摘要

人体肠道菌群中的抗药性细菌（ARB）和抗药性基因（ARGs）对人体健康具有重要影响。虽然高通量的宏基因组测序揭示了微生物群落的基因型，但人类肠道微生物群落的功能、表型和异质性仍然很难以捉摸。在本研究中，我们应用拉曼显微镜和氘同位素探针（Raman-DIP）在两个健康成人的肠道微生物群中的单细胞水平上原位检测具有代谢活性ARB（MA-ARB）。我们分析了不同浓度的阿莫西林、头孢氨苄、四环素、氟苯尼考和万古霉素对MA-ARB的相对丰度的影响。为了建立MA-ARB的表型和基因型之间的联系，使用拉曼激活细胞分选（RACS）从人类肠道微生物群中筛选MA-ARB，并对筛选出的细菌的微宏基因组DNA进行扩增、测序和分析。对分选的MA-ARB及其相关的ARGs进行了鉴定。我们的研究结果表明，人体肠道菌群中的ARB与个人病史有很强的关系。这项研究表明，Raman-DIP、RACS和DNA测序工具包可用于在单细胞水平上揭示人类肠道微生物群中ARB的表型和基因型。

The antibiotic‐resistant bacteria (ARB) and antibiotic‐resistant genes (ARGs) in human gut microbiota have significant impact on human health. While high throughput metagenomic sequencing reveals genotypes of microbial communities, the functionality, phenotype and heterogeneity of human gut microbiota are still elusive. In this study, we applied Raman microscopy and deuterium isotope probing (Raman–DIP) to detect metabolic active ARB (MA‐ARB) in situ at the single‐cell level in human gut microbiota from two healthy adults. We analysed the relative abundances of MA‐ARB under different concentrations of amoxicillin, cephalexin, tetracycline, florfenicol and vancomycin. To establish the link between phenotypes and genotypes of the MA‐ARB, Raman‐activated cell sorting (RACS) was used to sort MA‐ARB from human gut microbiota, and mini‐metagenomic DNA of the sorted bacteria was amplified, sequenced and analysed. The sorted MA‐ARB and their associated ARGs were identified. Our results suggest a strong relation between ARB in human gut microbiota and personal medical history. This study demonstrates that the toolkit of Raman–DIP, RACS and DNA sequencing can be useful to unravel both phenotypes and genotypes of ARB in human gut microbiota at the single‐cell level.