News Express: UM research team discovers key factors in utilisation of medicinal polysaccharides by human gut bacteria
新聞快訊：澳大團隊發現人類腸道細菌對中藥多糖利用的關鍵因素
單形擬桿菌特異性代謝石斛多糖的基因簇及關鍵酶GH26的發現與機制解析
Discovery and mechanistic analysis of the gene cluster and key enzyme GH26 for Dendrobium polysaccharide utilisation in human gut Bacteroides uniformis
澳大團隊發現人類腸道細菌對中藥多糖利用的關鍵因素
澳門大學健康科學學院教授梁麗嫻、中國科學院深圳先進技術研究院研究員戴磊、廣東省中醫院及中醫證候全國重點實驗室教授周華共同帶領的團隊在人體腸道擬桿菌和副擬桿菌選擇性利用中藥多糖的分子機制上取得了重大進展，對人類腸道微生物組、碳水化合物活性酶、膳食和中藥多糖的開發與應用等領域具有重要意義。相關研究成果已發表在國際知名期刊《自然—通訊》上。
該研究首次發現一種人體應答菌對特異代謝石斛多糖的選擇性利用。研究團隊以合成生物學交叉學科的方法，在該細菌中發現了特有的多糖利用基因座。通過結構比對、分子對接，進一步證明了GH26酶具有保守的催化位點（E415/E504）和底物結合位點，是石斛多糖代謝核心酶。研究開創發現了人類腸道細菌對中藥多糖利用的關鍵因素，強調中藥多糖具高度特異性利用，有助理解多糖的體內潛在用途及作用機理，突顯對腸道菌群進行精准靶向的潛力，為治療干預開闢了新路徑。
利用中藥多糖調控腸道微生物組，已被證明是治療人類疾病的一種具有前景的策略。人體腸道中的擬桿菌和副擬桿菌是膳食多糖的主要消費者，了解這些腸道共生細菌如何利用中藥多糖，對開發新型基於多糖的益生元和藥物從而改善人類健康至關重要。然而，目前尚缺乏對腸道細菌利用中藥多糖的系統性分析及相應的遺傳基礎研究。
研究團隊系統地繪製了28種人體腸道擬桿菌和副擬桿菌利用20種中藥多糖的生長表型的圖譜，發現腸道擬桿菌之間和中藥多糖之間存在顯著生長差異。其中，鐵皮石斛多糖（一種葡甘聚糖）能特別促進單形擬桿菌（B. uniformis DA183）的生長。為了揭示石斛多糖選擇性促進單形擬桿菌生長背後的遺傳機制，該研究進行了比較轉錄組分析和基因敲除實驗。結果表明，多糖利用基因簇PUL34和關鍵酶GH26_BuDA183對於單形擬桿菌DA183菌株利用石斛多糖至關重要。透過序列比對分析，發現只有單形擬桿菌DA183的基因組能編碼完整的PUL34_BuDA183基因簇。
最後，為了表徵單形擬桿菌GH26酶的催化活性及底物特異性機制，研究團隊將AlphaFold2預測的單形擬桿菌GH26酶蛋白結構與卵形擬桿菌GH26酶的晶體結構進行比對分析，發現這兩種GH26的催化位點和底物結合位點是相同的，這表明單形擬桿菌GH26酶與卵形擬桿菌GH26酶有相似的催化劑機制。隨後，研究團隊通過表達和純化GH26酶，在體外證明了其對多種甘露聚糖的水解活性。點突變實驗表明，谷氨酸殘基E415A或E504A的突變都會導致酶活性喪失，證明兩個催化位點對酶活性都是必要的。分子對接模擬顯示底物的反應性取決於其與催化殘基相互作用的能力。
總體而言，該研究提供了一個通用框架，用以分析人體腸道細菌對植物多糖的利用情況，並深入理解其背後的分子機制。這些發現對多個研究領域具有重要意義，包括人類腸道微生物組、碳水化合物活性酶、膳食和中藥多糖的開發與應用等。此外，一些中藥多糖（如石斛多糖）的高度特異性利用，也突顯了基於中藥多糖的益生元和藥物在靶向調節人類腸道微生物組方面的潛力。
梁麗嫻、戴磊及周華為該研究的共同通訊作者，澳門科技大學博士生曲澤鵬、中國科學院深圳先進技術研究院合成所助理研究員劉紅賓、廣東藥科大學中藥學院中藥藥理系教師楊繼為共同第一作者。研究獲得了中華人民共和國科學技術部和澳門科學技術發展基金（檔案編號：0063/2022/A2、0018/2024/RIB1和0137/2024/AMJ）資助；以及深圳市微生物藥物智能製造重點實驗室（檔案編號：ZDSYS20210623091810032）和中國國家自然科學基金（檔案編號：32201313）資助。研究同時得到了國家中醫藥管理局2020年青年岐黃學者專案、澳門科學技術發展基金博士後專項資助計劃（檔案編號：0017/2021/APD）、澳門大學（檔案編號：SRG2022-00020-FHS）、中藥質量研究國家重點實驗室（澳門大學）（檔案編號：SKL-QRCM-IRG2023-001和005/2023/SKL）、國家教育部澳門大學精準腫瘤學前沿科學中心的支持。全文可瀏覽：https://www.nature.com/articles/s41467-025-55845-7。
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UM research team discovers key factors in utilisation of medicinal polysaccharides by human gut bacteria
A research team jointly led by Elaine Leung Lai Han, professor in the Faculty of Health Sciences at the University of Macau (UM), Dai Lei, principal investigator at the Shenzhen Institute of Advanced Technology of the Chinese Academy of Sciences, and Zhou Hua, professor at the State Key Laboratory of Traditional Chinese Medicine Syndrome and Guangdong Provincial Hospital of Chinese Medicine, has made significant progress in understanding the molecular mechanism by which human gut Bacteroides and Parabacteroides selectively utilise medicinal polysaccharides. The study has important implications for several research areas, including the human gut microbiome, carbohydrate-active enzymes, and the development and application of dietary and medicinal polysaccharides. The research has been published in the prestigious international journal Nature Communications.
