The rumen microbiome: a crucial consideration when optimising milk and meat production and nitrogen utilisation efficiency

Effect of Dietary Rumen-Degradable Starch to Rumen-Degradable Protein Ratio on In Vitro Rumen Fermentation Characteristics and Microbial Protein Synthesis

The objective of this study was to investigate the effects of dietary rumen-degradable starch (RDS, g/kg of DM) to rumen-degradable protein (RDP, g/kg of DM) ratios (SPR) on in vitro rumen fermentation characteristics and microbial protein synthesis (MCPS). Treatments were eight diets with SPR of 1.9, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5 and 2.6 and were formulated to be isoenergetic, isonitrogenous, and isostarch. Substrates were anaerobically incubated in sealed culture vials (100 mL) for 6, 24 or 48 h. Three incubation runs were conducted within two consecutive weeks. With the increase of the dietary SPR, the gas production (GP), in vitro dry matter disappearance (IVDMD) and concentration of MCPS and total volatile fatty acids (TVFA) linearly increased after 6 h of incubation (p ≤ 0.01), whereas they quadratically increased and peaked at the SPR of 2.3 after 24 and 48 h of incubation (p < 0.05). In response to dietary SPR increasing, the in vitro neutral detergent fiber disappearance (IVNDFD) quadratically increased (p < 0.01), and the ammonia nitrogen (NH3-N) concentration linearly decreased (p < 0.01) after 6, 24 and 48 h of incubation. Based on the presented results, an SPR of 2.3 is recommended for formulating a diet due to its greatest IVDMD, IVNDFD, GP, TVFA and MCPS. However, as the results obtained are strictly dependent on the in vitro conditions, further in vivo studies are needed to verify our findings.

Influence of Using Various Levels of Protein Concentrate in Rations of Ayrshire Dairy Cows on Rumen Microbiome, Reproductive Traits and Economic Efficiency

Animal feeding research has revealed a close relationship between the chemical composition and nutritional value of cow rations, the number of rumen bacterial communities and animal productivity. Our present research aimed to investigate the outcome of inclusion of different levels of protein concentrate in rations of Ayrshire dairy cows in relation to the rumen microbiome, reproductive traits and economic value. Forty-five Ayrshire cows were divided into three groups (15 in each). The first control group 0 AM was fed the basal ration, while the second 1 AM and third 2 AM groups were fed the basic ration with the sunflower cake replaced by different levels of protein concentrate Agro-Matic (1 and 1.5 kg/head/day, respectively). Ruminal fluid samples, reproductive parameters and economic value were studied. During the early lactation period, 120 days in milk (DIM), the number of pathogenic microorganisms decreased in both the 1 AM and 2 AM groups when compared with the control group 0 AM; moreover, a significant decrease in Peptococcus bacteria was recorded in the 1 AM group, while Fusobacterium decreased in the 2 AM group. At the end of lactation, the total number of cellulolytic bacteria increased with the use of protein concentrate in animals of the 1 AM group when compared with the control group. Regarding undesirable bacteria, the 2 AM group recorded the highest value for Lactobacilli and Actinobacteria when compared with the 0 AM group (0.18 and 8.90 vs. 0.04 and 4.24), and the differences were significant (p < 0.05). The insemination index and the duration of the days open period decreased in the 2 AM group, while the differences were p > 0.05. The profitability of milk production increased by 2.76% and 6.28% in both supplemented groups, and the differences compared to the 0 AM group were significant. We conclude that the supplementation of Agro-Matic caused no deviations from the normal standards of cellulolytic, amylolytic, transit and pathogenic bacteria, no impact on reproductive functions and significantly improved the profitability of the milk production process of Ayrshire dairy cows.

Characterization of rumen, fecal, and milk microbiota in lactating dairy cows

Targeting the gastrointestinal microbiome for improvement of feed efficiency and reduction of production costs is a potential promising strategy. However little progress has been made in manipulation of the gut microbiomes in dairy cattle to improve milk yield and milk quality. Even less understood is the milk microbiome. Understanding the milk microbiome may provide insight into how the microbiota correlate with milk yield and milk quality. The objective of this study was to characterize similarities between rumen, fecal, and milk microbiota simultaneously, and to investigate associations between microbiota, milk somatic cell count (SCC), and milk yield. A total of 51 mid-lactation, multiparous Holstein dairy cattle were chosen for sampling of ruminal, fecal, and milk contents that were processed for microbial DNA extraction and sequencing. Cows were categorized based on low, medium, and high SCC; as well as low, medium, and high milk yield. Beta diversity indicated that ruminal, fecal, and milk populations were distinct (p &lt; 0.001). Additionally, the Shannon index demonstrated that ruminal microbial populations were more diverse (p &lt; 0.05) than were fecal and milk populations, and milk microbiota was the least diverse of all sample types (p &lt; 0.001). While diversity indices were not linked (p &gt; 0.1) with milk yield, milk microbial populations from cows with low SCC demonstrated a more evenly distributed microbiome in comparison to cows with high SCC values (p = 0.053). These data demonstrate the complexity of host microbiomes both in the gut and mammary gland. Further, we conclude that there is a significant relationship between mammary health (i.e., SCC) and the milk microbiome. Whether this microbiome could be utilized in efforts to protect the mammary gland remains unclear, but should be explored in future studies.

Effects of ruminal lipopolysaccharides on growth and fermentation end products of pure cultured bacteria

Elevated levels of ruminal lipopolysaccharides (LPS) have been linked to ruminal acidosis; however, they result in reduced endotoxicity compared to LPS derived from species like Escherichia coli. Additionally, there is a knowledge gap on the potential effect of LPS derived from ruminal microbiome on ruminal bacteria species whose abundance is associated with ruminal acidosis. The objective of this study was to evaluate the effects of LPS-free anaerobic water (CTRL), E. coli-LPS (E. COLI), ruminal-LPS (RUM), and a 1:1 mixture of E. coli and ruminal-LPS (MIX) on the growth characteristics and fermentation end products of lactate-producing bacteria (Streptococcus bovis JB1, Selenomonas ruminantium HD4) and lactate-utilizing bacterium (Megasphaera elsdenii T81). The growth characteristics were predicted based on the logistic growth model, the ammonia concentration was determined by the phenolic acid/hypochlorite method and organic acids were analyzed with high performance liquid chromatography. Results indicate that, compared to the CTRL, the maximum specific growth rate of S. bovis JB1 decreased by approximately 19% and 23% when RUM and MIX were dosed, respectively. In addition, acetate and lactate concentrations in Se. ruminantium HD4 were reduced by approximately 30% and 18%; respectively, in response to MIX dosing. Compared to CTRL, lactate concentration from S. bovis JB1 was reduced approximately by 31% and 22% in response to RUM and MIX dosing; respectively. In summary, RUM decreased the growth and lactate production of some lactate-producing bacteria, potentially mitigating the development of subacute ruminal acidosis by restricting lactate availability to some lactate-utilizing bacteria that metabolize lactate into VFAs thus further contributing to the development of acidosis. Also, RUM did not affect Megasphaera elsdenii T81 growth.

The SGNH hydrolase family: a template for carbohydrate diversity

The substitution and de-substitution of carbohydrate materials are important steps in the biosynthesis and/or breakdown of a wide variety of biologically important polymers. The SGNH hydrolase superfamily is a group of related and well-studied proteins with a highly conserved catalytic fold and mechanism composed of 16 member families. SGNH hydrolases can be found in vertebrates, plants, fungi, bacteria, and archaea, and play a variety of important biological roles related to biomass conversion, pathogenesis, and cell signaling. The SGNH hydrolase superfamily is chiefly composed of a diverse range of carbohydrate-modifying enzymes, including but not limited to the carbohydrate esterase families 2, 3, 6, 12 and 17 under the carbohydrate-active enzyme classification system and database (CAZy.org). In this review, we summarize the structural and functional features that delineate these subfamilies of SGNH hydrolases, and which generate the wide variety of substrate preferences and enzymatic activities observed of these proteins to date.

