Advances in chemical and biological methods to identify microorganisms—from past to present

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.C.F.R. would like to thank the Portuguese Foundation for Science and Technology (FCT–Portugal) for the C.F.R. for the project UID/EQU/00511/2019—Laboratory for Process Engineering, Environment, Biotechnology, and Energy—LEPABE funded by national funds through FCT/MCTES (PIDDAC) and N.M. for the Strategic project ref. UID/BIM/04293/2013 and “NORTE2020 - Programa Operacional Regional do Norte” (NORTE-01-0145-FEDER-000012)