A Multi-Kingdom Study Reveals the Plasticity of the Rumen Microbiota in Response to a Shift From Non-grazing to Grazing Diets in Sheep

Increasing feed efficiency is a key target in ruminant science which requires a better understanding of rumen microbiota. This study investigated the effect of a shift from a non-grazing to a grazing diet on the rumen bacterial, methanogenic archaea, fungal, and protozoal communities. A systems biology approach based on a description of the community structure, core microbiota, network analysis, and taxon abundance linked to the rumen fermentation was used to explore the benefits of increasing depth of the community analysis. A total of 24 sheep were fed ryegrass hay supplemented with concentrate (CON) and subsequently ryegrass pasture (PAS) following a straight through experimental design. Results showed that concentrate supplementation in CON-fed animals (mainly starch) promoted a simplified rumen microbiota in terms of network density and bacterial, methanogen and fungal species richness which favored the proliferation of amylolytic microbes and VFA production (+48%), but led to a lower (ca. 4-fold) ammonia concentration making the N availability a limiting factor certain microbes. The adaptation process from the CON to the PAS diet consisted on an increase in the microbial concentration (biomass of bacteria, methanogens, and protozoa), diversity (+221, +3, and +21 OTUs for bacteria, methanogens, and fungi, respectively), microbial network complexity (+18 nodes and +86 edges) and in the abundance of key microbes involved in cellulolysis (Ruminococcus, Butyrivibrio, and Orpinomyces), proteolysis (Prevotella and Entodiniinae), lactate production (Streptococcus and Selenomonas), as well as methylotrophic archaea (Methanomassiliicoccaceae). This microbial adaptation indicated that pasture degradation is a complex process which requires a diverse consortium of microbes working together. The correlations between the abundance of microbial taxa and rumen fermentation parameters were not consistent across diets suggesting a metabolic plasticity which allowed microbes to adapt to different substrates and to shift their fermentation products. The core microbiota was composed of 34, 9, and 13 genera for bacteria, methanogens, and fungi, respectively, which were shared by all sheep, independent of diet. This systems biology approach adds a new dimension to our understanding of the rumen microbial interactions and may provide new clues to describe the mode of action of future nutritional interventions.

Megasphaera elsdenii Lactate Degradation Pattern Shifts in Rumen Acidosis Models

Background:Megasphaera elsdenii is an ecologically important rumen bacterium that metabolizes lactate and relieves rumen acidosis (RA) induced by a high-grain-diet. Understanding the regulatory mechanisms of the lactate metabolism of this species in RA conditions might contribute to developing dietary strategies to alleviate RA.

Methods:Megasphaera elsdenii was co-cultured with four lactate producers (Streptococcus bovis, Lactobacilli fermentum, Butyrivibrio fibrisolvens, and Selenomonas ruminantium) and a series of substrate starch doses (1, 3, and 9 g/L) were used to induce one normal and two RA models (subacute rumen acidosis, SARA and acute rumen acidosis, ARA) under batch conditions. The associations between bacterial competition and the shift of organic acids’ (OA) accumulation patterns in both statics and dynamics manners were investigated in RA models. Furthermore, we examined the effects of substrate lactate concentration and pH on Megasphaera elsdenii’s lactate degradation pattern and genes related to the lactate utilizing pathways in the continuous culture.

Results and Conclusion: The positive growth of M. elsdenii and B. fibrisolvens caused OA accumulation in the SARA model to shift from lactate to butyrate and resulted in pH recovery. Furthermore, both the quantities of substrate lactate and pH had remarkable effects on M. elsdenii lactate utilization due to the transcriptional regulation of metabolic genes, and the lactate utilization in M. elsdenii was more sensitive to pH changes than to the substrate lactate level. In addition, compared with associations based on statics data, associations discovered from dynamics data showed greater significance and gave additional explanations regarding the relationships between bacterial competition and OA accumulation.

Composition of Rumen Bacterial Community in Dairy Cows With Different Levels of Somatic Cell Counts

Mastitis is an inflammatory disease, affects the dairy industry and has a severe economic impact. During subclinical mastitis, milk production and milk quality deteriorates. Recently, rumen microbial composition has been linked to rumen health, but few studies have investigated the effect of rumen microbiota on mammary health in cows. This study was undertaken to identify the rumen microbial composition and associated microbial fermentation in cows with different somatic cell counts (SCC), with the speculation that cows with different health statuses of the mammary gland have different rumen bacterial composition and diversity. A total of 319 Holstein dairy cows fed the same diet and under the same management were selected and divided into four groups as SCC1 (N = 175), SCC2 (N = 49), SCC3 (N = 49), and SCC4 (N = 46) with < 200,000, 200,001–500,000, 500,001–1,000,000, and >1,000,000 somatic cells/mL, respectively. Further, 20 cows with the lowest SCC and 20 cows with the highest SCC were identified. The rumen microbial composition was profiled using 16S rRNA sequencing, along with measurement of rumen fermentation parameters and milking performance. Compared to low SCC, cows with high SCC showed poorer milk yield, milk composition, and rumen volatile fatty acids concentration, but higher rumen bacterial diversity. Although the predominant rumen bacterial taxa did not vary among the SCC groups, the relative abundance of phyla SR1 and Actinobacteria, unclassified family Clostridiales and genus Butyrivibrio were significantly different. In addition, Proteobacteria and family Succinivibrionaceae were enriched in cows with low SCC. Our results suggest that specific rumen microbes are altered in cows with high SCC.

Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences

Background: Microbiome studies need to analyze massive sequencing data, which requires the use of sophisticated bioinformatics pipelines. Up to date, several tools are available, although the literature is scarce on studies that compare the performance of different bioinformatics pipelines on rumen microbiota when 16S rRNA amplicons are analyzed. The impact of the pipeline on the outcome of the results is also unknown, mainly in terms of the output from studies using these tools as an intermediate phenotype (pseudophenotypes). This study compares two commonly used software (Quantitative Insights Into Microbial Ecology) (QIIME) and mothur, and two microbial gene data bases (GreenGenes and SILVA) for 16S rRNA gene analysis, using metagenome read data collected from rumen content of a cohort of dairy cows.

Results: We compared the relative abundance (RA) of the identified OTUs at the genus level. Both tools presented a high degree of agreement at identifying the most abundant genera: Bifidobacterium, Butyrivibrio, Methanobrevibacter, Prevotella, and Succiniclasticum (RA > 1%), regardless the database. There were no statistical differences between mothur and QIIME (P > 0.05) at estimating the overall RA of the most abundant (RA > 10%) genera, either using SILVA or GreenGenes. However, differences were found at RA < 10% (P < 0.05) when using GreenGenes as database, with mothur assigning OTUs to a larger number of genera and in larger RA for these less frequent microorganisms. With this database mothur resulted in larger richness (P < 0.05), more favorable rarefaction curves and a larger analytic sensitivity. These differences caused significant and relevant differences between tools at identifying the dissimilarity of microbiotas between pairs of animals. However, these differences were attenuated, but not erased, when SILVA was used as the reference database.

Conclusion: The findings showed that the SILVA database seemed a preferred reference dataset for classifying OTUs from rumen microbiota. If this database was used, both QIIME and mothur produced comparable richness and diversity, and also in the RA of most common rumen microbes. However, important differences were found for less common microorganisms which impacted on the beta diversity calculated between pipelines. This may have relevant implications at studying global rumen microbiota.

Dietary starch and rhubarb supplement increase ruminal dissolved hydrogen without altering rumen fermentation and methane emissions in goats

Hydrogen is an important intermediate that is produced during carbohydrate fermentation to volatile fatty acid and utilized by methanogens to produce methane in the rumen. Ruminal volatile fatty acid and dissolved methane concentrations are more than 500 times greater than dissolved hydrogen concentration. Therefore, we hypothesized that dissolved hydrogen might have a higher sensitivity in response to dietary changes compared with volatile fatty acid and dissolved methane. Using goats, we investigated the effects of increasing dietary starch content (maize replaced with wheat bran) and supplementing with rhubarb rhizomes and roots on the relationships among dissolved hydrogen, dissolved methane and other fermentation end products. The study was conducted in a replicated 4×4 Latin square with a 2×2 factorial arrangement of four treatments: two starch levels (220 v. 320 g/kg dry matter (DM)), without and with rhubarb supplement (0% v. 2.8% of total mixed ration). Increased dietary starch and rhubarb supplementation did not alter volatile fatty acid concentrations or methane emissions in terms of g/day, g/g DM intake and g/g organic matter digested. However, goats fed the high-starch diet had greater dissolved hydrogen (P=0.005) and relative abundance of Selenomonas ruminantium (P&lt;0.01), and lower (P=0.02) copy number of protozoa than those fed the low-starch diet. Rhubarb increased ruminal dissolved H2 (P=0.03) and total volatile fatty acid concentration (P&lt;0.001), but decreased copies of bacteria (P=0.002). In conclusion, dissolved hydrogen appears to be more sensitive to dietary changes with starch content and rhubarb supplementation, when compared with volatile fatty acid concentrations and methane production.

Lactic acid treatment of by-products and phosphorus level in the diet modulate bacterial microbiome and the predicted metagenome functions using the rumen simulation technique

