alexa Identification of Host-Specific Genetic Markers within
ISSN: 2153-0602

Journal of Data Mining in Genomics & Proteomics
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Research Article

Identification of Host-Specific Genetic Markers within 16S rDNA Intervening Sequences of 73 Genera of Fecal Bacteria

Zhenyu Shen1,2, Ning Zhang3, Azlin Mustapha2, Mengshi Lin2, Dong Xu3, Daiyong Deng1, Mary Reed1 and Guolu Zheng1*

1Department of Agriculture and Environmental Sciences, Lincoln University in Missouri, 904 Chestnut Street, Jefferson City, MO 65101, USA

2Food Science Program, University of Missouri, Columbia, MO 65211, USA

3Department of Computer Science and C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA

*Corresponding Author:
Guolu Zheng
Department of Agriculture and Environmental Sciences
Lincoln University in Missouri, 904 Chestnut Street
Jefferson City, MO 65101, USA
Tel: 573-681-5964
Fax: 573-681-5955
E-mail: [email protected]

Received date: January 5, 2016 Accepted date: January 27, 2016 Published date: January 31, 2016

Citation:Shen Z, Zhang N, Mustapha A, Lin M, Xu D, et al. (2016) Identification of Host-Specific Genetic Markers within 16S rDNA Intervening Sequences of 73 Genera of Fecal Bacteria. J Data Mining Genomics Proteomics 7:186. doi:10.4172/2153-0602.1000186

Copyright: © 2016 Zhenyu S, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

 

Abstract

Ribosomal intervening sequences (IVSs) were recently proposed as genetic markers for microbial source tracking (MST). This study comprehensively investigated host specificities of IVSs within the 16S rDNA of 73 genera of dominant fecal bacteria using the approaches of bioinformatics and next generation sequencing (NGS). Thirteen types of IVSs were identified in silico to be associated with particular host species; they were found within bacteria of the genera Anaerovibrio, Bacteroides, Faecalibacterium, Mitsuokella, Peptostreptococcus, Phascolarctobacterium, and Subdoligranulum. Based on the DNA sequences of the thirteen types of IVSs, polymerase chain reaction (PCR) assays were developed. PCR amplifications using fecal DNA samples of target and non-target host species demonstrated that eight out of the 13 IVSs were highly associated with human, chicken/turkey, beef cattle/pig, or horse/pig/human feces. Based on the IVS polymorphisms, NGS was applied to search for single-host-associated IVSs from those linked to multiple host species. Consequently, a new type of IVS specific to beef cattle was found and confirmed by PCR amplification using cattle and non-cattle fecal samples. The results suggest that some IVSs may be used as the genetic markers for MST and that NGS may be useful in identifying novel host-specific genetic markers.

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