Microbiology

Microbiology (from Ancient Greek μῑκρος (mīkros) 'small', βίος (bíos) 'life', and -λογία (-
logía) 'study of') is the scientific study of microorganisms, those being of unicellular (single-
celled), multicellular (consisting of complex cells), or acellular (lacking cells).[1][2] Microbiology
encompasses numerous sub-disciplines including virology, bacteriology, protistology, mycology,
immunology, and parasitology.

An agar plate streaked with

microorganisms

Eukaryotic microorganisms possess membrane-bound organelles and include fungi and protists,
whereas prokaryotic organisms—all of which are microorganisms—are conventionally classified
as lacking membrane-bound organelles and include Bacteria and Archaea.[3][4] Microbiologists
traditionally relied on culture, staining, and microscopy for the isolation and identification of
microorganisms. However, less than 1% of the microorganisms present in common
environments can be cultured in isolation using current means.[5] With the emergence of
biotechnology, Microbiologists currently rely on molecular biology tools such as DNA sequence-
based identification, for example, the 16S rRNA gene sequence used for bacterial identification.

Viruses have been variably classified as organisms,[6] as they have been considered either as
very simple microorganisms or very complex molecules. Prions, never considered as
microorganisms, have been investigated by virologists, however, as the clinical effects traced to
them were originally presumed due to chronic viral infections, virologists took a search—
discovering "infectious proteins".

The existence of microorganisms was predicted many centuries before they were first observed,
for example by the Jains in India and by Marcus Terentius Varro in ancient Rome. The first
recorded microscope observation was of the fruiting bodies of moulds, by Robert Hooke in 1666,
but the Jesuit priest Athanasius Kircher was likely the first to see microbes, which he mentioned
observing in milk and putrid material in 1658. Antonie van Leeuwenhoek is considered a father
of microbiology as he observed and experimented with microscopic organisms in the 1670s,
using simple microscopes of his design. Scientific microbiology developed in the 19th century
through the work of Louis Pasteur and in medical microbiology Robert Koch.

History

Avicenna postulated the

existence of
microorganisms.

The existence of microorganisms was hypothesized for many centuries before their actual
discovery. The existence of unseen microbiological life was postulated by Jainism which is
based on Mahavira's teachings as early as 6th century BCE (599 BC - 527 BC).[7]: 24 Paul Dundas
notes that Mahavira asserted the existence of unseen microbiological creatures living in earth,
water, air and fire.[7]: 88 Jain scriptures describe nigodas which are sub-microscopic creatures
living in large clusters and having a very short life, said to pervade every part of the universe,
even in tissues of plants and flesh of animals.[8] The Roman Marcus Terentius Varro made
references to microbes when he warned against locating a homestead in the vicinity of swamps
"because there are bred certain minute creatures which cannot be seen by the eyes, which float
in the air and enter the body through the mouth and nose and thereby cause serious diseases."[9]
Persian scientists hypothesized the existence of microorganisms, such as Avicenna in his book
The Canon of Medicine, Ibn Zuhr (also known as Avenzoar) who discovered scabies mites, and
Al-Razi who gave the earliest known description of smallpox in his book The Virtuous Life (al-
Hawi).[10] The tenth-century Taoist Baoshengjing describes "countless micro organic worms"
which resemble vegetable seeds, which prompted Dutch sinologist Kristofer Schipper to claim
that "the existence of harmful bacteria was known to the Chinese of the time."[11]

In 1546, Girolamo Fracastoro proposed that epidemic diseases were caused by transferable
seedlike entities that could transmit infection by direct or indirect contact, or vehicle
transmission.[12]

Antonie van Leeuwenhoek

(1632–1723)

Statue of Robert Koch, one of the

founders of microbiology,[13] in Berlin
 Martinus Beijerinck is often
considered as a founder of
virology.

