Rumen Ecosystem Research Articles

The Rumen Microbiome Composition of Raramuri Criollo and European Cattle in an Extensive System

Understanding the relationship between Raramuri Criollo cattle (RC) and their microbial ruminal ecosystem will help identify advantageous characteristics of adapted cattle as alternatives to achieve sustainable beef production systems. Our objective was to characterize the rumen microbiome of RC in comparison to Angus and Hereford breeds (European, E) and the cross between them (E × RC). Ruminal fluid was collected from 63 cows in their second productive cycle after grazing in the same paddock for 45 d, in the dry (n = 28) and rain (n = 35) seasons. DNA from ruminal fluid was isolated for 16s rRNA gene next-generation sequencing. The data were analyzed with QIIME2 and compared against the SILVA 16s rRNA database. Beta diversity was different (p < 0.05) between RC and E in both seasons. A microbial core was represented by the most abundant phyla. Planctomycetes and Spirochaetes represented above 1% in the rain season and below 1% in the dry one, whereas Euryarchaeota was below 1% and around 3%, respectively. LEfSe analysis identified differentiated (p < 0.05) key microbial groups that explain the differences between lineages at different taxonomic levels, reflecting the ability of the rumen ecosystem of RC cattle to adapt to hostile environmental conditions by having microbial groups specialized in the degradation of highly fibrous content.

Viruses contribute to microbial diversification in the rumen ecosystem and are associated with certain animal production traits

BackgroundThe rumen microbiome enables ruminants to digest otherwise indigestible feedstuffs, thereby facilitating the production of high-quality protein, albeit with suboptimal efficiency and producing methane. Despite extensive research delineating associations between the rumen microbiome and ruminant production traits, the functional roles of the pervasive and diverse rumen virome remain to be determined.ResultsLeveraging a recent comprehensive rumen virome database, this study analyzes virus-microbe linkages, at both species and strain levels, across 551 rumen metagenomes, elucidating patterns of microbial and viral diversity, co-occurrence, and virus-microbe interactions. Additionally, this study assesses the potential role of rumen viruses in microbial diversification by analyzing prophages found in rumen metagenome-assembled genomes. Employing CRISPR–Cas spacer-based matching and virus-microbe co-occurrence network analysis, this study suggests that the viruses in the rumen may regulate microbes at strain and community levels through both antagonistic and mutualistic interactions. Moreover, this study establishes that the rumen virome demonstrates responsiveness to dietary shifts and associations with key animal production traits, including feed efficiency, lactation performance, weight gain, and methane emissions.ConclusionsThese findings provide a substantive framework for further investigations to unravel the functional roles of the virome in the rumen in shaping the microbiome and influencing overall animal production performance.3QAbSJqYZPn2njEBJ23VpAVideo

Yeasts isolated from bovine rumen selected to degrade lignocellulosic roughage

Abstract. Duarte ER, Lima SM, Nere JC, Freitas CES, Maia HAR, Júlio ADL, Abrão FO, Alves JMS, Santos VLD, Geraseev LC, Cota J. 2024. Yeasts isolated from bovine rumen selected to degrade lignocellulosic roughage. Biodiversitas 25: 1159-1166. Commercial yeast strains are viable alternatives to chemical additives in ruminants; however, they are not self to the rumen ecosystem. The present study was conducted to compare the degradation of Urochloa decumbens (Stapf) R.D.Webster (UD) hay and sugarcane bagasse (SB) by eight selected yeast strains, naturally present in the rumen cows and control without microorganisms. Eight yeast isolates that showed >6 log CFU per mL of ruminal fluid were selected and identified as four Pichia kudriavzevii isolates, three Rhodotorula mucilaginosa isolates and one Candida tropicalis isolate, according to their morphological and physiological characteristics and by analyses of the D1 - D2 variable domain sequences of the 28S rRNA gene. The strain V5 (R. mucilaginosa) showed higher cell biomass production than other strains of this species in fermentations with UD (P<0.05). Two isolates of Pichia kudriavzevii (V10 and V62) and one of R. mucilaginosa (V5) promoted a higher reduction of dry matter (DM) of UD than other yeast. The strain V5 was also the most efficient to reduce DM of SB (P <0.05). These selected yeasts could represent a potential alternative for use in animal diets and for industrial applications.

