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Dairy cows experience dramatic changes in host physiology from gestation to lactation period and dietary switch from high-forage prepartum diet to high-concentrate postpartum diet over the transition period (parturition +/- three weeks). Understanding the community structure and activity of the rumen microbiota and its associative patterns over the transition period may provide insight for e.g. improving animal health and production. In the present study, rumen samples from ten primiparous Holstein dairy cows were collected over seven weeks spanning the transition period. Total RNA was extracted from the rumen samples and cDNA thereof was subsequently used for characterizing the metabolically active bacterial (16S rRNA transcript amplicon sequencing) and archaeal (qPCR, T-RFLP and  mcrA  and 16S rRNA transcript amplicon sequencing) communities. The metabolically active bacterial community was dominated by three phyla, showing significant changes in relative abundance range over the transition period:  Firmicutes  (from prepartum 57% to postpartum 35%),  Bacteroidetes  (from prepartum 22% to postpartum 18%) and  Proteobacteria  (from prepartum 7% to postpartum 32%). For the archaea, qPCR analysis of 16S rRNA transcript number, revealed a significant prepartum to postpartum increase in  Methanobacteriales , in accordance with an observed increase (from prepartum 80% to postpartum 89%) in relative abundance of 16S rRNA transcript amplicons allocated to this order. On the other hand, a significant prepartum to postpartum decrease (from 15% to 2%) was observed in relative abundance of  Methanomassiliicoccales  16S rRNA transcripts. In contrast to qPCR analysis of the 16S rRNA transcripts, quantification of  mcrA  transcripts revealed no change in total abundance of metabolically active methanogens over the transition period. According to T-RFLP analysis of the  mcrA  transcripts, two  Methanobacteriales  genera,  Methanobrevibacter  and  Methanosphaera  (represented by the T-RFs 39 and 267 bp), represented more than 70% of the metabolically active methanogens, showing no significant changes over the transition period; minor T-RFs, likely to represent members of the order  Methanomassiliicoccales  and with a relative abundance below 5% in total, decreased significantly over the transition period. In accordance with the T-RFLP analysis, the  mcrA  transcript amplicon sequencing revealed  Methanobacteriales  to cover 99% of the total reads, dominated by the genera  Methanobrevibacter  (75%) and  Methanosphaera  (24%), whereas the  Methanomassiliicoccales  order covered only 0.2% of the total reads. In conclusion, the present study showed that the structure of the metabolically active bacterial and archaeal rumen communities changed over the transition period, likely in response to the dramatic changes in physiology and nutritional factors like dry matter intake and feed composition. It should be noted however that for the methanogens, the observed community changes were influenced by the analyzed gene ( mcrA  or 16S rRNA).

Community structure of the metabolically active rumen bacterial and archaeal communities of dairy cows over the transition period