title: Phylogenetic analysis of archaea in three fractions of cow rumen based on the 16S rDNA sequence.
abstract: Phylogenetic analysis of archaea in the rumen ecosystem was analysed by PCR of 16S rDNA from the bovine rumen using archaea-specific primers. The libraries were constructed from rumen fluid (AF), rumen solid (AS), and rumen epithelium (AE) from a rumen-fistulated Korean cow (Hanwoo). The 45 AF clones could be divided into three groups and the largest group was affiliated with the Methanomicrobiaceae family (96% of clones). The AF clones contained a high proportion of unidentifiable clones (67%). The 39 AE clones could be divided into two groups and the largest group was also affiliated with the Methanomicrobiaceae family (95% of clones). The AE clones contained a low proportion of unidentifiable clones (5%). The 20 AS clones could be divided into two groups that were affiliated with either the Methanobacteriaceae family (55%) or the Methanomicrobiaceae family (45%). The AS clones contained a moderate proportion of unidentifiable clones (40%). The predominant family of whole rumen archaea was found to belong to the Methanomicrobiaceae (85%). Methanomicrobiaceae were predominant in the rumen epithelium and the rumen fluid while Methanobacteriaceae were predominant in the rumen solid. One clone from the rumen fluid and two clones from the rumen epithelium contained rDNA sequences of Non-Thermophilic-Crenarchaeota (NTC) and Thermophilic-Crenarchaeota (TC), respectively, which have not previously been described from the rumen.
authors.affiliation: Division of Applied Life Science, Research Institute of Life Science, Gyeongsang National University, Chinju 660-701, Republic of Korea.
authors.forename: Eun Chule
authors.initials: EC
authors.lastname: Shin
authors.forename: Byoung Rock
authors.initials: BR
authors.lastname: Choi
authors.forename: Woo Jin
authors.initials: WJ
authors.lastname: Lim
authors.forename: Su Young
authors.initials: SY
authors.lastname: Hong
authors.forename: Chang Long
authors.initials: CL
authors.lastname: An
authors.forename: Kye Man
authors.initials: KM
authors.lastname: Cho
authors.forename: Young Kyun
authors.initials: YK
authors.lastname: Kim
authors.forename: Jin Mee
authors.initials: JM
authors.lastname: An
authors.forename: Jung Mi
authors.initials: JM
authors.lastname: Kang
authors.forename: Sung Sill
authors.initials: SS
authors.lastname: Lee
authors.forename: Hoon
authors.initials: H
authors.lastname: Kim
authors.forename: Han Dae
authors.initials: HD
authors.lastname: Yun