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.

Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water

“…In contrast, the Enterobacteriales order was highly prevalent in composite cattle wastewater samples. This is not in agreement with a previous study that reported that Firmicutes was the most abundant phylum across all communities in dairy cows (65). Such a discrepancy could be due to the fact that we collected cattle wastewater samples from wastewater drains in abattoirs, whereas Pitta and colleagues (65) collected ruminant contents from the stomachs of dairy cows.…”

Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers

“…Succiniclasticum (3.53; 1.52%) and Succinivibrio (0.26; 0.01%), represented differences between the PacBio V1-V8 and Miseq V1-V3 amplicons (P b 0.05), which have been identified in the rumen at abundances greater than 0.1% (Myer et al, 2015a;Pitta et al, 2014).…”

Aspects of rumen adaptation in dairy cattle : morphological, functional, and gene expression changes of the rumen papillae and changes of the rumen microbiota during the transition period

“…In comparison to some studies, where bacterial communities were dominated by Bacteroidales, and specifically its genus Prevotella (Jami et al, 2013;Pitta et al, 2014), in the present study multiple orders of bacteria have a sizable relative abundance. Such more diverse bacterial communities appear to be more common globally , and is likewise reported by Wang et al (2012), Petri et al (2013) and Lima et al (2015).…”

“…Various studies addressed this relationship between ration composition and the composition of the rumen microbiota (review by McCann et al, 2014). However, few studies (Mohammed et al, 2012;Pitta et al, 2014;Lima et al, 2015) focused on the transition period in dairy cattle. Unfortunately, these studies generally provide very little information about feed intake and no studies have reported peripartum changes in papillae morphology, VFA absorption capacity, and their relationship to the changes in the microbiota.…”

“…Various studies addressed the interrelationship between ration composition and the composition of the rumen microbiota (reviewed by McCann et al, 2014). However, few studies (Mohammed et al, 2012;Pitta et al, 2014;Lima et al, 2015) focused on the transition period in dairy cattle, and knowledge of rumen microbiota changes during this period is limited. In addition, the idea of functional redundancy requires the study of changes in the microbiota together with measurements of substrate degradation capacity by the microbiota to understand the functional impact of any changes in microbiota community composition.…”