Abstract
SummaryThe 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.
Highlights
The human intestine accommodates a large number of intestinal bacteria (Hao and Lee, 2004) which exert significant physiological functions including assisting host digestion and immunity, synthesis of essential vitamins such as vitamin K and resistance to pathogen invasion (O’Hara and Shanahan, 2006; Blaser, 2011; Iliev et al, 2012; Mills et al, 2013; Hillman et al, 2017; Thursby and Juge, 2017)
Our results demonstrated that there were a large number of MA-antibiotic-resistant bacteria (ARB) in the gut microbiota in two healthy individuals
The phenotypes of the metabolic active ARB (MA-ARB) exhibited distinct metabolic activity when exposing to minimal inhibitory concentration (MIC) and higher concentrations of antibiotics, detected by the C–D band of single-cell Raman spectra (SCRS) by Raman– DIP
Summary
The antibiotic-resistant bacteria (ARB) and antibioticresistant 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. 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. To establish the link between phenotypes and genotypes of the MA-ARB, Ramanactivated cell sorting (RACS) was used to sort MA-ARB from human gut microbiota, and minimetagenomic DNA of the sorted bacteria was amplified, sequenced and analysed. 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
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