Raman microspectroscopy for microbiology

Lee, Kang Soo; Landry, Zachary C.; Pereira, Fátima C.; Wagner, Michael; Berry, David; Huang, Wei E.; Taylor, Gordon T.; Kneipp, Janina; Popp, Juergen; Zhang, Meng; Cheng, Ji‐Xin; Stocker, Roman

doi:10.1038/s43586-021-00075-6

Cited by 86 publications

(69 citation statements)

References 249 publications

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“…2b, Table S1). Prior to acquisition of Raman spectra, cells were photobleached for 1-2 minutes to remove background from the FISH dyes (49). Alternatively, dyes such as FAM/FITC or Cy5, that are not excited by the 532 nm Raman laser, could be used (20).…”

Section: Resultsmentioning

confidence: 99%

“…While Raman can provide information on cellular isotope uptake, its sensitivity is 30-100x lower than NanoSIMS, depending on the isotope (1, 50). In contrast, NanoSIMS (a destructive technique) does not provide reliable information about the molecular composition of a sample, which is, however, achieved by Raman (1, 49). Depending on the exact research question, extent of metabolic activity, and available instruments, researchers need to decide whether the use of NanoSIMS and/or Raman is warranted (51).…”

Section: Resultsmentioning

confidence: 99%

“…In contrast, NanoSIMS is a destructive but fully quantitative technique capable of measuring the elemental and isotopic composition of a cell at atomic resolution. However, NanoSIMS does not provide reliable information about the molecular composition of a sample, which is, in turn, achieved by Raman (1, 52). These fundamentally different working mechanisms are a major reason for the discrepancy between the H/D ratios determined via Raman (11 %C-D for E. coli ) vs. NanoSIMS (5.2 atom % D).…”

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes

Schaible

Kohtz

Cliff

et al. 2022

Preprint

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Microscopic and spectroscopic techniques are commonly applied to study microbial cells but are typically used on separate samples, resulting in population-level datasets that are integrated across different cells with little spatial resolution. To address this shortcoming, we developed a workflow that correlates several microscopic and spectroscopic techniques to generate an in-depth analysis of individual cells. By combining stable isotope probing (SIP), fluorescence in situ hybridization (FISH), scanning electron microscopy (SEM), confocal Raman microspectroscopy (Raman), and nano-scale secondary ion mass spectrometry (NanoSIMS), we illustrate how individual cells can be thoroughly interrogated to obtain information about their taxonomic identity, structure, physiology, and metabolic activity. Analysis of an artificial microbial community demonstrated that our correlative approach was able to resolve the activity of single cells using heavy water SIP in conjunction with Raman and/or NanoSIMS and establish their taxonomy and morphology using FISH and SEM. This workflow was then applied to a sample of yet uncultured multicellular magnetotactic bacteria (MMB). In addition to establishing their identity and activity, backscatter electron microscopy (BSE), NanoSIMS, and energy-dispersive X-ray spectroscopy (EDS) were employed to characterize the magnetosomes within the cells. By integrating these techniques, we demonstrate a cohesive approach to thoroughly study environmental microbes on a single cell level.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes

Schaible

Kohtz

Cliff

et al. 2022

Preprint

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“…Rapid detection and identification of chemical substances are of utmost importance in many fields, such as food safety, drug monitoring, industrial wastewater discharging, etc. [1,2]. There are many detection methods which can achieve very accurate qualitative and quantitative detection for their respective application scenarios [3,4].…”

Section: Introductionmentioning

confidence: 99%

Review on All-Fiber Online Raman Sensor with Hollow Core Microstructured Optical Fiber

Ding

et al. 2022

Photonics

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Raman spectroscopy is widely used for qualitative and quantitative analysis of trace components in scientific fields such as food safety monitoring, drug testing, environmental monitoring, etc. In addition to its demonstrated advantages of fast response, non-destructive, and non-polluting characteristics, fast online Raman detection is drawing growing attention for development. To achieve this desirable capability, hollow core optical fibers are employed as a common transmission channel for light and fluid in the Raman sensor. By enhancing the interaction process between light and matter, the detection sensitivity is improved. At the same time, the Raman spectroscopy signal light collection efficiency is significantly improved. This article summarizes enhancement techniques reported for Raman sensors, followed by a detailed review on fiber-based Raman sensor techniques including theoretical analyses, fabrication, and application based on hollow core photonic crystal fibers and capillary-based hollow core fibers. The prospects of using these fibers for Raman spectroscopy are discussed.

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“…To realize chemical-specific label-free microscopy, vibrational spectroscopic imaging techniques have been developed to chemically image cellular morphology based on signals from intrinsic chemical bond vibrations 18,19 . Among numerous technical realizations, coherent Raman scattering microscopy has been developed for high-speed vibrational imaging and applied to address various biomedical problems [20][21][22] . Despite its success, Raman scattering is a weak scattering process with an extremely small absorption cross-section (~10 -30 -10 -28 cm 2 ).…”

Section: Introductionmentioning

confidence: 99%

Bond-selective intensity diffraction tomography

Zhao¹,

Matlock

Song

et al. 2022

Advanced Chemical Microscopy for Life Science and Translational Medicine 2022

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Recovering molecular information remains a grand challenge in the widely used holographic and computational imaging technologies. To address this challenge, we developed a computational mid-infrared photothermal microscope, termed Bond-selective Intensity Diffraction Tomography (BS-IDT). Based on a low-cost brightfield microscope with an add-on pulsed light source, BS-IDT recovers both infrared spectra and bond-selective 3D refractive index maps from intensity-only measurements. High-fidelity infrared fingerprint spectra extraction is validated. Volumetric chemical imaging of biological cells is demonstrated at a speed of ~20 seconds per volume, with a lateral and axial resolution of ~350 nm and ~1.1 µm, respectively. BS-IDT's application potential is investigated by chemically quantifying lipids stored in cancer cells and volumetric chemical imaging on Caenorhabditis elegans with a large field of view (~100 µm x 100 µm).

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Raman microspectroscopy for microbiology

Cited by 86 publications

References 249 publications

Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes

Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes

Review on All-Fiber Online Raman Sensor with Hollow Core Microstructured Optical Fiber

Bond-selective intensity diffraction tomography

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