Gut microbiota development in the growing dog: A dynamic process influenced by maternal, environmental and host factors

Microorganisms of the gastrointestinal tract play a crucial role in the health, metabolism and development of their host by modulating vital functions such as digestion, production of key metabolites or stimulation of the immune system. This review aims to provide an overview on the current knowledge of factors shaping the gut microbiota of young dogs. The composition of the gut microbiota is modulated by many intrinsic (i.e., age, physiology, pathology) and extrinsic factors (i.e., nutrition, environment, medication) which can cause both beneficial and harmful effects depending on the nature of the changes. The composition of the gut microbiota is quickly evolving during the early development of the dog, and some crucial bacteria, mostly anaerobic, progressively colonize the gut before the puppy reaches adulthood. Those bacterial communities are of paramount importance for the host health, with disturbance in their composition potentially leading to altered metabolic states such as acute diarrhea or inflammatory bowel disease. While many studies focused on the microbiota of young children, there is still a lack of knowledge concerning the development of gut microbiota in puppies. Understanding this early evolution is becoming a key aspect to improve dogs' short and long-term health and wellbeing.

Relationship between rumen microbial differences and traits among Hu sheep, Tan sheep, and Dorper sheep

Rumen microbes play an important role in the growth and development of ruminants. Differences in variety will affect the rumen community structure. The three excellent sheep breeds were selected for this study (Hu sheep, Tan sheep, and Dorper sheep) have different uses and origins. The sheep were raised on the same diet to 180 d of age in a consistent environment. 16S rDNA V3 to V4 region sequencing was used to assess the rumen microbes of 180 individuals (60 per breed). There were differences in microbial diversity among different sheep breeds (P < 0.05). Principal coordinate analysis showed that the three varieties were separated, but also partially overlapped. Linear discriminant analysis effect size identified a total of 19 biomarkers in three breeds. Of these biomarkers, five in Hu sheep were significantly negatively correlated with average feed conversion rate (P < 0.05). Six biomarkers were identified in the rumen of Dorper sheep, among which Ruminococcus was significantly positively correlated with body weight at 80 d (P < 0.05). In Tan sheep, Rikenellaceae_RC9_gut_group was significantly positively correlated with meat fat, and significantly positively correlated with volatile fatty acids (VFAs), such as butyric acid and isobutyric acid (P < 0.05). The Rikenellaceae_RC9_gut_group may regulate Tan mutton fat deposition by affecting the concentration of VFAs. Functional prediction revealed enrichment differences of functional pathways among different sheep breeds were small. All were enriched in functions, such as fermentation and chemoheterotrophy. The results show that there are differences in the rumen microorganisms of the different sheep breeds, and that the microorganisms influence the host.

Stable isotopes provide evidence that condensed tannins from sericea lespedeza are degraded by ruminal microbes

The objective of Trial 1 was to determine the effects of condensed tannins (CT) from sericea lespedeza [SL; Lespedeza cuneata (Dum. Cours.) G. Don] on in vitro digestible organic matter (IVDOM), total gas production (GP), methane (CH₄) emission, and ruminal fluid parameters after fermentation. Substrates used in four 48-h in vitro fermentations were 100% bermudagrass [(Cynodon dactylon (L.) Pers.] hay (0SL), 100% SL hay (100SL), and a mix of both hays (50SL). Linear reductions were observed for all parameters (P < 0.05) with the inclusion of SL, except for CH₄ in relation to GP, that presented a quadratic effect (P = 0.005). In Trial 2, SL plants were enriched with ¹³C-CO₂ to obtain pure enriched CT to identify the destination of fermentation end products of CT degradation. The enrichment of CT through the SL was successful (P < 0.001), and carbon originated from CT was detected in the fermentation end products [microbial mass, clarified rumen fluid, and in the CH₄ produced (P < 0.001)]. Therefore, inclusion of SL was effective in reducing in vitro CH₄ production and compound-specific tracing of δ¹³C abundance provided better quantitative understanding of the mechanisms of partitioning CT during ruminal fermentation processes.

Progressive microbial adaptation of the bovine rumen and hindgut in response to a step-wise increase in dietary starch and the influence of phytogenic supplementation

Microbial composition and activity in the gastrointestinal tract (GIT) of cattle has important implications for animal health and welfare, driving the focus of research toward ways to modify their function and abundance. However, our understanding of microbial adaption to nutritional changes remains limited. The aim of this study was to examine the progressive mechanisms of adaptation in the rumen and hindgut of cattle receiving increasing amounts of starch with or without dietary supplementation of a blended phytogenic feed additive (PFA; containing menthol, thymol and eugenol). We used 16S rRNA gene amplicon sequencing to assess the microbial composition and predicted metabolic pathways in ruminal solid and liquid digesta, and feces. Furthermore, we employed targeted liquid chromatography-mass spectrometry methods to evaluate rumen fluid metabolites. Results indicated a rapid microbial adaptation to diet change, starting on the second day of starch feeding for the particle associated rumen liquid (PARL) microbes. Solid rumen digesta- and feces-associated microbes started changing from the following day. The PARL niche was the most responsive to dietary changes, with the highest number of taxa and predicted pathways affected by the increase in starch intake, as well as by the phytogenic supplementation. Despite the differences in the microbial composition and metabolic potential of the different GIT niches, all showed similar changes toward carbohydrate metabolism. Metabolite measurement confirmed the high prevalence of glucose and volatile fatty acids (VFAs) in the rumen due to the increased substrate availability and metabolic activity of the microbiota. Families Prevotellaceae, Ruminococcaceae and Lachnospiraceae were found to be positively correlated with carbohydrate metabolism, with the latter two showing wide-ranging predicted metabolic capabilities. Phytogenic supplementation affected low abundant taxa and demonstrated the potential to prevent unwanted implications of feeding high-concentrate diet, such as reduction of microbial diversity. The inclusion of 50% concentrate in the diet caused a major shift in microbial composition and activity in the GIT of cattle. This study demonstrated the ability of microorganisms in various GIT niches to adjust differentially, yet rapidly, to changing dietary conditions, and revealed the potential beneficial effects of supplementation with a PFA during dietary adaptation.

Understanding microbial networks of farm animals through genomics, metagenomics and other meta-omic approaches for livestock wellness and sustainability – A Review

The association of microorganisms with livestock as endosymbionts, opportunists, and pathogens has been a matter of debate for a long time. Several livestock-associated bacterial and other microbial species have been identified and characterized through traditional culture-dependent genomic approaches. However, it is imperative to understand the comprehensive microbial network of domestic animals for their wellness, disease management, and disease transmission control. Since it is strenuous to provide a niche replica to any microorganisms while culturing them, thus a substantial number of microbial communities remain obscure. Metagenomics has laid out a powerful lens for gaining insight into the hidden microbial diversity by allowing the direct sequencing of the DNA isolated from any livestock sample like the gastrointestinal tract, udder, or genital system. Through metatranscriptomics and metabolomics, understanding gene expression profiles of the microorganisms and their molecular phenotype has become unchallenging. With large data sets emerging out of the genomic, metagenomic, and other meta-omics methods, several computational tools have also been developed for curation, assembly, gene prediction, and taxonomic profiling of the microorganisms. This review provides a detailed account of the beneficial and pathogenic organisms that dwell within or on farm animals. Besides, it highlights the role of meta-omics and computational tools in a comprehensive analysis of livestock-associated microorganisms.

Feedomics provides bidirectional omics strategies between genetics and nutrition for improved production in cattle

Increasing the efficiency and sustainability of cattle production is an effective way to produce valuable animal proteins for a growing human population. Genetics and nutrition are the 2 major research topics in selecting cattle with beneficial phenotypes and developing genetic potentials for improved performance. There is an inextricable link between genetics and nutrition, which urgently requires researchers to uncover the underlying molecular mechanisms to optimize cattle production. Feedomics integrates a range of omic techniques to reveal the mechanisms at different molecular levels related to animal production and health, which can provide novel insights into the relationships of genes and nutrition/nutrients. In this review, we summarized the applications of feedomics techniques to reveal the effect of genetic elements on the response to nutrition and investigate how nutrients affect the functional genome of cattle from the perspective of both nutrigenetics and nutrigenomics. We highlighted the roles of rumen microbiome in the interactions between host genes and nutrition. Herein, we discuss the importance of feedomics in cattle nutrition research, with a view to ensure that cattle exhibit the best production traits for human consumption from both genetic and nutritional aspects.