This study used a rumen simulation technique to evaluate the effects of soaking of by-product-rich concentrate (BPC) in 5% lactic acid (LAC; vol/vol) on the rumen microbiota, predicted metagenome, fermentation characteristics, and nutrient degradation without or with supplemented P. The diet was supplemented with 1.6 g of P in the form of monocalcium phosphate per kilogram of dry matter in addition to 284 mg of inorganic P/d per fermentor via artificial saliva. Fermentor fluid was collected for analyses of short-chain fatty acids, fermentation gases, redox potential, and microbiota and feed residues for calculation of nutrient degradation. The microbiota composition was assessed using paired-end Illumina (Illumina Inc., San Diego, CA) MiSeq sequencing of the V3 to V5 region of the 16S rRNA gene. Soaking in LAC reduced the contents of crude protein, neutral and acid detergent fibers, and organic matter fractions as well as ash and P content of the BPC. Both the LAC treatment of BPC and the inorganic P modified the relative bacterial abundances mainly within the predominant orders Bacteroidales and Clostridiales. Supervised DIABLO N-integration networking supported that operational taxonomic units related to BS11, Ruminococcaceae, Christensenellaceae, Eubacterium, and Selenomonas were the most discriminant for the LAC-treated BPC, whereas other operational taxonomic units related to BS11, RFN20, Ruminococcus, and Succiniclasticum were best correlated with the inorganic P supplementation. Integration networking also showed that carbohydrate and pyruvate metabolism, biosynthesis of unsaturated fatty acids, and degradation of several xenobiotics were stimulated by the LAC treatment of BPC. Those data supported the enhanced fermentation activity as indicated by increased total short-chain fatty acid concentration, especially propionate and butyrate, and methane, but decreased ruminal crude protein degradation, with the LAC-treated compared with control-treated BPC. In contrast, despite an increased abundance of imputed functions, such as inositol phosphate metabolism, phosphatidylinositol signaling, and fructose and mannose metabolism, the reduced abundance of the imputed Kyoto Encyclopedia of Genes and Genomes pathway "transcription machinery" as well as the decrease in total short-chain fatty acids and nutrient degradation indicated reduced bacterial metabolic activity with the inorganic P supplementation. In conclusion, soaking of BPC in LAC may favor the proliferation of certain fibrolytic bacterial taxa and stimulate their metabolic activity, whereas the supplemented P to a diet already meeting ruminal P needs may impair ruminal nutrient utilization.

Persistence of Cellulolytic Bacteria Fibrobacter and Treponema After Short-Term Corn Stover-Based Dietary Intervention Reveals the Potential to Improve Rumen Fibrolytic Function

Limited lignocellulose degradation is the primary obstacle to feed digestion efficiency in ruminant animals. Low-quality forage with high levels of fibrous components can favor the proliferation of fibrolytic bacteria, but whether this can result a profound microbial shift after dietary intervention remains unclear. In this study, we monitored the microbial communities in the rumens of five ruminally cannulated Hu sheep through dietary transition from alfalfa hay (AH, pre-CS) to corn stover (CS, post-CS) and then back to AH (post-AH), with each treatment lasting for 14 days. The CS intervention significantly increased the relative abundance of microorganisms involved in lignocellulose degradation, including Fibrobacter and Treponema. When the diet was switched back to AH, the microbial community did not completely return to a pre-CS treatment state. In the post-AH microbial community, the relative abundances of Fibrobacter and Treponema were persistently high, and were similar to those in the post-CS community. Meanwhile, the diversity of the microbial community increased after dietary transition from AH to CS and remained significantly higher after transition from CS to AH compared to those under the original AH diet. Enzyme activity measurement verified significant increase of carboxymethyl cellulase (CMCase) and xylanase catalytic activities in the rumen. Microbial functional predictions using Tax4Fun revealed that this microbial persistence may enhance the carbohydrate metabolism pathway in the rumen. In summary, persistence of Fibrobacter and Treponema can be enhanced through a low-quality forage intervention at least for 2 weeks, which may enlighten the reprogram of microbial population in the rumen in the future.

Alfalfa Intervention Alters Rumen Microbial Community Development in Hu Lambs During Early Life

The pre-weaning period is crucial for rumen developmental plasticity, which can have a long-term impact on animal performance. Understanding the rumen microbiota during early life is important to elucidate its potential role in rumen development. In this study, the rumen microbiota of 10-day-old Hu lambs fed either milk replacer (B-10), milk replacer and starter (STA) or milk replacer and starter supplemented with alfalfa (S-ALF) in the pre- (d17, 24, and 38) and post-weaning periods (d45 and 66) were assessed to characterize rumen microbial colonization during early life and its response to fiber intervention. In the rumens of B-10 lambs, 498 operational taxonomic units belonging to 33 predominant genera were observed, and the top six predicted functions included “Membrane transport,” “carbohydrate metabolism,” “amino acid metabolism,” “replication and repair,” “translation,” and “energy metabolism.” Prevotella, Succinivibrio, Bifidobacterium, and Butyrivibrio abundances were increased at d38 for both STA and S-ALF groups compared to the B-10 group, whereas fibrolytic bacteria of the taxa Lachnospiraceae and Treponema were only increased in the S-ALF group at d38. A number of saccharolytic bacteria (Bacteroidaceae), organic acid-producing bacteria (Coprococcus and Actinomyces), proteolytic and amino acid fermenters (Fusobacterium) and fibrolytic bacteria (unclassified Ruminococcaceae) were significantly decreased in the STA lambs but not in the S-ALF lambs at d38. After weaning and exposed to alfalfa, the rumen microbial composition in the STA group started to appear similar to that of the S-ALF lambs. The relative abundance of unclassified Clostridiales was higher in S-ALF lambs than STA lambs after weaning. Spearman’s correlation analysis showed positive relationships between unclassified Lachnospiraceae, unclassified Clostridiales, Treponema, unclassified Bacteroidales, Coprococcus and crude protein intake, neutral detergent fiber intake, and plasma β-hydroxybutyrate. The unclassified Lachnospiraceae and Treponema were also positively correlated with average daily gain. Our results revealed that alfalfa stimulated changes in rumen microbiota during the pre- and post-weaning periods and was consistent with rumen development for better feed intake and animal performance before and after weaning. The findings of this study provide clues for strategies to improve rumen function through manipulation of the rumen microbiota during early life.

