Bacterial single-cell transcriptomics: Recent technical advances and future applications in dentistry

Moon, Ji-Hoi; Roh, Dae-Hyun; Kwack, Kyu Hwan; Lee, Jae-Hyung

doi:10.1016/j.jdsr.2023.08.001

Cited by 2 publications

(2 citation statements)

References 55 publications

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“…Single-cell transcriptomics has ushered in formidable methodologies for determining microbial diversity. Pioneering-modified techniques, such as Fluidigm C1, Prokaryotic single-cell RNA sequencing (PETRI-seq), microbial split-pool ligation transcriptomics (microSPLiT), multiple annealing and dC-tailing-based quantitative single-cell RNA-seq (MATQ-seq), and Bacterial droplet-based single-cell RNA-seq (BacDrop), have been developed to effectively circumvent the limitations of 16S rDNA-based microbiota profiling ( 104 ). Techniques such as Smart‐seq, Smart‐seq2, MATQ‐seq (multiple annealing and dC‐tailing‐based quantitative single‐cell RNA‐seq), MARS‐seq (massively parallel single‐cell RNA‐sequencing), and CEL‐seq (Cell Expression by Linear amplification and sequencing) use fluorescence-activated cell sorting (FACS) for single-cell isolation ( 105 – 107 ).…”

Section: Single-cell Transcriptomics: Revolutionizing the Exploration...mentioning

confidence: 99%

Single cell genomics based insights into the impact of cell-type specific microbial internalization on disease severity

Soni,

Pandey

2024

Front. Immunol.

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Host-microbe interactions are complex and ever-changing, especially during infections, which can significantly impact human physiology in both health and disease by influencing metabolic and immune functions. Infections caused by pathogens such as bacteria, viruses, fungi, and parasites are the leading cause of global mortality. Microbes have evolved various immune evasion strategies to survive within their hosts, which presents a multifaceted challenge for detection. Intracellular microbes, in particular, target specific cell types for survival and replication and are influenced by factors such as functional roles, nutrient availability, immune evasion, and replication opportunities. Identifying intracellular microbes can be difficult because of the limitations of traditional culture-based methods. However, advancements in integrated host microbiome single-cell genomics and transcriptomics provide a promising basis for personalized treatment strategies. Understanding host-microbiota interactions at the cellular level may elucidate disease mechanisms and microbial pathogenesis, leading to targeted therapies. This article focuses on how intracellular microbes reside in specific cell types, modulating functions through persistence strategies to evade host immunity and prolong colonization. An improved understanding of the persistent intracellular microbe-induced differential disease outcomes can enhance diagnostics, therapeutics, and preventive measures.

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Section: Single-cell Transcriptomics: Revolutionizing the Exploration...mentioning

confidence: 99%

Single cell genomics based insights into the impact of cell-type specific microbial internalization on disease severity

Soni,

Pandey

2024

Front. Immunol.

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“…Over the years, much effort has been placed into establishing techniques to isolate novel and useful bacteria from the environment (Rodrigues and de Carvalho, 2022). In addition to the conventional Fluorescence In Situ Hybridization (FISH) approach, where specific bacteria can be fluorescently stained, identified, and isolated using flow cytometry or micromanipulation, recent efforts for large-scale screening and high-throughput systems using microfluidics and in combination with single-cell analytical techniques have allowed for a comprehensive understanding of bacterial communities (Moon et al, 2023), construction of near-complete draft genomes of novel and unique bacteria (Kogawa et al, 2018), and elucidation of highly efficient enzymes applicable for downstream processes (Baysoy et al, 2023). However, originally designed for nucleic acid analyses, most of these techniques have incorporated cell fixation or lysis, resulting in many isolated bacteria to be inapplicable for subsequent cultivation.…”

mentioning

confidence: 99%

Approaches for attaining clean bacterial fractions from complex environmental samples

Yu,

Kawahisa,

Kinoshita

et al. 2024

Front. Mar. Sci.

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Marine bacteria have been targeted by industry and pharmaceutics as genetic resources for highly active enzymes or novel lead compounds. Although numerous techniques have been introduced to isolate useful bacteria from the environment, we are still highly dependent on the conventional direct cultivation method to attain pure cultures. However, efficient bacterial isolation is hindered by several factors, including the presence of impurities. In this work, to demonstrate the significance of removing impurities and their impact on bacterial isolation, we employed two approaches: dielectrophoresis (DEP) and fluorescent D-amino acids (FDAA). We successfully attained clean bacterial fractions applicable for downstream processing using these approaches, uniquely designed to identify bacteria based on their characteristics and features. The diversity of bacteria attained by both approaches was investigated using 16S rRNA sequencing and compared to that attained by the standard differential centrifugation method. In addition, the viability of the isolates was also determined via direct cultivation. As a result, the separation of bacteria from impurities allowed for the identification of novel and useful bacteria unique to each approach. Successful cultivation also suggested that both approaches were applicable for attaining viable bacteria. In conclusion, removing impurities to attain clean bacterial fractions promotes the isolation of novel bacteria and thus could aid in the successful isolation of useful bacteria within complex environmental samples.

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Bacterial single-cell transcriptomics: Recent technical advances and future applications in dentistry

Cited by 2 publications

References 55 publications

Single cell genomics based insights into the impact of cell-type specific microbial internalization on disease severity

Single cell genomics based insights into the impact of cell-type specific microbial internalization on disease severity

Approaches for attaining clean bacterial fractions from complex environmental samples

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