Utilization of Waste Date Palm Leaves Biomass Ensiled with Malic or Lactic Acids in Diets of Farafra Ewes under Tropical Conditions

The aim of the current study was to evaluate the ensiling of date palm leaves (DPL) with organic acids (lactic or malic acid) for 45 day as a feed for lactating ewes under desert conditions. Two weeks before expected parturition, 50 multiparous lactating Farafra ewes (mean ± SD: 2 ± 0.3 parity, 34 ± 1.9 kg bodyweight, 25 ± 2.4 months of age, and 555 ± 13.0 g/day of previous milk production) were equally divided into five treatments in a completely randomized design for 90 day. The ewes in the control treatment were offered a diet composed of a concentrate feed mixture and DPL at 60:40 on a dry matter (DM) basis ensiled without additive. In the other treatments, DPL (ensiled without organic acids) in the control treatment was replaced with DPL ensiled with lactic or malic acid (at 5 g/kg DM) at 50 or 100% levels. Organic acids linearly and quadratically increased (p < 0.01) DPL and total intakes and digestibilities of DM, organic matter, crude protein, and nonstructural carbohydrates without affecting fiber digestibility. Malic and lactic acid treatment also increased the concentrations of ruminal total volatile fatty acids, acetate, propionate, and ammonia-N. Additionally, malic and lactic acid-treated DPL increased serum glucose concentration and total antioxidant capacity. Without affecting daily actual milk production, treatments increased (p < 0.001) the daily production of energy-corrected milk (ECM), fat-corrected milk (FCM), milk energy output, milk contents of fats, and feed efficiency. Organic acid-treated DPL increased (p < 0.05) the proportions of total polyunsaturated fatty acids and total conjugated linoleic acids and the unsaturated to saturated fatty acid ratio in milk. It is concluded that feeding DPL ensiled with malic or lactic acid at 20 or 40% of total diet DM increased daily ECM and FCM production, nutrient utilization efficiency, and milk quality. No differences were observed between lactic and malic acid treatment of DPL during ensiling; therefore, both of them are recommended to treat DPL for silage preparation.

Improvement of the Nutritional Quality of Psophocarpus tetragonolobus Tubers by Fermentation with Ruminal Crabtree-Negative Yeasts on the In Vitro Digestibility and Fermentation in Rumen Fluid

The purpose of this study was to determine how ruminal Crabtree-negative yeast affects the nutritional characteristics of winged bean (Psophocarpus tetragonolobus) tubers (WBT), in vitro gas and digestibility, and rumen fermentation. The experiment was carried out in a randomized complete design with a 5 × 2 (+1) factorial arrangement. Factor A determined the WBT products (a1 = dry WBT, a2 = fermented WBT without yeast in media solution, a3 = fermented WBT with Pichia kudriavzevii KKU20, a4 = fermented WBT with Candida tropicalis KKU20, and a5 = fermented WBT with Saccharomyces cerevisiae), whereas factor B determined the level of fermented WBT replacing cassava chips (b1 = WBT at 50% and b2 = 100% levels). The results of the experiment showed that the fermentation approach could increase the crude protein (CP) content of WBT by around 7% (p < 0.01). The WBT fermented with yeast lowered the number of aerobic bacteria during the fermentation process (p < 0.01). P. kudriazevii KKU20 yeast strain had a 17.3% higher final asymptotic gas volume (Vf) than the C. tropicalis KKU20. Crabtree-negative yeast had a higher in vitro dry matter digestibility (IVDMD) than Crabtree-positive yeast after 12 h of incubation (p < 0.01). Fermented WBT with yeast had a higher IVDMD after 24 h of incubation than fermented WBT without yeast in the media solution (p < 0.05). The fermented WBT with C. tropicalis KKU20 enhanced propionic acid (C3) concentrations when cassava chips were replaced for half of all of the diet (C3 ranged from 26.0 to 26.4 mol/100 mol; p < 0.01). Furthermore, Crabtree-negative yeast isolated from the rumen stimulates rumen bacteria more effectively than Crabtree-positive yeast (p < 0.01). According to our findings, nutritional enrichment with yeast might increase the in vitro gas production and digestibility of WBT. The study also demonstrated that Crabtree-negative yeast has a promising lead in terms of improving rumen fermentation quality. However, further research is required before deciding on an effective approach for optimizing the potential of WBT as a feed source.

Gut health benefit and application of postbiotics in animal production

Gut homeostasis is of importance to host health and imbalance of the gut usually leads to disorders or diseases for both human and animal. Postbiotics have been applied in manipulating of gut health, and utilization of postbiotics threads new lights into the host health. Compared with the application of probiotics, the characteristics such as stability and safety of postbiotics make it a potential alternative to probiotics. Studies have reported the beneficial effects of components derived from postbiotics, mainly through the mechanisms including inhibition of pathogens, strengthen gut barrier, and/or regulation of immunity of the host. In this review, we summarized the characteristics of postbiotics, main compounds of postbiotics, potential mechanisms in gut health, and their application in animal production.

Enteric Methane Emissions and Animal Performance in Dairy and Beef Cattle Production: Strategies, Opportunities, and Impact of Reducing Emissions

Enteric methane (CH4) emissions produced by microbial fermentation in the rumen resulting in the emission of greenhouse gases (GHG) into the atmosphere. The GHG emissions reduction from the livestock industry can be attained by increasing production efficiency and improving feed efficiency, by lowering the emission intensity of production, or by combining the two. In this work, information was compiled from peer-reviewed studies to analyze CH4 emissions calculated per unit of milk production, energy-corrected milk (ECM), average daily gain (ADG), dry matter intake (DMI), and gross energy intake (GEI), and related emissions to rumen fermentation profiles (volatile fatty acids [VFA], hydrogen [H2]) and microflora activities in the rumen of beef and dairy cattle. For dairy cattle, there was a positive correlation (p < 0.001) between CH4 emissions and DMI (R2 = 0.44), milk production (R2 = 0.37; p < 0.001), ECM (R2 = 0.46), GEI (R2 = 0.50), and acetate/propionate (A/P) ratio (R2 = 0.45). For beef cattle, CH4 emissions were positively correlated (p < 0.05−0.001) with DMI (R2 = 0.37) and GEI (R2 = 0.74). Additionally, the ADG (R2 = 0.19; p < 0.01) and A/P ratio (R2 = 0.15; p < 0.05) were significantly associated with CH4 emission in beef steers. This information may lead to cost-effective methods to reduce enteric CH4 production from cattle. We conclude that enteric CH4 emissions per unit of ECM, GEI, and ADG, as well as rumen fermentation profiles, show great potential for estimating enteric CH4 emissions.

A comparative analysis of carcass and meat traits, and rumen bacteria between Chinese Mongolian sheep and Dorper × Chinese Mongolian crossbred sheep

Mutton is one of the most widely consumed meats globally. The Chinese Mongolian sheep (MS) breed is an indigenous breed of sheep characterised by high-quality meat and strong adaptability. Dorper × Chinese Mongolian crossbred sheep (DS) is an improved breed with a rapid growth rate and high mutton yield found in parts of China. The rumen microbiota is known to play a key role in shaping host nutrition and health. However, the carcass traits and meat nutritional qualities of DS and MS remain poorly defined, as does how rumen microbes affect these characteristics. The objective of this study was to compare carcass profiles, rumen bacterial communities, and meat nutritional qualities between MS and DS and clarify the associations between rumen microbiota and meat nutritional composition. We found that DS had a faster growth rate and better carcass traits than MS, including BW, carcass weight, meat weight, and loin-eye area. We further found that metabolite and rumen bacterial community composition differed between the two sheep breeds. First, compared with MS, DS had lower contents of some sweet amino acids, monounsaturated fatty acids, n-3 polyunsaturated fatty acids, and beneficial metabolites. Secondly, MS and DS had distinct rumen bacterial compositions, and these differential bacteria were related to carcass traits as well as to contents of meat amino acids, free fatty acids, and other metabolites. Taken together, our data showed that DS had better carcass characteristics but lower meat nutritional quality, parameters that were associated with differences in rumen bacterial community composition. These findings may benefit future breeding strategies aimed at improving sheep carcass performance and meat quality worldwide.

