Microbiome analysis of dairy cows fed pasture or total mixed ration diets

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224

ABSTRACTFeed-efficient animals have lower production costs and reduced environmental impact. Given that rumen microbial fermentation plays a pivotal role in host nutrition, the premise that rumen microbiota may contribute to host feed efficiency is gaining momentum. Since diet is a major factor in determining rumen community structure and fermentation patterns, we investigated the effect of divergence in phenotypic residual feed intake (RFI) on ruminal community structure of beef cattle across two contrasting diets. PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) were performed to profile the rumen bacterial population and to quantify the ruminal populations ofEntodiniumspp., protozoa,Fibrobacter succinogenes,Ruminococcus flavefaciens,Ruminococcus albus,Prevotella brevis, the genusPrevotella, and fungi in 14 low (efficient)- and 14 high (inefficient)-RFI animals offered a low-energy, high-forage diet, followed by a high-energy, low-forage diet. Canonical correspondence and Spearman correlation analyses were used to investigate associations between physiological variables and rumen microbial structure and specific microbial populations, respectively. The effect of RFI on bacterial profiles was influenced by diet, with the association between RFI group and PCR-DGGE profiles stronger for the higher forage diet. qPCR showed thatPrevotellaabundance was higher (P< 0.0001) in inefficient animals. A higher (P< 0.0001) abundance ofEntodiniumandPrevotellaspp. and a lower (P< 0.0001) abundance ofFibrobacter succinogeneswere observed when animals were offered the low-forage diet. Thus, differences in the ruminal microflora may contribute to host feed efficiency, although this effect may also be modulated by the diet offered.

mentioning

confidence: 99%

Effect of Phenotypic Residual Feed Intake and Dietary Forage Content on the Rumen Microbial Community of Beef Cattle

Carberry

Kenny

Han

et al. 2012

262

224

“…In the rumen contents of dairy cows, deep amplicon sequencing of the 16S rRNA gene revealed a higher abundance of members of the Fibrobacteraceae family in total mixed-ration samples and a lower abundance of members of the propionate-producing Veillonellaceae than in pasture samples (8). Moreover, based on sequence information from the reference marker of PCR-denaturing gradient gel electrophoresis (DGGE), abundances of the phyla Firmicutes and Proteobacteria in the heifer ruminal epithelial bacterial community decreased in response to a rapid transition from a diet containing 97% hay to a diet containing 8% hay (9).…”

mentioning

confidence: 99%

Taxonomic Identification of Ruminal Epithelial Bacterial Diversity during Rumen Development in Goats

Jiao

Huang

Zhou

et al. 2015

bUnderstanding of the colonization process of epithelial bacteria attached to the rumen tissue during rumen development is very limited. Ruminal epithelial bacterial colonization is of great significance for the relationship between the microbiota and the host and can influence the early development and health of the host. MiSeq sequencing of 16S rRNA genes and quantitative realtime PCR (qPCR) were applied to characterize ruminal epithelial bacterial diversity during rumen development in this study. Seventeen goat kids were selected to reflect the no-rumination (0 and 7 days), transition (28 and 42 days), and rumination (70 days) phases of animal development. Alpha diversity indices (operational taxonomic unit [OTU] numbers, Chao estimate, and Shannon index) increased (P < 0.01) with age, and principal coordinate analysis (PCoA) revealed that the samples clustered together according to age group. Phylogenetic analysis revealed that Proteobacteria, Firmicutes, and Bacteroidetes were detected as the dominant phyla regardless of the age group, and the abundance of Proteobacteria declined quadratically with age (P < 0.001), while the abundances of Bacteroidetes (P ‫؍‬ 0.088) and Firmicutes (P ‫؍‬ 0.009) increased with age. At the genus level, Escherichia (80.79%) dominated at day zero, while Prevotella, Butyrivibrio, and Campylobacter surged (linearly; P < 0.01) in abundance at 42 and 70 days. qPCR showed that the total copy number of epithelial bacteria increased linearly (P ‫؍‬ 0.013) with age. In addition, the abundances of the genera Butyrivibrio, Campylobacter, and Desulfobulbus were positively correlated with rumen weight, rumen papilla length, ruminal ammonia and total volatile fatty acid concentrations, and activities of carboxymethylcellulase (CMCase) and xylanase. Taking the data together, colonization by ruminal epithelial bacteria is age related (achieved at 2 months) and might participate in the anatomic and functional development of the rumen. R ecent years have witnessed growing interest in the diversity and function of ruminal epithelial bacteria. It has been demonstrated that ruminal epithelial bacteria are involved in oxygen scavenging, tissue recycling, and urea digestion (1). Furthermore, in steers, the ruminal epithelial bacterial communities of acidosisresistant and acidosis-susceptible groups were different during subacute ruminal acidosis development, and this difference could be recognized by the host TLRs (Toll-like receptors), which are associated with changes in the function of the rumen epithelial tissue barrier (2). Similarly, in the mouse colon, epithelial bacterial diversity correlated with TLR2 and TLR4 gene expression (3). These findings reveal that since epithelial bacteria are directly attached to the epithelial surface, their end products may play a direct or indirect role in host immune responses and tissue barrier function.Ruminal epithelial bacteria are distinctly different at the taxonomic level from bacteria associated with rumen contents (4, 5). By use of culture-based tech...

