The application of rumen simulation technique (RUSITEC) for studying dynamics of the bacterial community and metabolome in rumen fluid and the effects of a challenge with Clostridium perfringens

Research updates and progress on nutritional significance of the amides I and II, alpha-helix and beta-sheet ratios, microbial protein synthesis, and steam pressure toasting condition with globar and synchrotron molecular microspectroscopic techniques with chemometrics

This article aims to review research updates and progress on the nutritional significance of the amides I and II, the alpha-helix and beta-sheet ratios, the microbial protein synthesis, and the steam pressure toasting condition in food and feed with globar and synchrotron molecular microspectroscopic techniques plus chemometrics (both univariate and multivariate techniques). The review focused on (I) impact of the amides I and II, and the alpha-helix and beta-sheet-structure ratios in food and feeds; (II) Current research progress and update in synchrotron technique and application in feed and food molecular structure studies that are associated with nutrition delivery; (III) Impact of thermal processing- steam pressure toasting condition on feed and food; (IV). Impact of the microbial protein synthesis and methodology on feed and food; and (V). Impact on performance and production of ruminants with Faba beans.

The intraruminal redox potential is stabilised by opposing influences during fermentation

An optimal fermentation process in the forestomach is pivotal for the wellbeing and performance of ruminants. Complex carbohydrates are broken down into short-chain fatty acids (SCFA) which form the major energy source for the animal. A strong interrelationship of this process with intraruminal pH and redox potential (Eh) exists. These parameters can be measured with intraruminal sensors, but the interpretation of the measurements, especially of Eh, and their meaning for intraruminal homeostasis is not completely clear. In this study, factors influencing intraruminal Eh were elucidated. We hypothesised that intraruminal Eh is influenced by the fermentation process as such, but not by its end products SCFA. We measured Eh and pH in ruminal fluid from fasting cannulated sheep after the addition of 0.06 m Na-acetate, -propionate, -butyrate or glucose in vitro. Furthermore, we assessed the interrelation of pH and Eh. Basal Eh and pH values were -120 ± 41 mV and 7.0 ± 0.3, respectively, in native ruminal fluid in vitro. While the addition of SCFA did not induce any changes, glucose addition caused a significant decrease in both pH and Eh compared to the values before the addition (paired Student's t-test, p < 0.05). We attribute the decrease in Eh to an increased production of H₂ in the process of generating SCFA, predominantly acetate. By titrating both native and particle-free ruminal fluid to more acidic and basic pH values (4.5-8.5), we found a non-linear inverse correlation of pH and Eh, counteracting the H₂ -driven decrease of Eh during fermentation. Thus, the intraruminal Eh is influenced by pH and H₂ output during SCFA formation. The opposed character of these factors stabilises the intraruminal homeostasis which might help maintain symbiotic microbiota in the rumen. Understanding, monitoring, and supporting this system will be an essential part of modern cattle production.

Effects of Different Formulations of Glyphosate on Rumen Microbial Metabolism and Bacterial Community Composition in the Rumen Simulation Technique System

The use of the herbicide glyphosate and its formulations on protein-rich feedstuff for cattle leads to a considerable intake of glyphosate into the rumen of the animals, where glyphosate may potentially impair the 5-enolpyruvylshikimate-3-phosphate pathway of the commensal microbiota, which could cause dysbiosis or proliferation of pathogenic microorganisms. Here, we evaluated the effects of pure glyphosate and the formulations Durano TF and Roundup® LB plus in different concentrations on the fermentation pattern, community composition and metabolic activity of the rumen microbiota using the Rumen Simulation Technique (RUSITEC). Application of the compounds in three concentrations (0.1 mg/l, 1.0 mg/l or 10 mg/l, n = 4 each) for 9 days did not affect fermentation parameters such as pH, redox potential, NH3-N concentration and production of short-chain fatty acids compared to a control group. Microbial protein synthesis and the degradation of different feed fractions did not vary among the treatments. None of the used compounds or concentrations did affect the microbial diversity or abundance of microbial taxa. Metaproteomics revealed that the present metabolic pathways including the shikimate pathway were not affected by addition of glyphosate, Durano TF or Roundup® LB plus. In conclusion, neither pure glyphosate, nor its formulations Durano TF and Roundup® LB plus did affect the bacterial communities of the rumen.