Distribution and Difference of Gastrointestinal Flora in Sheep with Different Body Mass Index

Fat deposition is the key factor affecting the efficiency of animal husbandry production. There are many factors affecting fat deposition, in which the gastrointestinal microbiota plays an important role. Therefore, the body mass index (BMI) was introduced into the evaluation of sheep fat deposition, and the different microbiota and functional pathways of the sheep gastrointestinal tract in different BMI groups were analyzed. We selected 5% of individuals with the highest and lowest BMI from a feed test population (357 in whole group). Microorganisms in 10 sites of the gastrointestinal tract in 36 individuals (18 in each group) were evaluated by 16S rRNA V3−V4 region sequencing. There were differences (p < 0.05) in fat deposition traits between different BMI groups. In the 10 parts of the gastrointestinal tract, the diversity and richness of cecal microflora in the high-BMI group were higher than those in low-BMI Hu sheep (p < 0.05). Principal coordinate analysis (PCoA) showed that there was separation of the cecum between groups, and there were differences in the cecal microbial community. Linear discriminant analysis effect size (LEfSe) showed that most biomarkers were in the cecum. On the basis of an indepth study of cecal microorganisms, 26 different bacterial genera were obtained (p < 0.05). Correlation analysis between them and the characteristics of fat deposition in sheep showed that Colidextribacter, Alloprevotella, and Succenivibrio were positively correlated with fat deposition, while Lachnospiraceae_ND3007_Group was negatively correlated (p < 0.05). The above results show that the cecum may be an important part leading to the difference of BMI in sheep, and its microorganisms may affect the level of fat deposition.

Strategies to Mitigate Enteric Methane Emissions from Ruminant Animals

Human activities account for approximately two-thirds of global methane emissions, wherein the livestock sector is the single massive methane emitter. Methane is a potent greenhouse gas of over 21 times the warming effect of carbon dioxide. In the rumen, methanogens produce methane as a by-product of anaerobic fermentation. Methane released from ruminants is considered as a loss of feed energy that could otherwise be used for productivity. Economic progress and growing population will inflate meat and milk product demands, causing elevated methane emissions from this sector. In this review, diverse approaches from feed manipulation to the supplementation of organic and inorganic feed additives and direct-fed microbial in mitigating enteric methane emissions from ruminant livestock are summarized. These approaches directly or indirectly alter the rumen microbial structure thereby reducing rumen methanogenesis. Though many inorganic feed additives have remarkably reduced methane emissions from ruminants, their usage as feed additives remains unappealing because of health and safety concerns. Hence, feed additives sourced from biological materials such as direct-fed microbials have emerged as a promising technique in mitigating enteric methane emissions.

Hydrogenosome, Pairing Anaerobic Fungi and H2-Utilizing Microorganisms Based on Metabolic Ties to Facilitate Biomass Utilization

Anaerobic fungi, though low in abundance in rumen, play an important role in the degradation of forage for herbivores. When only anaerobic fungi exist in the fermentation system, the continuous accumulation of metabolites (e.g., hydrogen (H2) and formate) generated from their special metabolic organelles-the hydrogenosome-inhibits the enzymatic reactions in the hydrogenosome and reduces the activity of the anaerobic fungi. However, due to interspecific H2 transfer, H2 produced by the hydrogenosome can be used by other microorganisms to form valued bioproducts. This symbiotic interaction between anaerobic fungi and other microorganisms can be used to improve the nutritional value of animal feeds and produce value-added products that are normally in low concentrations in the fermentation system. Because of the important role in the generation and further utilization of H2, the study of the hydrogensome is increasingly becoming an important part of the development of anaerobic fungi as model organisms that can effectively improve the utilization value of roughage. Here, we summarize and discuss the classification and the process of biomass degradation of anaerobic fungi and the metabolism and function of anaerobic fungal hydrogensome, with a focus on the potential role of the hydrogensome in the efficient utilization of biomass.

Relationships of the Microbial Communities with Rumen Epithelium Development of Nellore Cattle Finished in Feedlot Differing in Phenotypic Residual Feed Intake

The objective of this study was to examine the relationships among ruminal microbial community, rumen morphometrics, feeding behavior, feedlot performance, and carcass characteristics of Nellore cattle, classified by residual feed intake (RFI). Twenty-seven Nellore yearling bulls with an initial body weight (BW) of 423.84 ± 21.81 kg were fed in feedlot for 107 d in individual pens to determine the RFI phenotype. Bulls were categorized as high RFI (>0.5 SD above the mean, n = 8), medium RFI (±0.5 SD from the mean, n = 9), and low RFI (<0.5 SD below the mean, n = 10). At harvest, whole rumen content samples were collected from each bull to evaluate ruminal microbial community, including bacteria and protozoa. The carcass characteristics were determined by ultrasonography at the beginning and at the end of the experimental period, and behavior data were collected on d 88. As a result of ranking Nellore bulls by RFI, cattle from low-RFI group presented lesser daily dry matter intake (DMI), either in kilograms (p < 0.01) or as percentage of BW (p < 0.01) than high-RFI yearling bulls, resulting in improved gain:feed (G:F). However, variables, such as average daily gain (ADG), final BW, hot carcass weight (HCW) and other carcass characteristics did not differ (p > 0.05) across RFI groups. The eating rate of either dry matter (DM )(p = 0.04) or neutral detergent fiber (NDF) (p < 0.01) was slower in medium-RFI yearling bulls. For ruminal morphometrics an RFI effect was observed only on keratinized layer thickness, in which a thinner layer (p = 0.04) was observed in low-RFI Nellore yearling bulls. Likewise, Nellore yearling bulls classified by the RFI did not differ in terms of Shannon’s diversity (p = 0.57) and Chao richness (p = 0.98). Our results suggest that the differences in feed efficiency of Nellore bulls differing in phenotypic RFI should be attributed to metabolic variables other than ruminal microorganisms and epithelium, and deserves further investigation.

Contribution of Ruminal Bacteriome to the Individual Variation of Nitrogen Utilization Efficiency of Dairy Cows

High nitrogen utilization efficiency (NUE) is important for increasing milk protein production and decreasing the feed nitrogen cost and nitrogen emission to the environment. Currently, there is a limited whole picture of the relationship between ruminal bacteriome and the NUE of dairy cows, even though some information has been revealed about the bacteriome and milk or milk protein production of dairy cows. The purpose of this study was to compare the rumen bacterial community in dairy cows with different nitrogen utilization efficiency under the same diet. The natural abundance of 15N between the animal proteins and diet (Δ15N) was used as a simple, non-invasive, and accurate biomarker for NUE in ruminants to mark the individual variation. Dairy cows with high NUE (HE_HP, n = 7), medium NUE (ME_MP, n = 7), and low NUE (LE_LP, n = 7) were selected from 284 Holstein dairy cows with the same diet. Measurement of the rumen fermentation indices showed that the proportion of propionate was higher in HE_HP cows and ME_MP cows than in LE_LP cows (P < 0.05). The diversity of rumen bacterial community was higher in LE_LP cows than in ME_MP cows and HE_HP cows by 16S rRNA sequencing analysis (P < 0.05). Moreover, at the genus level, the relative abundances of Succinivibrionaceae_UCG_001, uncultured_Selenomonadaceae, and Acidaminococcus were higher in HE_HP cows than in LE_LP cows (P < 0.05). Interestingly, we found that these bacteria were positively correlated with milk protein yield and negatively correlated with Δ15N (P < 0.05). However, Clostridia_UCG_014, Saccharofermentans, Bacilli_RF39, and Desulfovibrio were lower in HE_HP cows and ME_MP cows than in LE_LP cows (P < 0.05), which were negatively correlated with milk protein yield and positively correlated with Δ15N (P < 0.05). In conclusion, the study showed that the diversity and relative abundances of rumen bacteria differed among different NUE cows, indicating that rumen bacteriome contributes to nitrogen metabolism in dairy cows.