Integrating microbial abundance time series with fermentation dynamics of the rumen microbiome via mathematical modelling.

The rumen represents a dynamic microbial ecosystem where fermentation metabolites and microbial concentrations change over time in response to dietary changes. The integration of microbial genomic knowledge and dynamic modelling can enhance our system-level understanding of rumen ecosystem's function. However, such an integration between dynamic models and rumen microbiota data is lacking. The objective of this work was to integrate rumen microbiota time series determined by 16S rRNA gene amplicon sequencing into a dynamic modelling framework to link microbial data to the dynamics of the volatile fatty acids (VFA) production during fermentation. For that, we used the theory of state observers to develop a model that estimates the dynamics of VFA from the data of microbial functional proxies associated with the specific production of each VFA. We determined the microbial proxies using CowPi to infer the functional potential of the rumen microbiota and extrapolate their functional modules from KEGG (Kyoto Encyclopedia of Genes and Genomes). The approach was challenged using data from an in vitro RUSITEC experiment and from an in vivo experiment with four cows. The model performance was evaluated by the coefficient of variation of the root mean square error (CRMSE). For the in vitro case study, the mean CVRMSE were 9.8% for acetate, 14% for butyrate and 14.5% for propionate. For the in vivo case study, the mean CVRMSE were 16.4% for acetate, 15.8% for butyrate and 19.8% for propionate. The mean CVRMSE for the VFA molar fractions were 3.1% for acetate, 3.8% for butyrate and 8.9% for propionate. Ours results show the promising application of state observers integrated with microbiota time series data for predicting rumen microbial metabolism.

Enrichment of ruminant meats with health enhancing fatty acids and antioxidants: feed-based effects on nutritional value and human health aspects – invited review

Optimising resource use efficiency in animal- agriculture-production systems is important for the economic, environmental, and social sustainability of food systems. Production of foods with increased health enhancing aspects can add value to the health and wellbeing of the population. However, enrichment of foods, especially meat with health enhancing fatty acids (HEFA) increases susceptibility to peroxidation, which adversely influences its shelf life, nutritional value and eating quality. The meat industry has been challenged to find sustainable strategies that enhance the fatty acid profile and antioxidant actions of meat while mitigating oxidative deterioration and spoilage. Currently, by-products or co-products from agricultural industries containing a balance of HEFA and antioxidant sources seem to be a sustainable strategy to overcome this challenge. However, HEFA and antioxidant enrichment processes are influenced by ruminal lipolysis and biohydrogenation, HEFA-antioxidant interactions in rumen ecosystems and muscle biofortification. A deep understanding of the performance of different agro-by-product-based HEFA and antioxidants and their application in current animal production systems is critical in developing HEFA-antioxidant co-supplementation strategies that would benefit modern consumers who desire nutritious, palatable, safe, healthy, affordable, and welfare friendly meat and processed meat products. The current review presents the latest developments regarding discovery and application of novel sources of health beneficial agro-by-product-based HEFA and antioxidants currently used in the production of HEFA-antioxidant enriched ruminant meats and highlights future research perspectives.

Multi-omics analyses reveal rumen microbes and secondary metabolites that are unique to livestock species.