Effect of hay supplementation timing on rumen microbiota in suckling calves

An animal feeding trial was conducted on 18 seven‐day‐old Holstein dairy bull calves weighing 42 ± 3 kg each. Calves were randomly assigned into three groups (n = 6 each). The dietary treatments were as follows: (1) milk and starter for the control group (MS), (2) supplementation of oat hay from week 2 on the basis of milk and starter (MSO2), and (3) supplementation of oat hay from week 6 on the basis of milk and starter (MSO6). All animals were fed starter and oat hay ad libitum. The major phyla in the different groups of rumen fluid included Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria, and Euryarchaeota. The major genera were identified, and major genera proportions in the three groups were as follows: Methanobrevibacter (Euryarchaeota), 2.1%, 1.7%, and 2.1%; Olsenella (Actinobacteria), 23.9%, 17.7%, and 12.8%; Prevotella (Bacteroidetes), 10.5%, 16.5%, and 19.2%; Dialister (Firmicutes), 3.3%, 4.1%, and 2.8%; Succiniclasticum (Firmicutes), 3.8%, 4.7%, and 9.2%; and Sharpea (Firmicutes), 0.4%, 2.5%, and 0.2%, respectively. There were no significant differences in the various phyla among the three groups (p > .05). The results showed that calves hay supplementation time did not affect the diversity of the rumen microbiota in the suckling calves. However, the hay supplementation altered the proportion of the various microbial populations, supplementation of oat hay from week 2 on the basis of milk and starter could improve calves rumen pH.

Enhancing the Resolution of Rumen Microbial Classification from Metatranscriptomic Data Using Kraken and Mothur

The advent of next generation sequencing and bioinformatics tools have greatly advanced our knowledge about the phylogenetic diversity and ecological role of microbes inhabiting the mammalian gut. However, there is a lack of information on the evaluation of these computational tools in the context of the rumen microbiome as these programs have mostly been benchmarked on real or simulated datasets generated from human studies. In this study, we compared the outcomes of two methods, Kraken (mRNA based) and a pipeline developed in-house based on Mothur (16S rRNA based), to assess the taxonomic profiles (bacteria and archaea) of rumen microbial communities using total RNA sequencing of rumen fluid collected from 12 cattle with differing feed conversion ratios (FCR). Both approaches revealed a similar phyla distribution of the most abundant taxa, with Bacteroidetes, Firmicutes, and Proteobacteria accounting for approximately 80% of total bacterial abundance. For bacterial taxa, although 69 genera were commonly detected by both methods, an additional 159 genera were exclusively identified by Kraken. Kraken detected 423 species, while Mothur was not able to assign bacterial sequences to the species level. For archaea, both methods generated similar results only for the abundance of Methanomassiliicoccaceae (previously referred as RCC), which comprised more than 65% of the total archaeal families. Taxon R4-41B was exclusively identified by Mothur in the rumen of feed efficient bulls, whereas Kraken uniquely identified Methanococcaceae in inefficient bulls. Although Kraken enhanced the microbial classification at the species level, identification of bacteria or archaea in the rumen is limited due to a lack of reference genomes for the rumen microbiome. The findings from this study suggest that the development of the combined pipelines using Mothur and Kraken is needed for a more inclusive and representative classification of microbiomes.

Camelina Seed Supplementation at Two Dietary Fat Levels Change Ruminal Bacterial Community Composition in a Dual-Flow Continuous Culture System

This experiment aimed to determine the effects of camelina seed (CS) supplementation at different dietary fat levels on ruminal bacterial community composition and how it relates to changes in ruminal fermentation in a dual-flow continuous culture system. Diets were randomly assigned to 8 fermenters (1,200–1,250 mL) in a 2 × 2 factorial arrangement of treatments in a replicated 4 × 4 Latin square with four 10-day experimental periods that consisted of 7 days for diet adaptation and 3 days for sample collection. Treatments were: (1) no CS at 5% ether extract (EE, NCS5); (2) no CS at 8% EE (NCS8); (3) 7.7% CS at 5% EE (CS5); and (4) 17.7% CS at 8% EE (CS8). Megalac was used as a control to adjust EE levels. Diets contained 55% orchardgrass hay and 45% concentrate, and fermenters were equally fed a total of 72 g/day (DM basis) twice daily. The bacterial community was determined by sequencing the V4 region of the 16S rRNA gene using the Illumina MiSeq platform. Sequencing data were analyzed using mothur and statistical analyses were performed in R and SAS. The most abundant phyla across treatments were the Bacteroidetes and Firmicutes, accounting for 49 and 39% of the total sequences, respectively. The bacterial community composition in both liquid and solid fractions of the effluent digesta changed with CS supplementation but not by dietary EE. Including CS in the diets decreased the relative abundances of Ruminococcus spp., Fibrobacter spp., and Butyrivibrio spp. The most abundant genus across treatments, Prevotella, was reduced by high dietary EE levels, while Megasphaera and Succinivibrio were increased by CS supplementation in the liquid fraction. Correlatively, the concentration of acetate was decreased while propionate increased; C18:0 was decreased and polyunsaturated fatty acids, especially C18:2 n-6 and C18:3 n-3, were increased by CS supplementation. Based on the correlation analysis between genera and fermentation end products, this study revealed that CS supplementation could be energetically beneficial to dairy cows by increasing propionate-producing bacteria and suppressing ruminal bacteria associated with biohydrogenation. However, attention should be given to avoid the effects of CS supplementation on suppressing cellulolytic bacteria.

