Successional colonization of perennial ryegrass by rumen bacteria

Integrated Multi-Omics Reveals New Ruminal Microbial Features Associated with Peanut Vine Efficiency in Dairy Cattle

The aim of this study was to improve the utilization of peanut vines as forage material for ruminants by investigating the degradation pattern of peanut vines in the dairy cow rumen. Samples of peanut vine incubated in cow rumens were collected at various time points. Bacterial diversity was investigated by scanning electron microscopy (SEM) and 16S rRNA gene sequencing. Carbohydrate-active enzymes (CAZymes) were analyzed by metagenomics. The peanut vines degraded rapidly from 2 to 24 h, before slowing from 24 to 72 h. SEM images confirmed dynamic peanut vine colonization. Firmicutes and Bacteroidetes were the two most dominant bacterial phyla throughout. Principal coordinates analysis indicated significant microbial composition changes at 6 and 24 h. This may be because, in the early stage, soluble carbohydrates that are easily degradable were degraded, while in the later stage, fibrous substances that are difficult to degrade were mainly degraded. Glycoside hydrolases (GHs) were the most abundant CAZymes, with peak relative abundance at 6 h (56.7 trans per million, TPM), and reducing at 24 (55.9 TPM) and 72 h (55.3 TPM). Spearman correlation analysis showed that Alistipes_sp._CAG:435, Alistipes_sp._CAG:514, Bacteroides_sp._CAG:1060, Bacteroides_sp._CAG:545, Bacteroides_sp._CAG:709, Bacteroides_sp._CAG:770, bacterium_F082, bacterium_F083, GH29, GH78, and GH92 were important for plant fiber degradation. These findings provide fundamental knowledge about forage degradation in the cow rumen, and will be important for the targeted improvement of ruminant plant biomass utilization efficiency.

- Invited Review - Chemical signalling within the rumen microbiome

Ruminants possess a specialized four-compartment forestomach, consisting of the reticulum, rumen, omasum, and abomasum. The rumen, the primary fermentative chamber, harbours a dynamic ecosystem comprising bacteria, protozoa, fungi, archaea, and bacteriophages. These microorganisms engage in diverse ecological interactions within the rumen microbiome, primarily benefiting the host animal by deriving energy from plant material breakdown. These interactions encompass symbiosis, such as mutualism and commensalism, as well as parasitism, predation, and competition. These ecological interactions are dependent on many factors, including the production of diverse molecules, such as those involved in quorum sensing (QS). QS is a density-dependent signalling mechanism involving the release of autoinducer (AIs) compounds, when cell density increases AIs bind to receptors causing the altered expression of certain genes. These AIs are classified as mainly being N-acyl-homoserine lactones (AHL; commonly used by Gram-negative bacteria) or autoinducer-2 based systems (AI-2; used by Gram-positive and Gram-negative bacteria); although other less common AI systems exist. Most of our understanding of QS at a gene-level comes from pure culture in vitro studies using bacterial pathogens, with much being unknown on a commensal bacterial and ecosystem level, especially in the context of the rumen microbiome. A small number of studies have explored QS in the rumen using 'omic' technologies, revealing a prevalence of AI-2 QS systems among rumen bacteria. Nevertheless, the implications of these signalling systems on gene regulation, rumen ecology, and ruminant characteristics are largely uncharted territory. Metatranscriptome data tracking the colonization of perennial ryegrass by rumen microbes suggest that these chemicals may influence transitions in bacterial diversity during colonization. The likelihood of undiscovered chemicals within the rumen microbial arsenal is high, with the identified chemicals representing only the tip of the iceberg. A comprehensive grasp of rumen microbial chemical signalling is crucial for addressing the challenges of food security and climate targets.

A Combination of Lactic Acid Bacteria and Molasses Improves Fermentation Quality, Chemical Composition, Physicochemical Structure, in vitro Degradability and Rumen Microbiota Colonization of Rice Straw

Aims

This study aims to evaluate the effect of lactic acid bacteria (LAB) and LAB-molasses (LAB + M) combination on the fermentation quality, chemical composition, physicochemical properties, in vitro degradability of rice straw and the characteristics of rumen microbial colonization on rice straw surface.

Methods and Results

There were three pretreatments, including control (not treated, Con), treated with LAB, or LAB + M. The results showed that both LAB and LAB + M treatments altered the physical and chemical structures of rice straw and were revealed by scanning electron microscopy (SEM) and X-ray diffraction analysis (XRD) spectroscopy, respectively. Moreover, both LAB and LAB + M pretreated rice straw increased the crude protein (CP) content, dry matter (DM) recovery, and in vitro digestibility and decreased the pH value, neutral detergent fiber (NDF), and acid detergent fiber (ADF) contents. The LAB + M pretreated rice straw increased the gas production (GP72) and rumen microbial colonization on the rice straw surface.

Conclusions

It is observed that LAB + M treatment could increase digestibility and the rumen microbial colonization on the rice straw surface. Therefore, LAB + M treatment can provide an alternative strategy to improve the quality of rice straw. Significance and impact of the study: This study provides an optimal pretreatment to improve the rice straw digestibility and rumen microbial colonization.

Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates

Rumen microbiota facilitates nutrition through digestion of recalcitrant lignocellulosic substrates into energy-accessible nutrients and essential metabolites. Despite the high similarity in rumen microbiome structure, there might be distinct functional capabilities that enable different ruminant species to thrive on various lignocellulosic substrates as feed. Here, we applied genome-centric metagenomics to explore phylogenetic diversity, lignocellulose-degrading potential and fermentation metabolism of biofilm-forming microbiota colonizing 11 different plant substrates in the camel rumen. Diversity analysis revealed significant variations in the community of rumen microbiota colonizing different substrates in accordance with their varied physicochemical properties. Metagenome reconstruction recovered genome sequences of 590 bacterial isolates and one archaeal lineage belonging to 20 microbial phyla. A comparison to publicly available reference genomes and rumen metagenome-assembled genomes revealed that most isolates belonged to new species with no well-characterized representatives. We found that certain low abundant taxa, including members of Verrucomicrobiota, Planctomycetota and Fibrobacterota, possessed a disproportionately large number of carbohydrate active enzymes per Mb of genome, implying their high metabolic potential to contribute to the rumen function. In conclusion, we provided a detailed picture of the diversity and functional significance of rumen microbiota colonizing feeds of varying lignocellulose composition in the camel rumen. A detailed analysis of 591 metagenome-assembled genomes revealed a network of interconnected microbiota and highlighted the key roles of certain taxonomic clades in rumen function, including those with minimal genomes (e.g., Patescibacteria). The existence of a diverse array of gene clusters encoding for secondary metabolites unveiled the specific functions of these biomolecules in shaping community structure of rumen microbiota.

