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Advances in Chemical and Biological Methods to Identify Microorganisms—From Past to Present

CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, 4710-057 Braga, Portugal
Institute of Science and Innovation for Bio-Sustainability (IB-S), University of Minho, 4710-057 Braga, Portugal
Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
Ramalingaswami Re-entry Fellowship, Department of Biotechnology, Government of India, Pune 411045, India
Student Research Committee, School of Medicine, Bam University of Medical Sciences, Bam 14665-354, Iran
Department of the Science of Agriculture, Food and Environment, University of Foggia, 71121 Foggia, Italy
Institute of Fermentation Technology and Microbiology, Department of Biotechnology and Food Science, Lodz University of Technology, Wolczanska 171/173, 90-924 Lodz, Poland
Laboratory of Industrial Biotechnology, Bionanopark Ltd., Dubois 114/116, 93-465 Lodz, Poland
Laboratory of Microbiology and Molecular Biology (LMBM), Department of Biological Chemistry/CCBS/URCA, Crato 63105-000, Brazil
Departamento of Microbiology, Instituto Aggeu Magalhães/Fiocruz, Recife 50670-420, Brazil
Zabol Medicinal Plants Research Center, Zabol University of Medical Sciences, Zabol 61615-585, Iran
Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135 Porto, Portugal
LEPABE–Dep. of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal
Authors to whom correspondence should be addressed.
These authors have contributed equally to this work.
Microorganisms 2019, 7(5), 130;
Received: 12 April 2019 / Revised: 30 April 2019 / Accepted: 8 May 2019 / Published: 13 May 2019
(This article belongs to the Special Issue Identification of Microorganisms: Old, New and Future Methods)
PDF [659 KB, uploaded 28 May 2019]


Fast detection and identification of microorganisms is a challenging and significant feature from industry to medicine. Standard approaches are known to be very time-consuming and labor-intensive (e.g., culture media and biochemical tests). Conversely, screening techniques demand a quick and low-cost grouping of bacterial/fungal isolates and current analysis call for broad reports of microorganisms, involving the application of molecular techniques (e.g., 16S ribosomal RNA gene sequencing based on polymerase chain reaction). The goal of this review is to present the past and the present methods of detection and identification of microorganisms, and to discuss their advantages and their limitations. View Full-Text
Keywords: identification methods; PCR; real-time PCR; RAPD PCR; MALDI-TOF; microscopy techniques; chromogenic media; DNA fingerprinting; WGS identification methods; PCR; real-time PCR; RAPD PCR; MALDI-TOF; microscopy techniques; chromogenic media; DNA fingerprinting; WGS

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Franco-Duarte, R.; Černáková, L.; Kadam, S.; S. Kaushik, K.; Salehi, B.; Bevilacqua, A.; Corbo, M.R.; Antolak, H.; Dybka-Stępień, K.; Leszczewicz, M.; Relison Tintino, S.; Alexandrino de Souza, V.C.; Sharifi-Rad, J.; Melo Coutinho, H.D.; Martins, N.; Rodrigues, C.F. Advances in Chemical and Biological Methods to Identify Microorganisms—From Past to Present. Microorganisms 2019, 7, 130.

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