Quantitative Community Fingerprinting Methods for Estimating the Abundance of Operational Taxonomic Units in Natural Microbial Communities

Ramette, Alban Nicolas (2009). Quantitative Community Fingerprinting Methods for Estimating the Abundance of Operational Taxonomic Units in Natural Microbial Communities. Applied and environmental microbiology, 75(8), pp. 2495-2505. American Society for Microbiology 10.1128/AEM.02409-08

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Molecular fingerprinting techniques offer great promise for analyzing changes in microbial community structure, especially when dealing with large number of samples. However, a serious limitation has been the lack of quantification offered by such techniques since the relative abundances of the identified operational taxonomic units (OTUs) in the original samples are not measured. A quantitative fingerprinting approach designated "qfingerprinting" is proposed here. This method involves serial dilutions of the sample of interest and further systematic fingerprinting of all dilution series. Using the ultimate dilutions for which OTU are still PCR amplifiable and taking into account peak size inaccuracy and peak reproducibility, the relative abundance of each OTU is then simultaneously determined over a scale spanning several orders of magnitude. The approach was illustrated by using a quantitative version of automated ribosomal intergenic spacer analysis (ARISA), here called qARISA. After validating the concept with a synthetic mixture of known DNA targets, qfingerprinting was applied to well-studied marine sediment samples to examine specific changes in OTU abundance associated with sediment depth. The new strategy represents a major advance for the detailed quantitative description of specific OTUs within complex communities. Further ecological applications of the new strategy are also proposed.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases
04 Faculty of Medicine > Pre-clinic Human Medicine > Institute of Social and Preventive Medicine (ISPM)

UniBE Contributor:

Ramette, Alban Nicolas

Subjects:

500 Science > 570 Life sciences; biology
300 Social sciences, sociology & anthropology > 360 Social problems & social services
600 Technology > 610 Medicine & health

ISSN:

0099-2240

Publisher:

American Society for Microbiology

Language:

English

Submitter:

Alban Nicolas Ramette

Date Deposited:

20 Mar 2017 11:32

Last Modified:

20 Mar 2017 11:32

Publisher DOI:

10.1128/AEM.02409-08

PubMed ID:

19201961

BORIS DOI:

10.7892/boris.91409

URI:

https://boris.unibe.ch/id/eprint/91409

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