Role of Age-Related Shifts in Rumen Bacteria and Methanogens in Methane Production in Cattle

Rumen microbiota are essential for maintaining digestive and metabolic functions, producing methane as a byproduct. Dairy heifers produce large amounts of methane based on fermentation of digested organic matter, with adverse consequences for feed efficiency and the environment. It is therefore important to understand the influence of host age on the relationship between microbiota and methane production. This study explored the age effect on the relationship between microbial communities and enteric methane production in dairy cows and heifers using high-throughput sequencing. Methane production and volatile fatty acid concentrations were age-related. Heifers (9-10 months) had lower methane production but higher methane production per dry matter intake (DMI). The acetate:propionate ratio decreased significantly with increasing age. Age-related microbiota changes in the rumen were reflected by a significant shift in bacterial taxa, but relatively stable archaeal taxa. Prevotella, Ruminococcus, Flavonifractor, Succinivibrio, and Methanobrevibacter were affected by age. This study revealed different associations between predominant bacterial phylotypes and Methanobrevibacter with increasing age. Prevotella was strongly correlated with Methanobrevibacter in heifers; howerver, in older cows (96-120 months) this association was replaced by a correlation between Succinivibrio and Methanobrevibacter. This shift may account for the age-related difference in rumen fermentation and methane production per DMI.

Effect of Sunflower and Marine Oils on Ruminal Microbiota, In vitro Fermentation and Digesta Fatty Acid Profile

This study using the rumen simulation technique (RUSITEC) investigated the changes in the ruminal microbiota and anaerobic fermentation in response to the addition of different lipid supplements to a ruminant diet. A basal diet with no oil added was the control, and the treatment diets were supplemented with sunflower oil (2%) only, or sunflower oil (2%) in combination with fish oil (1%) or algae oil (1%). Four fermentation units were used per treatment. RUSITEC fermenters were inoculated with rumen digesta. Substrate degradation, fermentation end-products (volatile fatty acids, lactate, gas, methane, and ammonia), and microbial protein synthesis were determined. Fatty acid profiles and microbial community composition were evaluated in digesta samples. Numbers of representative bacterial species and microbial groups were determined using qPCR. Microbial composition and diversity were based on T-RFLP spectra. The addition of oils had no effect on substrate degradation or microbial protein synthesis. Differences among diets in neutral detergent fiber degradation were not significant (P = 0.132), but the contrast comparing oil–supplemented diets with the control was significant (P = 0.039). Methane production was reduced (P < 0.05) with all oil supplements. Propionate production was increased when diets containing oil were fermented. Compared with the control, the addition of algae oil decreased the percentage C18:3 c9c12c15 in rumen digesta, and that of C18:2 c9t11 was increased when the control diet was supplemented with any oil. Marine oils decreased the hydrogenation of C18 unsaturated fatty acids. Microbial diversity was not affected by oil supplementation. Cluster analysis showed that diets with additional fish or algae oils formed a group separated from the sunflower oil diet. Supplementation with marine oils decreased the numbers of Butyrivibrio producers of stearic acid, and affected the numbers of protozoa, methanogens, Selenomonas ruminantium and Streptococcus bovis, but not total bacteria. In conclusion, there is a potential to manipulate the rumen fermentation and microbiota with the addition of sunflower, fish or algae oils to ruminant diets at appropriate concentrations. Specifically, supplementation of ruminant mixed rations with marine oils will reduce methane production, the acetate to propionate ratio and the fatty acid hydrogenation in the rumen.

Alterations in the Rumen Liquid-, Particle- and Epithelium-Associated Microbiota of Dairy Cows during the Transition from a Silage- and Concentrate-Based Ration to Pasture in Spring