Bovine Animal Model for Studying the Maternal Microbiome, in utero Microbial Colonization and Their Role in Offspring Development and Fetal Programming

Recent developments call for further research on the timing and mechanisms involved in the initial colonization of the fetal/infant gut by the maternal microbiome and its role in Developmental Origins of Health and Disease (DOHaD). Although progress has been made using primarily preterm infants, ethical and legal constraints hinder research progress in embryo/fetal-related research and understanding the developmental and mechanistic roles of the maternal microbiome in fetal microbial imprinting and its long-term role in early-life microbiome development. Rodent models have proven very good for studying the role of the maternal microbiome in fetal programming. However, some inherent limitations in these animal models make it challenging to study perinatal microbial colonization from a biomedical standpoint. In this review, we discuss the potential use of bovine animals as a biomedical model to study the maternal microbiome, in utero microbial colonization of the fetal gut, and their impact on offspring development and DOHaD.

Integration of Multiplied Omics, a Step Forward in Systematic Dairy Research

Due to their unique multi-gastric digestion system highly adapted for rumination, dairy livestock has complicated physiology different from monogastric animals. However, the microbiome-based mechanism of the digestion system is congenial for biology approaches. Different omics and their integration have been widely applied in the dairy sciences since the previous decade for investigating their physiology, pathology, and the development of feed and management protocols. The rumen microbiome can digest dietary components into utilizable sugars, proteins, and volatile fatty acids, contributing to the energy intake and feed efficiency of dairy animals, which has become one target of the basis for omics applications in dairy science. Rumen, liver, and mammary gland are also frequently targeted in omics because of their crucial impact on dairy animals’ energy metabolism, production performance, and health status. The application of omics has made outstanding contributions to a more profound understanding of the physiology, etiology, and optimizing the management strategy of dairy animals, while the multi-omics method could draw information of different levels and organs together, providing an unprecedented broad scope on traits of dairy animals. This article reviewed recent omics and multi-omics researches on physiology, feeding, and pathology on dairy animals and also performed the potential of multi-omics on systematic dairy research.

Whole-Genome Sequencing and Comparative Genomic Analysis of Antimicrobial Producing Streptococcus lutetiensis from the Rumen

Antimicrobial peptides (AMPs) can efficiently control different microbial pathogens and show the potential to be applied in clinical practice and livestock production. In this work, the aim was to isolate AMP-producing ruminal streptococci and to characterize their genetic features through whole-genome sequencing. We cultured 463 bacterial isolates from the rumen of Nelore bulls, 81 of which were phenotypically classified as being Streptococcaceae. Five isolates with broad-range activity were genome sequenced and confirmed as being Streptococcus lutetiensis. The genetic features linked to their antimicrobial activity or adaptation to the rumen environment were characterized through comparative genomics. The genome of S. lutetiensis UFV80 harbored a putative CRISPR-Cas9 system (Type IIA). Computational tools were used to discover novel biosynthetic clusters linked to the production of bacteriocins. All bacterial genomes harbored genetic clusters related to the biosynthesis of class I and class II bacteriocins. SDS-PAGE confirmed the results obtained in silico and demonstrated that the class II bacteriocins predicted in the genomes of three S. lutetiensis strains had identical molecular mass (5197 Da). These results demonstrate that ruminal bacteria of the Streptococcus bovis/equinus complex represent a promising source of novel antimicrobial peptides.

The microbiome of the buffalo digestive tract

Buffalo is an important livestock species. Here, we present a comprehensive metagenomic survey of the microbial communities along the buffalo digestive tract. We analysed 695 samples covering eight different sites in three compartments (four-chambered stomach, intestine, and rectum). We mapped ~85% of the raw sequence reads to 4,960 strain-level metagenome-assembled genomes (MAGs) and 3,255 species-level MAGs, 90% of which appear to correspond to new species. In addition, we annotated over 5.8 million nonredundant proteins from the MAGs. In comparison with the rumen microbiome of cattle, the buffalo microbiota seems to present greater potential for fibre degradation and less potential for methane production. Our catalogue of microbial genomes and the encoded proteins provides insights into microbial functions and interactions at distinct sites along the buffalo digestive tract.

Homo-Acetogens: Their Metabolism and Competitive Relationship with Hydrogenotrophic Methanogens

Homo-acetogens are microbes that have the ability to grow on gaseous substrates such as H₂/CO₂/CO and produce acetic acid as the main product of their metabolism through a metabolic process called reductive acetogenesis. These acetogens are dispersed in nature and are found to grow in various biotopes on land, water and sediments. They are also commonly found in the gastro-intestinal track of herbivores that rely on a symbiotic relationship with microbes in order to breakdown lignocellulosic biomass to provide the animal with nutrients and energy. For this motive, the fermentation scheme that occurs in the rumen has been described equivalent to a consolidated bioprocessing fermentation for the production of bioproducts derived from livestock. This paper reviews current knowledge of homo-acetogenesis and its potential to improve efficiency in the rumen for production of bioproducts by replacing methanogens, the principal H₂-scavengers in the rumen, thus serving as a form of carbon sink by deviating the formation of methane into bioproducts. In this review, we discuss the main strategies employed by the livestock industry to achieve methanogenesis inhibition, and also explore homo-acetogenic microorganisms and evaluate the members for potential traits and characteristics that may favor competitive advantage over methanogenesis, making them prospective candidates for competing with methanogens in ruminant animals.

Comparative analysis of gut microbial composition and potential functions in captive forest and alpine musk deer

Gut microbiota forms a unique microecosystem and performs various irreplaceable metabolic functions for ruminants. The gut microbiota is important for host health and provides new insight into endangered species conservation. Forest musk deer (FMD) and alpine musk deer (AMD) are typical small ruminants, globally endangered due to excessive hunting and habitat loss. Although nearly 60 years of captive musk deer breeding has reduced the hunting pressure in the wild, fatal gastrointestinal diseases restrict the growth of captive populations. In this study, 16S rRNA high-throughput sequencing revealed the differences in gut microbiota between FMD and AMD based on 166 fecal samples. The alpha diversity was higher in FMD than in AMD, probably helping FMD adapt to different and wider habitats. The ß-diversity was higher between adult FMD and AMD than juveniles and in winter than late spring. The phylum Firmicutes and the genera Christensenellaceae R7 group, Ruminococcus, Prevotellaceae UCG-004, and Monoglobus were significantly higher in abundance in FMD than in AMD. However, the phylum Bacteroidetes and genera Bacteroides, UCG-005, Rikenellaceae RC9 gut group, and Alistipes were significantly higher in AMD than FMD. The expression of metabolic functions was higher in AMD than in FMD, a beneficial pattern for AMD to maintain higher energy and substance metabolism. Captive AMD may be at higher risk of intestinal diseases than FMD, with higher relative abundances of most opportunistic pathogens and the expression of disease-related functions. These results provide valuable data for breeding healthy captive musk deer and assessing their adaptability in the wild. KEY POINTS: • Alpha diversity of gut microbiota was higher in FMD than that in AMD • Expression of metabolic and disease-related functions was higher in AMD than in FMD.

Nutrient Digestibility, Microbial Fermentation, and Response in Bacterial Composition to Methionine Dipeptide: An In Vitro Study

Simple Summary

The rumen microbiota plays an important role in maintaining microbiota homeostasis and promoting milk production synthesis through utilizing amino acids and non-protein nitrogen. Furthermore, various nitrogen sources have shown distinct effects on microbial growth rates. The methionine dipeptide (MD) is a bioactive peptide consisting of two methionine (Met) residues linked by a peptide bond. Although the role of MD in milk protein synthesis is established, little is known about its role in bacterial fermentation. The present study demonstrates that the various nitrogen sources could reshape microbiota differently, and MD could be more efficient than free Met in the rumen to support acetate producer growth. Our study provides some new insights into the relationship between ruminal microbiota of dairy cows and small peptides and points to potential strategies to effectively enhance the health condition and digestion ability of dairy cows.

