Evaluations of different hypervariable regions of archaeal 16S rRNA genes in profiling of methanogens by Archaea-specific PCR and denaturing gradient gel electrophoresis.
Different hypervariable (V) regions of the archaeal 16S rRNA gene (rrs) were compared systematically to establish a preferred V region(s) for use in Archaea-specific PCR-denaturing gradient gel electrophoresis (DGGE). The PCR products of the V3 region produced the most informative DGGE profiles and permitted identification of common methanogens from rumen samples from sheep. This study also showed that different methanogens might be detected when different V regions are targeted by PCR-DGGE. Dietary fat appeared to transiently stimulate Methanosphaera stadtmanae but inhibit Methanobrevibacter sp. strain AbM4 in rumen samples.
Yu
Zhongtang
Z
The MAPLE Research Initiative, Department of Animal Sciences, The Ohio State University, Columbus, Ohio 43210, USA. yu.226@osu.edu
García-González
Rubén
R
Schanbacher
Floyd L
FL
Morrison
Mark
M
D000821:Animal Feed; D000818:Animals; D022801:Complementarity Determining Regions / Q000235:genetics*; D017931:DNA Primers; D004041:Dietary Fats; D004587:Electrophoresis, Agar Gel / Q000379:methods*; D019766:Genes, Archaeal; D008697:Methane / Q000378:metabolism; D017013:Methanobacteriaceae / Q000145:classification* / Q000235:genetics; D041581:Methanobrevibacter / Q000145:classification / Q000235:genetics; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012417:Rumen / Q000382:microbiology; D017422:Sequence Analysis, DNA; D012756:Sheep; D013045:Species Specificity
D022801:Complementarity Determining Regions; D017931:DNA Primers; D004041:Dietary Fats; D012336:RNA, Ribosomal, 16S; D008697:Methane