In spring dairy cows are often gradually transitioned from a silage- and concentrate-based ration (total mixed ration, TMR) to pasture. Rumen microbiota adaptability is a key feature of ruminant survival strategy. However, only little is known on the temporal and spatial microbial alterations involved. This study aims to investigate how the rumen liquid (LAAB), particle (PAAB), and epithelium (EAAB) associated archaea and bacteria are influenced by this nutritional change. A 10-wk trial was performed, including 10 rumen-fistulated dairy cows, equally divided into a pasture- and a confinement- group (PG and CG). The CG stayed on a TMR-based ration, while the PG was gradually transitioned from TMR to pasture (wk 1: TMR-only, wk 2: 3 h/day on pasture, wk 3 & 4: 12 h/day on pasture, wk 5-10: pasture-only). In wk 1, wk 5, and wk 10 samples of solid and liquid rumen contents, and papillae biopsies were collected. The DNA was isolated, and PCR-SSCP and 16S rRNA gene amplicon sequencing analysis were performed. Cluster analysis revealed a higher similarity between LAAB and PAAB, compared to the EAAB, characterized by higher species diversity. At all three locations the microbiota was significantly influenced by the ration change, opposite the generally acknowledged hypothesis that the EAAB remain more consistent throughout dietary changes. Even though the animals in the PG were already on a full-grazing ration for 4-6 days in wk 5, the microbiota at all three locations was significantly different compared to wk 10, suggesting an adaptation period of several days to weeks. This is in line with observations made on animal level, showing a required time for adaptation of 2-3 weeks for production and metabolic variables. A large part of the rumen prokaryote species remained unaltered upon transition to pasture and exhibited a strong host influence, supporting the hypothesis that the rumen microbiota consists of a core and a variable microbiota. For the effect of the location as well as the ration change either very similar or opposite trends among member species of common taxa were observed, demonstrating that microbes that are phylogenetically close may still exhibit substantially different phenotypes and functions.

Linking Peripartal Dynamics of Ruminal Microbiota to Dietary Changes and Production Parameters

During the peripartal period, proper acclimatization of rumen microorganisms to variations in nutritional management can facilitate the transition into lactation. This study characterized the temporal shifts in the composition and functional properties of ruminal microbiota during the periparturient period in dairy cows subjected to a typical two-tiered feeding management approach. Ruminal digesta samples from eight multiparous fistulated Holstein cows were collected on days -14, -7, 10, 20, and 28 relative to parturition. High-throughput Illumina sequencing of the V4 region of the bacterial 16S rRNA gene revealed distinct clustering patterns between pre- and postpartal ruminal microbiota. During the prepartal period, when the voluntary dry matter intake was lower, we observed strikingly lower inter-animal variations in the composition of the ruminal microbiota. Genera Ruminococcus and Butyrivibrio, which are considered major fibrolytic rumen dwellers, were overrepresented in the prepartal rumen ecosystem. In contrast, increased postpartal voluntary DMI was associated with enrichment of bacterial genera mainly consisting of proteolytic, amylolytic, and lactate-producer species (including Prevotella, Streptococcus, and Lactobacillus). These, together with the postpartal enrichment of energy metabolism pathways, suggested a degree of acclimatization of the ruminal microbiota to harvest energy from the carbohydrate-dense lactation diet. In addition, correlations between ruminal microbiota and parameters such as milk yield and milk composition underscored the metabolic contribution of this microbial community to the cow's performance and production.

Ginkgo fruit extract as an additive to modify rumen microbiota and fermentation and to mitigate methane production

Ginkgo fruit, an unused byproduct of the ginkgo nut industry, contains antimicrobial compounds known as anacardic acids. Two major cultivars of ginkgo, Kyuju (K) and Tokuro (T), were evaluated for their potential as a feed additive for ruminants. In batch culture, we incubated a mixture of hay and concentrate in diluted rumen fluid with or without 1.6% (fruit equivalent) ginkgo fruit extract. We conducted another series of batch culture studies to determine the dose response of fermentation. We also conducted continuous culture using the rumen simulation technique (RUSITEC) with cultivar K and carried out a pure culture study to monitor the sensitivity of 17 representative rumen bacterial species to ginkgo extract and component phenolics. Although both K and T extracts led to decreased methane and increased propionate production, changes were more apparent with K extract, and were dose-dependent. Total gas production was depressed at doses ≥3.2%, suggesting that 1.6% was the optimal supplementation level. In RUSITEC fermentation supplemented with 1.6% ginkgo K, methane decreased by 53% without affecting total gas or total VFA production, but with decreased acetate and increased propionate. Disappearance of dry matter, neutral detergent fiber, and acid detergent fiber were not affected by ginkgo, but ammonia levels were decreased. Quantitative PCR indicated that the abundance of protozoa, fungi, methanogens, and bacteria related to hydrogen and formate production decreased, but the abundance of bacteria related to propionate production increased. MiSeq analysis (Illumina Inc., San Diego, CA) confirmed these bacterial changes and identified archaeal community changes, including a decrease in Methanobrevibacter and Methanomassiliicoccaceae and an increase in Methanoplanus. Pure culture study results supported the findings for the above bacterial community changes. These results demonstrate that ginkgo fruit can modulate rumen fermentation toward methane mitigation and propionate enhancement via microbial selection.

