Rethinking Sterile: The Hospital Microbiome
Rethinking Sterile: The Hospital Microbiome
Historically, microbiologists have studied bacteria in pure culture, growing one species at a time. Although this allowed them to create large numbers of microbes relatively quickly, the method had several limitations.
Many microbes found in the environment are difficult, if not impossible, to grow in culture, which caused microbiologists to dramatically underestimate the number of microbes that make up human microbiomes. As well, given the significant public health threat of infectious diseases, researchers preferentially focused their efforts on harmful bacteria rather than neutral or beneficial species.
(Enlarge Image)
As recently as 50 years ago, when much of what scientists knew of microbes was related to pathogens, stripping surfaces of their thin layer of microbes made sense. But that's not the case today. Beginning in the late 1990s and early 2000s, genetic sequencing technology began a series of exponential improvements, which lowered both the time and the cost to sequence genes. This allowed Eisen, Gilbert, and others to improve upon methods pioneered by microbial ecologist Norman R. Pace in the 1980s to survey the environment for microorganisms that cannot be grown in the laboratory; these studies showed that our world is awash in microbes. Surveys of the environment reveal that culturable bacteria such as Streptococcus and Staphylococcus species represent only a tiny fraction of the microbes we encounter every day.
Different types of bacteria contain a unique version of the 16S rRNA gene that acts as a fingerprint. By swabbing a surface and then sequencing the various 16S rRNA genes present in that sample, scientists can quickly, cheaply, and easily discover the types of bacteria present in any given location. The biodiversity present on a table, bed rail, or patch of floor can rival that seen in any Amazonian rainforest, researchers have discovered.
"It's very hard to clear out all of the microbes from a particular ecosystem," Eisen says. In a review published in Genome Biology, Gilbert and coauthor Scott Kelley wrote that there "probably exists a microbe that will survive on almost any [built environment] surface or condition." Simply put, sterility doesn't exist.
Rethinking Sterile
Historically, microbiologists have studied bacteria in pure culture, growing one species at a time. Although this allowed them to create large numbers of microbes relatively quickly, the method had several limitations.
Many microbes found in the environment are difficult, if not impossible, to grow in culture, which caused microbiologists to dramatically underestimate the number of microbes that make up human microbiomes. As well, given the significant public health threat of infectious diseases, researchers preferentially focused their efforts on harmful bacteria rather than neutral or beneficial species.
(Enlarge Image)
As recently as 50 years ago, when much of what scientists knew of microbes was related to pathogens, stripping surfaces of their thin layer of microbes made sense. But that's not the case today. Beginning in the late 1990s and early 2000s, genetic sequencing technology began a series of exponential improvements, which lowered both the time and the cost to sequence genes. This allowed Eisen, Gilbert, and others to improve upon methods pioneered by microbial ecologist Norman R. Pace in the 1980s to survey the environment for microorganisms that cannot be grown in the laboratory; these studies showed that our world is awash in microbes. Surveys of the environment reveal that culturable bacteria such as Streptococcus and Staphylococcus species represent only a tiny fraction of the microbes we encounter every day.
Different types of bacteria contain a unique version of the 16S rRNA gene that acts as a fingerprint. By swabbing a surface and then sequencing the various 16S rRNA genes present in that sample, scientists can quickly, cheaply, and easily discover the types of bacteria present in any given location. The biodiversity present on a table, bed rail, or patch of floor can rival that seen in any Amazonian rainforest, researchers have discovered.
"It's very hard to clear out all of the microbes from a particular ecosystem," Eisen says. In a review published in Genome Biology, Gilbert and coauthor Scott Kelley wrote that there "probably exists a microbe that will survive on almost any [built environment] surface or condition." Simply put, sterility doesn't exist.
