title: Metagenomic assessment of the functional potential of the rumen microbiome in Holstein dairy cows.
abstract: The microbial ecology of the rumen microbiome is influenced by the diet and the physiological status of the dairy cow and can have tremendous influence on the yield and components of milk. There are significant differences in milk yields between first and subsequent lactations of dairy cows, but information on how the rumen microbiome changes as the dairy cow gets older has received little attention. We characterized the rumen microbiome of the dairy cow for phylogeny and functional pathways by lactation group and stage of lactation using a metagenomics approach. Our findings revealed that the rumen microbiome was dominated by Bacteroidetes (70%), Firmicutes (15-20%) and Proteobacteria (7%). The abundance of Firmicutes and Proteobacteria were independently influenced by diet and lactation. Bacteroidetes contributed to a majority of the metabolic functions in first lactation dairy cows while the contribution from Firmicutes and Proteobacteria increased incrementally in second and third lactation dairy cows. We found that nearly 70% of the CAZymes were oligosaccharide breaking enzymes which reflect the higher starch and fermentable sugars in the diet. The results of this study suggest that the rumen microbiome continues to evolve as the dairy cow advances in lactations and these changes may have a significant role in milk production.
authors.affiliation: Department of Clinical Studies, Center for Animal Health and Productivity, School of Veterinary Medicine, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348, USA. Electronic address: dpitta@vet.upenn.edu.
authors.forename: Dipti W
authors.initials: DW
authors.lastname: Pitta
authors.affiliation: Department of Clinical Studies, Center for Animal Health and Productivity, School of Veterinary Medicine, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348, USA.
authors.forename: Nagaraju
authors.initials: N
authors.lastname: Indugu
authors.affiliation: Department of Clinical Studies, Center for Animal Health and Productivity, School of Veterinary Medicine, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348, USA.
authors.forename: Sanjay
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Department of Clinical Studies, Center for Animal Health and Productivity, School of Veterinary Medicine, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348, USA.
authors.forename: Bonnie
authors.initials: B
authors.lastname: Vecchiarelli
authors.affiliation: Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, PA, USA; Center for Infection and Immunity, Columbia University, New York 10027, USA.
authors.forename: Rohini
authors.initials: R
authors.lastname: Sinha
authors.affiliation: Department of Clinical Studies, Center for Animal Health and Productivity, School of Veterinary Medicine, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348, USA.
authors.forename: Linda D
authors.initials: LD
authors.lastname: Baker
authors.affiliation: Department of Clinical Studies, Center for Animal Health and Productivity, School of Veterinary Medicine, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348, USA.
authors.forename: Bhima
authors.initials: B
authors.lastname: Bhukya
authors.affiliation: Department of Clinical Studies, Center for Animal Health and Productivity, School of Veterinary Medicine, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348, USA.
authors.forename: James D
authors.initials: JD
authors.lastname: Ferguson
mesh_terms: D000818:Animals; D001105:Archaea / Q000145:classification / Q000235:genetics; D001419:Bacteria / Q000145:classification / Q000235:genetics; D002417:Cattle; D019295:Computational Biology / Q000379:methods; D007774:Lactation; D054892:Metagenome; D056186:Metagenomics / Q000379:methods; D064307:Microbiota; D010802:Phylogeny; D012417:Rumen / Q000382:microbiology* / Q000502:physiology
keywords: CAZymes; Dairy cattle; Functional potential; Metagenomics; Phylogeny; Rumen microbiome