The Contribution of Mathematical Modeling to Understanding Dynamic Aspects of Rumen Metabolism

All mechanistic rumen models cover the main drivers of variation in rumen function, which are feed intake, the differences between feedstuffs and feeds in their intrinsic rumen degradation characteristics, and fractional outflow rate of fluid and particulate matter. Dynamic modeling approaches are best suited to the prediction of more nuanced responses in rumen metabolism, and represent the dynamics of the interactions between substrates and micro-organisms and inter-microbial interactions. The concepts of dynamics are discussed for the case of rumen starch digestion as influenced by starch intake rate and frequency of feed intake, and for the case of fermentation of fiber in the large intestine. Adding representations of new functional classes of micro-organisms (i.e., with new characteristics from the perspective of whole rumen function) in rumen models only delivers new insights if complemented by the dynamics of their interactions with other functional classes. Rumen fermentation conditions have to be represented due to their profound impact on the dynamics of substrate degradation and microbial metabolism. Although the importance of rumen pH is generally acknowledged, more emphasis is needed on predicting its variation as well as variation in the processes that underlie rumen fluid dynamics. The rumen wall has an important role in adapting to rapid changes in the rumen environment, clearing of volatile fatty acids (VFA), and maintaining rumen pH within limits. Dynamics of rumen wall epithelia and their role in VFA absorption needs to be better represented in models that aim to predict rumen responses across nutritional or physiological states. For a detailed prediction of rumen N balance there is merit in a dynamic modeling approach compared to the static approaches adopted in current protein evaluation systems. Improvement is needed on previous attempts to predict rumen VFA profiles, and this should be pursued by introducing factors that relate more to microbial metabolism. For rumen model construction, data on rumen microbiomes are preferably coupled with knowledge consolidated in rumen models instead of relying on correlations with rather general aspects of treatment or animal. This helps to prevent the disregard of basic principles and underlying mechanisms of whole rumen function.

Rapid Fermentable Substance Modulates Interactions between Ruminal Commensals and Toll-Like Receptors in Promotion of Immune Tolerance of Goat Rumen

Whether dietary non-fiber carbohydrate (NFC), a rapid fermentable substance, affects immune homeostasis of rumen through the modulation of interactions of ruminal microbiota and epithelial toll-like receptors (TLRs) remains unclear. A combination of 16S rRNA amplicon sequencing and quantitative PCRs was applied to study the synergetic responses of ruminal microbiota and epithelial TLRs to the dietary NFC switch from 15 to 31% in the goat model. The results showed that the 31% NFC diet caused the radical increases on the richness and diversity of rumen microbiota. The phylum Verrucomicrobia was most significantly expanded, whereas opportunistic pathogens, namely Rikenella, Anaeroplasma, and Olsenella, were significantly decreased. In rumen epithelium, the significantly increased expressions of TLR1, 6, 10 were associated with the significantly decreased expressions of pro-inflammatory cytokines interleukin-1beta (IL-1ß), IL-6, and anti-inflammatory cytokine IL-10. Constrained correlation analysis indicated that the increased abundance of commensal bacteria in Verrucomicrobia subdivision 5 contributed to the upregulation of TLR10 expression. Finally, the significantly increased concentrations of rumen short-chain fatty acids (SCFAs), coupled with the significantly upregulated expressions of epithelial genes related to SCFA absorption were observed in goats fed with 31% NFC diet. Thus, the NFC-induced expansion of rumen microbiota promoted epithelium tolerance by enhancement of the intensity of TLR10 signaling. The newly established equilibrium benefited to the transport of ruminal energy substances into the blood.

Taxonomic Assessment of Rumen Microbiota Using Total RNA and Targeted Amplicon Sequencing Approaches

Taxonomic characterization of active gastrointestinal microbiota is essential to detect shifts in microbial communities and functions under various conditions. This study aimed to identify and quantify potentially active rumen microbiota using total RNA sequencing and to compare the outcomes of this approach with the widely used targeted RNA/DNA amplicon sequencing technique. Total RNA isolated from rumen digesta samples from five beef steers was subjected to Illumina paired-end sequencing (RNA-seq), and bacterial and archaeal amplicons of partial 16S rRNA/rDNA were subjected to 454 pyrosequencing (RNA/DNA Amplicon-seq). Taxonomic assessments of the RNA-seq, RNA Amplicon-seq, and DNA Amplicon-seq datasets were performed using a pipeline developed in house. The detected major microbial phylotypes were common among the three datasets, with seven bacterial phyla, fifteen bacterial families, and five archaeal taxa commonly identified across all datasets. There were also unique microbial taxa detected in each dataset. Elusimicrobia and Verrucomicrobia phyla; Desulfovibrionaceae, Elusimicrobiaceae, and Sphaerochaetaceae families; and Methanobrevibacter woesei were only detected in the RNA-Seq and RNA Amplicon-seq datasets, whereas Streptococcaceae was only detected in the DNA Amplicon-seq dataset. In addition, the relative abundances of four bacterial phyla, eight bacterial families and one archaeal taxon were different among the three datasets. This is the first study to compare the outcomes of rumen microbiota profiling between RNA-seq and RNA/DNA Amplicon-seq datasets. Our results illustrate the differences between these methods in characterizing microbiota both qualitatively and quantitatively for the same sample, and so caution must be exercised when comparing data.

