Phylogenetic analysis of methanogens in the pig feces.
In order to assess methanogen diversity in feces of pigs, archaeal 16S rRNA gene clone libraries were constructed from feces of the pig. After the amplification by PCR using primers Met86F and Met1340R, equal quantities of PCR products from each of the five pigs were mixed together and used to construct the library. Sequence analysis showed that the 74 clones were divided into ten phylotypes as defined by RFLP analysis. Phylogenetic analysis showed that three phylotypes were most closely affiliated with the genus Methanobrevibacter (46% of clones). The library comprised 55.4% unidentified euryarchaeal clones. Three phylotypes (LMG4, LMG6, LMG8) were not closely related to any known Euryarchaeota sequences. The phylogenetic analysis indicated that the archaea found in the libraries were all clustered into the Euryarchaeota. The data from the phylogenetic tree showed that those sequences belonged to three monophyletic groups. Phylotypes LGM2 and LGM7 grouped within the genus Methanobrevibacter. Phylotypes LGM4, LGM6, LGM8 and LGM9 grouped within the genus Methanosphaera. Other phylotypes grouped together, and formed a distantly related sister group to Aciduliprofundum boonei and species of the Thermoplasmatales including Thermoplasma volcanium and Thermoplasm acidophilum. Our results showed that methanogens belonging to the genus Methanobrevibacter were predominant in pig feces, and that many unique unknown archaea sequences were also found in the library. Nevertheless, whether these unique sequences represent new taxonomic groups and their role in the pig gut need further investigation.
Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China. maoshengyong@njau.edu.cn
Sheng-Yong
SY
Mao
Cui-Feng
CF
Yang
Wei-Yun
WY
Zhu
D000818:Animals; D001105:Archaea / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D019641:DNA, Archaeal / Q000235:genetics; D005243:Feces / Q000382:microbiology*; D008697:Methane / Q000378:metabolism*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013552:Swine
D019641:DNA, Archaeal; D012336:RNA, Ribosomal, 16S; D008697:Methane
Appl Environ Microbiol. 2007 Jul;73(13):4206-10
17483285
Anaerobe. 2006 Jun;12(3):134-9
16765859
Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576-9
2112744
Appl Environ Microbiol. 2004 Mar;70(3):1263-70
15006742
Animal. 2010 Jan;4(1):20-9
22443614
J Microbiol Methods. 2003 Nov;55(2):337-49
14529955
BMC Microbiol. 2001;1:5
11384509
Appl Environ Microbiol. 1998 Oct;64(10):3854-9
9758810