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Appl Environ Microbiol. Sep 1980; 40(3): 578–586.
PMCID: PMC291624

Aspects of Diversity Measurement for Microbial Communities


A useful measure of diversity was calculated for microbial communities collected from lake water and sediment samples using the Shannon index (H′) and rarefaction [E(S)]. Isolates were clustered by a numerical taxonomy approach in which limited (<20) tests were used so that the groups obtained represented a level of resolution other than species. The numerical value of diversity for each sample was affected by the number of tests used; however, the relative diversity compared among several sampling locations was the same whether 11 or 19 characters were examined. The number of isolates (i.e., sample size) strongly influenced the value of H′ so that unequal sized samples could not be compared. Rarefaction accounts for differences in sample size inherently so that such comparisons are made simple. Due to the type of sampling carried out by microbiologists, H′ is estimated and not determined and therefore requires a statement of error associated with it. Failure to report error provided potentially misleading results. Calculation of the variance of H′ is not a simple matter and may be impossible when handling a large number of samples. With rarefaction, the variance of E(S) is readily determined, facilitating the comparison of many samples.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Debette J, Losfeld J, Blondeau R. Taxonomie numérique de bactéries telluriques non fermentantes à Gram-négatif. Can J Microbiol. 1975 Sep;21(9):1322–1334. [PubMed]
  • Dubos RJ. THE DECOMPOSITION OF CELLULOSE BY AEROBIC BACTERIA. J Bacteriol. 1928 Apr;15(4):223–234. [PMC free article] [PubMed]
  • Gamble TN, Betlach MR, Tiedje JM. Numerically dominant denitrifying bacteria from world soils. Appl Environ Microbiol. 1977 Apr;33(4):926–939. [PMC free article] [PubMed]
  • Hood MA, Bishop WS, Bishop FW, Meyers SP, Whelan T. Microbial indicators of oil-rich salt marsh sediments. Appl Microbiol. 1975 Dec;30(6):982–987. [PMC free article] [PubMed]
  • Hutcheson K. A test for comparing diversities based on the Shannon formula. J Theor Biol. 1970 Oct;29(1):151–154. [PubMed]

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