Proper motility enhances rumen fermentation and microbial protein synthesis with decreased saturation of dissolved gases in rumen simulation technique

The physiological function of the reticulorumen plays an essential role in ruminant nutrition, and detailed knowledge of rumen motility can further advance understanding of ruminant nutrition and physiology. Rumen motility was simulated by setting different stirrer rotation speeds in a rumen simulation technique (RUSITEC) system. The aim of this study was to investigate the effects of rotation speeds on rumen fermentation, saturation factor of dissolved gases, hydrogen (H₂) and methane (CH₄) emissions, microbial protein synthesis, and selected microbial population using RUSITEC. The experiment was performed according to a balanced 3 × 3 Latin square design, and each period included 7 d for adaptation and 3 d for sampling. Three motility treatments included 5, 15, and 25 rpm rotation speeds. Daily total gas and H₂ and CH₄ emissions had quadratic responses to the increasing rotation speed and were highest at 15 rpm. Quadratic and linear responses (highest at 5 rpm) to increasing rotation speed were observed for saturation factors of H₂ and CH₄, liquid-dissolved H₂ and CH₄ concentrations, and headspace concentration of H₂ in the gas phase, whereas increasing rotation speed linearly decreased saturation factors of CO₂ and liquid-dissolved CO₂ concentration. Quadratic and linear responses to increasing rotation speed were observed for molar percentages of acetate, ammonia, and microbial protein concentration, whereas increasing rotation speed quadratically increased pH and decreased total volatile fatty acid concentration and acetate-to-propionate ratio. The 15-rpm rotation speed had the highest values of total volatile fatty acids, acetate molar percentage, and microbial protein concentration. Quadratic and linear responses to increasing rotation speed were observed for copy numbers of solid-associated fungi and fluid-associated bacteria, fungi, and protozoa, while increasing rotation speed linearly increased copy numbers of solid-associated protozoa. Rotation at 15 rpm increased populations of fungi and protozoa in the solid rumen contents and the population of bacteria and fungi in the liquid rumen contents. In summary, this study provides insights on the biofunction of proper rumen motility (i.e., at a rotation speed of 15 rpm), such as improving feed fermentation, increasing gas emissions with decreased dissolved gas concentrations and saturation factors, and promoting microbial colonization and microbial protein synthesis, although further increase in rotation speed (i.e., to 25 rpm) decreases feed fermentation and microbial protein synthesis.

Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches

BACKGROUND

Gut microbiomes, such as the rumen, greatly influence host nutrition due to their feed energy-harvesting capacity. We investigated temporal ecological interactions facilitating energy harvesting at the fresh perennial ryegrass (PRG)-biofilm interface in the rumen using an in sacco approach and prokaryotic metatranscriptomic profiling.

RESULTS

Network analysis identified two distinct sub-microbiomes primarily representing primary (≤ 4 h) and secondary (≥ 4 h) colonisation phases and the most transcriptionally active bacterial families (i.e Fibrobacteriaceae, Selemondaceae and Methanobacteriaceae) did not interact with either sub-microbiome, indicating non-cooperative behaviour. Conversely, Prevotellaceae had most transcriptional activity within the primary sub-microbiome (focussed on protein metabolism) and Lachnospiraceae within the secondary sub-microbiome (focussed on carbohydrate degradation). Putative keystone taxa, with low transcriptional activity, were identified within both sub-microbiomes, highlighting the important synergistic role of minor bacterial families; however, we hypothesise that they may be 'cheating' in order to capitalise on the energy-harvesting capacity of other microbes. In terms of chemical cues underlying transition from primary to secondary colonisation phases, we suggest that AI-2-based quorum sensing plays a role, based on LuxS gene expression data, coupled with changes in PRG chemistry.

CONCLUSIONS

In summary, we show that fresh PRG-attached prokaryotes are resilient and adapt quickly to changing niches. This study provides the first major insight into the complex temporal ecological interactions occurring at the plant-biofilm interface within the rumen. The study also provides valuable insights into potential plant breeding strategies for development of the utopian plant, allowing optimal sustainable production of ruminants. Video Abstract.

The rumen eukaryotome is a source of novel antimicrobial peptides with therapeutic potential

BACKGROUND

The rise of microbial antibiotic resistance is a leading threat to the health of the human population. As such, finding new approaches to tackle these microbes, including development of novel antibiotics is vital.

RESULTS

In this study, we mined a rumen eukaryotic metatranscriptomic library for novel Antimicrobial peptides (AMPs) using computational approaches and thereafter characterised the therapeutic potential of the AMPs. We identified a total of 208 potentially novel AMPs from the ruminal eukaryotome, and characterised one of those, namely Lubelisin. Lubelisin (GIVAWFWRLAR) is an α-helical peptide, 11 amino acid long with theoretical molecular weight of 1373.76 D. In the presence of Lubelisin, strains of methicillin-resistant Staphylococcus aureus (MRSA) USA300 and EMRSA-15 were killed within 30 min of exposure with ≥103 and 104 CFU/mL reduction in viable cells respectively. Cytotoxicity of Lubelisin against both human and sheep erythrocytes was low resulting in a therapeutic index of 0.43. Membrane permeabilisation assays using propidium iodide alongside transmission electron microscopy revealed that cytoplasmic membrane damage may contribute to the antimicrobial activities of Lubelisin.

CONCLUSIONS

We demonstrate that the rumen eukaryotome is a viable source for the discovery of antimicrobial molecules for the treatment of bacterial infections and further development of these may provide part of the potential solution to the ongoing problem of antimicrobial resistance. The role of these AMPs in the ecological warfare within the rumen is also currently unknown.

Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen

Rumen microbiota play a key role in the digestion and utilization of plant materials by the ruminant species, which have important implications for greenhouse gas emission. Yet, little is known about the key taxa and potential gene functions involved in the digestion process. Here, we performed a genome-centric analysis of rumen microbiota attached to six different lignocellulosic biomasses in rumen-fistulated cattle. Our metagenome sequencing provided novel genomic insights into functional potential of 523 uncultured bacteria and 15 mostly uncultured archaea in the rumen. The assembled genomes belonged mainly to Bacteroidota, Firmicutes, Verrucomicrobiota, and Fibrobacterota and were enriched for genes related to the degradation of lignocellulosic polymers and the fermentation of degraded products into short chain volatile fatty acids. We also found a shift from copiotrophic to oligotrophic taxa during the course of rumen fermentation, potentially important for the digestion of recalcitrant lignocellulosic substrates in the physiochemically complex and varying environment of the rumen. Differential colonization of forages (the incubated lignocellulosic materials) by rumen microbiota suggests that taxonomic and metabolic diversification is an evolutionary adaptation to diverse lignocellulosic substrates constituting a major component of the cattle's diet. Our data also provide novel insights into the key role of unique microbial diversity and associated gene functions in the degradation of recalcitrant lignocellulosic materials in the rumen.

Diversity of microbes colonizing forages of varying lignocellulose properties in the sheep rumen

Background

The rumen microbiota contributes strongly to the degradation of ingested plant materials. There is limited knowledge about the diversity of taxa involved in the breakdown of lignocellulosic biomasses with varying chemical compositions in the rumen.

Method

We aimed to assess how and to what extent the physicochemical properties of forages influence the colonization and digestion by rumen microbiota. This was achieved by placing nylon bags filled with candidate materials in the rumen of fistulated sheep for a period of up to 96 h, followed by measuring forage's chemical characteristics and community structure of biofilm-embedded microbiota.

Results

Rumen degradation for all forages appeared to have occurred mainly during the first 24 h of their incubation, which significantly slowed down after 48 h of rumen incubation, depending on their chemical properties. Random Forest analysis predicted the predominant role of Treponema and Butyrivibrio in shaping microbial diversity attached to the forages during the course of rumen incubation. Exploring community structure and composition of fiber-attached microbiota revealed significant differential colonization rates of forages depending on their contents for NDF and cellulose. The correlation analysis highlighted the significant contribution of Lachnospiraceae and Veillonellaceae to fiber degradation in the sheep rumen.

Conclusion

Our findings suggested that forage cellulose components are critical in shaping the pattern of microbial colonization and thus their final digestibility in the rumen.