In 1676, Antonie van Leeuwenhoek, who lived most of his life in Delft, Netherlands, observed
bacteria and other microorganisms using a single-lens microscope of his own design.[14][2] He is
considered a father of microbiology as he used simple single-lensed microscopes of his own
design.[14] While Van Leeuwenhoek is often cited as the first to observe microbes, Robert Hooke
made his first recorded microscopic observation, of the fruiting bodies of moulds, in 1665.[15] It
has, however, been suggested that a Jesuit priest called Athanasius Kircher was the first to
observe microorganisms.[16]

Kircher was among the first to design magic lanterns for projection purposes, and so he was
well acquainted with the properties of lenses.[16] He wrote "Concerning the wonderful structure
of things in nature, investigated by Microscope" in 1646, stating "who would believe that vinegar
and milk abound with an innumerable multitude of worms." He also noted that putrid material is
full of innumerable creeping animalcules. He published his Scrutinium Pestis (Examination of the
Plague) in 1658, stating correctly that the disease was caused by microbes, though what he saw
was most likely red or white blood cells rather than the plague agent itself.[16]
The birth of bacteriology

Innovative laboratory
glassware and experimental
methods developed by Louis
Pasteur and other biologists
contributed to the young field
of bacteriology in the late
19th century.

The field of bacteriology (later a subdiscipline of microbiology) was founded in the 19th century
by Ferdinand Cohn, a botanist whose studies on algae and photosynthetic bacteria led him to
describe several bacteria including Bacillus and Beggiatoa. Cohn was also the first to formulate a
scheme for the taxonomic classification of bacteria, and to discover endospores.[17] Louis
Pasteur and Robert Koch were contemporaries of Cohn, and are often considered to be the
fathers of modern microbiology[16] and medical microbiology, respectively.[18] Pasteur is most
famous for his series of experiments designed to disprove the then widely held theory of
spontaneous generation, thereby solidifying microbiology's identity as a biological science.[19]
One of his students, Adrien Certes, is considered the founder of marine microbiology.[20] Pasteur
also designed methods for food preservation (pasteurization) and vaccines against several
diseases such as anthrax, fowl cholera and rabies.[2] Koch is best known for his contributions to
the germ theory of disease, proving that specific diseases were caused by specific pathogenic
microorganisms. He developed a series of criteria that have become known as the Koch's
postulates. Koch was one of the first scientists to focus on the isolation of bacteria in pure
culture resulting in his description of several novel bacteria including Mycobacterium
tuberculosis, the causative agent of tuberculosis.[2]
While Pasteur and Koch are often considered the founders of microbiology, their work did not
accurately reflect the true diversity of the microbial world because of their exclusive focus on
microorganisms having direct medical relevance. It was not until the late 19th century and the
work of Martinus Beijerinck and Sergei Winogradsky that the true breadth of microbiology was
revealed.[2] Beijerinck made two major contributions to microbiology: the discovery of viruses
and the development of enrichment culture techniques.[21] While his work on the tobacco
mosaic virus established the basic principles of virology, it was his development of enrichment
culturing that had the most immediate impact on microbiology by allowing for the cultivation of
a wide range of microbes with wildly different physiologies. Winogradsky was the first to develop
the concept of chemolithotrophy and to thereby reveal the essential role played by
microorganisms in geochemical processes.[22] He was responsible for the first isolation and
description of both nitrifying and nitrogen-fixing bacteria.[2] French-Canadian microbiologist Felix
d'Herelle co-discovered bacteriophages in 1917 and was one of the earliest applied
microbiologists.[23]

Joseph Lister was the first to use phenol disinfectant on the open wounds of patients.[24]

Branches

A university food microbiology

laboratory

The branches of microbiology can be classified into applied sciences, or divided according to
taxonomy, as is the case with bacteriology, mycology, protozoology, virology, phycology, and
microbial ecology. There is considerable overlap between the specific branches of microbiology
with each other and with other disciplines, and certain aspects of these branches can extend
beyond the traditional scope of microbiology[25][26] A pure research branch of microbiology is
termed cellular microbiology.
Applications
While some people have fear of microbes due to the association of some microbes with various
human diseases, many microbes are also responsible for numerous beneficial processes such
as industrial fermentation (e.g. the production of alcohol, vinegar and dairy products), antibiotic
production and act as molecular vehicles to transfer DNA to complex organisms such as plants
and animals. Scientists have also exploited their knowledge of microbes to produce
biotechnologically important enzymes such as Taq polymerase,[27] reporter genes for use in
other genetic systems and novel molecular biology techniques such as the yeast two-hybrid
system.[28]

