The very first observations of microorganisms by Antonie Van Leeuwenhoek and Louis Joblot in the 17th century paved the way to what we now know as modern microbiology. It has been estimated that 50% of the earth’s biomass is microbial (parasites, diatoms, microalgae, fungi, bacteria, and viruses) and of these, viruses (living parasitic organisms that thrive off the cells they infect) have reached an astronomical number (10). Humankind and animals are equally dependent on the activity of microorganisms within their environments, because microorganisms are fundamental to all geochemical cycles. Different observers have perceived microorganisms in different ways. Medical doctors have invariably seen microorganisms as harmful, which is logical when we take into account the history of medicine, whereas biotechnologists have tried to understand and use them in a range of traditional procedures such as bread making and in promising new techniques such as molecule biosynthesis for therapeutic purposes. It is the latter context, i.e. emphasis on the positive side of microorganisms and their function when it comes to analysis (in its broadest sense) within the health sector, the food industry, and the environment sector, that has inspired this special issue. Microorganisms (mainly bacteria) have been used unequivocally in the field of health in order to assess the impact of chemotherapeutic agents, as initially discovered by Paul Ehrlich from 1904 onwards. Antibiograms were the first bioassays developed between 1940 and 1945 to determine the activity of newly discovered antibiotics in relation to bacteria test samples which would now be referred to as “sensitive bioelements”. After having achieved incredible scientific and medical advances, researchers during the 1960s became concerned about the effects of chemical substances on the environment and how they could alter key geochemical cycles. The field of ecotoxicology brought about the introduction of a significant number of tests using various typical microbial bioelements to assess the impact of chemical pollutants on their surroundings and their potential impact on microbial ecosystems. We have to acknowledge the work, begun in 1968 by Kempner and Hanson, then continued by Bulich, Isenberg, and Ulitzur in the 1980s, which established the status of a simple bioassay based on the reduced bioluminescence of Vibrio fischeri (now Aliivibrio fischeri), a marine bacterium, when placed in contact with a toxic substance. This test, sold under the name Microtox, is internationally renowned and has without doubt contributed to progress in modern day microbial bioassays. Besides the effect of toxic substances on the environment, studies published in the 1960s demonstrated the ability of microorganisms to biodegrade organic matter; this led to the publication of articles after 1963 on examination of the measurement of biodegradation. The objective was to assess the biodegradation of chemical substances under the action of microorganisms in a closed reactor (before these substances became available commercially) and to estimate their environmental persistence. This issue continues to be of utmost importance, certainly since the implementation of the European Chemicals Regulation, REACH 1907/2006 (Registration, Evaluation and Authorisation of Chemicals). Published in the special issue Microorganisms for Analysis with Guest Editor Gerald Thouand.