetoxydeoxycholic acid synthases (ADS), was discovered. These enzymes can produce the previously unreported carbon-skeleton bile acid 3-acetoxydeoxycholic acid (3-acetoDCA) via an aldol condensation reaction. It was confirmed that Bacteroides ovatus is the primary producer of 3-acetoDCA, and its ADS gene knockout strain completely loses the ability to synthesize 3-acetoDCA. Structural biology studies revealed that BoADS (ADS derived from Bacteroides ovatus) belongs to the 1-deoxy-D-xylulose-5-phosphate synthase (DXPS) family. It binds to the substrate 3-oxodeoxycholic acid (3-oxoDCA) through a unique "sandwich"-style hydrophobic interaction and catalyzes the reaction between 3-oxoDCA and pyruvate to generate 3-acetoDCA. Analysis of clinical samples showed that 3-acetoDCA is widely present in human feces, and its concentration is positively correlated with the abundance of Bacteroides ovatus and the read count of the ADS gene. At physiological concentrations, 3-acetoDCA does not act on traditional BA receptors such as FXR, VDR, PXR, and TGR5. Instead, it regulates gut microbiota composition by promoting the growth of Lactobacilli (particularly Lactobacillus gasseri) in the presence of arginine/ornithine, thereby increasing the levels of tryptophan metabolites ((such as indole-3-lactic acid) in mouse feces and colons—a effect that may play a protective role in metabolic diseases. The application of BEAUT and the discovery of novel BA-metabolizing enzymes provide a "top-down" paradigm for research on microbial BA metabolism and expand the understanding of BA chemical diversity and microbe-host interactions.

總結(jié)：該研究開發(fā)了一種人工智能輔助流程BEAUT（膽汁酸酶播報單元工具），用于挖掘腸道微生物中的膽汁酸（BA）代謝酶。BEAUT 基于蛋白質(zhì)語言模型ESM2生成蛋白質(zhì)功能感知表征，并通過密集神經(jīng)網(wǎng)絡(luò)從宏基因組數(shù)據(jù)中篩選BA代謝酶，結(jié)合已知BA代謝酶序列及具有相似底物結(jié)合口袋的擴(kuò)展序列進(jìn)行訓(xùn)練，從人類腸道微生物基因組序列中預(yù)測出超60萬個潛在BA代謝酶，并構(gòu)建人類通用微生物BA代謝酶（HGBME）數(shù)據(jù)庫（https://beaut.bjmu.edu.cn）供公開訪問。通過功能驗證，研究發(fā)現(xiàn)了40多種未被記錄的BA代謝酶，其中單酸?；疊A水解酶（MABH）來自Hungatella hathewayi，負(fù)責(zé)單酸3-酰膽酸（如3-乙酰膽酸、3-丙酰膽酸）的水解，對3-琥珀酰膽酸無活性；還發(fā)現(xiàn)一類依賴硫胺素焦磷酸（ThDP）的新型BA代謝酶——3-乙酰DCA合成酶（ADS），其能通過羥醛縮合反應(yīng)生成此前未被報道的碳骨架膽汁酸3-乙酰DCA（3-acetoDCA），明確多形擬桿菌（Bacteroides ovatus）是3-acetoDCA的主要產(chǎn)生菌，且其ADS基因敲除菌株完全喪失3-acetoDCA合成能力。結(jié)構(gòu)生物學(xué)研究揭示，BoADS（多形擬桿菌來源的ADS）屬于1-脫氧-D-木酮糖-5-磷酸合成酶（DXPS）家族，通過特殊的“三明治”式疏水相互作用結(jié)合底物3-氧代脫氧膽酸（3-oxoDCA），催化其與丙酮酸反應(yīng)生成3-acetoDCA。臨床樣本分析顯示，3-acetoDCA 在人類糞便中廣泛存在，且其濃度與多形擬桿菌豐度及ADS基因正相關(guān)；生理濃度下的3-acetoDCA不作用于FXR、VDR、PXR、TGR5等傳統(tǒng)BA受體，而是通過促進(jìn)精氨酸/鳥氨酸存在時乳桿菌（尤其是加氏乳桿菌）的生長來調(diào)節(jié)腸道菌群組成，進(jìn)而增加小鼠糞便和結(jié)腸中吲哚-3-乳酸等色氨酸代謝物水平，在代謝疾病中發(fā)揮保護(hù)作用。BEAUT的應(yīng)用及新型BA代謝酶的發(fā)現(xiàn)，為微生物BA代謝研究提供了“自上而下”的新范式，拓展了對BA化學(xué)多樣性及微生物-宿主相互作用的認(rèn)知。