Ruminant livestock, including cattle, sheep, goats, and camels, possess a distinctive digestive system with complex microbiota communities critical for feed conversion and secondary metabolite production, including greenhouse gases. Yet, there is limited knowledge regarding the diversity of rumen microbes and metabolites benefiting livestock physiology, productivity, climate impact, and defense mechanisms across ruminant species. In this study, we utilized metataxonomics and metabolomics data from four evolutionarily distinct livestock species, which had fed on diverse plant materials like grass, shrubs, and acacia trees, to uncover the unique signature microbes and secondary metabolites. We established the presence of a distinctive anaerobic fungus called Oontomyces in camels, while cattle exhibited a higher prevalence of unique microbes like Psychrobacter, Anaeromyces, Cyllamyces, and Orpinomyces. Goats hosted Cleistothelebolus, and Liebetanzomyces was unique to sheep. Furthermore, we identified a set of conserved core microbes, including Prevotella, Rickenellaceae, Cladosporium, and Pecoramyces, present in all the ruminants, irrespective of host genetics and dietary composition. This underscores their indispensable role in maintaining crucial physiological functions. Regarding secondary metabolites, camel's rumen is rich in organic acids, goat's rumen is rich in alcohols and hydrocarbons, sheep's rumen is rich in indoles, and cattle's rumen is rich in sesquiterpenes. Additionally, linalool propionate and terpinolene were uniquely found in sheep rumen, while valencene was exclusive to cattle. This may suggest the existence of species-specific microbes and metabolites that require host rumen-microbes' environment balance. These results have implications for manipulating the rumen environment to target specific microbes and secondary metabolite networks, thereby enhancing livestock productivity, resilience, reducing susceptibility to vectors, and environmentally preferred livestock husbandry.IMPORTANCERumen fermentation, which depends on feed components and rumen microbes, plays a crucial role in feed conversion and the production of various metabolites important for the physiological functions, health, and environmental smartness of ruminant livestock, in addition to providing food for humans. However, given the complexity and variation of the rumen ecosystem and feed of these various livestock species, combined with inter-individual differences between gut microbial communities, how they influence the rumen secondary metabolites remains elusive. Using metagenomics and metabolomics approaches, we show that each livestock species has a signature microbe(s) and secondary metabolites. These findings may contribute toward understanding the rumen ecosystem, microbiome and metabolite networks, which may provide a gateway to manipulating rumen ecosystem pathways toward making livestock production efficient, sustainable, and environmentally friendly.

Integrated microbiota-host-metabolome approaches reveal adaptive ruminal changes to prolonged high-grain feeding and phytogenic supplementation in cattle.

Diets rich in readily fermentable carbohydrates primarily impact microbial composition and activity, but can also impair the ruminal epithelium barrier function. By combining microbiota, metabolome, and gene expression analysis, we evaluated the impact of feeding a 65% concentrate diet for 4 weeks, with or without a phytogenic feed additive (PFA), on the rumen ecosystem of cattle. The breaking point for rumen health seemed to be the second week of high grain (HG) diet, with a dysbiosis characterized by reduced alpha diversity. While we did not find changes in histological evaluations, genes related with epithelial proliferation (IGF-1, IGF-1R, EGFR, and TBP) and ZO-1 were affected by the HG feeding. Integrative analyses allowed us to define the main drivers of difference for the rumen ecosystem in response to a HG diet, identified as ZO-1, MyD88, and genus Prevotella 1. PFA supplementation reduced the concentration of potentially harmful compounds in the rumen (e.g. dopamine and 5-aminovaleric acid) and increased the tolerance of the epithelium toward the microbiota by altering the expression of TLR-2, IL-6, and IL-10. The particle-associated rumen liquid microbiota showed a quicker adaptation potential to prolonged HG feeding compared to the other microenvironments investigated, especially by the end of the experiment.

- Invited Review - Hydrogen production and hydrogen utilization in the rumen: key to mitigating enteric methane production.

Molecular hydrogen (H2) and formate (HCOO-) are metabolic end products of many primary fermenters in the rumen ecosystem. Both play a vital role in fermentation where they are electron sinks for individual microbes in an anaerobic environment that lacks external electron acceptors. If H2 and/or formate accumulate within the rumen, the ability of primary fermenters to regenerate electron carriers may be inhibited and microbial metabolism and growth disrupted. Consequently, H2- and/or formate-consuming microbes such as methanogens and possibly homoacetogens play a key role in maintaining the metabolic efficiency of primary fermenters. There is increasing interest in identifying approaches to manipulate the rumen ecosystem for the benefit of the host and the environment. As H2 and formate are important mediators of interspecies interactions, an understanding of their production and utilization could be a significant starting point for the development of successful interventions aimed at redirecting electron flow and reducing methane emissions. We conclude by discussing in brief ruminant methane mitigation approaches as a model to help understand the fate of H2 and formate in the rumen ecosystem.

