Only Simpson diversity can be estimated accurately from microbial community fingerprints.

Bart Haegeman (1) , Biswarup Sen (2) , Jean-Jacques Godon (3) , Jérôme Hamelin (3)

1 SEEM - Station d’Ecologie Expérimentale du CNRS à Moulis
2 Department of Environmental Engineering and Science
3 LBE - Laboratoire de Biotechnologie de l'Environnement [Narbonne]

Lalande et al. (Microb. Ecol. 66(3):647-658, 2013) introduced a promising approach to quantify microbial diversity from fingerprinting profiles. Their analysis is based on extrapolating the abundance of the phylotypes detectable in a fingerprint towards the rare phylotypes of the community. By considering a set of reconstructed communities, Lalande et al. obtained a range of estimates for phylotype richness, Shannon diversity and Simpson diversity. They reported narrow ranges indicating accurate estimation, especially for Shannon and Simpson diversities. Here, we show that a much larger set of reconstructed communities than the one considered by Lalande et al. is consistent with the fingerprint. We find that the estimates for phylotype richness and Shannon diversity vary over orders of magnitude, but that the estimates for Simpson diversity are restricted to a narrow range (around 10 %). We conclude that only Simpson diversity can be estimated accurately from fingerprints.

Mots clés: Terminal Restriction Fragment Length Polymorphism; Estimation Range; Abundance Distribution; Diversity Metrics; Simpson Diversity

Domaines: Sciences du Vivant [q-bio]

Bart Haegeman, Biswarup Sen, Jean-Jacques Godon, Jérôme Hamelin. Only Simpson diversity can be estimated accurately from microbial community fingerprints.. Microbial ecology, 2014, 68 (2), pp.169-72. ⟨10.1007/s00248-014-0394-5⟩. ⟨hal-01190153⟩