Abstract

It is well known that the methionine dipeptide (MD) could enhance the dairy cows milking performance. However, there is still a knowledge gap of the effects of MD on the rumen fermentation characteristics, microbiota composition, and digestibility. This experiment was conducted to determine the effect of different nitrogen sources with a total mixed ration on in vitro nutrient digestibility, fermentation characteristics, and bacterial composition. The treatments included 5 mg urea (UR), 25.08 mg methionine (Met), 23.57 mg MD, and no additive (CON) in fermentation culture medium composed of buffer solution, filtrated Holstein dairy cow rumen fluid, and substrate (1 g total mixed ration). Nutrient digestibility was measured after 24 h and 48 h fermentation, and fermentation parameters and microbial composition were measured after 48 h fermentation. Digestibility of dry matter, crude protein, neutral detergent fiber (NDF), and acid detergent fiber (ADF) in the MD group at 48 h were significantly higher than in the CON and UR groups. The total volatile fatty acid concentration was higher in the MD group than in the other groups. In addition, 16S rRNA microbial sequencing results showed MD significantly improved the relative abundances of Succinivibrio, Anaerotruncus, and Treponema_2, whereas there was no significant difference between Met and UR groups. Spearman’s correlation analysis showed the relative abundance of Succinivibrio and Anaerotruncus were positively correlated with gas production, NDF digestibility, ADF digestibility, and acetate, propionate, butyrate, and total volatile fatty acid concentrations. Overall, our results suggested that the microbiota in the fermentation system could be affected by additional nitrogen supplementation and MD could effectively enhance the nutrient utilization in dairy cows.

Fluorescence activated cell sorting and fermentation analysis to study rumen microbiome responses to administered live microbials and yeast cell wall derived prebiotics

Rapid dietary changes, such as switching from high-forage to high-grain diets, can modify the rumen microbiome and initiate gastrointestinal distress, such as bloating. In such cases, feed additives, including prebiotics and live microbials, can be used to mitigate these negative consequences. Bio-Mos® is a carbohydrate-based prebiotic derived from yeast cells that is reported to increase livestock performance. Here, the responses of rumen bacterial cells to Bio-Mos® were quantified, sorted by flow cytometry using fluorescently-labeled yeast mannan, and taxonomically characterized using fluorescence in situ hybridization and 16S rRNA sequencing. Further, to evaluate the effects of bovine-adapted Bacteroides thetaiotaomicron administration as a live microbial with and without Bio-Mos® supplementation, we analyzed microbial fermentation products, changes to carbohydrate profiles, and shifts in microbial composition of an in vitro rumen community. Bio-Mos® was shown to be an effective prebiotic that significantly altered microbial diversity, composition, and fermentation; while addition of B. thetaiotaomicron had no effect on community composition and resulted in fewer significant changes to microbial fermentation. When combined with Bio-Mos®, there were notable, although not significant, changes to major bacterial taxa, along with increased significant changes in fermentation end products. These data suggest a synergistic effect is elicited by combining Bio-Mos® and B. thetaiotaomicron. This protocol provides a new in vitro methodology that could be extended to evaluate prebiotics and probiotics in more complex artificial rumen systems and live animals.

Applications of Metagenomics for Unrevealing the Extended Horizons of Microbiota Prevalence from Soil to Human Health

Phylogenetic analysis of different ecosystems has shown that the number of microbial communities in a single sample exceeds their cultured counterparts. Microbes have been found throughout nature and can thrive in adverse conditions. Besides inhabiting diverse environments, they also play a key role in the maintenance of the ecosystem. Most of these microbes are either unculturable or difficult to culture with conventional culturing methods. Metagenomics is an emerging field of science that has been in the light for a decade and offers a potential way to assess microbial diversity. The development of metagenomics opens new ways to study genetic material directly from the environmental samples. DNA sequencing and synthesis technologies are making it possible to read and write entire genomes. The huge amount of data obtained from genome sequencing inevitably requires bioinformatics tools to handle and further process them for analysis. Advances in DNA sequencing and high-performance computing have brought about exemplar improvement in metagenomics, allowing in-depth study of the largely unexplored frontier of microbial life. This culture-independent method provides extensive information regarding the structure, composition, and function of the diverse assemblages of the environmental microbes. The current review presents an overview of the technical aspects of metagenomics along with its diverse applications.

The Effect of Yeast and Roughage Concentrate Ratio on Ruminal pH and Protozoal Population in Thai Native Beef Cattle

Simple Summary

As a result of the recent ban on antibiotics in feed, animal probiotics are becoming increasingly popular. Yeast is extensively used as both a probiotic and prebiotic in the gastrointestinal tracts of ruminants. The purpose of this study is to determine how adding yeast (Saccharomyces cerevisiae) to the diet and changing the roughage-to-concentrate ratio (R:C ratio) affects nutrient consumption, rumen fermentation, microbial protein synthesis, and protozoal population in Thai native beef cattle. The roughage source was urea–calcium-hydroxide-treated rice straw. The findings suggest that supplementing with a R:C ratio of 40:60 and a LY of 4 g/hd/d boosted nutrient digestibility, volatile fatty acid (VFA) production, propionic acid (C₃) in particular, and microbial protein synthesis while lowering protozoal population.

Abstract

The objective of this research is to investigate the effect of yeast (Saccharomyces cerevisiae) adding and roughage-to-concentrate ratio (R:C ratio) on nutrients utilization, rumen fermentation efficiency, microbial protein synthesis, and protozoal population in Thai native beef cattle. Four Thai native beef cattle, weighing an average of 120 ± 10 kg live weight, were randomly assigned to four dietary treatments using a 2 × 2 factorial arrangement in a 4 × 4 Latin square design. Factor A was the level of roughage-to-concentrate ratio (R:C ratio) at 60:40 and 40:60; factor B was the levels of live yeast (LY) supplementation at 0 and 4 g/hd/d; urea–calcium-hydroxide-treated rice straw were used as a roughage source. Findings revealed that total intake and digestibility of dry matter (DM), organic matter (OM), and crude protein (CP) were increased (p < 0.05) by both factors, being greater for steers fed a R:C ratio of 40:60 supplemented with 4 g LY/hd/d. Ruminal ammonia nitrogen, total volatile fatty acid (VFA), and propionate (C₃) were increased (p < 0.05) at the R:C ratio of 40:60 with LY supplementation at 4 g/hd/d, whereas rumen acetate (C₂) and the C₂ to C₃ ratio were decreased (p < 0.05). With a high level of concentrate, LY addition increased total bacterial direct counts and fungal zoospores (p < 0.05), but decreased protozoal populations (p < 0.05). High-concentrate diet and LY supplementation increased nitrogen absorption and the efficiency of microbial nitrogen protein production. In conclusion, feeding beef cattle with 4 g/hd/d LY at a R:C ratio of 40:60 increased C₃ and nutritional digestibility while lowering protozoal population.

FI: The Fecobiome Initiative

Animal husbandry has been key to the sustainability of human societies for millennia. Livestock animals, such as cattle, convert plants to protein biomass due to a compartmentalized gastrointestinal tract (GIT) and the complementary contributions of a diverse GIT microbiota, thereby providing humans with meat and dairy products. Research on cattle gut microbial symbionts has mainly focused on the rumen (which is the primary fermentation compartment) and there is a paucity of functional insight on the intestinal (distal end) microbiota, where most foodborne zoonotic bacteria reside. Here, we present the Fecobiome Initiative (or FI), an international effort that aims at facilitating collaboration on research projects related to the intestinal microbiota, disseminating research results, and increasing public availability of resources. By doing so, the FI can help mitigate foodborne and animal pathogens that threaten livestock and human health, reduce the emergence and spread of antimicrobial resistance in cattle and their proximate environment, and potentially improve the welfare and nutrition of animals. We invite all researchers interested in this type of research to join the FI through our website: www.fecobiome.com

Effects of Management, Dietary Intake, and Genotype on Rumen Morphology, Fermentation, and Microbiota, and on Meat Quality in Yaks and Cattle

Traditionally, yaks graze only natural grassland, even in harsh winters. Meat from grazing yaks is considered very healthy; however, feedlot fattening, which includes concentrate, has been introduced. We questioned whether this change in management and diet would have an impact on the rumen and meat quality of yaks. This study examined the morphology, fermentation, and microbiota of the rumen and the quality of meat of three groups of bovines: (1) grazing yaks (GYs, 4-year olds), without dietary supplements; (2) yaks (FYs, 2.5-year olds) feedlot-fattened for 5 months after grazing natural pasture; and (3) feedlot-fattened cattle (FC, Simmental, 2-year olds). This design allowed us to determine the role of diet (with and without concentrate) and genotype (yaks vs. cattle) on variables measured. Ruminal papillae surface area was greater in the FYs than in the GYs (P = 0.02), and ruminal microbial diversity was greater but richness was lesser in the GYs than in the FC and FYs. Concentrations of ruminal volatile fatty acids were greater in the yaks than in the cattle. In addition, both yak groups had higher protein and lower fat contents in meat than the FC. Meat of GY had a lower n6:n3 ratio than FY and FC, and was the only group with a ratio below r, which is recommended for healthy food. Essential amino acids (EAA), as a proportion of total AA and of non-essential AA of yak meat, met WHO criteria for healthy food; whereas FC did not.

