title: Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools.
abstract: The temporal sequence of microbial establishment in the rumen of the neonatal ruminant has important ecological and pathophysiological implications. In this study, we characterized the rumen microbiota of pre-ruminant calves fed milk replacer using two approaches, pyrosequencing of hypervariable V3-V5 regions of the 16S rRNA gene and whole-genome shotgun approach. Fifteen bacterial phyla were identified in the microbiota of pre-ruminant calves. Bacteroidetes was the predominant phylum in the rumen microbiota of 42-day-old calves, representing 74.8% of the 16S sequences, followed by Firmicutes (12.0%), Proteobacteria (10.4%), Verrucomicrobia (1.2%) and Synergistetes (1.1%). However, the phylum-level composition of 14-day-old calves was distinctly different. A total of 170 bacterial genera were identified while the core microbiome of pre-ruminant calves included 45 genera. Rumen development seemingly had a significant impact on microbial diversity. The dazzling functional diversity of the rumen microbiota was reflected by identification of 8298 Pfam and 3670 COG protein families. The rumen microbiota of pre-ruminant calves displayed a considerable compositional heterogeneity during early development. This is evidenced by a profound difference in rumen microbial composition between the two age groups. However, all functional classes between the two age groups had a remarkably similar assignment, suggesting that rumen microbial communities of pre-ruminant calves maintained a stable function and metabolic potentials while their phylogenetic composition fluctuated greatly. The presence of all major types of rumen microorganisms suggests that the rumen of pre-ruminant calves may not be rudimentary. Our results provide insight into rumen microbiota dynamics and will facilitate efforts in formulating optimal early-weaning strategies.
authors: Bovine Functional Genomics Laboratory, Animal and Natural Resources Institute, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA. robert.li@ars.usda.gov
authors: Robert W
authors: RW
authors: Li
authors: Erin E
authors: EE
authors: Connor
authors: Congjun
authors: C
authors: Li
authors: Ransom L
authors: RL
authors: Baldwin Vi
authors: Michael E
authors: ME
authors: Sparks
mesh_terms: D000821:Animal Feed; D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D002417:Cattle; D004269:DNA, Bacterial / Q000235:genetics; D008297:Male; D054892:Metagenome; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012417:Rumen / Q000382:microbiology*; D017422:Sequence Analysis, DNA; D014886:Weaning
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S