Microorganisms

Carl A Batt, Cornell University, Ithaca, NY, USA

Ó 2016 Elsevier Inc. All rights reserved.

While we humans might consider ourselves to be at the top of the pyramid of living organisms on Earth, we are vastly outnum-
bered by the microorganisms that we share the planet, if not the universe with. Even within our own bodies, microorganisms
outnumber our own cells by several orders of magnitude. They are not just passengers hopping a ride as we go to work or sit
down to eat a meal. Microorganisms are intimately involved in all aspects from digestion to the feeling we get when we have
eaten something delicious (or bad) to the odor we produce. The discovery of microorganisms was a bifurcated event, with early
observations that there were unseen agents that impacted food and our health. These early observations would then be followed
by the work of Antonie van Leeuwenhoek whose handmade lenses would reveal the microorganisms found in common environ-
ments (van Leeuwenhoek, 1800).
Microorganisms is a broad term used to encompass bacteria, yeast, fungi, and in some definition viruses. The classification is
broad and includes both microorganisms that are capable of replication outside of any host and those that require a host to survive.
They range in size from less than 100 nm to almost a millimeter, the latter exemplified by Thiomargarita namibiensis which is approx-
imately 750 mm in length (Schulz and Jørgensen, 2001). The further classification of microorganisms can be rooted in a number of
different frameworks but with the advent of DNA sequencing, a common framework has evolved to allow for relationships to be
built across all of these different microorganisms. That framework based upon rRNA has given rise to the ‘tree of life’ a popular
representation of all living organisms (except for viruses) (Figure 1). Within this framework, the relationship between man and
the microorganisms that inhabit the Earth and our bodies can be examined (http://tolweb.org).
Microorganisms involved in the production, safety, and other aspects of foods are predominately located among the ‘bacteria’
and also the ‘eukarya.’ For reference, we are a branch of the ‘animalia.’ Among the bacteria, classical classification begins with the
Gram’s stain, resulting in gram-positive and gram-negative. The gram-positive are a distinct group in the tree while the gram-
negative are predominately found in the proteobacteria. Further classification into more typical genus and species taxonomy is
typically accomplished using a series of biochemical tests but 16S rRNA sequences has proven to be a very good (but not perfect)
corollary to the more traditional taxonomy (Gutell et al., 1994). Within the eukarya, a number of microorganisms important for
foods can be found, and these include yeast and fungi which are found in the fungi branch. While perhaps not really a microor-
ganism, but certainly important as a food-borne parasite, Trichomonas is a member of the ‘trichomonads.’ The archaea are not typi-
cally important for foods, but this branch includes organisms that have revolutionized food microbiology. A key technique in the
detection of microorganisms, the polymerase chain reaction, owes it success to an archaea, Thermus aquaticus, which was the source
of a thermostable DNA polymerase (Erlich, 1989). Taq polymerase made a curious but impractical technique of amplifying targeted
sequences of nucleic acid into a universal method for the detection of virtually any organism which contained a nucleic acid.
Microorganisms that cause food-borne illness are varied and span both the ‘bacteria’ and ‘eukarya’ branches. They can be further
divided into organisms that cause intoxication as compared to those that cause infection. Toxigenic organisms are typically found
among the gram-positive organisms while infectious organisms can be found in both ‘bacteria’ and ‘eukarya’ branches. This is not
a perfect divide (infection vs intoxication) and some organisms can do both depending upon the route of introduction. For
example, Clostridium botulinum, which is most famous for the deadly consequences of ingesting it along with its toxin, can also
be introduced and cause infection via a wound (Davis et al., 1951). It fails, however, to infect via the gastrointestinal system as

Figure 1 Phylogenetic tree of life.

Reference Module in Food Sciences http://dx.doi.org/10.1016/B978-0-08-100596-5.03436-3 1

2 Microorganisms

compared to an organism such as Listeria monocytogenes. Listeria monocytogenes has the remarkable capability of transiting from the
gastrointestinal system and eventually migrating to the brain where it can cause encephalitis.
In addition to food-borne illness, microorganisms are responsible for the spoilage of food products. Spoilage is a function of the
initial contamination of the food product coupled to a set of intrinsic and extrinsic conditions that allow the spoilage flora to prolif-
erate. Estimates are that approximately 1/3 of all food for human consumption is lost to spoilage and other forms of waste. The
control of spoilage is not simple as it is dependent upon the infrastructure of system that transports and stores the food along
the supply chain to the consumer. It is also a matter of economics as the means to prevent food spoilage while resulting in
more food available for consumption is a net contributor to the final cost of the food. In affluent-developed countries, there is
an economic basis for flying berries produced in one part of the world to another. The microorganisms that cause food spoilage
are varied depending upon the type of food and the storage conditions (Gram et al., 2002). Gram-negative bacteria including Pseu-
domonas cause spoilage of foods with relatively high water activity. In contrast, molds will be the dominant spoilage flora on foods
with a relatively low water activity. Finally, the organoleptic changes that are associated with the spoilage of food are a result of the
microbial action not unlike those that occur during fermentation. Texture is affected as a result of spoilage, and off-flavors and odors
are generated by the conversion of substrates into metabolic end products.
Finally the discovery that microorganisms could positively affect the organoleptic quality and storage life of foods, a process that
includes numerous chemical and physical changes, was accidental. In general, the fermentation process involves the breakdown of
complex macromolecules and the conversion of the resulting substrate into other metabolic end products. In most cases, this specif-
ically involves the breakdown of a complex carbohydrate and the production of an acid or alcohol as the end product. The devel-
opment of a particular acidogenic or alcoholic fermentation process may be more a function of the interest in and exploitation of
these types of fermentation rather than a fundamental thermodynamic driving force. Fermentative microorganisms carry out this
process to alter their environment by reducing the available substrate, as well as to generate a concentration of metabolite that
would discourage the growth of competitors. Fermentations may also be a combination of enzymatic and microbial processes,
with the former contributed by the raw ingredients, and the latter by endogenous microflora. Modern adaptations of these natural
fermentations have mastered these previously haphazard events to ensure the uniformity and predictability of the processes.

References

Davis, J.B., Mattman, L.H., Wiley, M., 1951. Clostridium botulinum in a fatal wound infection. J. Am. Med. Assoc. 146 (7), 646–648.
Erlich, H.A., 1989. Polymerase chain reaction. J. Clin. Immunol. 9 (6), 437–447.
Gram, L., Ravn, L., Rasch, M., Bruhn, J.B., Christensen, A.B., Givskov, M., 2002. Food spoilagedinteractions between food spoilage bacteria. Int. J. Food Microbiol. 78 (1), 79–97.
Gutell, R.R., Larsen, N., Woese, C.R., 1994. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbiol. Rev. 58 (1), 10–26.
van Leeuwenhoek, A., 1800. The Select Works of Anthony van Leeuwenhoek: Containing His Microscopical Discoveries in Many of the Works of Nature. Translator, vol. 1.
Schulz, H.N., Jørgensen, B.B., 2001. Big bacteria. Annu. Rev. Microbiol. 55 (1), 105–137.