Human intestinal microbiota is important to host health and is associated with various diseases. It is a challenge to identify the functions and metabolic activity of microorganisms at the single‐cell level in gut microbial community. In this study, we applied Raman microspectroscopy and deuterium isotope probing (Raman–DIP) to quantitatively measure the metabolic activities of intestinal bacteria from two individuals and analysed lipids and phenylalanine metabolic pathways of functional microorganisms in situ. After anaerobically incubating the human faeces with heavy water (D₂O), D₂O with specific substrates (glucose, tyrosine, tryptophan and oleic acid) and deuterated glucose, the C–D band in single‐cell Raman spectra appeared in some bacteria in faeces, due to the Raman shift from the C–H band. Such Raman shift was used to indicate the general metabolic activity and the activities in response to the specific substrates. In the two individuals' intestinal microbiota, the structures of the microbial communities were different and the general metabolic activities were 76 ± 1.0% and 30 ± 2.0%. We found that glucose, but not tyrosine, tryptophan and oleic acid, significantly stimulated metabolic activity of the intestinal bacteria. We also demonstrated that the bacteria within microbiota preferably used glucose to synthesize fatty acids in faeces environment, whilst they used glucose to synthesize phenylalanine in laboratory growth environment (e.g. LB medium). Our work provides a useful approach for investigating the metabolic activity in situ and revealing different pathways of human intestinal microbiota at the single‐cell level.

中文翻译：

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拉曼氘同位素探测，以研究人类肠道菌群中单个细菌细胞的代谢活性。

人体肠道菌群对于宿主健康很重要，并且与各种疾病有关。在肠道微生物群落中，在单细胞水平上鉴定微生物的功能和代谢活性是一项挑战。在这项研究中，我们应用拉曼光谱和氘同位素探测（Raman-DIP）定量测量了两个个体的肠道细菌的代谢活性，并就地分析了功能性微生物的脂质和苯丙氨酸代谢途径。将人类粪便与重水（D ₂ O）厌氧孵育后，D ₂O具有特定的底物（葡萄糖，酪氨酸，色氨酸和油酸）和氘代葡萄糖，单细胞拉曼光谱中的C–D谱带出现在粪便中的某些细菌中，这是由于拉曼光谱从C–H谱带移出的缘故。这种拉曼位移用于指示一般的代谢活性和对特定底物的响应活性。在两个人的肠道菌群中，微生物群落的结构不同，总体代谢活性分别为76±1.0％和30±2.0％。我们发现葡萄糖而不是酪氨酸，色氨酸和油酸显着刺激了肠道细菌的代谢活性。我们还证明了微生物群中的细菌最好在粪便环境中使用葡萄糖来合成脂肪酸，他们使用葡萄糖在实验室生长环境（例如LB培养基）中合成苯丙氨酸。我们的工作为研究代谢活动提供了有用的方法原位并在单细胞水平揭示人类肠道菌群的不同途径。