The small size and low DNA amount of bacterial cells have hindered establishing phenome–genome links in a precisely indexed, one‐cell‐per‐reaction manner. Here, Raman‐Activated Gravity‐driven single‐cell Encapsulation and Sequencing (RAGE‐Seq) is presented, where individual cells are phenotypically screened via single‐cell Raman spectra (SCRS) in an aquatic, vitality‐preserving environment, then the cell with targeted SCRS is precisely packaged in a picoliter microdroplet and readily exported in a precisely indexed, “one‐cell‐one‐tube” manner. Such integration of microdroplet encapsulation to Raman‐activated sorting ensures high‐coverage one‐cell genome sequencing or cultivation that is directly linked to metabolic phenotype. For clinical Escherichia coli isolates, genome assemblies derived from precisely one cell via RAGE‐Seq consistently reach >95% coverage. Moreover, directly from a urine sample of urogenital tract infection, metabolic‐activity‐based antimicrobial susceptibility phenotypes and genome sequence of 99.5% coverage are obtained simultaneously from precisely one cell. This single‐cell global mutation map corroborates resistance phenotype and genotype, and unveils epidemiological features with high specificity and sensitivity. The ability to profile and correlate bacterial metabolic phenome and high‐quality genome sequences at one‐cell resolution suggests broad application of RAGE‐Seq.
Soil is home to an enormous and complex microbiome that features arguably the highest genomic diversity and metabolic heterogeneity of cells on Earth. Their
in situ
metabolic activities drive many natural processes of pivotal ecological significance or underlie industrial production of numerous valuable bioactivities.
Detecting matter at a single-molecule level is the ultimate target in many branches of study. Nanosensors based on plasmonics have garnered significant interest owing to their ultrahigh sensitivity even at single-molecule level. However, currently, plasmonic-enhanced nanosensors have not achieved excellent performances in practical applications and their detection at femtomolar or attomolar concentrations remains highly challenging. Here we show a plasmonic sensing strategy, called buoyant plasmonic-particulate-based few-to-single particle-nanosensors. Large-sized floating particles combined with a slippery surface may prevent the coffee-ring effect and enhance the spatial enrichment capability of the analyte in plasmonic sensitive sites via the aggregation and lifting effect. Dimer and single particle-nanosensors demonstrate an enhanced surface-enhanced Raman spectroscopy (SERS) and a high fluorescence sensitivity with an enrichment factor up to an order of ∼104 and the limit of detection of CV molecules down to femto- or attomolar levels. The current buoyant particulate strategy can be exploited in a wide range of plasmonic enhanced sensing applications for a cost-effective, simple, fast, flexible, and portable detection.
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