title: PCR detection and 16S rRNA sequence-based phylogeny of a novel Propionibacterium acidipropionici applicable for enhanced fermentation of high moisture corn.
abstract: OBJECTIVE
  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.
  
  
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Microbiology and Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA. romanoff@msu.edu
authors.forename: M N
authors.initials: MN
authors.lastname: Romanov
authors.forename: R V
authors.initials: RV
authors.lastname: Bato
authors.forename: M T
authors.initials: MT
authors.lastname: Yokoyama
authors.forename: S R
authors.initials: SR
authors.lastname: Rust
mesh_terms: D000818:Animals; D001483:Base Sequence; D002417:Cattle; D004269:DNA, Bacterial / Q000032:analysis*; D005285:Fermentation; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D011424:Propionibacterium / Q000145:classification / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000032:analysis*; D012417:Rumen / Q000382:microbiology; D012820:Silage; D003313:Zea mays
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S