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Detection of Fiber-Digesting Bacteria in the Ceca of Ostrich Using Specific Primer Sets

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Abstract

The purpose of this study was to detect three fibrolytic bacteria, Fibrobacter succinogenes, Ruminococcus flavefaciens, and Ruminococcus albus, in the cecal digesta of the ostrich (Struthio camelus) by PCR using a species-specific primer set for each 16S ribosomal RNA gene (16S rDNA). Although amplified DNA fragments obtained from each primer set had the expected size, the clone library derived from the amplimer contained non-specific sequences. The F. succinogenes-specific primer set recovered a partial 16S rDNA sequence of an uncultivated Fibrobacter with low similarity (<95%) and distantly related phylogenetic positioning to Fibrobacter sequences deposited in the databases, indicating a novel species of Fibrobacter. The sequence was considered to be identical to a clone detected in our previous experiment. Thus, we confirm that the gastrointestinal tract of the ostrich is one of the habitats of Fibrobacter species. The clone library derived from the R. flavefaciens-specific primer set contained a 16S rDNA sequence with 97% similarity to R. flavefaciens, indicating it could be one of a major fibrolytic bacterium in the ostrich ceca. No R. albus 16S rDNA sequence was found in the clone library of the R. albus-specific primer set.

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Acknowledgments

The authors thank Professor Kazunari Ushida and his colleagues (Kyoto Prefectural University, Kyoto, Japan) for their instruction of DNA extraction. The present study was financially supported by Grants-in-Aid for Scientific Research, Japan Society for the Promotion of Science (17380157). Nucleotide sequencing was carried out at Life Science Research Center (Center for Molecular Biology and Genetics, Mie University (Tsu, Japan).

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Authors and Affiliations

  1. Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie, 514-8507, Japan

    Hiroki Matsui, Tomomi Ban-Tokuda & Masaaki Wakita

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  1. Hiroki Matsui
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  2. Tomomi Ban-Tokuda
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  3. Masaaki Wakita
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Correspondence to Hiroki Matsui.

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Matsui, H., Ban-Tokuda, T. & Wakita, M. Detection of Fiber-Digesting Bacteria in the Ceca of Ostrich Using Specific Primer Sets. Curr Microbiol 60, 112–116 (2010). https://doi.org/10.1007/s00284-009-9513-9

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  • DOI: https://doi.org/10.1007/s00284-009-9513-9

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