Viruses help to culture "the unculturable"

You probably know it: less than 1% of bacteria from environmental samples can be cultured in the laboratory; so, the 99% silent majority is called the "unculturable bacteria". But let's make it clear: "unculturable" only means that we haven't found a way to grow them yet.

The word "unculturable" is impressive and widely used, although perhaps misleading, and might be replaced by "yet to be cultured", "uncultured" or "uncultivated". Why are most microorganisms so fastidious, not growing in common media? Possible reasons: a required nutrient or "growth factor" is missing (perhaps produced in the natural environment by other bacteria), a component of the medium is toxic, or other bacteria in the sample produce an inhibitory substance.

One obvious method of eliminating common microorganisms of a complex sample is by the addition of antibiotics to the culture media. Hence, for the isolation of actinomycetes, cycloheximide and nalidixic acid can be used to inhibit the growth of fungi and Gram-negative bacteria, respectively. But additional removal of unwanted bacteria can get much more precise, thanks to phages (or bacteriophages, i.e. bacterial viruses). As a neat example, see a recent article that reports on the use of phages for the isolation of novel actinomycetes from termite guts. The authors utilized four sets of phages, which selectively targeted various groups of bacteria. The first set was specific for bacteria commonly culturable from termite guts: Bacillus, Enterococcus, Staphylococcus, Lactococcus, Paenibacillus. The other three groups of phages were specifically directed against actinomycetes of the genera Streptomyces, Micromonospora and Nocardia/Rhodococcus, respectively. By sequentially using the sets of phages, the researchers were able to uncover and grow a number of new actinomycetes, which could not be identified without the phage treatment.

Culture-independent techniques such as metagenomics are a centre of attention, as they are providing a wealth of information from uncultured microorganisms. But efforts directed to "culturing the unculturable" are still needed for a better understanding of the microbial universe, don't you think so?

Reference:
Kurtböke, D., French, J. (2007). Use of phage battery to investigate the actinofloral layers of termite gut microflora. Journal of Applied Microbiology, 103(3), 722-734. DOI: 10.1111/j.1365-2672.2007.03308.x

Image credits:
Electron micrographs of a bacteriophage (phi HAU3) negatively stained with uranyl acetate. Reproduced from: Zhou X, Deng Z, Hopwood DA, Kieser T. Characterization of phi HAU3, a broad-host-range temperate Streptomyces phage, and development of phasmids. J. Bacteriol. (1994) 176, 2096-2099. Copyright 1994, American Society for Microbiology.