Temporal changes in microbial communities attached to forages with different lignocellulosic compositions in cattle rumen

The attachment of rumen microbes to feed particles is critical to feed fermentation, degradation and digestion. However, the extent to which the physicochemical properties of feeds influence the colonization by rumen microbes is still unclear. We hypothesized that rumen microbial communities may have differential preferences for attachments to feeds with varying lignocellulose properties. To this end, the structure and composition of microbial communities attached to six common forages with different lignocellulosic compositions were analyzed following in situ rumen incubation in male Taleshi cattle. The results showed that differences in lignocellulosic compositions significantly affected the inter-sample diversity of forage-attached microbial communities in the first 24 h of rumen incubation, during which the highest dry matter degradation was achieved. However, extension of the incubation to 96 h resulted in the development of more uniform microbial communities across the forages. Fibrobacteres were significantly overrepresented in the bacterial communities attached to the forages with the highest neutral detergent fiber contents. Ruminococcus tended to attach to the forages with low acid detergent lignin contents. The extent of dry matter fermentation was significantly correlated with the populations of Fibrobacteraceae, unclassified Bacteroidales, Ruminococcaceae and Spirochaetacea. Our findings suggested that lignocellulosic compositions, and more specifically the cellulose components, significantly affected the microbial attachment to and thus the final digestion of the forages.

Influence of probiotics on biofilm formation and diversity of bacteria colonising crop sorghum ensiled with unsalable vegetables

The objective of this study was to characterise in situ digestion kinetics and bacterial colonisation of crop sorghum ensiled with unsalable carrot or pumpkin at 0, 20 or 40% dry matter (DM). Silages with or without the application of a commercial probiotic were incubated in situ for 0, 3, 6, 9, 24 and 48 h. Calculation of in situ digestion kinetics was conducted for DM, organic matter and neutral detergent fibre (aNDF). The V4 region of the 16S rRNA gene was sequenced to determine the composition and diversity of bacteria colonising the silage. Organic matter and DM digestion kinetics indicated that greater vegetable inclusion increased (P < 0.05) the soluble fraction and effective degradability. Bacterial richness at 48 h incubation was greater (P = 0.02) in 20% carrot and 40% pumpkin treatments, compared with the control. An effect of level × probiotic was observed with increased Shannon diversity (P = 0.01) for 40% carrot and 20% pumpkin probiotic treatments, respectively. Primary colonising bacteria were members of the Prevotella genus, dominating after 3 and 6 h of incubation. The abundance of Prevotella increased by 4.1% at 3 h (P < 0.01) and by 4.7% at 9 h incubation with probiotics, compared with the control. Secondary biofilm colonisers included members of Treponema, Saccharofermentans, Fibrobacter, Ruminobacter and Anaerosporobacter genera, dominant from 9 h incubation onward. This study demonstrated that including unsalable vegetables at 20 or 40% DM increases the soluble fraction and effective degradability of sorghum silage during in situ digestion and increases diversity of bacteria colonising ensiled vegetables within the rumen. KEY POINTS: • Ensiling unsalable vegetables is a viable strategy to reduce food waste. • Ensiled vegetables increased in situ soluble fraction and effective degradability. • Bacterial richness at 48 h incubation improved with 20% carrot or 40% pumpkin. • Diversity of colonising rumen bacteria increased with carrot or pumpkin inclusion.

Pretreatment of crop residues by ammonia fiber expansion (AFEX) alters the temporal colonization of feed in the rumen by rumen microbes

This study examines the colonization of barley straw (BS) and corn stover (CS) by rumen bacteria and how this is impacted by ammonia fiber expansion (AFEX) pre-treatment. A total of four ruminally cannulated beef heifers were used to investigate in situ microbial colonization in a factorial design with two crop residues, pre-treated with or without AFEX. Crop residues were incubated in the rumen for 0, 2, 4, 8 and 48 h and the colonizing profile was determined using 16 s rRNA gene sequencing. The surface colonizing community clustered based on incubation time and pre-treatment. Fibrobacter, unclassified Bacteroidales, and unclassified Ruminococcaceae were enriched during late stages of colonization. Prevotella and unclassified Lachnospiraceae were enriched in the early stages of colonization. The microbial community colonizing BS-AFEX and CS was less diverse than the community colonizing BS and CS-AFEX. Prevotella, Coprococcus and Clostridium were enriched in both AFEX crop residues, while untreated crop residues were enriched with Methanobrevibacter. Several pathways associated with simple carbohydrate metabolism were enriched in the primary colonizing community of AFEX crop residues. This study suggests that AFEX improves the degradability of crop residues by increasing the accessibility of polysaccharides that can be metabolized by the dominant taxa responsible for primary colonization.

Temporal stability of the rumen microbiota in beef cattle, and response to diet and supplements

BACKGROUND

Dietary intake is known to be a driver of microbial community dynamics in ruminants. Beef cattle go through a finishing phase that typically includes very high concentrate ratios in their feed, with consequent effects on rumen metabolism including methane production. This longitudinal study was designed to measure dynamics of the rumen microbial community in response to the introduction of high concentrate diets fed to beef cattle during the finishing period. A cohort of 50 beef steers were fed either of two basal diet formulations consisting of approximately 10:90 or 50:50 forage:concentrate ratios respectively. Nitrate and oil rich supplements were also added either individually or in combination. Digesta samples were taken at time points over ~ 200 days during the finishing period of the cattle to measure the adaptation to the basal diet and long-term stability of the rumen microbiota.

RESULTS

16S rRNA gene amplicon libraries were prepared from 313 rumen digesta samples and analysed at a depth of 20,000 sequences per library. Bray Curtis dissimilarity with analysis of molecular variance (AMOVA) revealed highly significant (p < 0.001) differences in microbiota composition between cattle fed different basal diets, largely driven by reduction of fibre degrading microbial groups and increased relative abundance of an unclassified Gammaproteobacteria OTU in the high concentrate fed animals. Conversely, the forage-based diet was significantly associated with methanogenic archaea. Within basal diet groups, addition of the nitrate and combined supplements had lesser, although still significant, impacts on microbiota dissimilarity compared to pre-treatment time points and controls. Measurements of the response and stability of the microbial community over the time course of the experiment showed continuing adaptation up to 25 days in the high concentrate groups. After this time point, however, no significant variability was detected.

CONCLUSIONS

High concentrate diets that are typically fed to finishing beef cattle can have a significant effect on the microbial community in the rumen. Inferred metabolic activity of the different microbial communities associated with each of the respective basal diets explained differences in methane and short chain fatty acid production between cattle. Longitudinal sampling revealed that once adapted to a change in diet, the rumen microbial community remains in a relatively stable alternate state.

Bacterial colonisation of reeds and cottonseed hulls in the rumen of Tarim red deer (Cervus elaphus yarkandensis)

The rumen microbiome contributes greatly to the degradation of plant fibres to volatile fatty acids and microbial products, affecting the health and productivity of ruminants. In this study, we investigated the dynamics of colonisation by bacterial communities attached to reeds and cottonseed hulls in the rumen of Tarim red deer, a native species distributed in the desert of the Tarim Basin. The reed and cottonseed hull samples incubated in nylon bags for 1, 6, 12, and 48 h were collected and used to examine the bacterial communities by next-generation sequencing of the bacterial 16S rRNA gene. Prevotella1 and Rikenellaceae RC9 were the most abundant taxa in both the reed and cottonseed hull groups at various times, indicating a key role of these organisms in rumen fermentation in Tarim red deer. The relative abundances of cellulolytic bacteria, such as members of Fibrobacter, Treponema 2, Ruminococcaceae NK4A214 and Succiniclasticum increased, while that of the genus Prevotella 1 decreased, with increasing incubation time in both reeds and cottonseed hulls. Moreover, the temporal changes in bacterial diversity between reeds and cottonseed hulls were different, as demonstrated by the variations in the taxa Ruminococcaceae UCG 010 and Papillibacter in the reed group and Sphaerochaeta and Erysipelotrichaceae UCG 004 in the cottonseed hull group; the abundances of these bacteria first decreased and then increased. In conclusion, our results reveal the dynamics of bacterial colonisation of reeds and cottonseed hulls in the rumen of Tarim red deer.

