title: Temporal dynamics in the ruminal microbiome of dairy cows during the transition period.
abstract: The transition period in dairy cows refers to the period from 3 wk before calving to 3 wk post-calving and is a critical time for influencing milk production and cow health. We hypothesize that the ruminal microbiome shifts as dairy cows transition from a non-lactation period into lactation due to changes in dietary regimen. The purpose of this study was to identify differences in the ruminal microbiome of primiparous and multiparous (study group) cows during the transition period. Five primiparous and 5 multiparous cows were randomly selected from a herd, and ruminal contents were sampled, via stomach tube, 4 times (study day) at 3 wk before calving date (S1), 1 to 3 d post-calving (S2), and 4 (S3) and 8 wk (S4) into lactation and were evaluated for bacterial diversity using 16S pyrotags. Both groups received the same pre-fresh diet (14.6% CP, 44.0% NDF, 21.9% starch) and 3 different lactation diets (L1, L2, and L3) varying in forage base but not amount and formulated to have similar nutrient specifications (16.8% to 17.7% CP; 32.5% to 33.6% NDF; 26.2% to 29.1% starch) post-calving. Forty bacterial communities were analyzed on the basis of annotations of 100,000 reads, resulting in 15,861 operational taxonomic units grouped into 17 bacterial phyla. The UniFrac distance metric revealed that both study group and study day had an effect on the community compositions (P < 0.05; permutational multivariate ANOVA test). The most abundant phyla observed were Bacteroidetes and Firmicutes across all the communities. As the cows transitioned into lactation, the ratio of Bacteroidetes to Firmicutes increased from 6:1 to 12:1 (P < 0.05; Mann-Whitney U test), and this ratio was greater in primiparous cows than in multiparous cows (P < 0.05). This report is the first to explore the effect of parity on dynamics in the ruminal microbiome of cows during the transition period.
authors.affiliation: Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348 dpitta@vet.upenn.edu.
authors.forename: D W
authors.initials: DW
authors.lastname: Pitta
authors.affiliation: Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348.
authors.forename: S
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348.
authors.forename: B
authors.initials: B
authors.lastname: Vecchiarelli
authors.affiliation: Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104.
authors.forename: D J
authors.initials: DJ
authors.lastname: Shirley
authors.affiliation: Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104.
authors.forename: K
authors.initials: K
authors.lastname: Bittinger
authors.affiliation: Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348.
authors.forename: L D
authors.initials: LD
authors.lastname: Baker
authors.affiliation: Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348.
authors.forename: J D
authors.initials: JD
authors.lastname: Ferguson
authors.affiliation: Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Kennett Square 19348.
authors.forename: N
authors.initials: N
authors.lastname: Thomsen
mesh_terms: D000818:Animals; D002417:Cattle / Q000382:microbiology*; D004032:Diet / Q000662:veterinary; D005260:Female; D007774:Lactation / Q000502:physiology; D064307:Microbiota / Q000502:physiology*; D010298:Parity; D058725:Peripartum Period; D011247:Pregnancy; D012417:Rumen / Q000382:microbiology*; D013045:Species Specificity; D013997:Time Factors
keywords: 16S pyrotags; dairy cows; ruminal microbiome; total mixed ration; transition period