Unraveling differences in fecal microbiota stability in mammals: from high variable carnivores and consistently stable herbivores

BACKGROUND

Through the rapid development in DNA sequencing methods and tools, microbiome studies on a various number of species were performed during the last decade. This advance makes it possible to analyze hundreds of samples from different species at the same time in order to obtain a general overview of the microbiota. However, there is still uncertainty on the variability of the microbiota of different animal orders and on whether certain bacteria within a species are subject to greater fluctuations than others. This is largely due to the fact that the analysis in most extensive comparative studies is based on only a few samples per species or per study site. In our study, we aim to close this knowledge gap by analyzing multiple individual samples per species including two carnivore suborders Canoidea and Feloidea as well as the orders of herbivore Perissodactyla and Artiodactyla held in different zoos. To assess microbial diversity, 621 fecal samples from 31 species were characterized by sequencing the V3-V4 region of the 16S rRNA gene using Illumina MiSeq.

RESULTS

We found significant differences in the consistency of microbiota composition and in fecal microbial diversity between carnivore and herbivore species. Whereas the microbiota of Carnivora is highly variable and inconsistent within and between species, Perissodactyla and Ruminantia show fewer differences across species boundaries. Furthermore, low-abundance bacterial families show higher fluctuations in the fecal microbiota than high-abundance ones.

CONCLUSIONS

Our data suggest that microbial diversity is significantly higher in herbivores than in carnivores, whereas the microbiota in carnivores, unlike in herbivores, varies widely even within species. This high variability has methodological implications and underlines the need to analyze a minimum amount of about 10 samples per species. In our study, we found considerable differences in the occurrence of different bacterial families when looking at just three and six samples. However, from a sample number of 10 onwards, these within-species fluctuations balanced out in most cases and led to constant and more reliable results.

Dietary Energy Levels Affect Carbohydrate Metabolism-Related Bacteria and Improve Meat Quality in the Longissimus Thoracis Muscle of Yak (Bos grunniens)

The effects of different dietary energy levels on the ruminal bacterial population, selected meat quality indices, and their relationship in yak longissimus thoracis (LT) muscle were assessed in this study. A total of 15 castrated yaks were randomly assigned to three groups with low- (NEg: 5.5 MJ/Kg, LE), medium- (NEg: 6.2 MJ/Kg, ME), and high- (NEg: 6.9 MJ/Kg, HE) dietary energy levels and occurred in the cold season (March to May). All yaks from each treatment group were humanely slaughtered and sampled on the day of completion of their feeding treatment. The results showed that the water content and crude fat levels of the LT muscle were markedly elevated in the HE group (P < 0.05), while the shear force was drastically reduced (P = 0.001). Methionine, aspartic acid, and glycine levels in the LT muscle were higher in the LE group compared with the ME and HE groups (P < 0.05). The glutamic acid level in the ME group was greater in comparison to the LE and HE groups (P < 0.05), while the histidine level in the ME group was higher than that in the HE group (P < 0.05). Additionally, the HE diet significantly elevated (P < 0.05) the abundance of carbohydrate metabolism-associated bacteria including Prevotella_1, Lachnospiraceae_NK4A136_group, U29_B03, Ruminiclostridium_6, and Ruminococcaceae_UCG_013 in the rumen. The results of the Spearman's rank correlation analysis showed that the abundance of uncultured_bacterium_f_vadinBE97 and uncultured_bacterium_f_Lachnospiraceae showed a significant influence on the indicator of IMF and SF. In conclusion, a high dietary energy level improved the meat quality in the LT muscle of yak mainly by increasing the relative abundance of ruminal amylolytic bacteria to provide substrates for fatty acid synthesis.

The Nasopharyngeal, Ruminal, and Vaginal Microbiota and the Core Taxa Shared across These Microbiomes in Virgin Yearling Heifers Exposed to Divergent In Utero Nutrition during Their First Trimester of Gestation and in Pregnant Beef Heifers in Response to Mineral Supplementation

In the present study, we evaluated whether the nasopharyngeal, ruminal, and vaginal microbiota would diverge (1) in virgin yearling beef heifers (9 months old) due to the maternal restricted gain during the first trimester of gestation; and (2) in pregnant beef heifers in response to the vitamin and mineral (VTM) supplementation during the first 6 months of pregnancy. As a secondary objective, using the microbiota data obtained from these two cohorts of beef heifers managed at the same location and sampled at the same time, we performed a holistic assessment of the microbial ecology residing within the respiratory, gastrointestinal, and reproductive tract of cattle. Our 16S rRNA gene sequencing results revealed that both α and β-diversity of the nasopharyngeal, ruminal and vaginal microbiota did not differ between virgin heifers raised from dams exposed to either a low gain (targeted average daily gain of 0.28 kg/d, n = 22) or a moderate gain treatment (0.79 kg/d, n = 23) during the first 84 days of gestation. Only in the vaginal microbiota were there relatively abundant genera that were affected by maternal rate of gain during early gestation. Whilst there was no significant difference in community structure and diversity in any of the three microbiota between pregnant heifers received no VTM (n = 15) and VTM supplemented (n = 17) diets, the VTM supplementation resulted in subtle compositional alterations in the nasopharyngeal and ruminal microbiota. Although the nasopharyngeal, ruminal, and vaginal microbiota were clearly distinct, a total of 41 OTUs, including methanogenic archaea, were identified as core taxa shared across the respiratory, gastrointestinal, and reproductive tracts of both virgin and pregnant heifers.

Oscillating dietary crude protein concentrations increase N retention of calves by affecting urea-N recycling and nitrogen metabolism of rumen bacteria and epithelium

The purpose of this study was to investigate the effects of oscillating crude protein (CP) concentration diet on the nitrogen utilization efficiency (NUE) of calves and determine its mechanism. Twelve Holstein calves were assigned randomly into static protein diet (SP, 149 g/kg CP) and oscillating protein diet (OP, 125 and 173 g/kg CP diets oscillated at 2-d intervals) groups. After 60 days of feeding, the weights of total stomach, rumen and omasum tended to increase in calves fed OP. The apparent crude fat digestibility, NUE and energy metabolism also increased. In terms of urea-N kinetics evaluated by urea-¹⁵N¹⁵N isotope labeling method, the urea-N production and that entry to gastrointestinal tended to increase, and urea-N reused for anabolism increased significantly in calves fed OP during the low protein phase. These data indicate that urea-N recycling contributed to improving NUE when dietary protein concentration was low. In addition, the differentially expressed genes in rumen epithelium and the rumen bacteria involved in protein and energy metabolism promoted the utilization of dietary protein in calves fed OP.

Gut Microbiota and Their Role in Health and Metabolic Disease of Dairy Cow

Ruminants are mostly herbivorous animals that employ rumen fermentation for the digestion of feed materials, including dairy cows. Ruminants consume plant fibre as their regular diet, but lack the machinery for their digestion. For this reason, ruminants maintain a symbiotic relation with microorganisms that are capable of producing enzymes to degrade plant polymers. Various species of microflora including bacteria, protozoa, fungi, archaea, and bacteriophages are hosted at distinct concentrations for accomplishing complete digestion. The ingested feed is digested at a defined stratum. The polysaccharic plant fibrils are degraded by cellulolytic bacteria, and the substrate formed is acted upon by other bacteria. This sequential degradative mechanism forms the base of complete digestion as well as harvesting energy from the ingested feed. The composition of microbiota readily gets tuned to the changes in the feed habits of the dairy cow. The overall energy production as well as digestion is decided by the intactness of the resident communal flora. Disturbances in the homogeneity gastrointestinal microflora has severe effects on the digestive system and various other organs. This disharmony in communal relationship also causes various metabolic disorders. The dominance of methanogens sometimes lead to bloating, and high sugar feed culminates in ruminal acidosis. Likewise, disruptive microfloral constitution also ignites reticuloperitonitis, ulcers, diarrhoea, etc. The role of symbiotic microflora in the occurrence and progress of a few important metabolic diseases are discussed in this review. Future studies in multiomics provides platform to determine the physiological and phenotypical upgradation of dairy cow for milk production.