Polyomic tools for an emerging livestock parasite, the rumen fluke Calicophoron daubneyi; identifying shifts in rumen functionality

BACKGROUND

Diseases caused by parasitic flatworms of rumen tissues (paramphistomosis) are a significant threat to global food security as a cause of morbidity and mortality in ruminant livestock in subtropical and tropical climates. Calicophoron daubneyi is currently the only paramphistome species commonly infecting ruminant livestock in temperate European climates. However, recorded incidences of C. daubneyi infection in European livestock have been increasing over the last decade. Whilst clinical paramphistomosis caused by adult worms has not been confirmed in Europe, fatalities have been attributed to severe haemorrhagic enteritis of the small intestine resulting from the migration of immature paramphistomes. Large numbers of mature adults can reside in the rumen, yet to date, the impact on rumen fermentation, and consequently on productivity and economic management of infected livestock, have not been resolved. Limited publicly available nucleotide and protein sequences for C. daubneyi underpin this lack of biological and economic understanding. Here we present for the first time a de novo assembled transcriptome, with functional annotations, for adult C. daubneyi, which provides a reference database for protein and nucleotide sequence identification to facilitate fundamental biology, anthelmintic, vaccine and diagnostics discoveries.

RESULTS

This dataset identifies a number of genes potentially unique to C. daubneyi and, by comparison to an existing transcriptome for the related Paramphistomum cervi, identifies novel genes which may be unique to the paramphistome group of platyhelminthes. Additionally, we present the first coverage of the excretory/secretory and soluble somatic proteome profiles for adult C. daubneyi and identify the release of extracellular vesicles from adult C. daubneyi parasites during in vitro, ex-host culture. Finally, we have performed the first analysis of rumen fluke impacting upon rumen fermentation parameters using an in vitro gas production study resulting in a significant increase in propionate production.

CONCLUSIONS

The resulting data provide a discovery platform (transcriptome, proteomes, EV isolation pipeline and in vitro fermentation system) to further study C. daubneyi-host interaction. In addition, the acetate: propionate ratio has been demonstrated to decrease with rumen fluke infection suggesting that acidotic conditions in the rumen may occur.

Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future

The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in “omic” data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent “omics” approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.

Using 'Omic Approaches to Compare Temporal Bacterial Colonization of Lolium perenne, Lotus corniculatus, and Trifolium pratense in the Rumen

Understanding rumen plant-microbe interactions is central for development of novel methodologies allowing improvements in ruminant nutrient use efficiency. This study investigated rumen bacterial colonization of fresh plant material and changes in plant chemistry over a period of 24 h period using three different fresh forages: Lolium perenne (perennial ryegrass; PRG), Lotus corniculatus (bird's foot trefoil; BFT) and Trifolium pratense (red clover; RC). We show using 16S rRNA gene ion torrent sequencing that plant epiphytic populations present pre-incubation (0 h) were substantially different to those attached post incubations in the presence of rumen fluid on all forages. Thereafter primary and secondary colonization events were evident as defined by changes in relative abundances of attached bacteria and changes in plant chemistry, as assessed using Fourier transform infrared (FTIR) spectroscopy. For PRG colonization, primary colonization occurred for up to 4 h and secondary colonization from 4 h onward. The changes from primary to secondary colonization occurred significantly later with BFT and RC, with primary colonization being up to 6 h and secondary colonization post 6 h of incubation. Across all 3 forages the main colonizing bacteria present at all time points post-incubation were Prevotella, Pseudobutyrivibrio, Ruminococcus, Olsenella, Butyrivibrio, and Anaeroplasma (14.2, 5.4, 1.9, 2.7, 1.8, and 2.0% on average respectively), with Pseudobutyrivibrio and Anaeroplasma having a higher relative abundance during secondary colonization. Using CowPI, we predict differences between bacterial metabolic function during primary and secondary colonization. Specifically, our results infer an increase in carbohydrate metabolism in the bacteria attached during secondary colonization, irrespective of forage type. The CowPI data coupled with the FTIR plant chemistry data suggest that attached bacterial function is similar irrespective of forage type, with the main changes occurring between primary and secondary colonization. These data suggest that the sward composition of pasture may have major implications for the temporal availability of nutrients for animal.

Lactobacilli Are Prominent Members of the Microbiota Involved in the Ruminal Digestion of Barley and Corn

The chemical composition of barley grain can vary among barley varieties (Fibar, Xena, McGwire, and Hilose) and result in different digestion efficiencies in the rumen. It is not known if compositional differences in barley can affect the microbiota involved in the ruminal digestion of barley. The objective of this study was to characterize the in situ rumen degradability and microbiota of four barley grain varieties and to compare these to corn. Three ruminally cannulated heifers were fed a low (60% barley silage, 37% barley grain, and 3% supplement) or high grain (37% barley silage, 60% barley grain, and 3% supplement) diet. One set of bags was used to estimate dry matter (DM), starch and crude protein (CP) degradability. A second set was used to extract DNA from the adherent microbiota and visualize grain after incubation using scanning electron microscopy (SEM). DNA was subjected to amplicon 16S rRNA gene sequencing followed by analysis using QIIME. In the low grain diet, McGwire had the highest effective degradability (ED) of DM (P < 0.01). The ED of starch was highest (P < 0.01) for Fibar, McGwire, and Xena, but the ED of CP was not affected by variety. For the high grain diet, Xena and McGwire had the highest ED of DM (P < 0.01). The ED of starch was highest (P < 0.01) for Xena and Fibar. The ED of protein was highest (P < 0.01) for Xena and McGwire. Although the microbiota did not differ among barley varieties, they did differ from corn and with incubation time. Lactobacilli were dominant members of the mature biofilms associated with corn and barley and were accompanied by a notable increase in the lactic acid utilizing genera, Megasphaera. As none of the cattle exhibited subclinical or clinical acidosis during the study, our results suggest that lactobacilli play a more prominent role in routine starch digestion than presently surmised.

Invited review: Current perspectives on eating and rumination activity in dairy cows

Many early studies laid the foundation for our understanding of the mechanics of chewing, the physiological role of chewing for the cow, and how chewing behavior is affected by dietary characteristics. However, the dairy cow has changed significantly over the past decades, as have the types of diets fed and the production systems used. The plethora of literature published in recent years provides new insights on eating and ruminating activity of dairy cows. Lactating dairy cows spend about 4.5 h/d eating (range: 2.4-8.5 h/d) and 7 h/d ruminating (range: 2.5-10.5 h/d), with a maximum total chewing time of 16 h/d. Chewing time is affected by many factors, most importantly whether access to feed is restricted, intake of neutral detergent fiber from forages, and mean particle size of the diet. Feed restriction and long particles (≥19 mm) have a greater effect on eating time, whereas intake of forage neutral detergent fiber and medium particles (4-19 mm) affects rumination time. It is well entrenched in the literature that promoting chewing increases salivary secretion of dairy cows, which helps reduce the risk of acidosis. However, the net effect of a change in chewing time on rumen buffing is likely rather small; therefore, acidosis prevention strategies need to be broad. Damage to plant tissues during mastication creates sites that provide access to fungi, adhesion of bacteria, and formation of biofilms that progressively degrade carbohydrates. Rumination and eating are the main ways in which feed is reduced in particle size. Contractions of the rumen increase during eating and ruminating activity and help move small particles to the escapable pool and into the omasum. Use of recently developed low-cost sensors that monitor chewing activity of dairy cows in commercial facilities can provide information that is helpful in management decisions, especially when combined with other criteria. Although accuracy and precision can be somewhat variable depending on sensor and conditions of use, relative changes in cow behavior, such as a marked decrease in rumination time of a cow or sustained low rumination time compared with a contemporary group of cows, can be used to help detect estrus, parturition, and some illnesses. This review provides a comprehensive understanding of the dietary, animal, and management factors that affect eating and ruminating behavior in dairy cows and presents an overview of the physiological importance of chewing with emphasis on recent developments and practical implications for feeding and managing the modern housed dairy cow.