Characterization of Microbial Intolerances and Ruminal Dysbiosis Towards Different Dietary Carbohydrate Sources Using an in vitro Model

AIM

This study aimed to characterize the critical points for determining the development of dysbiosis associated with feed intolerances and ruminal acidosis.

METHODS AND RESULTS

A metabologenomics approach was used to characterize dynamic microbial and metabolomics shifts using the rumen simulation technique (RUSITEC) by feeding native cornstarch (ST), chemically-modified cornstarch (CMS), or sucrose (SU). SU and CMS elicited the most drastic changes as rapidly as 4 h after feeding. This was accompanied by a swift accumulation of D-lactate, and the decline of benzoic and malonic acid. A consistent increase in Bifidobacterium and Lactobacillus as well as a decrease in fibrolytic bacteria was observed for both CMS and ST after 24 h, indicating intolerances within the fiber degrading populations. However, an increase in Lactobacillus was already evident in SU after 8 h. An inverse relationship between Fibrobacter and Bifidobacterium was observed in ST. In fact, Fibrobacter was positively correlated with several short-chain fatty acids (SCFA), while Lactobacillus was positively correlated with lactic acid, hexoses, hexose-phosphates, pentose phosphate pathway (PENTOSE-P-PWY) and heterolactic fermentation (P122-PWY).

CONCLUSIONS

The feeding of sucrose and modified starches, followed by native cornstarch, had a strong disruptive effect in the ruminal microbial community. Feed intolerances were shown to develop at different rates based on the availability of glucose for ruminal microorganisms.

SIGNIFICANCE OF THE STUDY

These results can be used to establish patterns of early dysbiosis (biomarkers) and develop strategies for preventing undesirable shifts in the ruminal microbial ecosystem.

Long-Term Mootral Application Impacts Methane Production and the Microbial Community in the Rumen Simulation Technique System

Methane emissions by ruminants contribute to global warming and result in a loss of dietary energy for the animals. One possibility of reducing methane emissions is by dietary strategies. In the present trial, we investigated the long-term effects of Mootral, a feed additive consisting of garlic powder (Allium sativum) and bitter orange extracts (Citrus aurantium), on fermentation parameters and the microbial community in the rumen simulation technique (RUSITEC) system. The experiment lasted 38 days and was divided into three phases: an equilibration period of 7 days, a baseline period (BL) of 3 days, and experimental period (EP) of 28 days. Twelve fermentation vessels were divided into three groups (n = 4): control (CON), short-term (ST), and long-term (LT) application. From day 11 to day 27, 1.7 g of Mootral was added to the ST vessels; LT vessels received 1.7 g of Mootral daily for the entire EP. With the onset of Mootral application, methane production was significantly reduced in both groups until day 18. Thereafter, the production rate returned to the initial quantity. Furthermore, the short chain fatty acid fermentation profile was significantly altered by Mootral application; the molar proportion of acetate decreased, while the proportions of propionate and butyrate increased. Metabolomic analysis revealed further changes in metabolite concentrations associated with the Mootral supplementation period. The methyl coenzyme-M reductase gene copy number was reduced in the liquid and solid phase, whereas the treatment did not affect the abundance of bacteria. At the end of the BL, Methanomicrobia was the most abundant archaeal class. Mootral supplementation induced an increase in the relative abundance of Methanomassiliicoccales and a reduction in the relative abundance of Methanomicrobia, however, this effect was transient. Abundances of bacterial families were only marginally altered by the treatment. In conclusion, Mootral has the transient ability to reduce methane production significantly due to a selective effect on archaea numbers and archaeal community composition with little effect on the bacterial community.

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.

Ruminal Fistulation and Cannulation: A Necessary Procedure for the Advancement of Biotechnological Research in Ruminants

Simple Summary

This article addresses the role of ruminal fistulation and cannulation as an essential procedure in the advancement of research related to several items: fermentation in the ruminant forestomach, effects of new food sources, rumen diseases as well as the minimization of methane emissions, implicated in the so-called greenhouse gases. The aim is also to diminish the alarmist news promoted by animalist sectors, which accuse this technique of being an act of cruelty. This paper describes the importance of this procedure as a necessary in vivo tool for biotechnological research. In addition, we highlight the necessary management measures to ensure animal welfare. This review ends with a description of current in vitro methods as an alternative to in vivo studies, assessing their applicability as a complementary tool to the knowledge of rumen dynamics.

