Friday, May 07, 2010

Request - information on the fraction of microbes that can be cultured

To all - I am looking for some information on the fraction of microbes that can currently be cultured from different environments. If you know of any good review papers or databases or other information on this topic, it would be very useful.

Here are examples of some information I have found:
  • From Jo Handelsman's review on metagenomics in 2004: "One of the indicators that cultured microorganisms did not represent much of the microbial world was the oft-observed "great plate count anomaly" (135)—the discrepancy between the sizes of populations estimated by dilution plating and by microscopy. This discrepancy is particularly dramatic in some aquatic environments, in which plate counts and viable cells estimated by acridine orange staining can differ by four to six orders of magnitude (66), and in soil, in which 0.1 to 1% of bacteria are readily culturable on common media under standard conditions (138, 139)."
  • From Phil Hugenholtz's review in 2002: "under aerobic conditions, at moderate temperatures. Easily isolated organisms are the ‘weeds’ of the microbial world and are estimated to constitute less than 1% of all microbial species (this figure was estimated by comparing plate counts with direct microscopic counts of microorganisms in environmental samples; it has been called the “great plate-count anomaly” [1]). " Reference 1 is Staley JT and Kanopka 1985.
But what I am looking for is some sort of review or database that has information for lots of different ecosystems.
Anyone know of anything like this?


  1. This comment has been removed by the author.

  2. maybe in the articles of Slava Epstein?

  3. Table 1 in Ammann et al. 1995 ("Phylogenetic Identification and In Situ Detection of Individual Microbial Cells without Cultivation") contains estimates of culturability in 7 different habitats based on published studies. The estimates range from 0.001-0.03%.

  4. Thanks Steve.

    However, the #s depend on what you mean. Amann et al. I think (not read it in years) refer to % of cells that are culturable

    However, perhaps more useful #s are the % of TYPES of microbes in samples (e.g., OTUs) that are culturable. This is usually very different --- b/c many of the cells from culturable species do not grow.

    What I am trying to track down is #s that correspond to the % of TYPES ...

  5. I think a wrench in the works of this question might be the definition of "culturable" or "cultured". If you use the plate count definition (sensible, but limiting) then the <1% cited above holds up, I think. But if you talk to Kim Lewis or Mary Lidstrom about their work in different veins on coaxing bugs into growth (or at least metabolism), I think the number could be much higher. But then you have to counter that with the astronomical numbers out there in the deep sea and deep earth, if you are talking about the fraction of all bugs that can be cultured, v. the culturable fraction. Sounds talmudic....

  6. Talmudic sounds fine to me. My question here was part rhetorical.

  7. There is a work where the authors even show that the cultivable ones are not even the most abundant, which would, perhaps, answer your question, if only I remembered the article, or the authors ... perhaps the proper person to ask is some environmental microbiologist who is not reading your blog. :-)


  8. Sen et al. cultured and 454-screened for microbes in a quite specialized niche: the bodies of leafcutter ants.

    Sen R, et al. (2009) Generalized antifungal activity and 454-screening of Pseudonocardia and Amycolatopsis bacteria in nests of fungus-growing ants. in Proc. Natl. Acad. Sci. U.S.A.), pp 17805-17810.

  9. This is not the exhaustive data you are looking for, but specifically in the oral cavity, my colleague Vladimir pointed this out: Just spit it out. Gura T. Nat Med. 2008 Jul;14(7):706-9.

    "Paster and Dewhirst have now identified and classified an estimated 600 different microbial species, 60% of which cannot be cultivated outside the mouth."


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