Comparison of feed intake, digestion and rumen function among domestic ruminant species grazing in upland vegetation communities

This study aimed to compare feed intake, digestion, rumen fermentation parameters and bacterial community of 5 beef cows, 12 crossed ewes and 12 goats grazing together in spring-early summer on heather-gorse vegetation communities with an adjacent area of improved pasture. Organic matter intake (OMI) and digestibility (OMD) were estimated using alkane markers. Ruminal fluid samples were collected for measuring fermentation parameters, and studying the bacterial community using terminal restriction fragment length polymorphism (T-RFLP). Spot samples of urine were taken to determine purine derivative (PD) and creatinine concentrations to estimate microbial protein synthesis in the rumen. Herbaceous species were the main dietary component in all animal species. Cattle had higher (p < 0.05) daily OMI (g/kg LW^0.75 ) and OMD, whereas sheep and goats showed similar values. The highest ammonia concentration was observed in sheep. Total VFA, acetate and butyrate concentrations were not influenced by animal species, while propionate concentrations in goats were 1.8 times lower (p < 0.05) than in sheep. Acetate:propionate ratio was greater (p < 0.05) in goats, whereas cattle excreted more allantoin (p < 0.05). Estimated supply of microbial N was higher in cows (p < 0.01), whereas the efficiency of microbial protein synthesis was lower (p < 0.01) in this animal species. Hierarchical clustering analysis indicated a clear effect of animal species on rumen bacterial structure. Differences among animal species were also observed in the relative frequency of several T-RFs. Certain T-RFs compatible with Lachnospiraceae, Proteobacteria and Clostridiales species were not found in goats, while these animals showed high relative frequencies of some fragments compatible with the Ruminococcaceae family that were not detected in sheep and cattle. Results suggest a close relationship between animals' grazing behaviour and rumen bacterial structure and its function. Goats seem to show a greater specialization of their microbial populations to deal with the greater fibrous and tannin content of their diet.

Treatment of grain with organic acids at 2 different dietary phosphorus levels modulates ruminal microbial community structure and fermentation patterns in vitro

Recent data indicate positive effects of treating grain with citric (CAc) or lactic acid (LAc) on the hydrolysis of phytate phosphorus (P) and fermentation products of the grain. This study used a semicontinuous rumen simulation technique to evaluate the effects of processing of barley with 50.25 g/L (wt/vol) CAc or 76.25 g/L LAc on microbial composition, metabolic fermentation profile, and nutrient degradation at low or high dietary P supply. The low P diet [3.1g of P per kg of dry matter (DM) of dietary P sources only] was not supplemented with inorganic P, whereas the high P diet was supplemented with 0.5 g of inorganic P per kg of DM through mineral premix and 870 mg of inorganic P/d per incubation fermenter via artificial saliva. Target microbes were determined using quantitative PCR. Data showed depression of total bacteria but not of total protozoa or short-chain fatty acid (SCFA) concentration with the low P diet. In addition, the low P diet lowered the relative abundance of Ruminococcus albus and decreased neutral detergent fiber (NDF) degradation and acetate proportion, but increased the abundance of several predominantly noncellulolytic bacterial species and anaerobic fungi. Treatment of grain with LAc increased the abundance of total bacteria in the low P diet only, and this effect was associated with a greater concentration of SCFA in the ruminal fluid. Interestingly, in the low P diet, CAc treatment of barley increased the most prevalent bacterial group, the genus Prevotella, in ruminal fluid and increased NDF degradation to the same extent as did inorganic P supplementation in the high P diet. Treatment with either CAc or LAc lowered the abundance of Megasphaera elsdenii but only in the low P diet. On the other hand, CAc treatment increased the proportion of acetate in the low P diet, whereas LAc treatment decreased this variable at both dietary P levels. The propionate proportion was significantly increased by LAc at both P levels, whereas butyrate increased only with the low P diet. Treatments with CAc or LAc reduced the degradation of CP and ammonia concentration compared with the control diet at both P levels. In conclusion, the beneficial effects of CAc and LAc treatment on specific ruminal microbes, fermentation profile, and fiber degradation in the low P diet suggest the potential for the treatment to compensate for the lack of inorganic P supplementation in vitro. Further research is warranted to determine the extent to which the treatment can alleviate the shortage of inorganic P supplementation under in vivo conditions.

Mining of luxS genes from rumen microbial consortia by metagenomic and metatranscriptomic approaches

Although rumen bacterial communities vary depending on many factors such as diet, age and physiological conditions, a core microbiota exists within the rumen. In many natural environments, some bacteria use a quorum-sensing (QS) system to regulate their physiological activities. However, very limited information is available about QS systems in rumen. To investigate the autoinducer 2 (AI-2)-mediated QS system in rumen, we detected genes (luxS) encoding the AI-2 synthase (LuxS), from three datasets embedded in metagenomics RAST server (MG-RAST) and from a metatranscriptome dataset. We collected 135 luxS genes from the metagenomic datasets, which were presumed to originate from Bacteroidetes, Firmicutes, Fusobacteria and Actinobacteria, and 34 luxS genes from the metatranscriptome dataset, which probably originated from Bacteroidetes, Firmicutes and Spirochaetes. Because the essential amino acids for LuxS activity were conserved in the LuxS homologues predicted from luxS gene sequences from both datasets, the LuxS homologues probably function in the rumen. Since the largest number of sequences of luxS genes were collected from the genera Prevotella, Ruminococcus and Eubacterium, which include many fibrolytic bacteria and constituent members of biofilm on feed particles, an AI-2-mediated QS system is likely involved in biofilm formation and fibrolytic activity in the rumen.