- Invited Review - Ruminal ciliates as modulators of the rumen microbiome.

Ruminal ciliates are a fundamental constituent within the rumen microbiome of ruminant animals. The complex interactions between ruminal ciliates and other microbial guilds within the rumen ecosystems are of paramount importance for facilitating the digestion and fermentation processes of ingested feed components. This review underscores the significance of ruminal ciliates by exploring their impact on key factors, such as methane production, nitrogen utilization efficiency, feed efficiency, and other animal performance measurements. Various methods are employed in the study of ruminal ciliates including culture techniques and molecular approaches. This review highlights the pressing need for further investigations to discern the distinct roles of various ciliate species, particularly relating to methane mitigation and the enhancement of nitrogen utilization efficiency. The promotion of establishing robust reference databases tailored specifically to ruminal ciliates is encouraged, alongside the utilization of genomics and transcriptomics that can highlight their functional contributions to the rumen microbiome. Collectively, the progressive advancement in knowledge concerning ruminal ciliates and their inherent biological significance will be helpful in the pursuit of optimizing rumen functionality and refining animal production outcomes.

Plasmid-encoded toxin defence mediates mutualistic microbial interactions

Gut environments harbour dense microbial ecosystems in which plasmids are widely distributed. Plasmids facilitate the exchange of genetic material among microorganisms while enabling the transfer of a diverse array of accessory functions. However, their precise impact on microbial community composition and function remains largely unexplored. Here we identify a prevalent bacterial toxin and a plasmid-encoded resistance mechanism that mediates the interaction between Lactobacilli and Enterococci. This plasmid is widespread across ecosystems, including the rumen and human gut microbiota. Biochemical characterization of the plasmid revealed a defence mechanism against reuterin, a toxin produced by various gut microbes, such as Limosilactobacillus reuteri. Using a targeted metabolomic approach, we find reuterin to be prevalent across rumen ecosystems with impacts on microbial community structure. Enterococcus strains carrying the protective plasmid were isolated and their interactions with L. reuteri, the toxin producer, were studied in vitro. Interestingly, we found that by conferring resistance against reuterin, the plasmid mediates metabolic exchange between the defending and the attacking microbial species, resulting in a beneficial relationship or mutualism. Hence, we reveal here an ecological role for a plasmid-coded defence system in mediating a beneficial interaction.

A Comparison of Three Artificial Rumen Systems for Rumen Microbiome Modeling

The rumen contains a complex mixture of microbes, crucial for the animal’s ability to degrade feed. Some of the feed-derived carbon is released as methane, a potent greenhouse gas, into the atmosphere. There is growing interest in reducing the loss of feed-derived carbon, making it available to the animal and improving animal productivity. Artificial rumen systems (ARSs) have been widely used to evaluate novel feed additives in terms of their ability to reduce methane production in the rumen and their effect on the rumen microbiome function prior to conducting resource-intensive animal trials. While the value of ARSs is widely acknowledged, it remains unclear which of these in vitro systems simulate the natural system most accurately. Here, we evaluated three different ARSs and compared them to in vivo rumen metrics. The results showed that all systems were capable of maintaining stable pH, redox potential, and temperature over time. The batch-style ARS simulated the rumen over 48 h. The semi-continuous ARS mimicked the volatile fatty acid profile and microbiota of the in vivo rumen for up to 120 h. Similarly, all ARSs maintained the prokaryotic and eukaryotic rumen populations over the duration of the study, with the semi-continuous ARS maintaining the natural rumen microbiome more accurately and for up to 120 h. In sum, our results suggest that three of the widely used ARSs simulate the rumen ecosystem adequately for many short-term rumen microbiome studies, with the more advanced semi-continuous ARS being more accurate when rumen simulation is extended to over 48 h.