Abstract

Rumen content is a complex mixture of feed, water, fermentation products, and living organisms such as bacteria, fungi, and protozoa, which vary over time and with different feeds. As it is impossible to reproduce this complex system in the laboratory, surgical fistulation and cannulation of the rumen is a powerful tool for the study (in vivo and in situ) of the physiology and biochemistry of the ruminant digestive system. Rumen fistulation in cattle, sheep, and goats has been performed extensively to advance our understanding of digestive physiology and development, nutrient degradability, and rumen microbial populations. The literature reports several fistulation and cannulation procedures in ruminants, which is not the focus of this paper. However, this method questions the ethical principles that alter the opinions of certain animal groups or those opposed to animal experimentation. In this article, we analyze the objectives of fistulation and cannulation of ruminants and the care needed to ensure that the welfare of the animal is maintained at all times. Due to the ethical issues raised by this technique, several in vitro digestion methods for simulating ruminal fermentation have been developed. The most relevant ones are described in this article. Independently of the procedure, we want to point out that research carried out with animals is obliged by legislation to follow strict ethical protocols, following the well-being and health status of the animal at all times.

Culturing Human Gut Microbiomes in the Laboratory

The human gut microbiota is a complex community of prokaryotic and eukaryotic microbes and viral particles that is increasingly associated with many aspects of host physiology and health. However, the classical microbiology approach of axenic culture cannot provide a complete picture of the complex interactions between microbes and their hosts in vivo. As such, recently there has been much interest in the culture of gut microbial ecosystems in the laboratory as a strategy to better understand their compositions and functions. In this review, we discuss the model platforms and methods available in the contemporary microbiology laboratory to study human gut microbiomes, as well as current knowledge surrounding the isolation of human gut microbes for the potential construction of defined communities for use in model systems. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

PacBio and Illumina MiSeq Amplicon Sequencing Confirm Full Recovery of the Bacterial Community After Subacute Ruminal Acidosis Challenge in the RUSITEC System

The impact of subacute rumen acidosis (SARA) on the rumen bacterial community has been frequently studied in in vivo trials. Here we investigated whether these alterations can be mirrored by using the rumen simulation technique (RUSITEC) as an in vitro model for this disease. We hypothezised that the bacterial community fully recovers after a subacute ruminal acidosis challenge. We combined a PacBio nearly full-length 16S rRNA gene analysis with 16S rRNA gene Illumina MiSeq sequencing of the V4 hypervariable region. With this hybrid approach, we aimed to get an increased taxonomic resolution of the most abundant bacterial groups and an overview of the total bacterial diversity. The experiment consisted of a control period I and a SARA challenge and ended after a control period II, of which each period lasted 5 d. Subacute acidosis was induced by applying two buffer solutions, which were reduced in their buffering capacity (SARA buffers) during the SARA challenge. Two control groups were constantly infused with the standard buffer solution. Furthermore, the two SARA buffers were combined with three different feeding variations, which differed in their concentrate-to-hay ratio. The induction of SARA led to a decrease in pH below 5.8, which then turned into a steady-state SARA. Decreasing pH values led to a reduction in bacterial diversity and richness. Moreover, the diversity of solid-associated bacteria was lower for high concentrate groups throughout all experimental periods. Generally, Firmicutes and Bacteroidetes were the predominant phyla in the solid and the liquid phase. During the SARA period, we observed a decrease in fibrolytic bacteria although lactate-producing and -utilizing families increased in certain treatment groups. The genera Lactobacillus and Prevotella dominated during the SARA period. With induction of the second control period, most bacterial groups regained their initial abundance. In conclusion, this in vitro model displayed typical bacterial alterations related to SARA and is capable of recovery from bouts of SARA. Therefore, this model can be used to mimic SARA under laboratory conditions and may contribute to a reduction in animal experiments.

