One-Cell Metabolic Phenotyping and Sequencing of Soil Microbiome by Raman-Activated Gravity-Driven Encapsulation (RAGE)

Jing, Xiaoyan; Gong, Yanhai; Xu, Teng; Meng, Yu; Han, Xiao; Su, Xiaolu; Wang, Jianmei; Ji, Yicai; Li, Yuandong; Jia, Zhilong; Ma, Bo; Xu, Jian

doi:10.1128/msystems.00181-21

Cited by 31 publications

(53 citation statements)

References 81 publications

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“…Likewise, 2bRAD-M does not provide information about the presence of antimicrobial resistance genes, thus the detection of potentially antibiotic-resistant pathogens only provides an indication of exposure risk. Future studies based on microbial single-cell technologies instead, such as ramanome and Raman-activated Cell Sorting and Sequencing (RACS-Seq), can potentially assess the risks regarding strain type, viability, vitality, and antibiotic resistance (both phenotype and the underlying genotype; Xu et al, 2020 ; Jing et al, 2021 ) at the level of individual bacterial cells. Moreover, it should be noted that many of the detected taxa with potential implications for human health were also opportunistic pathogens such as Actinomyces naeslundii and Streptococcus mitis , which can lead to infections in oral lesions and immune-compromised patients, respectively, but also asymptomatically colonize the human body ( Mitchell, 2011 ; Könönen and Wade, 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Species-Resolved Metagenomics of Kindergarten Microbiomes Reveal Microbial Admixture Within Sites and Potential Microbial Hazards

Tzehau¹,

Chew²,

Zhao³

et al. 2022

Front. Microbiol.

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Microbiomes on surfaces in kindergartens, the intermediate transfer medium for microbial exchange, can exert significant impact on the hygiene and wellbeing of young children, both individually and as a community. Here employing 2bRAD-M, a novel species-resolved metagenomics approach for low-biomass microbiomes, we surveyed over 100 samples from seven frequently contacted surfaces by children, plus individual children’s palms, in two kindergartens. Microbiome compositions, although kindergarten-specific, were grouped closely based on the type of surface within each kindergarten. Extensive microbial admixture were found among the various sampled sites, likely facilitated by contact with children’s hands. Notably, bacterial species with potential human health concerns and potentially antibiotic-resistant, although found across all sampled locations, were predominantly enriched on children’s hands instead of on the environmental sites. This first species-resolved kindergarten microbiome survey underscores the importance of good hand hygiene practices in kindergartens and provides insights into better managing hygiene levels and minimizing spread of harmful microbes in susceptible indoor environments.

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Section: Discussionmentioning

confidence: 99%

Species-Resolved Metagenomics of Kindergarten Microbiomes Reveal Microbial Admixture Within Sites and Potential Microbial Hazards

Tzehau¹,

Chew²,

Zhao³

et al. 2022

Front. Microbiol.

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“…However, the detection of metabolites and proteins using flow cytometry usually relies on specific stains or antibodies, and may influence the viability of target cells for further axenic culture. To overcome this limitation, several techniques based on Raman spectra have been developed and successfully adapted to microbial single-cell metabolic profiling and phenotypic screening ( He et al, 2019 ; Su et al, 2020 ; Wang et al, 2020 ; Xu et al, 2020 ; Heidari Baladehi et al, 2021 ; Jing et al, 2021 ). The profiling of metabolites based on Raman spectrum dispenses with cell fixing or staining, and provides better experimental flexibility and higher cell viability for downstream analysis.…”

Section: Phenotypic Analysis: Non-invasive Detecting With Spectrummentioning

confidence: 99%

“…The profiling of metabolites based on Raman spectrum dispenses with cell fixing or staining, and provides better experimental flexibility and higher cell viability for downstream analysis. In addition, the phenotypic analysis step of both flow cytometry and Raman spectra techniques are high-throughput and can combined with cell sorting system or microfluidics, making it easier for further axenic culture or genotypic analysis ( He et al, 2019 ; Xu et al, 2020 ; Jing et al, 2021 ).…”

Section: Phenotypic Analysis: Non-invasive Detecting With Spectrummentioning

confidence: 99%

“…With these sorting methods, scientists can either select microbes with specific phenotype or randomly choose an ideal number of cells, then eject them to agar plates, microplates, or even small oil-water particles for either axenic culture or genotypic analysis. More importantly, if the sorting is phenotype-based, it is possible to unify the phenotype and genotype (genome or transcriptome) in every cell ( Xu et al, 2020 ; Jing et al, 2021 ). Simultaneously profile phenotype (like metabolites with Ramanome) and genotype (genome or transcriptome) from the same cell could be very helpful in some specific fields, such as finding the related gene clusters for producing specific natural products ( Xu et al, 2020 ; Jing et al, 2021 ).…”