90 Microbiome-Derived Bioactive Molecules to Reduce Enteric Methane Emissions

Abstract Microorganisms are pivotal for the development, health, and productivity of livestock. In adult ruminants, the microbiota colonizing the rumen is essential for efficient depolymerization of indigestible carbohydrates from plant biomass and their conversion into microbial protein and fermentation end-products that are used by the host for growth. In the last decades, next-generation sequencing and omics technologies provided unparalleled insights into the composition, structure, and function of the gastrointestinal (GI) tract microbiome of ruminants and helped improve our understanding of relationships between the rumen microbiota with cattle performance (efficiency) traits, as well as health and disease and greenhouse gas emissions. The ecological interactions between microbes within the rumen ecosystem are complex and involve, among others, cross-feeding, predation, parasitism, antagonism, and competition for novel (empty) niches and available resources. These diverse associations of ecological traits across distinct microbial populations that coexist in the same ecosystem represent a goldmine for the discovery of novel bioactive molecules, including compounds with potential to modulate rumen fermentation and inhibit methane emissions from enteric fermentation. These effects often result from metabolic shifts in the rumen fermentation that lead to increased production of propionate, but can also be caused by direct inhibition of methanogenic archaea or through a reduction in the production of substrates for methanogenesis. Culture-independent approaches based on genome mining and functional metagenomics demonstrated that the rumen is an underexplored resource for bioactive molecules, such as antimicrobial peptides, non-ribosomal peptides, polyketides, and secondary metabolites involved in intercellular (microbe-microbe) communication. Rumen metatranscriptomic data indicate that the expression of genes potentially encoding some of these molecules is increased during the colonization of plant biomass that enters the rumen. Nonetheless, some representatives of key taxa from the core rumen microbiome cannot be found in culture collections, which is critical to validate phenotypic predictions from genomic and metagenomic data and obtain ecological insights about the interplay between individual microbial populations in the microbiome. Culturomic technologies and high-throughput identification and characterization of microbial species that colonize the rumen could contribute to building a unique biotechnological resource that can be explored for sourcing novel bioactive compounds with anti-methanogenic activity and developing fermentation products that could reduce rumen methanogenesis while improving the health status and productivity of cattle.

Potential use of garlic products in ruminant feeding: A review.

The addition of antibiotics as growth promoters to ruminant feed can result in bacterial resistance and antibiotic residues in ruminant products. Correspondingly, there is serious public concern regarding the presence of antibiotic residue in ruminant products and the consequent threat to human health. As a result, the addition of plants and their products to ruminant feeds, as an alternative to antibiotics, has received much attention recently. Garlic and its products are rich in organosulphur compounds, which have a variety of biological activities and have been widely used as natural additives in animal production. This review presents recent knowledge on the addition of garlic products (powder, skin, oil, leaf and extracts) to the diets of ruminants. In this paper, garlic products are evaluated with respect to their chemical composition, bioactive compounds, and their impacts on the rumen ecosystem, antioxidant status, immune response, parasitic infection, growth performance and product quality of ruminants. This review provides valuable guidance and a theoretical basis for the development of garlic products as green, highly efficient and safe additives, with the aims of promoting ruminant growth and health, reducing methane emissions and improving ruminant product quality. Garlic extracts have the potential to control parasite infections by decreasing the faecal egg count. Garlic powder, oil and allicin are able to reduce the methane emissions of ruminants. Organosulphur compounds such as allicin, which is present in garlic products, have the potential to inhibit membrane lipid synthesis of the archaeal community, thus influencing the population of methanogenic archaea and resulting in a reduction in methane emissions. Some garlic products are also able to increase the average daily gain (garlic skin, water extract, and leaf) and the feed conversion ratio (garlic skin and leaf) of ruminants. Garlic stalk silage fed to sheep has the potential to improve the nutritional value of mutton by increasing the concentrations of linoleic and linolenic acids and essential amino acids. Sheep fed a diet containing garlic powder or oil are able to produce milk with higher concentrations of the conjugated linoleic acids and n-3 fatty acids, which has health benefits for consumers, due to the widely recognized positive impact of n-3 polyunsaturated fatty acids and conjugated linoleic acids on human heart health, improving platelet aggregation, vasodilation and thrombotic tendency. Overall, garlic products have the potential to enhance growth performance and product quality and reduce parasite infections, as well as methane emissions of ruminants.