Alterations in fermentation parameters during and after induction of a subacute rumen acidosis in the rumen simulation technique

Subacute rumen acidosis (SARA) is a common problem in dairy cattle. High-concentrate rations lead to an accumulation of short-chain fatty acids (SCFA) in the rumen and a subsequent decrease in ruminal pH. As SARA impairs animal welfare and productivity, numerous in vivo studies are focusing on evaluation of prevention strategies. In vitro models can support this research and reduce animal numbers and experimental costs. We used different diets and buffer compositions to induce SARA in the rumen simulation technique (Rusitec) and investigated the recovery process. The experiment consisted of an equilibration period (7 days), a first control period, a SARA period and a second control period (5 days each). During the SARA period, SARA was induced by infusing SARA1 or SARA2 buffer with reduced bicarbonate (20 mmol/L and 25 mmol/L) and phosphate (both 10 mmol/L) contents compared to a modified McDougall's buffer (bicarbonate 97.9 mmol/L, phosphates 20 mmol/L). Additionally, we compared three feeding strategies, which differed in the concentrate-to-roughage ratio (30:70, 70:30, changing ratio: 30% concentrate in control periods and 70% concentrate in SARA period). During the SARA period, the pH decreased to a constant value below the SARA thresholds of pH 5.8 and 5.6, whereas lactate concentrations remained low. The total SCFA production rate declined 3 days after SARA induction, and the molar proportion of acetate decreased. The decrease in pH and SCFA production was more pronounced for SARA1 buffer. The high-concentrate diet reduced the molar proportion of acetate and increased NH₃ -N concentrations. During the second control period, most parameters recovered. In conclusion, SARA conditions were successfully induced in the Rusitec. However, we observed a higher influence of buffer composition than of concentrate proportions on most biochemical parameters. Nearly all changes were reversible. This model can be applied to test acidosis prevention strategies prior to animal experiments.

Differently Pre-treated Alfalfa Silages Affect the in vitro Ruminal Microbiota Composition

Alfalfa (Medicago sativa L.) silage (AS) is an important feedstuff in ruminant nutrition. However, its high non-protein nitrogen content often leads to poor ruminal nitrogen retention. Various pre-ensiling treatments differing with respect to dry matter concentrations, wilting intensities and sucrose addition have been previously shown to improve the quality and true protein preservation of AS, and have substantial effects on in vitro ruminal fermentation of the resulting silages. However, it is unknown how these pre-ensiling treatments affect the ruminal microbiota composition, and whether alterations in the microbiota explain previously observed differences in ruminal fermentation. Therefore, during AS incubation in a rumen simulation system, liquid and solid phases were sampled 2 and 7 days after first incubating AS, representing an early (ET) and late (LT) time point, respectively. Subsequently, DNA was extracted and qPCR (bacteria, archaea, and anaerobic fungi) and prokaryotic 16S rRNA gene amplicon sequence analyses were performed. At the ET, high dry matter concentration and sucrose addition increased concentrations of archaea in the liquid phase (P = 0.001) and anaerobic fungi in the solid phase (P < 0.001). At the LT, only sucrose addition increased archaeal concentration in the liquid phase (P = 0.014) and anaerobic fungal concentration in the solid phase (P < 0.001). Bacterial concentrations were not affected by pre-ensiling treatments. The prokaryotic phylogenetic diversity index decreased in the liquid phase from ET to LT (P = 0.034), whereas the solid phase was not affected (P = 0.060). This is suggestive of a general adaption of the microbiota to the soluble metabolites released from the incubated AS, particularly regarding the sucrose-treated AS. Redundancy analysis of the sequence data at the genus level indicated that sucrose addition (P = 0.001), time point (P = 0.001), and their interaction (P = 0.001) affected microbial community composition in both phases. In summary, of the pre-ensiling treatments tested sucrose addition had the largest effect on the microbiota, and together with sampling time point affected microbiota composition in both phases of the rumen simulation system. Thus, microbiota composition analysis helped to understand the ruminal fermentation patterns, but could not fully explain them.

Administration of Streptococcus bovis isolated from sheep rumen digesta on rumen function and physiology as evaluated in a rumen simulation technique system

BACKGROUND AND AIM

Little information about the stability and changes of sheep ruminal microbiota due to pathogen intervention in the rumen simulation technique (RUSITEC) is available. This study aimed to investigate the effect of administration of a novel isolated Streptococcus bovis strain on rumen microbiology and physiology. In addition, the isolation of pigment-producing Streptococcus lutetiensis is described.

MATERIALS AND METHODS

Microbial strains were isolated from sheep rumen digesta. An isolated strain of S. bovis was evaluated in the RUSITEC system fed with mixed cattle feed and compared with an in-house developed probiotic formulation (PF), PF 1, containing Bacillus amyloliquifaciens, Bacillus subtilis, and Propionibacterium freudenreichii. The parameters of volatile fatty acid, lactic acid, pH profiling, and the coliform anti-pathogenicity were evaluated to determine the effect of S. bovis on rumen function and physiology.

