Changes in the Rumen Epimural Bacterial Diversity of Beef Cattle as Affected by Diet and Induced Ruminal Acidosis

bAnalysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R ‫؍‬ 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R ‫؍‬ 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants. Intensive farming of ruminant livestock for the production of human food and everyday commodities has wide implications for the environment (1). Apart from the well-described impacts of animals and their effluents on soils and waterways through nitrate leaching (2, 3), ruminants also represent a major anthropogenic source of the potent greenhouse gas methane through the microbial processes occurring in the rumen during fermentation of ingested feed (4). There is also great interest in the role of rumen microorganisms in feed conversion to animal products and in the association of differences in feed provided or animal genetics with the rumen microbial community. With the rapid development of highly resolving high-throughput sequencing technologies, there has been increased interest and opportunity to better understand the structure of bacterial, archaeal, and eukaryotic microbial communities in the rumen and to resolve the contributions of individual taxa to methane emission or animal productivity. Over the past years, this knowledge has provided valuable leads to new methane mitigation strategies, such as the use of low-greenhousegas feeds, feed supplements, vaccines, and inhibitors, and selective breeding for animals that show a naturally low-methane-emission phenotype (for a recent review, see reference 5). For example, i...

Section: Discussionsupporting

confidence: 81%

Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen

Kittelmann

Kirk

Jonker

et al. 2015

“…In all age groups, Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phyla in the epithelial microbiota, and their abundances and genus compositions differed remarkably, in line with previous studies (7,32). Similarly, at the genus level, although the abundances of some genera changed with age, they were present in all groups, representing a core microbiome in the ruminal epithelial microbiota of goats.…”

Section: Figsupporting

confidence: 68%

“…(22.4%), Selenomonas ruminantium (9.9%), Succinivibrio dextrinosolvens (8.7%) and Streptococcus bovis (8.1%) predominate (6). At the class level, ruminal epithelial bacteria were found by pyrosequencing to be composed mainly of Clostridia (67%), Bacteroidia (9%), Deltaproteobacteria (4%), and Erysipelotrichia (3%) (7).…”

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

161

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...