Interrogating the viral dark matter of the rumen ecosystem with a global virome database

The diverse rumen virome can modulate the rumen microbiome, but it remains largely unexplored. Here, we mine 975 published rumen metagenomes for viral sequences, create a global rumen virome database (RVD), and analyze the rumen virome for diversity, virus-host linkages, and potential roles in affecting rumen functions. Containing 397,180 species-level viral operational taxonomic units (vOTUs), RVD substantially increases the detection rate of rumen viruses from metagenomes compared with IMG/VR V3. Most of the classified vOTUs belong to Caudovirales, differing from those found in the human gut. The rumen virome is predicted to infect the core rumen microbiome, including fiber degraders and methanogens, carries diverse auxiliary metabolic genes, and thus likely impacts the rumen ecosystem in both a top-down and a bottom-up manner. RVD and the findings provide useful resources and a baseline framework for future research to investigate how viruses may impact the rumen ecosystem and digestive physiology.

Sigla storax (Liquidambar orientalis) mitigates in vitro methane production without disturbances in rumen microbiota and nutrient fermentation in comparison to monensin.

The aim of this study was to investigate the in vitro dose-dependent effects of sigla storax (Styrax liquidus) on rumen microbiota and rumen microbial fermentation in comparison to monensin as a positive control. This study was carried out using a rumen simulation model (Rusitec). Treatments consisted of no additive (control), 10mg l-1 of monensin sodium salt, 100mg l-1 (Low-Sigla), and 500mg l-1 (High-Sigla) of sigla storax (n=6/treatment). In addition to rumen fermentation characteristics, rumen microbial composition was investigated using 16S rRNA sequencing. The methane variables and the acetate to propionate ratio decreased in the both High-Sigla and monensin groups (P<0.05). High-Sigla had no effect on ammonia, total SCFA and nutrition degradation, while monensin decreased these parameters (P<0.05). Unlike monensin, the sigla storax treatments did not affect the alpha or beta diversity indexes of the microbiota. The relative abundance of Methanomethylophilaceae and Ruminococcaceae decreased with High-Sigla and monensin (P<0.05), and Atopobiaceae and Eggerthellaceae decreased with the both doses of sigla storax as well as monensin treatments (P<0.05). Syntrophococcus, DNF00809, and Kandleria were among the genera that most decreased with High-Sigla and monensin (Q<0.07) and were strongly positively correlated with methane production (r=0.52-0.56). The high dose of sigla storax (500mg l-1) decreased methane in the rumen ecosystem without adverse effects on nutrient degradation and SCFA production, and without dramatically impacting the microbial composition. Sigla storax might be a novel feed additive to mitigate methane in cattle.

Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacterium Fibrobacter succinogenes S85.

Fibrobacter succinogenes is a cellulolytic bacterium that plays an essential role in the degradation of plant fibers in the rumen ecosystem. It converts cellulose polymers into intracellular glycogen and the fermentation metabolites succinate, acetate, and formate. We developed dynamic models of F. succinogenes S85 metabolism on glucose, cellobiose, and cellulose on the basis of a network reconstruction done with the automatic reconstruction of metabolic model workspace. The reconstruction was based on genome annotation, five template-based orthology methods, gap filling, and manual curation. The metabolic network of F. succinogenes S85 comprises 1,565 reactions with 77% linked to 1,317 genes, 1,586 unique metabolites, and 931 pathways. The network was reduced using the NetRed algorithm and analyzed for the computation of elementary flux modes. A yield analysis was further performed to select a minimal set of macroscopic reactions for each substrate. The accuracy of the models was acceptable in simulating F. succinogenes carbohydrate metabolism with an average coefficient of variation of the root mean squared error of 19%. The resulting models are useful resources for investigating the metabolic capabilities of F. succinogenes S85, including the dynamics of metabolite production. Such an approach is a key step toward the integration of omics microbial information into predictive models of rumen metabolism. IMPORTANCE F. succinogenes S85 is a cellulose-degrading and succinate-producing bacterium. Such functions are central for the rumen ecosystem and are of special interest for several industrial applications. This work illustrates how information of the genome of F. succinogenes can be translated to develop predictive dynamic models of rumen fermentation processes. We expect this approach can be applied to other rumen microbes for producing a model of rumen microbiome that can be used for studying microbial manipulation strategies aimed at enhancing feed utilization and mitigating enteric emissions.

