Proper Usage of Terms and Scientific Names
Singular vs. Plural Usage of Some Common Terms
Aside from an understanding of the terms and concepts involved in the course, it is necessary that proper communication be observed regarding usage of terms. One area in which too many microbiologists have difficulty is in singular vs. plural usage. The following is a summary of the proper forms for some important terms:
Proper Presentation of Genus and Species
The way in which scientific names are written is also very important. You can always refer to scientific papers, your textbook, and (hopefully) your lab manual for proper examples. Each named species of living thing is always referred to by its genus and species name, never the species name alone. Two examples are a common bacterium, Escherichia coli and humans, Homo sapiens. Also, these names must always be italicized or (alternately) underlined (never both) – with only (and always) the genus name capitalized. All too often, we see E. coli written as E. Coli.
One should retain from any high school-level biology course the basic elements of taxonomy. It is sad to teach a college course in microbiology and see a general mis-understanding of terms such as genus and species. We should not have to take (or make) the time to do remedial work in this intrinsic element of biological science.
To refer to members of a given genus in the plural sense, using Bacillus, Micrococcus and Mycobacterium as examples, one cannot change the genus name directly to a plural form. Bacilli, Micrococci and Mycobacteria would be improper. To get around the problem, one can write such as the following examples: "species of Bacillus," "isolates of Micrococcus," "strains of Mycobacterium." If the genus names were to be reduced to common forms (made into conventional English words – not capitalized, italicized or underlined), then plural alteration would be valid, as follows: bacilli, micrococci, mycobacteria. Use the term "bacilli" with caution; this term (depending on context) can mean rod-shaped cells in general or members of the genus Bacillus more specifically.
Furthermore, according to recently-added conventions in taxonomy, Bacilli (as so written, additionally in quotation marks) is applied to a taxonomic rank higher than genus as follows: The bacterial phylum Firmicutes contains at least three classes, one of which is "Bacilli." Then follow the order Bacillales and the family Bacillaceae before the genus Bacillus is reached in descending the taxonomic heirarchy. This is according to Bergey's Manual of Systematic Bacteriology (2nd Edition, Volume 3, 2009) in which a number of species of the classic endospore-forming genera are reassigned into new genera of varying degrees of relatedness to each other and the revised genera Bacillus and Clostridium.
So, What Is a "Strain"?
One of the really neat things about a laboratory course such as Bacteriology 102 (since 2006, Microbiology 102) is the probability of working with strains of bacteria and bacteriophages from nature that were most likely never isolated and studied before. Also possible is finding a previously unknown bacterial species or, at least, a rarely isolated one. Finding rare or new species is helped along by playing around with various selective and differential plating media, perhaps "programming" these media to detect certain physiological types of bacteria such as what we discuss in our Differential Media Site.
When we inoculate a sample (soil, water, clinical, etc.) onto the medium in a petri plate, the bacterial cells in the sample will begin to replicate on the medium by repeated binary fission, forming colonies. A colony is a discrete mass of millions of cells – visible to the naked eye – and the original cell (or cells) that begin colony formation is called a colony-forming unit (CFU). (Naturally this depends on whether the bacteria find the nutrients and conditions suitable for metabolism and replication. There is no one medium which will support the growth of all of the different types of bacteria.) Cells of many of our more common species of bacteria can double their population 2 to 4 times an hour, and their colonies can become easily visible overnight.
An example showing colonies on a plate which had been inoculated with a sample of soil is seen here. The different shapes, sizes, colors, etc. of colonies represent the various species of bacteria whose cells constitute these colonies.
One can usually expect a homogenously-appearing, well-isolated colony as being a "pure culture" which arose from one common source – i.e., the colony-forming unit. Once cells from such a colony are transferred to another plate or tube of medium and allowed to multiply by themselves (as a pure culture), this culture is considered an isolate – having been isolated from the original sample. And once this isolate has been studied in the laboratory and something becomes known about how the cells appear and behave, it is considered a strain. By extension, the population of identical cells in the environment from which this culture was ultimately derived would be considered as belonging to the same strain.
In the microbial habitat (soil, lake water, infected human, etc.) from which a sample can be taken, there are various specific populations of cells which each arose from a common source (a cell or group of cells) "placed" into that habitat. If more than one isolate is obtained from any of these specific populations, they may be thought of as being of the same strain. It may be difficult or impossible to prove that a number of separate isolates indeed belong to the same strain when one performs isolations from natural sources such as soil and lake water. However, in an epidemic situation when a pathogen can spread from a common source – a contaminated food product, for example – it may not take too much to establish that the isolates from infected individuals are similar enough such that one can eventually trace back to that food product. Such is the essence of epidemiology.
For the known, speciated cultures that we provide in the lab, some are strains purchased from a national culture center such as the American Type Culture Collection, and their designations may be well-known around the world. Most strains we use are from isolations we have made here over the years, and whatever designations we give them (such as our phage strains "JL-1" and "KX-32") may never see the light of day in a scientific journal. We should be keeping a stock culture collection of all of the strains we isolate in the enrichment/isolation experiments for Bacteriology 102. Most of these strains may be known to genus, but probably none are known to species with what few tests and observations we do on them. An exception is Bacillus mycoides which is immediately recognizable by its distinctive filamentous and spreading type of growth.
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