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Pathogens 2014, 3(1), 109-120; doi:10.3390/pathogens3010109
Article

Evaluation of Automated Ribosomal Intergenic Spacer Analysis for Bacterial Fingerprinting of Rumen Microbiome Compared to Pyrosequencing Technology

1,2
, 1
 and 1,*
1 Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, PO Box 6, Bet Dagan 50250, Israel 2 Department of Molecular Microbiology and Biotechnology , The George S. Wise Faculty of Life Science, Tel Aviv University, Ramat-Aviv 69978, Israel
* Author to whom correspondence should be addressed.
Received: 24 November 2013 / Revised: 18 December 2013 / Accepted: 9 January 2014 / Published: 22 January 2014
(This article belongs to the Special Issue Gut Microbiome)
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Abstract

The mammalian gut houses a complex microbial community which is believed to play a significant role in host physiology. In recent years, several microbial community analysis methods have been implemented to study the whole gut microbial environment, in contrast to classical microbiological methods focusing on bacteria which can be cultivated. One of these is automated ribosomal intergenic spacer analysis (ARISA), an inexpensive and popular way of analyzing bacterial diversity and community fingerprinting in ecological samples. ARISA uses the natural variability in length of the DNA fragment found between the 16S and 23S genes in different bacterial lineages to infer diversity. This method is now being supplanted by affordable next-generation sequencing technologies that can also simultaneously annotate operational taxonomic units for taxonomic identification. We compared ARISA and pyrosequencing of samples from the rumen microbiome of cows, previously sampled at different stages of development and varying in microbial complexity using several ecological parameters. We revealed close agreement between ARISA and pyrosequencing outputs, especially in their ability to discriminate samples from different ecological niches. In contrast, the ARISA method seemed to underestimate sample richness. The good performance of the relatively inexpensive ARISA makes it relevant for straightforward use in bacterial fingerprinting analysis as well as for quick cross-validation of pyrosequencing data.
Keywords: ARISA; pyrosequencing; rumen microbiome ARISA; pyrosequencing; rumen microbiome
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Jami, E.; Shterzer, N.; Mizrahi, I. Evaluation of Automated Ribosomal Intergenic Spacer Analysis for Bacterial Fingerprinting of Rumen Microbiome Compared to Pyrosequencing Technology. Pathogens 2014, 3, 109-120.

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