Chelerythrine Chloride: A Potential Rumen Microbial Urease Inhibitor Screened by Targeting UreG

Inhibition of ruminal microbial urease is of particular interest due to its crucial role in regulating urea-N utilization efficiency and nitrogen pollution in the livestock industry. Acetohydroxamic acid (AHA) is currently the only commercially available urease inhibitor, but it has adverse side effects. The urease accessory protein UreG, which facilitates the functional incorporation of the urease nickel metallocentre, has been proposed in developing urease inhibitor through disrupting urease maturation. The objective of this study was to screen natural compounds as potential urease inhibitors by targeting UreG in a predominant ruminal microbial urease. In silico screening and in vitro tests for potential inhibitors were performed using molecular docking and an assay for the GTPase activity of UreG. Chelerythrine chloride was selected as a potential urease inhibitor of UreG with an inhibition concentration IC₅₀ value of 18.13 μM. It exhibited mixed inhibition, with the K_i value being 26.28 μM. We further explored its inhibition mechanism using isothermal titration calorimetry (ITC) and circular dichroism (CD) spectroscopy, and we found that chelerythrine chloride inhibited the binding of nickel to UreG and induced changes in the secondary structure, especially the α-helix and β-sheet of UreG. Chelerythrine chloride formed a pi-anion interaction with the Asp41 residue of UreG, which is an important residue in initiating the conformational changes of UreG. In conclusion, chelerythrine chloride exhibited a potential inhibitory effect on urease, which provided new evidence for strategies to develop novel urease inhibitors targeting UreG to reduce nitrogen excretion from ruminants.

Disentangling the Complexity of the Rumen Microbial Diversity Through Fractionation Using a Sucrose Density Gradient

The ruminal microbial community is an important element in health, nutrition, livestock productivity, and climate impact. Despite the historic and current efforts to characterize this microbial diversity, many of its members remain unidentified, making it challenging to associate microbial groups with functions. Here we present a low-cost methodology for rumen sample treatment that separates the microbial community based on cell size, allowing for the identification of subtle compositional changes. In brief, the sample is centrifuged through a series of sucrose density gradients, and cells migrate to their corresponding density fraction. From each fraction, DNA is extracted and 16S rRNA gene amplicons are sequenced. We tested our methodology on four animals under two different conditions, fasting, and post-feeding. Each fraction was examined by confocal microscopy showing that the same sucrose fraction consistently separated similar cell-sized microorganisms independent of the animal or treatment. Microbial composition analysis using metabarcoding showed that our methodology detected low abundance bacterial families and population changes between fasting and post-feeding treatments that could not be observed by bulk DNA analysis. In conclusion, the sucrose-based method is a powerful low-cost approximation to untwine, enrich, and potentially isolate uncharacterized members of the ruminal microbiome.

Bovine Immunology: Implications for Dairy Cattle

The growing world population (7.8 billion) exerts an increased pressure on the cattle industry amongst others. Intensification and expansion of milk and beef production inevitably leads to increased risk of infectious disease spread and exacerbation. This indicates that improved understanding of cattle immune function is needed to provide optimal tools to combat the existing and future pathogens and improve food security. While dairy and beef cattle production is easily the world's most important agricultural industry, there are few current comprehensive reviews of bovine immunobiology. High-yielding dairy cattle and their calves are more vulnerable to various diseases leading to shorter life expectancy and reduced environmental fitness. In this manuscript, we seek to fill this paucity of knowledge and provide an up-to-date overview of immune function in cattle emphasizing the unresolved challenges and most urgent needs in rearing dairy calves. We will also discuss how the combination of available preventative and treatment strategies and herd management practices can maintain optimal health in dairy cows during the transition (periparturient) period and in neonatal calves.

Inter and intraspecies comparison of the level of selected bacterial phyla in in cattle and sheep based on feces

Background

The microbiome of the digestive tract of ruminants contains microbial ecosystem that is affected by both environmental and genetic factors. The subject of this study concerns the influence of selected genetic factors, such as species of animals and “host” individual differences on the digestive tract microbiome composition. The results show the core microbiological composition (Firmicutes and Bacteroidetes) of ruminants digestive tract (based on feces) depending on breed and “host”. The Bacteroidetes and Firmicutes phyla are the most abundant in ruminants digestive tract. The aim of the study was to determine the differences prevalence level of Bacteroidetes and Firmicutes phyla in feces of Charolaise cattle and Polish Olkuska Sheep with respect to intra- and inter-species variability.

Results

The research group in the experiment consisted of animals at the age of 3 months kept in the same environmental conditions – rams of Polish Olkuska Sheep (n = 10) and Charolaise bulls (n = 10). Feces were collected individually from each animal (animals without disease symptoms were selected), living on the same environmental conditions. The analysis of the results in terms of species showed differences in the Firmicutes phylum level and Lactobacillaceae family between rams and bulls. Subsequently, the analysis performed for the “host effect” showed differentiation in the levels of the Bacteroidetes and Firmicutes phyla between individuals in a group and also between the groups.

Conclusion

The obtained results suggest that, apart from the diet and the environment, the species and the individual host are equally important factors influencing the microbiological composition of the digestive system of ruminants.

Effects of Lactobacillus rhamnosus and Enterococcus faecalis Supplementation as Direct-Fed Microbials on Rumen Microbiota of Boer and Speckled Goat Breeds

The effects on rumen microbial communities of direct-fed probiotics, Lactobacillus rhamnosus and Enterococcus faecalis, singly and in combination as feed supplements to both the Boer and Speckled goats were studied using the Illumina Miseq platform targeting the V3-V4 region of the 16S rRNA microbial genes from sampled rumen fluid. Thirty-six goats of both the Boer and Speckled were divided into five experimental groups: (T1) = diet + Lactobacillus rhamnosus; (T2) = diet + Enterococcus faecalis; (T3) = diet + Lactobacillus rhamnosus + Enterococcus faecalis; (T4, positive control) = diet + antibiotic and (T5, negative control) = diet without antibiotics and without probiotics. Our results revealed that Bacteroidetes, Firmicutes, TM7, Proteobacteria, and Euryarchaeota dominate the bacterial communities. In our observations, Lactobacillus rhamnosus and Enterococcus faecalis supplements reduced the archaeal population of Methanomassiliicocca in the T1, T2 and T3 groups, and caused an increase in the T4 group. Chlamydiae were present only in the T5 group, suggesting that probiotic and antibiotic inhibit the growth of pathogens in the rumen. We inferred, based on our results, that Lactobacillus rhamnosus and Enterococcus faecalis favour the survival of beneficial microbial communities in the goats’ rumen. This may lead to an overall improved feed efficacy and growth rate.

Effects of the dietary grain content on rumen and fecal microbiota of dairy cows

Six non-lactating Holstein dairy cows received diets with forage to grain mixture ratios of 100:0 (G0), 75:25 (G25), and 50:50 (G50) that contained 0.5%, 10.0%, and 19.5% dry matter (DM) of starch, respectively. Rumen fluid and feces were sampled, and methane emissions were determined during the last week of 5 wk experimental periods. Taxonomic compositions of microbiota were determined using Illumina 16S rRNA sequencing. Increased grain feeding increased the acidity and volatile fatty acid concentrations of rumen fluid and feces, and decreased methane emissions expressed as L·kg−1 DM. Microbial diversities were highest for G25. The numbers of identified genera in rumen fluid were 185, 182, and 171 for G0, G25, and G50, respectively. In feces, these numbers were 197, 182, and 171 for these diets, respectively. In rumen digesta, seven genera were correlated positively to G0 and negatively to G50, and six genera were correlated negatively to G0 and positively to G50. In feces, 16 genera were correlated positively to G0 and negatively to G50, and 13 genera were correlated negatively to G0 and positively to G50. Increasing grain feeding affected a limited number of genera in rumen digesta and feces. This could not explain treatment effects on the functionalities of microbiota.