Temporal changes of the bacterial community colonizing wheat straw in the cow rumen

This study used Miseq pyrosequencing and scanning electron microscopy to investigate the temporal changes in the bacterial community tightly attached to wheat straw in the cow rumen. The wheat straw was incubated in the rumens and samples were recovered at various times. The wheat straw degradation exhibited three phases: the first degradation phase occurred within 0.5 h, and the second degradation phase occurred after 6 h, with a stalling phase occurring between 0.5 and 6 h. Scanning electron microscopy revealed the colonization of the microorganisms on the wheat straw over time. The bacterial communities at 0.5, 6, 24, and 72 h were determined, corresponding to the degradation phases. Firmicutes and Bacteroidetes were the two most dominant phyla in the bacterial communities at the four time points. Principal coordinate analysis (PCoA) showed that the bacterial communities at the four time points were distinct from each other. The wheat straw-associated bacteria stabilized at the phylum level after 0.5 h of rumen incubation, and only modest phylum-level and family-level changes were observed for most taxa between 0.5 h and 72 h. The relative abundance of the dominant genera, Butyrivibrio, Coprococcus, Ruminococcus, Succiniclasticum, Clostridium, Prevotella, YRC22, CF231, and Treponema, changed significantly over time (P < .05). However, at the genus level, unclassified taxa accounted for 70.3% ± 6.1% of the relative abundance, indicating their probable importance in the degradation of wheat straw as well as in the temporal changes of the bacterial community. Thus, understanding the function of these unclassified taxa is of great importance for targeted improvement of forage use efficiency in ruminants. Collectively, our results revealed distinct degradation phases of wheat straw and corresponding changes in the colonized bacterial community.

Unravelling methanogenesis in ruminants, horses and kangaroos: the links between gut anatomy, microbial biofilms and host immunity

The present essay aims to resolve the question as to why macropod marsupials (e.g. kangaroos and wallabies, hereinafter termed ‘macropods) and horses produce much less methane (CH4) than do ruminants when digesting the same feed. In herbivores, gases produced during fermentation of fibrous feeds do not pose a major problem in regions of the gut that have mechanisms to eliminate them (e.g. eructation in the rumen and flatus in the lower bowel). In contrast, gas pressure build-up in the tubiform forestomach of macropods or in the enlarged tubiform caecum of equids would be potentially damaging. It is hypothesised that, to prevent this problem, evolution has favoured development of controls over gut microbiota that enable enteric gas production (H2 and CH4) to be differently regulated in the forestomach of macropods and the caecum of all three species, from the forestomach of ruminants. The hypothesised regulation depends on interactions between their gut anatomy and host-tissue immune responses that have evolved to modify the species composition of their gut microbiota which, importantly, are mainly in biofilms. Obligatory H2 production during forage fermentation is, thus, captured in CH4 in the ruminant where ruminal gases are readily released by eructation, or in acetate in the macropod forestomach and equid caecum–colon where a build-up in gas pressure could potentially damage these organs. So as to maintain appropriate gut microbiota in different species, it is hypothesised that blind sacs at the cranial end of the haustral anatomy of the macropod forestomach and the equid caecum are sites of release of protobiofilm particles that develop in close association with the mucosal lymphoid tissues. These tissues release immune secretions such as antimicrobial peptides, immunoglobulins, innate lymphoid cells and mucin that eliminate or suppress methanogenic Archaea and support the growth of acetogenic microbiota. The present review draws on microbiological studies of the mammalian gut as well as other microbial environments. Hypotheses are advanced to account for published findings relating to the gut anatomy of herbivores and humans, the kinetics of digesta in ruminants, macropods and equids, and also the composition of biofilm microbiota in the human gut as well as aquatic and other environments where the microbiota exist in biofilms.

The rumen microbiome: an underexplored resource for novel antimicrobial discovery

Antimicrobial peptides (AMPs) are promising drug candidates to target multi-drug resistant bacteria. The rumen microbiome presents an underexplored resource for the discovery of novel microbial enzymes and metabolites, including AMPs. Using functional screening and computational approaches, we identified 181 potentially novel AMPs from a rumen bacterial metagenome. Here, we show that three of the selected AMPs (Lynronne-1, Lynronne-2 and Lynronne-3) were effective against numerous bacterial pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). No decrease in MRSA susceptibility was observed after 25 days of sub-lethal exposure to these AMPs. The AMPs bound preferentially to bacterial membrane lipids and induced membrane permeability leading to cytoplasmic leakage. Topical administration of Lynronne-1 (10% w/v) to a mouse model of MRSA wound infection elicited a significant reduction in bacterial counts, which was comparable to treatment with 2% mupirocin ointment. Our findings indicate that the rumen microbiome may provide viable alternative antimicrobials for future therapeutic application.

Anti-microbial molecules made by microbes in the gut of ruminant animals could become new weapons against antibiotic-resistant infections. An international team of researchers led by Sharon Huws at Queen’s University Belfast, UK, identified three anti-microbial peptides in the rumen of animals such as cattle, sheep and goats. The peptides—short proteins—were highly active in laboratory trials against several clinically important drug-resistant infections. These included methicillin resistant Staphylococcus aureus (MRSA), a notorious cause of life-threatening infections, especially in patients with weakened immunity. There is growing interest in using peptides as alternatives to existing antibiotics. The findings, initiated by examining a ‘library’ of molecular data, suggest that the rumen is an under-explored resource that may harbor many medically useful antimicrobials. The possibilities should be investigated further, with promising molecules being tested in clinical conditions.

Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing

The aim of this study was to improve the utilization of rice straw as forage in ruminants by investigating the degradation pattern of rice straw in the dairy cow rumen. Ground up rice straw was incubated in situ in the rumens of three Holstein cows over a period of 72 h. The rumen fluid at 0 h and the rice straw at 0.5, 1, 2, 4, 6, 12, 24, 48, and 72 h were collected for analysis of the bacterial community and the degradation of the rice straw. The bacterial community and the carbohydrate-active enzymes in the rumen fluid were analyzed by metagenomics. The diversity of bacteria loosely and tightly attached to the rice straw was investigated by scanning electron microscopy and Miseq sequencing of 16S rRNA genes. The predominant genus in the rumen fluid was Prevotella, followed by Bacteroides, Butyrivibrio, unclassified Desulfobulbaceae, Desulfovibrio, and unclassified Sphingobacteriaceae. The main enzymes were members of the glycosyl hydrolase family, divided into four categories (cellulases, hemicellulases, debranching enzymes, and oligosaccharide-degrading enzymes), with oligosaccharide-degrading enzymes being the most abundant. No significant degradation of rice straw was observed between 0.5 and 6 h, whereas the rice straw was rapidly degraded between 6 and 24 h. The degradation then gradually slowed between 24 and 72 h. A high proportion of unclassified bacteria were attached to the rice straw and that Prevotella, Ruminococcus, and Butyrivibrio were the predominant classified genera in the loosely and tightly attached fractions. The composition of the loosely attached bacterial community remained consistent throughout the incubation, whereas a significant shift in composition was observed in the tightly attached bacterial community after 6 h of incubation. This shift resulted in a significant reduction in numbers of Bacteroidetes and a significant increase in numbers of Firmicutes. In conclusion, the degradation pattern of rice straw in the dairy cow rumen indicates a strong contribution by tightly attached bacteria, especially after 6 h incubation, but most of these bacteria were not taxonomically characterized. Thus, these bacteria should be further identified and subjected to functional analysis to improve the utilization of crop residues in ruminants.

