Counter-culture revolution: understanding “the great plate anomaly”

For much of the time that microbes have been studied, great attention has been paid to microbes that can be grown in cultures. Indeed, much of what we know about the microscopic world is due toknowledge acquired through studying these organisms that are relatively easy to cultivate. In his study of pathogens, Robert Koch went so far as to postulate that bacteria must be isolated and culturedin order to be studied.1 It seems, however, that bacteria that grow in traditional cultures represent only the very lowest hanging fruit of the microbial world. Many of the bacteria observed throughthe lens of a microscope, despite not easily growing in traditional culture medium, can nonetheless have a significant impact on their environment. Peptic ulcers2,cavities3, Leprosy, and Syphilis4are among the many effects that humans experience from these difficult to culture microbes.
As technology has progressed, more and more tools have become available for the analysis of the microbialrealm. Among these tools, genetic analysis has proved particularly useful. Since the early 1980’s, 16S rRNA gene sequencing has spurred a five-fold increase in the number of named bacterial species5.Molecular genetics has emerged as a promising alternative to traditional culture methodology. Based on evidence from 16S rRNA gene sequencing, it is estimated that about 99% of all bacterialspecies are not cultivable in traditional culture medium6. Bacterial diversity is immense; bacteria grow in the most surprising locations. Many have evolved to fill very specific niches in theirenvironment and thus have very specific biochemical and environmental requirements. Building a culture to fulfill these needs “from scratch” can be exceedingly difficult and often requires a bit of serendipityto get it right. A promising alternative methodology allows bacteria to grow in its own environment. Diffusion chambers isolate and immobilize the bacteria while simultaneously allowing it to...