Elaborating, can we use these indices to determine diversity/abundance of 2 microorganisms at different skin sites (e.g. stomach, neck and hand) rather than determining the complete microbial composition at the 3 skin sites and then determining the Shannon and Simpson indices for 2 selected micro organisms?
Indexes of diversity, such as Shannon and Simpson, assume as input abundances per species over some space/time. So you can't use them to determine abundances. Moreover, the diversity in ecology is property of a community, thus it cannot be used to determine the diversity of a single species (please remember that a microorganism is a single observation of a species, so diversity is not applicable to microoganisms, but to a community composed of microoganisms categorized into different species).
Now if you really need to determine the diversity for two species, I can only think that you have identified different strains for those species. In this case, you might assume that your community now is represented by the abundances of your different strains for your two species, then you can still apply a community index of diversity over the abundances of these strains. In this case you can construct a new dataset restricted only to the abundances for the different strains for your two selected species over the three sites you mention.
I hope that helps. Best regards.
Studies of bacterial diversity from environments ranging from anaerobic digesters to arid soils are producing ever-larger libraries of 16S rDNA clones. Whatever method is used to define operational taxonomic units (OTUs), suitable measures are required to describe and, more importantly, compare these highly diverse communities. There are many ways to measure diversity. Methods vary in the particular aspect, or aspects, of diversity that they measure, their sensitivity to different abundance classes and their failings. Particular measures can be chosen to suit the goal of the study, or a suite of measures can be applied to obtain a diversity profile.
you may refer the following papers from the link supplied below.
Article Rethinking microbial diversity analysis in the high throughp...
http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6941.2003.tb01040.x/full
I suggest, you observe and calculate species abundance for ith species from your data set separately. Shannon and Simpson indices represent the diversity of a community as whole.
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