Bacteria can be used for the industrial production of amino acids. Corynebacterium glutamicum
is one of the most important bacterial species with an annual production of more than two
million tons of amino acids, mainly L-glutamate and L-lysine.[29] Since some bacteria have the
ability to synthesize antibiotics, they are used for medicinal purposes, such as Streptomyces to
make aminoglycoside antibiotics.[30]

Fermenting tanks with yeast

being used to brew beer

A variety of biopolymers, such as polysaccharides, polyesters, and polyamides, are produced by

microorganisms. Microorganisms are used for the biotechnological production of biopolymers
with tailored properties suitable for high-value medical application such as tissue engineering
and drug delivery. Microorganisms are for example used for the biosynthesis of xanthan,
alginate, cellulose, cyanophycin, poly(gamma-glutamic acid), levan, hyaluronic acid, organic
acids, oligosaccharides polysaccharide and polyhydroxyalkanoates.[31]

Microorganisms are beneficial for microbial biodegradation or bioremediation of domestic,

agricultural and industrial wastes and subsurface pollution in soils, sediments and marine
environments. The ability of each microorganism to degrade toxic waste depends on the nature
of each contaminant. Since sites typically have multiple pollutant types, the most effective
approach to microbial biodegradation is to use a mixture of bacterial and fungal species and
strains, each specific to the biodegradation of one or more types of contaminants.[32]

Symbiotic microbial communities confer benefits to their human and animal hosts health
including aiding digestion, producing beneficial vitamins and amino acids, and suppressing
pathogenic microbes. Some benefit may be conferred by eating fermented foods, probiotics
(bacteria potentially beneficial to the digestive system) or prebiotics (substances consumed to
promote the growth of probiotic microorganisms).[33][34] The ways the microbiome influences
human and animal health, as well as methods to influence the microbiome are active areas of
research.[35]

Research has suggested that microorganisms could be useful in the treatment of cancer.
Various strains of non-pathogenic clostridia can infiltrate and replicate within solid tumors.
Clostridial vectors can be safely administered and their potential to deliver therapeutic proteins
has been demonstrated in a variety of preclinical models.[36]

Some bacteria are used to study fundamental mechanisms. An example of model bacteria used
to study motility[37] or the production of polysaccharides and development is Myxococcus
xanthus.[38]

See also

Biosafety
Microbes and Man
Professional organizations

American Society for Microbiology

 Federation of European Microbiological
Societies
Society for Applied Microbiology
Society for General Microbiology
Journals

Critical Reviews in Microbiology

International Journal of Systematic and
Evolutionary Microbiology
Journal of Bacteriology
Nature Reviews Microbiology

Portal: Biology

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Further reading

Kreft JU, Plugge CM, Grimm V, Prats C,

Leveau JH, Banitz T, et al. (November 2013).
"Mighty small: Observing and modeling
individual microbes becomes big science" (ht
tps://www.ncbi.nlm.nih.gov/pmc/articles/PM
C3831448) . Proceedings of the National
Academy of Sciences of the United States of
America. 110 (45): 18027–18028.
Bibcode:2013PNAS..11018027K (https://ui.a
dsabs.harvard.edu/abs/2013PNAS..1101802
7K) . doi:10.1073/pnas.1317472110 (https://
doi.org/10.1073%2Fpnas.1317472110) .
PMC 3831448 (https://www.ncbi.nlm.nih.go
v/pmc/articles/PMC3831448) .
PMID 24194530 (https://pubmed.ncbi.nlm.ni
h.gov/24194530) .
Madigan MT, Martinko JM, Bender KS,
Buckley DH, Stahl DA (2015-06-05). Brock
Biology of Microorganisms, Global Edition (htt
 ps://books.google.com/books?id=eBnLCQA
AQBAJ) . Pearson Education Limited.
ISBN 978-1-292-06831-2.

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