Rumen microbial community and milk quality in Holstein lactating cows fed olive oil pomace as part in a sustainable feeding strategy

The use of alternative feed ingredients from the Agro-industry could be an efficient tool to improve the sustainability of dairy cow production. Since the richness in polyphenols, olive oil pomace (OOP), produced during olive oil milling, seems a promising by-product to ameliorate milk’s nutritional value. The aim of this study was to test the use of OOP produced by means of a new technology (biphasic with stone deprivation) in dairy cow feeding strategy to evaluate the effect on animal performances, rumen microbiota, biohydrogenation processes and milk quality by a multidisciplinary approach. Forty multiparous Italian-Friesian dairy cows, at middle lactation, were randomly allotted into two homogenous groups and fed respectively a commercial diet (CON) and the experimental diet (OOPD) obtained by adding OOP to CON as partial replacement of maize silage. The two diets were formulated to be isoproteic and isoenergetic. The same diets were tested also in an in vitro trial aimed to evaluate their rumen degradability (% DEG). The dietary supplementation with OOP did not affect DM intake, rumen % DEG and milk production. The milk’s nutritional quality was improved by increasing several important functional fatty acids (FAs; i.e., linoleic acid, conjugated linoleic acid, oleic acid, vaccenic acid). This finding was related to a decrease in rumen liquor biohydrogenation rate of unsaturated FAs. The stochiometric relation between volatile FA production in the rumen and methanogenesis suggested that OOP lowers the methane potential production (CON = 0.050 mol/L vs OOPD = 0.024 mol/L, SEM = 0.005, P = 0.0011). Rumen microbiota and fungi community did not be strongly altered by OOP dietary inclusion because few bacteria were affected at the genus level only. Particularly, Acetobacter, Prevotellaceae_UCG-004, Prevotellaceae_UCG-001, Eubacterium coprostanoligenes, Lachnospira, Acetitomaulatum, Lachnospiraceae_NK3A20 group were more abundant with OOPD condition (P < 0.05). Data reported in this study confirm that the use of OOP in dairy cow feeding can be an interesting strategy to improve milk nutritional quality increasing functional FA content without compromising the rumen degradability of the diet or causing strong perturbation of rumen ecosystem and maintaining animal performances.

Profiling of Fatty Acids and Rumen Ecosystem of Sheep Fed on a Palm Kernel Cake-Based Diet Substituted with Corn

The purpose of this study was to analyze the effects of corn substitution on the rumen functions and fatty acid profile of Dorper lambs fed a diet based on palm kernel cake (PKC). Corn was replaced with PKC basal diet at the following levels: C0% = (0% corn + 75.3% PKC), C1% = (5% corn + 70.3% PKC) and C2% = (10% corn + 65.3% PKC) of diet. The rumen fermentation was carried out in vitro, and feeding trials were in vivo. Twenty-seven lambs were used to determine gastrointestinal tract content and rumen fluid fatty acid. Rumen liquor was obtained from four fistulae Dorper sheep and incubated with 200 mg of each treatment for 24 and 72 h. In vitro organic matter digestibility (IVOMD), in vitro dry matter digestibility (IVDMD), volatile fatty acids (VFA), methane estimation (CH4), rumen microbial population and fatty acid biohydrogenation were determined. The results of the in vitro study showed there were no significant differences in IVDMD, IVOMD, NH3-N, pH and VFA at 72 h. Higher significant CH4 production was observed in C0% when compared with C1% and C2%. Microbial population did not differ significantly between treatment groups. The rates of biohydrogenation were not affected by corn substitution, although a significant difference was observed in C18:1n9 (in vitro) and C18:1 t-11 (in vivo). In conclusion, the present study indicated that the corn substitution in the PKC diets maintained fermentation characteristics with an increase in unsaturated fatty acids in the rumen.

