Metagenomics - Arriving At Estimates Of Diversity

Question

[Monzoor]

What experiments did one perform to estimate that 99% of microbes are yet to be discovered.

[Michael]

I think that is just an estimate, maybe a reasonable one, but where did you read this? I believe, this claim is very hard to deal with, as it refers to an unknown quantity and makes claims about it, but how would one count something that is per definition not discovered yet?

[Monzoor]

Sort of agree. Please see my other comments below

Answer 1

[Dave Lunt]

Maybe you are referring to the estimates that indicate that only about 1% of bacteria can be cultured? These come from staining and counting bactera in environmental samples versus trying to grow them and then counting colonies.

Answer 2

[Adam Monier]

This estimate of uncultured microbial diversity was determined before the use of environmental clone libraries. I think it was Staley and Konopka that came first with that number by reviewing the literature: in their famous "great plate-count anomaly" paper, they pointed out the discrepancy in numbers between plate (culture media) and direct-microspcopy counts:

only approximately 0.1-1.0% of the total bacteria can be enumerated by the plating procedure. Indeed, as a general rule we have found that the maximum recovery of heterotrophic bacteria [bacteria that don't use photosynthesis] is 1% of the total direct count using plating procedures or other viable enumeration methods…. From a microbiological perspective, only a few percent of the bacterial cells enumerated by direct microscopic count can be cultured and identified

This anomaly was already noted by Razumov in 1932!

Answer 3

[Neilfws]

Dave is correct: the observation is that 99% or more of cells in environmental samples cannot be cultured, not that we known only of 1% of species.

The issue is reviewed (and the 99% figure quoted) in Metagenomics for studying unculturable microorganisms: cutting the Gordian knot - freely available review at PubMed Central. The authors cite the article "Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations" - also free at PMC as the source for the estimate.

Incidentally, this observation is responsible for the development of sequence-based methods to study microbial diversity, such as 16S rDNA probes and metagenomics.

[Monzoor]

I sort of agree. But these experiments have been performed say from a sample or many samples obtained from a particular environment. Unless one has sort of analyzed almost all types of environments, how does one come to the conclusion that 99% or more are unculturable ? I know this argument is somewhat impractical, but it is something to think about. I am sure you may not agree ..

[Neilfws]

Well, clearly you cannot analyse "all types" of environment - just as many as is practical. The observation holds: in all cases examined thus far, there are far more cells than can be cultured.

Answer 4

[Prateek]

This is a good resource to find out how J Craig Venter Institute's global ocean sampling project is trying to make sense of oceanic metagenomic ecosystems.

[Monzoor]

Thanks Prateek. That was a good link. Where are you based from. Im from India