Gut methanogenic archaea of monogastric animals are considered to be related to energy metabolism and adipose deposition of the host; however, information on their development in young piglets is limited. Thus, to investigate early methanogenic colonisation in the faeces of Meishan and Yorkshire piglets, faecal samples were collected from piglets at 1, 3, 7, and 14 days after birth and used to analyse the methanogenic community with 16S rRNA gene pyrosequencing. Results showed that the diversity of the methanogenic community in the faeces of neonatal piglets decreased from one to 14 days of age, as the total methanogen populations increased. The age of piglets, but not the breed, significantly affected the diversity of the methanogenic community which was dominated by the genus Methanobrevibacter. From the ages of one to 14 days, the abundance of M. smithii-related operational taxonomic units (OTUs) increased significantly, while the abundances of M. thaueri- and M. millerae-related OTUs decreased significantly. The substitution of M. smithii for M. thaueri/M. millerae was faster in Yorkshire piglets than in Meishan piglets. These results suggest that the early establishment of microbiota in neonatal piglets is accompanied by dramatic changes in the methanogenic community, and that the changes vary among pigs of different genotypes. 1. Introduction Methanogenic archaea exist widely in the gastrointestinal (GI) tract of many vertebrates and invertebrates [1–3]. Methanogens can use hydrogen and other compounds such as formate, methanol, and acetate, as electron donors for the production of methane. Methane formation not only contributes to global warming as a greenhouse gas, but it also represents an energy loss for the animal [4]. Recently, methanogenic archaea in the gut of monogastric animals, including humans, have been studied intensively because gut methanogens are considered to be related to energy metabolism and adipose deposition of the host [5]. In addition, methane produced by methanogens might play an important role in the pathogenesis of several intestinal disorders, including colon cancer, inflammatory bowel disease, irritable bowel syndrome, and diverticulosis [6]. Thus far, only limited reports on gut methanogens in pigs have been available. Based on archaeal 16S ribosomal RNA (rRNA) gene clone library analysis, methanogens belonging to the genus Methanobrevibacter were found to be predominant in pig faeces [7, 8]. The GI microbiota of newborn animals play a fundamentally important role in the development of intestinal function and the
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