A Systems Biology Approach Reveals Differences in the Dynamics of Colonization and Degradation of Grass vs. Hay by Rumen Microbes with Minor Effects of Vitamin E Supplementation

Increasing the efficiency of utilization of fresh and preserved forage is a key target for ruminant science. Vitamin E is often used as additive to improve product quality but its impact of the rumen function is unknown. This study investigated the successional microbial colonization of ryegrass (GRA) vs. ryegrass hay (HAY) in presence of zero or 50 IU/d supplementary vitamin E, using a rumen simulation technique. A holistic approach was used to link the dynamics of feed degradation with the structure of the liquid-associated (LAB) and solid-associated bacteria (SAB). Results showed that forage colonization by SAB was a tri-phasic process highly affected by the forage conservation method: Early colonization (0-2 h after feeding) by rumen microbes was 2× faster for GRA than HAY diets and dominated by Lactobacillus and Prevotella which promoted increased levels of lactate (+56%) and ammonia (+18%). HAY diets had lower DM degradation (-72%) during this interval being Streptococcus particularly abundant. During secondary colonization (4-8 h) the SAB community increased in size and decreased in diversity as the secondary colonizers took over (Pseudobutyrivibrio) promoting the biggest differences in the metabolomics profile between diets. Secondary colonization was 3× slower for HAY vs. GRA diets, but this delay was compensated by a greater bacterial diversity (+197 OTUs) and network complexity resulting in similar feed degradations. Tertiary colonization (>8 h) consisted of a slowdown in the colonization process and simplification of the bacterial network. This slowdown was less evident for HAY diets which had higher levels of tertiary colonizers (Butyrivibrio and Ruminococcus) and may explain the higher DM degradation (+52%) during this interval. The LAB community was particularly active during the early fermentation of GRA and during the late fermentation for HAY diets indicating that the availability of nutrients in the liquid phase reflects the dynamics of feed degradation. Vitamin E supplementation had minor effects but promoted a simplification of the LAB community and a slight acceleration in the SAB colonization sequence which could explain the higher DM degradation during the secondary colonization. Our findings suggest that when possible, grass should be fed instead of hay, in order to accelerate feed utilization by rumen microbes.

Buwchitin: A Ruminal Peptide with Antimicrobial Potential against Enterococcus faecalis

Antimicrobial peptides (AMPs) are gaining popularity as alternatives for treatment of bacterial infections and recent advances in omics technologies provide new platforms for AMP discovery. We sought to determine the antibacterial activity of a novel antimicrobial peptide, buwchitin, against Enterococcus faecalis. Buwchitin was identified from a rumen bacterial metagenome library, cloned, expressed and purified. The antimicrobial activity of the recombinant peptide was assessed using a broth microdilution susceptibility assay to determine the peptide's killing kinetics against selected bacterial strains. The killing mechanism of buwchitin was investigated further by monitoring its ability to cause membrane depolarization (diSC₃(5) method) and morphological changes in E. faecalis cells. Transmission electron micrographs of buwchitin treated E. faecalis cells showed intact outer membranes with blebbing, but no major damaging effects and cell morphology changes. Buwchitin had negligible cytotoxicity against defibrinated sheep erythrocytes. Although no significant membrane leakage and depolarization was observed, buwchitin at minimum inhibitory concentration (MIC) was bacteriostatic against E. faecalis cells and inhibited growth in vitro by 70% when compared to untreated cells. These findings suggest that buwchitin, a rumen derived peptide, has potential for antimicrobial activity against E. faecalis.

Characterization of the Microbiome along the Gastrointestinal Tract of Growing Turkeys

The turkey microbiome is largely understudied, despite its relationship with bird health and growth, and the prevalence of human pathogens such as Campylobacter spp. In this study we investigated the microbiome within the small intestine (SI), caeca (C), large intestine (LI), and cloaca (CL) of turkeys at 6, 10, and 16 weeks of age. Eight turkeys were dissected within each age category and the contents of the SI, C, LI, and CL were harvested. 16S rDNA based QPCR was performed on all samples and samples for the four locations within three birds/age group were sequenced using ion torrent-based sequencing of the 16S rDNA. Sequencing data showed on a genus level, an abundance of Lactobacillus, Streptococcus, and Clostridium XI (38.2, 28.1, and 13.0% respectively) irrespective of location and age. The caeca exhibited the greatest microbiome diversity throughout the development of the turkey. PICRUSt data predicted an array of bacterial function, with most differences being apparent in the caeca of the turkeys as they matured. QPCR revealed that the caeca within 10 week old birds, contained the most Campylobacter spp. Understanding the microbial ecology of the turkey gastrointestinal tract is essential in terms of understanding production efficiency and in order to develop novel strategies for targeting Campylobacter spp.

Biofilm compartmentalisation of the rumen microbiome: modification of fermentation and degradation of dietary toxins

Many deleterious chemicals in plant materials ingested by ruminants produce clinical effects, varying from losses of production efficiency through to death. Many of the effects are insidious, often going unrecognised by animal managers. When secondary plant compounds enter the rumen, they may undergo modification by rumen microbes, which often removes the deleterious compounds, but in specific instances, the deleterious effect may be enhanced. Improved understanding of rumen ecology, particularly concerning the biofilm mode of microbial fermentation, has led to major advances in our understanding of fermentation. In the present review, the potential impact of the physical structuring of the rumen microbiome is discussed in relation to how several economically important secondary plant compounds and other toxins are metabolised by the rumen microbiome and how their toxic effects may be remedied by providing inert particles with a large surface area to weight ratio in the diet. These particles provide additional surfaces for attachment of rumen microorganisms that help alleviate toxicity problems associated with deleterious compounds, including fluoroacetate, mimosine, mycotoxins, cyanoglycosides and hydrogen cyanide. The review first summarises the basic science of biofilm formation and describes the properties of biofilms and their roles in the rumen. It then addresses how biofilms on inert solids and fermentable particulates may assist in detoxification of potentially toxic compounds. A hypothesis that explains how nitrate poisoning may occur as a result of compartmentalisation of nitrate and nitrite reduction in the rumen is included.

Temporal Metagenomic and Metabolomic Characterization of Fresh Perennial Ryegrass Degradation by Rumen Bacteria

Understanding the relationship between ingested plant material and the attached microbiome is essential for developing methodologies to improve ruminant nutrient use efficiency. We have previously shown that perennial ryegrass (PRG) rumen bacterial colonization events follow a primary (up to 4 h) and secondary (after 4 h) pattern based on the differences in diversity of the attached bacteria. In this study, we investigated temporal niche specialization of primary and secondary populations of attached rumen microbiota using metagenomic shotgun sequencing as well as monitoring changes in the plant chemistry using mid-infrared spectroscopy (FT-IR). Metagenomic Rapid Annotation using Subsystem Technology (MG-RAST) taxonomical analysis of shotgun metagenomic sequences showed that the genera Butyrivibrio, Clostridium, Eubacterium, Prevotella, and Selenomonas dominated the attached microbiome irrespective of time. MG-RAST also showed that Acidaminococcus, Bacillus, Butyrivibrio, and Prevotella rDNA increased in read abundance during secondary colonization, whilst Blautia decreased in read abundance. MG-RAST Clusters of Orthologous Groups (COG) functional analysis also showed that the primary function of the attached microbiome was categorized broadly within “metabolism;” predominantly amino acid, carbohydrate, and lipid metabolism and transport. Most sequence read abundances (51.6, 43.8, and 50.0% of COG families pertaining to amino acid, carbohydrate and lipid metabolism, respectively) within these categories were higher in abundance during secondary colonization. Kyoto encyclopedia of genes and genomes (KEGG) pathways analysis confirmed that the PRG-attached microbiota present at 1 and 4 h of rumen incubation possess a similar functional capacity, with only a few pathways being uniquely found in only one incubation time point only. FT-IR data for the plant residues also showed that the main changes in plant chemistry between primary and secondary colonization was due to increased carbohydrate, amino acid, and lipid metabolism. This study confirmed primary and secondary colonization events and supported the hypothesis that functional changes occurred as a consequence of taxonomical changes. Sequences within the carbohydrate metabolism COG families contained only 3.2% of cellulose activities, on average across both incubation times (1 and 4 h), suggesting that degradation of the plant cell walls may be a key rate-limiting factor in ensuring the bioavailability of intra-plant nutrients in a timely manner to the microbes and ultimately the animal. This suggests that a future focus for improving ruminant nutrient use efficiency should be altering the recalcitrant plant cell wall components and/or improving the cellulolytic capacity of the rumen microbiota.

