Applications of Optical DNA Mapping in Microbiology

Abstract

Optical mapping (OM) has been used in microbiology for the past 20 years, initially as a technique to facilitate DNA sequence-based studies; however, with decreases in DNA sequencing costs and increases in sequence output from automated sequencing platforms, OM has grown into an important auxiliary tool for genome assembly and comparison. Currently, there are a number of new and exciting applications for OM in the field of microbiology, including investigation of disease outbreaks, identification of specific genes of clinical and/or epidemiological relevance, and the possibility of single-cell analysis when combined with cell-sorting approaches. In addition, designing lab-on-a-chip systems based on OM is now feasible and will allow the integrated and automated microbiological analysis of biological fluids. Here, we review the basic technology of OM, detail the current state of the art of the field, and look ahead to possible future developments in OM technology for microbiological applications.

Advances in optical mapping for genomic research

“…1 ). Initially, optical mapping was used to assist genome assembly of microorganisms , such as yeast and bacteria [29] . However, due to its low throughput, high error rate, and imprecise DNA-length measurement, optical mapping has not been widely adopted for genomic studies in higher species [14] .…”

“…To solve this problem, in 1995 Cai et al [30] and Meng et al [31] fixed DNA molecules on glass surfaces that had been treated with specific chemicals. Consequently, the DNA stretch rate was improved to 60% of its contour length, compared with 30% on agarose [29] . The number of cut sites was also increased.…”

Microbiological Sensing Technologies: A Review

“…The development of different high affinity molecules, such as antibodies, phage, and other natural/synthetic factors for the detection of specific moieties, such as antigenic epitopes, receptors and specific hydrocarbon, respectively, on the surface of bacteria have been improving optical based devices for the detection of microorganisms [ 66 ]. Furthermore, scientists have been focusing on a way to resolve the limitation of the sample preparation step using the application of so-called label free optical methods, such as Surface Plasmon Resonance (SPR) ( Figure 5 ) [ 67 ].…”

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“…Antonio Bennasar, Rafael Bosch, Sara Díaz, Francisca Font, Joan Francisco Gago, Elena García-Valdés, Margarita Gomila, Jorge Lalucat, Ana Menéndez, María Montaner, Magdalena Mulet, Raúl Muñoz, Balbina Nogales, Cristina Ramón, Ramon Rosselló-Móra, Guillermo Seguí, Mercedes Urdiain y Tomeu Viver grupos nacionales e internacionales para mantener el nivel de competitividad exigido en la investigación. En estos momentos, se colabora con grupos de investigación en Suecia y Portugal para utilizar la técnica de "optical mapping" (mapeo óptico) para facilitar el ensamblaje de lecturas largas de DNA o en la secuenciación de plásmidos (Bogas et al, 2017). También se colabora con USA y Alemania para conseguir que la diversidad microbiana no cultivable disponga de un reconocimiento en la taxonomía de procariotas mediante la clasifi cación de especies por metagenómica ( 2017).…”