Microchip-Based Terminal Restriction Fragment Length Polymorphism for On-Site Analysis of Bacterial Communities in Freshwater

Yamaguchi, Naohito; Matsukawa, Syuhei; Shintome, Yoko; Ichijo, Tomoaki; Nasu, Masao

doi:10.1248/bpb.b13-00118

Cited by 5 publications

(3 citation statements)

References 17 publications

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“…29) PCR for T-RFLP analysis was performed according to the procedure reported by Yamaguchi et al 30) PCR products were purified and concentrated using MiniElute PCR purification Kit (QIAGEN, Hilden, Germany). The purified PCR products were then digested with MspI (TaKaRa Bio, Shiga, Japan) for 3 h at 37°C.…”

Section: )mentioning

confidence: 99%

Abundance and Community Structure of Bacteria on Asian Dust Particles Collected in Beijing, China, during the Asian Dust Season

Yamaguchi

Baba

Ichijo

et al. 2016

Biological & Pharmaceutical Bulletin

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Approximately 180 t/km2 of Asian dust particles are estimated to fall annually on Beijing, China, and there is significant concern about the influence of microbes transported by Asian dust events on human health and downwind ecosystems. In this study, we collected Asian dust particles in Beijing, and analyzed the bacterial communities on these particles by culture-independent methods. Bacterial cells on Asian dust particles were visualized first by laser scanning microscopy, which demonstrated that Asian dust particles carry bacterial cells to Beijing. Bacterial abundance, as determined by quantitative polymerase chain reaction (PCR), was 10 8 to 10 9 cells/g, a value about 10 times higher than that in Asian dust source soils. Interseasonal variability of bacterial community structures among Asian dust samples, as compared by terminal restriction fragment length polymorphism (T-RFLP), was low during the Asian dust season. Several viable bacteria, including intestinal bacteria, were found in Asian dust samples by denaturing gradient gel electrophoresis (DGGE). Clone library analysis targeting 16S ribosomal RNA (rRNA) gene sequences demonstrated that bacterial phylogenetic diversity was high in the dust samples, and most of these were environmental bacteria distributed in soil and air. The dominant species in the clone library was Segetibacter aerophilus (Bacteroidetes), which was first isolated from an Asian dust sample collected in Korea. Our results also indicate the possibility of a change in the bacterial community structure during transportation and increases in desiccation-tolerant bacteria such as Firmicutes.

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Section: )mentioning

confidence: 99%

Abundance and Community Structure of Bacteria on Asian Dust Particles Collected in Beijing, China, during the Asian Dust Season

Yamaguchi

Baba

Ichijo

et al. 2016

Biological & Pharmaceutical Bulletin

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“…The detection limit for targeted bacteria reached 10 3 cells/mL, and the analysis was completed within 15 min. These findings indicate that T‐RFLP‐MCE is a sensitive, rapid, and effective tool for analyzing the bacterial community in fresh water (Yamaguchi and others ).…”

Section: Procedures For Food Analysis Based On Ce‐based Nucleic Acid Dmentioning

confidence: 75%

Capillary Electrophoresis Based on Nucleic Acid Detection as Used in Food Analysis

Lian

Zeng

2017

Comp Rev Food Sci Food Safe

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Food safety and food production are closely related to the health of consumers. Food-related accidents often cause tremendous losses of personnel and property. Thus, rapid detection and analysis of ingredients in food, tracing food sources, studying the optimal conditions for food production, and more are vital for preventing incidents related to safety. Conventional analysis based on proteomics, microbial cultures, and morphology, as well as biochemical tests based on metabonomics, are considered gold standards and used frequently, but they are labor-intensive, time-consuming, tedious, error-prone, and incapable of meeting the demand for rapid and precise detection at a large scale. Alternative detection methods that utilize capillary electrophoresis have the advantages of high efficiency, high throughput, high speed, and automation; these methods are coupled with various nucleic acid detection strategies to overcome the drawbacks of traditional identification methods, and to prevent false results. Therefore, this review focuses on the application of capillary electrophoresis based on nucleic acid detection in food analysis and provides an introduction to the limitations, advantages, and future developments of this approach.

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“…Thus, the development of the analytical techniques for this purpose is critical. Yamaguchi et al [37] used MCE for rapid microbial community analysis and developed a microchip-based terminal restriction fragment length polymorphism (T-RFLP) to analyze bacterial communities in freshwater within 15 min, by which time the limit of detection (LOD) of the targeted bacteria was reduced to 1% (10 3 cells/mL). Their results indicate that T-RFLP-MCE analysis is a sensitive tool for rapidly analyzing bacterial number and community stucture in freshwater sources used for human activities.…”

Section: Detecting and Diagnosing Bacteriamentioning

confidence: 99%

Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease

Lian

Zhao

2016

Clinical Chemistry and Laboratory Medicine (CCLM)

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Rapid transmission, high morbidity, and mortality are the features of human infectious diseases caused by microorganisms, such as bacteria, fungi, and viruses. These diseases may lead within a short period of time to great personal and property losses, especially in regions where sanitation is poor. Thus, rapid diagnoses are vital for the prevention and therapeutic intervention of human infectious diseases. Several conventional methods are often used to diagnose infectious diseases, e.g. methods based on cultures or morphology, or biochemical tests based on metabonomics. Although traditional methods are considered gold standards and are used most frequently, they are laborious, time consuming, and tedious and cannot meet the demand for rapid diagnoses. Disease diagnosis using capillary electrophoresis methods has the advantages of high efficiency, high throughput, and high speed, and coupled with the different nucleic acid detection strategies overcomes the drawbacks of traditional identification methods, precluding many types of false positive and negative results. Therefore, this review focuses on the application of capillary electrophoresis based on nucleic detection to the diagnosis of human infectious diseases, and offers an introduction to the limitations, advantages, and future developments of this approach.

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Microchip-Based Terminal Restriction Fragment Length Polymorphism for On-Site Analysis of Bacterial Communities in Freshwater

Cited by 5 publications

References 17 publications

Abundance and Community Structure of Bacteria on Asian Dust Particles Collected in Beijing, China, during the Asian Dust Season

Abundance and Community Structure of Bacteria on Asian Dust Particles Collected in Beijing, China, during the Asian Dust Season

Capillary Electrophoresis Based on Nucleic Acid Detection as Used in Food Analysis

Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease

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