“…Over 27,000 carbohydrate-active genes, 50 proteins with enzymatic activity against cellulosic substrates, and 15 uncultured microbial genomes were revealed in a study of rumen samples using high-throughput sequencing (4). Diet can be a significant factor shaping the microbial diversity of the rumen content of dairy cows (5) and beef cows (6). Variation in the rumen microbiome of dairy cattle has also been linked to levels of methane emission (7), and metagenomic profiling of the rumen microbiome can actually be used to predict phenotypes related to enteric methane gas production (8).…”

mentioning

confidence: 99%

Prepartum and Postpartum Rumen Fluid Microbiomes: Characterization and Correlation with Production Traits in Dairy Cows

Lima

Oikonomou

Lima

et al. 2015

169

138

cMicrobes present in the rumen of dairy cows are essential for degradation of cellulosic and nonstructural carbohydrates of plant origin. The prepartum and postpartum diets of high-producing dairy cows are substantially different, but in what ways the rumen microbiome changes in response and how those changes may influence production traits are not well elucidated. Here, we sequenced the 16S and 18S rRNA genes using the MiSeq platform to characterize the prepartum and postpartum rumen fluid microbiomes in 115 high-producing dairy cows, including both primiparous and multiparous animals. Discriminant analysis identified differences between the microbiomes of prepartum and postpartum samples and between primiparous and multiparous cows. 18S rRNA sequencing revealed an overwhelming dominance of the protozoan class Litostomatea, with over 90% of the eukaryotic microbial population belonging to that group. Additionally, fungi were relatively more prevalent and Litostomatea relatively less prevalent in prepartum samples than in postpartum ones. The core rumen microbiome (common to all samples) consisted of 64 bacterial taxa, of which members of the genus Prevotella were the most prevalent. The Chao1 richness index was greater for prepartum multiparous cows than for postpartum multiparous cows. Multivariable models identified bacterial taxa associated with increased or reduced milk production, and general linear models revealed that a metagenomically based prediction of productivity is highly associated with production of actual milk and milk components. In conclusion, the structure of the rumen fluid microbiome shifts between the prepartum and first-week postpartum periods, and its profile within the context of this study could be used to accurately predict production traits. Rumen microbiology studies in the last 4 to 5 decades have contributed to the advancement of the field of anaerobic microbiology (1, 2) and have explained much regarding the nature of ruminal fermentation, its effect on ruminant nutrition, and the physiological importance of volatile fatty acid production by ruminal microorganisms to the nutrition of the host. Additionally, ruminal microbiology provided vital concepts and quantitative data that are essential for the construction of the mathematical models that allow for precision nutrition of ruminants, which has been adopted throughout the world in modern meat and milk production systems (3). However, direct manipulation of fermentation by biotechnological means has so far been restricted to a few antimicrobial compounds and some microorganisms that can be added to the feed.High-throughput sequencing technologies have opened new frontiers in microbial analysis by allowing cost-effective characterization of complex microbial communities in biological samples, and they have significantly improved our knowledge of bovine rumen microbial diversity. Over 27,000 carbohydrate-active genes, 50 proteins with enzymatic activity against cellulosic substrates, and 15 uncultured microbial genomes were reveal...