Characterization and comparison of the temporal dynamics of ruminal bacterial microbiota colonizing rice straw and alfalfa hay within ruminants

Three ruminally cannulated Holstein cows were used to characterize the dynamics of bacterial colonization of rice straw and alfalfa hay and to assess the differences in the composition and inferred gene function of the colonized microbiota between these 2 forages. Nonincubated (0h) rice straw and alfalfa hay samples and residues in nylon bags incubated for 0.5, 2, 6, 16, and 48h were analyzed for dry matter and were used for DNA extraction and MiSeq (Illumina Inc., San Diego, CA) sequencing of the 16S rRNA gene. The microbial communities that colonized the air-dried and nonincubated (0h) rice straw and alfalfa hay were both dominated by members of the Proteobacteria (contributing toward 70.47% of the 16S RNA reads generated). In situ incubation of the 2 forages revealed major shifts in the community composition: Proteobacteria were replaced within 30min by members belonging to the Bacteroidetes and Firmicutes, contributing toward 51.9 and 36.6% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 6h of rumen incubation, when members of the Spirochaetes and Fibrobacteria phyla became abundant in the forage-adherent community. During the first 30min of rumen incubation, ~20.7 and 36.1% of the rice straw and alfalfa hay, respectively, were degraded, whereas little biomass degradation occurred between 30min and 2h after the rice straw or alfalfa hay was placed in the rumen. Significant differences were noted in attached bacterial community structure between the 2 forage groups, and the abundances of dominant genera Anaeroplasma, Butyrivibrio, Fibrobacter, and Prevotella were affected by the forage types. Real-time PCR results showed that the 16S rRNA copies of total bacteria attached to these 2 forages were affected by the forage types and incubation time, and higher numbers of attached bacterial 16S rRNA were observed in the alfalfa hay samples than in the rice straw from 0.5 to 16h of incubation. The metagenomes predicted by phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) revealed that the forage types significantly affected 21 metabolic pathways identified in the Kyoto Encyclopedia of Genes and Genomes, and 33 were significantly changed over time. Collectively, our results reveal a difference in the dynamics of bacterial colonization and the inferred gene function of microbiota associated with rice straw and alfalfa hay within the rumen. These findings are of great importance for the targeted improvement of forage nutrient use efficiency in ruminants.

The effects of PPO activity on the proteome of ingested red clover and implications for improving the nutrition of grazing cattle

Increasing the rumen-stable protein content of feed would lead to improved nitrogen utilisation in cattle, and less nitrogenous waste. Red clover (Trifolium pratense L.) is a high protein ruminant feed containing high polyphenol oxidase (PPO) activity. PPO mediated protein-quinone binding has been linked to protecting plant proteins from proteolysis. To explore the mechanism underlying the effect of PPO on protein protection in fresh forage feeds, proteomic components of feed down-boli produced from wild-type red clover and a low PPO mutant, at point of ingestion and after 4h in vitro incubation with rumen inoculum were analysed. Significant differences in proteomic profiles between wild-type and mutant red clover were determined after 4h incubation, with over 50% less spots in mutant than wild-type proteomes, indicating decreased proteolysis in the latter. Protein identifications revealed preferentially retained proteins localised within the chloroplast, suggesting that PPO mediated protection in the wild-type operates due to the proximity of target proteins to the enzyme and substrates, either diffusing into this compartment from the vacuole or are present in the chloroplast. This increased understanding of protein targets of PPO indicates that wider exploitation of the trait could contribute to increased protein use efficiency in grazing cattle.

BIOLOGICAL SIGNIFICANCE

One of the main challenges for sustainable livestock farming is improving capture of dietary nitrogen by ruminants. Typically up to 70% of ingested protein-N is excreted representing a loss of productivity potential and a serious environmental problem in terms of nitrogenous pollution of lands and water. Identification of key characteristics of rumen-protected protein will deliver target traits for selection in forage breeding programmes. The chloroplastic enzyme PPO catalyzes the oxidation of phenols to quinones, which react with protein. Little is currently known about the intracellular protein targets of the products of PPO activity or the mechanism underlying protein complexing, including whether there is any specificity to the reaction. Here we have determined significant differences in the proteomes of freshly ingested down boli corresponding to the presence or absence of active PPO. These results show that in the presence of PPO the forage protein is less amenable to proteolysis and provide the novel information that the protected proteins are putatively chloroplastically located. These data also contribute to a growing evidence base that a chloroplastic PPO substrate exists in red clover in addition to the currently known vacuolar substrates.

Temporal dynamics of the metabolically active rumen bacteria colonizing fresh perennial ryegrass

This study investigated successional colonization of fresh perennial ryegrass (PRG) by the rumen microbiota over time. Fresh PRG was incubated in sacco in the rumens of three Holstein × Friesian cows over a period of 8 h, with samples recovered at various times. The diversity of attached bacteria was assessed using 454 pyrosequencing of 16S rRNA (cDNA). Results showed that plant epiphytic communities either decreased to low relative abundances or disappeared following rumen incubation, and that temporal colonization of the PRG by the rumen bacteria was biphasic with primary (1 and 2 h) and secondary (4-8 h) events evident with the transition period being with 2-4 h. A decrease in sequence reads pertaining to Succinivibrio spp. and increases in Pseudobutyrivibrio, Roseburia and Ruminococcus spp. (the latter all order Clostridiales) were evident during secondary colonization. Irrespective of temporal changes, the continually high abundances of Butyrivibrio, Fibrobacter, Olsenella and Prevotella suggest that they play a major role in the degradation of the plant. It is clear that a temporal understanding of the functional roles of these microbiota within the rumen is now required to unravel the role of these bacteria in the ruminal degradation of fresh PRG.

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.

Isolation and characterization of novel lipases/esterases from a bovine rumen metagenome

Improving the health beneficial fatty acid content of meat and milk is a major challenge requiring an increased understanding of rumen lipid metabolism. In this study, we isolated and characterized rumen bacterial lipases/esterases using functional metagenomics. Metagenomic libraries were constructed from DNA extracted from strained rumen fluid (SRF), solid-attached bacteria (SAB) and liquid-associated rumen bacteria (LAB), ligated into a fosmid vector and subsequently transformed into an Escherichia coli host. Fosmid libraries consisted of 7,744; 8,448; and 7,680 clones with an average insert size of 30 to 35 kbp for SRF, SAB and LAB, respectively. Transformants were screened on spirit blue agar plates containing tributyrin for lipase/esterase activity. Five SAB and four LAB clones exhibited lipolytic activity, and no positive clones were found in the SRF library. Fosmids from positive clones were pyrosequenced and twelve putative lipase/esterase genes and two phospholipase genes retrieved. Although the derived proteins clustered into diverse esterase and lipase families, a degree of novelty was seen, with homology ranging from 40 to 78 % following BlastP searches. Isolated lipases/esterases exhibited activity against mostly short- to medium-chain substrates across a range of temperatures and pH. The function of these novel enzymes recovered in ruminal metabolism needs further investigation, alongside their potential industrial uses.

Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling

The rumen microbial ecosystem is known for its biomass-degrading and methane-producing phenotype. Fermentation of recalcitrant plant material, comprised of a multitude of interwoven fibers, necessitates the synergistic activity of diverse microbial taxonomic groups that inhabit the anaerobic rumen ecosystem. Although interspecies hydrogen (H₂) transfer, a process during which bacterially generated H₂ is transferred to methanogenic Archaea, has obtained significant attention over the last decades, the temporal variation of the different taxa involved in in situ biomass-degradation, H₂ transfer and the methanogenesis process remains to be established. Here we investigated the temporal succession of microbial taxa and its effect on fiber composition during rumen incubation using 16S rRNA amplicon sequencing. Switchgrass filled nylon bags were placed in the rumen of a cannulated cow and collected at nine time points for DNA extraction and 16S pyrotag profiling. The microbial community colonizing the air-dried and non-incubated (0 h) switchgrass was dominated by members of the Bacilli (recruiting 63% of the pyrotag reads). During in situ incubation of the switchgrass, two major shifts in the community composition were observed: Bacilli were replaced within 30 min by members belonging to the Bacteroidia and Clostridia, which recruited 34 and 25% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 16 h of rumen incubation, when members of the Spirochaetes and Fibrobacteria classes became more abundant in the fiber-adherent community. During the first 30 min of rumen incubation ~13% of the switchgrass dry matter was degraded, whereas little biomass degradation appeared to have occurred between 30 min and 4 h after the switchgrass was placed in the rumen. Interestingly, methanogenic members of the Euryarchaeota (i.e., Methanobacteria) increased up to 3-fold during this period of reduced biomass-degradation, with peak abundance just before rates of dry matter degradation increased again. We hypothesize that during this period microbial-mediated fibrolysis was temporarily inhibited until H₂ was metabolized into CH₄ by methanogens. Collectively, our results demonstrate the importance of inter-species interactions for the biomass-degrading and methane-producing phenotype of the rumen microbiome—both microbially facilitated processes with global significance.

Ruminal Prevotella spp. may play an important role in the conversion of plant lignans into human health beneficial antioxidants

Secoisolariciresinol diglucoside (SDG), the most abundant lignan in flaxseed, is metabolized by the ruminal microbiota into enterolignans, which are strong antioxidants. Enterolactone (EL), the main mammalian enterolignan produced in the rumen, is transferred into physiological fluids, with potentially human health benefits with respect to menopausal symptoms, hormone-dependent cancers, cardiovascular diseases, osteoporosis and diabetes. However, no information exists to our knowledge on bacterial taxa that play a role in converting plant lignans into EL in ruminants. In order to investigate this, eight rumen cannulated cows were used in a double 4 × 4 Latin square design and fed with four treatments: control with no flax meal (FM), or 5%, 10% and 15% FM (on a dry matter basis). Concentration of EL in the rumen increased linearly with increasing FM inclusion. Total rumen bacterial 16S rRNA concentration obtained using Q-PCR did not differ among treatments. PCR-T-RFLP based dendrograms revealed no global clustering based on diet indicating between animal variation. PCR-DGGE showed a clustering by diet effect within four cows that had similar basal ruminal microbiota. DNA extracted from bands present following feeding 15% FM and absent with no FM supplementation were sequenced and it showed that many genera, in particular Prevotella spp., contributed to the metabolism of lignans. A subsequent in vitro study using selected pure cultures of ruminal bacteria incubated with SDG indicated that 11 ruminal bacteria were able to convert SDG into secoisolariciresinol (SECO), with Prevotella spp. being the main converters. These data suggest that Prevotella spp. is one genus playing an important role in the conversion of plant lignans to human health beneficial antioxidants in the rumen.

Interactions between microbial consortia in biofilms: a paradigm shift in rumen microbial ecology and enteric methane mitigation

Minimising enteric CH4 emissions from ruminants is a current research priority because CH4 contributes to global warming. The most effective mitigation strategy is to adjust the animal’s diet to complement locally available feed resources so that optimal production is gained from a minimum of animals. This essay concentrates on a second strategy – the use of feed additives that are toxic to methanogens or that redirect H2 (and electrons) to inhibit enteric CH4 emissions from individual animals. Much of the published research in this area is contradictory and may be explained when the microbial ecology of the rumen is considered. Rumen microbes mostly exist in organised consortia within biofilms composed of self-secreted extracellular polymeric substances attached to or within feed particles. In these biofilms, individual colonies are positioned to optimise their use of preferred intermediates from an overall process of organic matter fermentation that generates end-products the animal can utilise. Synthesis of CH4 within biofilms prevents a rise in the partial pressure of H2 (pH2) to levels that inhibit bacterial dehydrogenases, and so reduce fermentation rate, feed intake and digestibility. In this context, hypotheses are advanced to explain changes in hydrogen disposal from the biofilms in the rumen resulting from use of anti-methanogenic feed additives as follows. Nitrate acts as an alternative electron sink when it is reduced via NO2– to NH3 and CH4 synthesis is reduced. However, efficiency of CH4 mitigation is always lower than that predicted and decreases as NO3– ingestion increases. Suggested reasons include (1) variable levels of absorption of NO3–or NO2– from the rumen and (2) increases in H2 production. One suggestion is that NO3– reduction may lower pH2 at the surface of biofilms, thereby creating an ecological niche for growth of syntrophic bacteria that oxidise propionate and/or butyrate to acetate with release of H2. Chlorinated hydrocarbons also inhibit CH4 synthesis and increase H2 and formate production by some rumen methanogens. Formate diffuses from the biofilm and is converted to HCO3– and H2 in rumen fluid and is then excreted via the breath. Short-chain nitro-compounds inhibit both CH4 and formate synthesis when added to ruminal fluid but have little or no effect in redirecting H2 to other sinks, so the pH2 within biofilms may increase to levels that support reductive acetogenesis. Biochar or activated charcoal may also alter biofilm activity and reduce net CH4 synthesis; direct electron transfer between microbes within biofilms may also be involved. A final suggestion is that, during their sessile life stage, protozoa interact with biofilm communities and help maintain pH2 in the biofilm, supporting methanogenesis.

Comparative metabolite fingerprinting of the rumen system during colonisation of three forage grass (Lolium perenne L.) varieties

The rumen microbiota enable ruminants to degrade complex ligno-cellulosic compounds to produce high quality protein for human consumption. However, enteric fermentation by domestic ruminants generates negative by-products: greenhouse gases (methane) and environmental nitrogen pollution. The current lack of cultured isolates representative of the totality of rumen microbial species creates an information gap about the in vivo function of the rumen microbiota and limits our ability to apply predictive biology for improvement of feed for ruminants. In this work we took a whole ecosystem approach to understanding how the metabolism of the microbial population responds to introduction of its substrate. Fourier Transform Infra Red (FTIR) spectroscopy-based metabolite fingerprinting was used to discriminate differences in the plant-microbial interactome of the rumen when using three forage grass varieties (Lolium perenne L. cv AberDart, AberMagic and Premium) as substrates for microbial colonisation and fermentation. Specific examination of spectral regions associated with fatty acids, amides, sugars and alkanes indicated that although the three forages were apparently similar by traditional nutritional analysis, patterns of metabolite flux within the plant-microbial interactome were distinct and plant genotype dependent. Thus, the utilisation pattern of forage nutrients by the rumen microbiota can be influenced by subtleties determined by forage genotypes. These data suggest that our interactomic approach represents an important means to improve forages and ultimately the livestock environment.