Characterization of the Dynamic Changes of Ruminal Microbiota Colonizing Citrus Pomace Waste during Rumen Incubation for Volatile Fatty Acid Production.

Rumen microorganisms are promising for efficient bioconversion of lignocellulosic wastes to biofuels and industrially relevant products. Investigating the dynamic changes of the rumen microbial community colonizing citrus pomace (CtP) will advance our understanding of the utilization of citrus processing waste by rumen fluid. Citrus pomace in nylon bags was incubated in the rumen of three ruminally cannulated Holstein cows for 1, 2, 4, 8, 12, 24, and 48 h. Results showed that total volatile fatty acids concentrations and proportions of valerate and isovalerate were increased over time during the first 12 h. Three major cellulose enzymes attached to CtP rose initially and then decreased during the 48-h incubation. Primary colonization happened during the initial hours of CtP incubation, and microbes compete to attach CtP for degrading easily digestible components and/or utilizing the waste. The 16S rRNA gene sequencing data revealed the diversity and structure of microbiota adhered to CtP were distinctly different at each time point. The increased abundance of Fibrobacterota, Rikenellaceae_RC9_gut_group, and Butyrivibrio may explain the elevated volatile fatty acids concentrations. This study highlighted key metabolically active microbial taxa colonizing citrus pomace in a 48-h in situ rumen incubation, which could have implications for promoting the biotechnological process of CtP. IMPORTANCE As a natural fermentation system, the rumen ecosystem of ruminants can efficiently degrade plant cellulose, indicating that the rumen microbiome offers an opportunity for anaerobic digestion to utilize biomass wastes containing cellulose. Knowledge of the response of the in situ microbial community to citrus pomace during anaerobic fermentation will help improve the current understanding of citrus biomass waste utilization. Our results demonstrated that a highly diverse rumen bacterial community colonized citrus pomace rapidly and continuously changed during a 48-h incubation period. These findings may provide a deep understanding of constructing, manipulating, and enriching rumen microorganisms to improve the anaerobic fermentation efficiency of citrus pomace.

Zearalenone and Its Emerging Metabolites Promptly Affect the Rumen Microbiota in Holstein Cows Fed a Forage-Rich Diet.

The study investigated the short-term effects of a single oral bolus of zearalenone (ZEN) on the rumen microbiota and fermentation patterns in four rumen-cannulated Holstein cows fed a forage diet with daily 2 kg/cow concentrate. During the baseline day, cows received uncontaminated concentrate, followed by ZEN-contaminated concentrate on the second day, and again the uncontaminated concentrate on day three. Free rumen liquid (FRL) and particle-associated rumen liquid (PARL) were collected at different hours post-feeding on all days to analyze the prokaryotic community composition, absolute abundances of bacteria, archaea, protozoa, and anaerobic fungi, as well as short-chain fatty acid (SCFA) profiles. The ZEN reduced the microbial diversity in FRL but not in the PARL fraction. The abundance of protozoa was higher after ZEN exposure in PARL, which may be related to their strong biodegradation capacity that, therefore, promoted protozoal growth. In contrast, α-zearalenol might compromise anaerobic fungi as indicated by reduced abundances in FRL and fairly negative correlations in both fractions. Total SCFA significantly increased in both fractions after ZEN exposure, while the SCFA profile only changed marginally. Concluding, a single ZEN challenge caused changes in the rumen ecosystem soon after intake, including ruminal eukaryotes, that should be the subject of future studies.