The study is the first to report the selective utilisation of Dendrobium polysaccharides by Bacteroides uniformis, a human gut commensal bacterium. Using an interdisciplinary synthetic biology approach, the researchers discovered a unique polysaccharide utilisation locus in this bacterium. Structural alignment and molecular docking analyses further revealed that the GH26 enzyme, with conserved catalytic sites (E415/E504) and substrate-binding sites, is a key enzyme in Dendrobium polysaccharide metabolism. This research pioneers the discovery of critical factors in the utilisation of medicinal polysaccharides by the human gut microbiota, highlighting the highly specific utilisation of medicinal polysaccharides. It advances our understanding of their potential in vivo applications and mechanisms of action, and underscores the potential for precise targeting of the gut microbiota, opening up new avenues for therapeutic intervention.
Manipulation of the gut microbiome using medicinal polysaccharides has emerged as a promising therapeutic strategy for human disease. Human gut Bacteroides and Parabacteroides are known to be the primary consumers of dietary polysaccharides. Understanding how human gut commensal bacteria utilise medicinal polysaccharides is important for the development of novel polysaccharide-based prebiotics and drugs to improve human health. However, a systematic profiling of gut bacterial utilisation of medicinal polysaccharides and the underlying genetic basis is still lacking.
The research team systematically mapped the utilisation profiles of 20 different medicinal polysaccharides by 28 human gut Bacteroides and Parabacteroides species. They found that different Bacteroides and Parabacteroides species showed distinct utilisation profiles of medicinal polysaccharides. Notably, Dendrobium polysaccharides (DPs, a type of glucomannan) specifically induced the growth of Bacteroides uniformis DA183. Transcriptomics and gene knock-out were performed to reveal the genetic mechanism behind the selective utilisation of DPs. The research team identified the key gene cluster PUL34 and the critical enzyme GH26_BuDA183 involved in DPs utilisation. Sequence alignment revealed that only the genome of B. uniformis DA183 encodes the complete PUL34_BuDA183 gene cluster.
Finally, to characterise the activity and substrate specificity of the GH26 enzyme from B. uniformis, the research team compared the protein structure of B. uniformis GH26 predicted by AlphaFold2 with the crystal structure of B. ovatus GH26. They found that the catalytic sites and substrate-binding sites are conserved between these two GH26 enzymes. This suggests that the GH26 enzyme from B. uniformis has a similar catalytic mechanism to that of B. ovatus. The team then expressed and purified the GH26 enzyme and demonstrated its hydrolytic activity against multiple mannans in vitro. Point mutation experiments showed that mutation of either the glutamate residue E415A or E504A leads to loss of enzyme activity, confirming that both catalytic sites are essential for enzyme function. Molecular docking simulations showed that substrate reactivity depends on the ability of the substrates to interact with the catalytic residues.
In general, the study provides a general framework for profiling the utilisation of plant-derived polysaccharides by human gut bacteria and understanding the underlying molecular mechanisms. These findings have important implications for several research areas, including the human gut microbiome, carbohydrate-active enzymes, and the development and application of dietary and medicinal polysaccharides. In addition, the highly specific utilisation of some medicinal polysaccharides (e.g. Dendrobium polysaccharides) also highlights the potential of glycan-based prebiotics and drugs for targeted modulation of the human gut microbiome.
Prof Leung, Dr Dai, and Prof Zhou are the co-corresponding authors of the study. Qu Zepeng, a PhD student at Macau University of Science and Technology; Liu Hongbin, an assistant researcher at the Shenzhen Institute of Advanced Technology of the Chinese Academy of Sciences; and Yang Ji, a faculty member in the School of Chinese Materia Medica at Guangdong Pharmaceutical University, are the co-first authors. The research was supported by regular grants of the Ministry of Science and Technology of the People’s Republic of China and the Science and Technology Development Fund (FDCT) of Macao (File No: 0063/2022/A2, 0018/2024/RIB1, and 0137/2024/AMJ), the Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines (File No: ZDSYS20210623091810032), the National Natural Science Foundation of China (File no. 32201313), the 2020 Young Qihuang Scholar of the National Administration of Traditional Chinese Medicine and the FDCT Funding Scheme for Postdoctoral Researchers of Higher Education Institutions (File No: 0017/2021/APD), UM (File No: SRG2022-00020-FHS), the State Key Laboratory of Quality Research in Chinese Medicine (UM) (File No: SKL-QRCM-IRG2023-001 and 005/2023/SKL), and the Ministry of Education Frontiers Science Center for Precision Oncology, UM. The full text of the study is available at: https://www.nature.com/articles/s41467-025-55845-7.
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https://www.um.edu.mo/news-and-press-releases/campus-news/detail/60372/