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http://dx.doi.org/10.5762/KAIS.2020.21.7.312

Methanogenic Archaeal Census of Ruminal Microbiomes  

Lee, Seul (Animal Nutrition and Physiology Team, National Institute of Animal Science)
Baek, Youlchang (Animal Nutrition and Physiology Team, National Institute of Animal Science)
Lee, Jinwook (Animal Genetic Resources Research Center, National Institute of Animal Science)
Kim, Minseok (Department of Animal Science, College of Agriculture and Life Sciences, Chonnam National University)
Publication Information
Journal of the Korea Academia-Industrial cooperation Society / v.21, no.7, 2020 , pp. 312-320 More about this Journal
Abstract
The objective of the study was to undertake a phylogenetic diversity census of ruminal archaea based on a meta-analysis of 16S rRNA gene sequences that were publicly available in the Ribosomal Database Project. A total of 8,416 sequences were retrieved from the Ribosomal Database Project (release 11, update 5) and included in the construction of a taxonomy tree. Species-level operational taxonomic units (OTUs) were analyzed at a 97% sequence similarity by using the QIIME program. Of the 8,416 sequences, 8,412 were classified into one of three phyla; however, the remaining four sequences could not be classified into a known phylum. The Euryarchaeota phylum was predominant and accounted for 99.8% of the archaeal sequences examined. Among the Euryarchaeota, 65.4% were assigned to Methanobrevibacter, followed by Methanosphaera (10.4%), Methanomassillicoccus (10.4%), Methanomicrobium (7.9%), Methanobacterium (1.9%), Methanimicrococcus (0.5%), Methanosarcina (0.1%), and Methanoculleus (0.1%). The 7,544 sequences that had been trimmed to the V2 and V3 regions clustered into 493 OTUs. Only 17 of those 493 OTUs were dominant groups and accounted for more than 1% of the 7,544 sequences. These results can help guide future research into the dominant ruminal methanogens that significantly contribute to methane emissions from ruminants, research that may lead to the development of anti-methanogenic compounds that inhibit these methanogens regardless of diet or animal species.
Keywords
16S rRNA Gene; Meta-Analysis; Phylogenetic Diversity; Ribosomal Database Project; Ruminal Microbiome; Methanogenic Archaea;
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