Section: Future Perspectivesmentioning

confidence: 99%

“…More importantly, if the sorting is phenotype-based, it is possible to unify the phenotype and genotype (genome or transcriptome) in every cell ( Xu et al, 2020 ; Jing et al, 2021 ). Simultaneously profile phenotype (like metabolites with Ramanome) and genotype (genome or transcriptome) from the same cell could be very helpful in some specific fields, such as finding the related gene clusters for producing specific natural products ( Xu et al, 2020 ; Jing et al, 2021 ). In addition, the state-of-the-art techniques for single-cell analysis prefer to use microfluidics as the bridge between phenotypic sorting and genotypic analysis ( Liu et al, 2021 ).…”

Section: Future Perspectivesmentioning

confidence: 99%

See 2 more Smart Citations

Microbial Single-Cell Analysis: What Can We Learn From Mammalian?

Chen

Lei

et al. 2022

Front. Cell Dev. Biol.

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High‐Throughput Raman‐Activated Cell Sorting in the Fingerprint Region

Lindley

Pablo

Peterson

et al. 2022

Adv Materials Technologies

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Cell sorting is the workhorse of biological research and medicine. [1] Cell sorters are commonly used to sort heterogeneous populations of cells based on their intrinsic features and have numerous applications in microbiology, immunology, virology, stem cell biology, and metabolic engineering. [2][3][4][5][6] While several schemes have been developed for sorting cells based on features such as size, [7] morphology, [8][9][10] viability, [11,12] and surface antigens, [13] those able to sort at high throughput for intracellular chemical content are limited to fluorescence-activated and Raman-activated cell sorting (FACS and RACS, respectively). [1,14] In both methods, sorting is accomplished by a stepwise automatic process: 1) measurement of chemical content with single-cell resolution, 2) analysis of the measurement data to identify cells of interest, and 3) mechanical separation of target cells from the original sample. [1] FACS machines commonly identify molecular targets by signals from attached exogenous fluorophores or coexpressed transgenic fluorescent proteins. This indirect detection scheme is often referred to as labeled detection. [1] Although fluorescent labeling is essential for microbiological research, the use of labels has inherrent drawbacks. These include reduced cellular vitality due to the cytotoxicity of labels themselves, nonspecific binding of labels, a lack of labels or transfection methods for many molecular targets and species, incompatibility with human-targeted cell therapies, and increased experimental complexity imposed by labeling protocols. [14] On the other hand, RACS machines directly identify target molecules in a label-free manner via Raman spectroscopy, which measures the inelastic scattering of incident photons by characteristic molecular vibrations. [14] The chemical specificity of this optical measurement contrasts with non-chemically-specific label-free methods such as impedance-based sorting for cell viability and image-based sorting for morphology or deformability. [10][11][12] To date, FACS technology is well developed, commercialized, and broadly adopted, while RACS is nascent and comprised of a small number of lab-based demonstrations. [14][15][16][17][18][19][20][21][22][23][24][25][26] A major hurdle in the broad deployment of RACS for biomedical applications is the weak signal produced by the Raman scattering process. This necessitates comparatively Cell sorting is the workhorse of biological research and medicine. Cell sorters are commonly used to sort heterogeneous cell populations based on their intrinsic features. Raman-activated cell sorting (RACS) has recently received considerable interest by virtue of its ability to discriminate cells by their intracellular chemical content, in a label-free manner. However, the broad deployment of RACS beyond lab-based demonstrations is hindered by a fundamental trade-off between throughput and measurement bandwidth (i.e., cellular information content). Here this trade-off is overcome and broadband RACS in the fingerprint reg...

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One-Cell Metabolic Phenotyping and Sequencing of Soil Microbiome by Raman-Activated Gravity-Driven Encapsulation (RAGE)

Cited by 31 publications

References 81 publications

Species-Resolved Metagenomics of Kindergarten Microbiomes Reveal Microbial Admixture Within Sites and Potential Microbial Hazards

Species-Resolved Metagenomics of Kindergarten Microbiomes Reveal Microbial Admixture Within Sites and Potential Microbial Hazards

Microbial Single-Cell Analysis: What Can We Learn From Mammalian?

High‐Throughput Raman‐Activated Cell Sorting in the Fingerprint Region

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