RESULTS

Administration of S. bovis reduced the coliform count by 31.20% from 7.2×1010 colony-forming units (CFU)/mLto 1.7×106 CFU/mL. Agar diffusion assays revealed the extracellular antimicrobial activity of S. bovis against coliforms; Escherichia coli and Salmonella enterica with 12 and 14 mm zones of inhibition, respectively. Simultaneously, an increase of 61.62% in the rumen yeast count was noted. The physiological changes resulted in a 5% reduction in acetic acid concentration from 431 to 405 mg/L.

CONCLUSION

The present research indicates that S. bovis is highly capable of altering rumen physiology and function on colonization and is a key transition microbe to be studied during rumen intervention studies. A decrease in the coliform count could be attributed to extracellular production of a bacteriocin-like substance, as illustrated through agar diffusion assays.

Invited review: Advances and challenges in application of feedomics to improve dairy cow production and health

Dairy cattle science has evolved greatly over the past century, contributing significantly to the improvement in milk production achieved today. However, a new approach is needed to meet the increasing demand for milk production and address the increased concerns about animal health and welfare. It is now easy to collect and access large and complex data sets consisting of molecular, physiological, and metabolic data as well as animal-level data (such as behavior). This provides new opportunities to better understand the mechanisms regulating cow performance. The recently proposed concept of feedomics could help achieve this goal by increasing our understanding of interactions between the different components or levels and their impact on animal production. Feedomics is an emerging field that integrates a range of omics technologies (e.g., genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, and metatranscriptomics) to provide these insights. In this way, we can identify the best strategies to improve overall animal productivity, product quality, welfare, and health. This approach can help research communities elucidate the complex interactions among nutrition, environment, management, animal genetics, metabolism, physiology, and the symbiotic microbiota. In this review, we summarize the outcomes of the most recent research on omics in dairy cows and highlight how an integrated feedomics approach could be applied in the future to improve dairy cow production and health. Specifically, we focus on 2 topics: (1) improving milk yield and milk quality, and (2) understanding metabolic physiology in transition dairy cows, which are 2 important challenges faced by the dairy industry worldwide.

Humic Substances Alter Ammonia Production and the Microbial Populations Within a RUSITEC Fed a Mixed Hay - Concentrate Diet

Humic substances are a novel feed additive which may have the potential to mitigate enteric methane (CH4) production from ruminants as well as enhance microbial activity in the rumen. The aim of this study was to examine the effects of humic substances on fermentation characteristics and microbial communities using the rumen stimulation technique (RUSITEC). The experiment was conducted as a completely randomized design with 3 treatments duplicated in 2 runs (a 15-day period each run) with 2 replicates per run. Treatments consisted of a control diet (forage:concentrate; 60:40) without humic substances or humic substances added at either 1.5 g/d or 3.0 g/d. Dry matter disappearance, pH, fermentation parameters and gas production were measured from day 8 to 15. Samples for microbial profiling were taken on day 5, 10, and 15 using the digested feed bags for solid- associated microbes (SAM) and fermenter fluid for liquid- associated microbes (LAM). The inclusion of humic substances had no effect (P ≥ 0.19) on DM disappearance, pH or the concentrations of VFA. The production of NH3 was linearly decreased (P = 0.04) with increasing levels of humic substances in the diet. There was no effect (P ≥ 0.43) of humic substances on total gas, CO2 or CH4 production. The number of OTUs was significantly reduced in the 3.0 g/d treatment compared to the control on d 10 and 15; however, the microbial community structure was largely unaffected (P > 0.05). In the SAM samples, the genera Lachnospiraceae XPB1014 group, Succiniclasticum, and Fibrobacter were reduced in the 3.0 g/d treatment and Anaeroplasma, Olsenella, and Pseudobutyrivibrio were increased on day 5, 10, and 15. Within the LAM samples, Christensenellaceae R-7 and Succiniclasticum were the most differentially abundant genera between the control and 3.0 g/d HS treatment samples (P < 0.05). This study highlights the potential use of humic substances as a natural feed additive which may play a role in nitrogen metabolism without negatively affecting the ruminal microbiota.