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Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
Published on: April 14, 2016
PCR detection and 16S rRNA sequence-based phylogeny of a novel Propionibacterium acidipropionici applicable for
M N Romanov1, R V Bato, M T Yokoyama
1Department of Microbiology and Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA. romanoff@msu.edu
Aims:
The aims of this study were to develop a sensitive and more rapid detection of Propionibacterium acidipropionici DH42 in silage and rumen fluid samples, and to explore its 16S rRNA sequence-based phylogeny.
Methods And Results:
Nested polymerase chain reaction (PCR) was used with DH42-specific primers dhb1 and dhb2 for the secondary amplification of a 1267-bp fragment of 16S rRNA encoding gene. Using the established protocols for PCR amplification, as low as 10(2) and 10(3) CFU ml(-1) of strain DH42 in silage extracts and rumen fluid, respectively, were detected. To determine phylogenetic relationships between DH42 and other representatives of Propionibacterineae, a 1529-bp fragment of its 16S rRNA was amplified by PCR and sequenced. The propionibacterium DH42 formed a cluster with Eubacterium combesii, P. acidipropionici and P. microaerophilus.
Conclusions:
16S rRNA-based PCR detection technique was developed for DH42 in silage and rumen fluid samples. The 16S rRNA sequence confirmed the earlier identification of strain DH42 as P. acidipropionici. However, variable nucleotide positions were revealed.
Significance And Impact Of The Study:
Variability of 16S rRNA sequence within the species P. acidipropionici, determined in this study, poses the need of re-sequencing for some species of the suborder Propionibacterineae for a more reliable classification.
