Effects of Nitrate Addition on Rumen Fermentation, Bacterial Biodiversity and Abundance

Feed additives for methane mitigation: A guideline to uncover the mode of action of antimethanogenic feed additives for ruminants

This publication aims to provide guidelines of the knowledge required and the potential research to be conducted in order to understand the mode of action of antimethanogenic feed additives (AMFA). In the first part of the paper, we classify AMFA into 4 categories according to their mode of action: (1) lowering dihydrogen (H2) production; (2) inhibiting methanogens; (3) promoting alternative H2-incorporating pathways; and (4) oxidizing methane (CH4). The second part of the paper presents questions that guide the research to identify the mode of action of an AMFA on the rumen CH4 production from 5 different perspectives: (1) microbiology; (2) cell and molecular biochemistry; (3) microbial ecology; (4) animal metabolism; and (5) cross-cutting aspects. Recommendations are provided to address various research questions within each perspective, along with examples of how aspects of the mode of action of AMFA have been elucidated before. In summary, this paper offers timely and comprehensive guidelines to better understand and reveal the mode of action of current and emerging AMFA.

Effect of nitrate supplementation on diurnal emission of enteric methane and nitrous oxide

The objective of this study was to investigate the effect of nitrate supplementation on diurnal enteric methane (CH4) and nitrous oxide (N2O) emissions in dairy cows. Four Danish Holstein dairy cows fitted with ruminal cannulas were used in a 2 × 2 crossover design with 2 periods of 14 d duration. Cows were fed ad libitum with 2 experimental diets based on either urea or nitrate (8.6 g ofN O 3 - / k g o f D M ) supplementation. Samples of ruminal fluid, blood, and rumen headspace gas samples were collected. Gas exchange was measured in respiration chambers during a 96-h period. Emission of N2O was calculated from the ratio between CH4 and N2O in the rumen headspace and the measured CH4 emission. Nitrate supplementation resulted in a lower daily CH4 production (g/d), CH4 yield (g/kg of DMI), and CH4 per kilogram of fat- and protein-corrected milk yield; a tendency of lower CH4 intensity (g/kg ECM); and higher daily hydrogen (H2) production, H2 yield, and daily N2O production compared with urea supplementation. The only difference in ruminal VFA composition was a higher valerate proportion in cows receiving nitrate compared with urea supplementation. In conclusion, nitrate compared with urea supplementation reduced CH4 production, mainly just after feeding, but also increased N2O production.

Rumen microbiota helps Tibetan sheep obtain energy more efficiently to survive in the extreme environment of the Qinghai-Tibet Plateau

Introduction

T-sheep and H-sheep exhibit different environmental adaptability and production performance. The rumen microbiome has co-evolved with hosts and plays a vital role in nutrient digestion and energy metabolism. In our previous study, we found that T-sheep have a higher efficiency in energy metabolism than H-sheep, but the rumen microbial community remains unclear.

Methods

In this study, we determined the rumen bacterial profile and rumen fermentation parameters to reveal the bacterial profiles and predictive functions among breeds and diets with four different energy levels, as well as the correlation between bacterial profiles and rumen fermentation characteristics.

Results

The results showed that the rumen total volatile fatty acids (VFAs), acetate, butyrate, total branched-chain VFAs, iso-butyrate, and iso-valerate were higher in T-sheep than H-sheep. The alpha diversity of ruminal bacteria is not affected by dietary energy, but it shows a distinction between the sheep breeds. Specifically, T-sheep rumen bacteria exhibit higher alpha diversity than H-sheep. The beta diversity of ruminal bacteria is not influenced by dietary energy or sheep breeds, indicating similar communities of ruminal bacteria between different diets and sheep breeds. The phyla of Bacteroidetes and Firmicutes predominate in the rumen, with a higher relative abundance of Firmicutes observed in T-sheep than H-sheep. The two most abundant genera in the rumen were Prevotella 1 and Rikenellaceae RC9 gut group. Prevotella 1 is the predominant bacterial genus in the rumen of H-sheep, while the Rikenellaceae RC9 gut group dominates in the rumen of T-sheep. Microbial co-occurrence network analysis reveals that variations in rumen fermentation characteristics result from differences in module abundance, with a higher abundance of VFA-producing modules observed in the rumen of T-sheep. Microbial function prediction analysis showed that dietary energy rarely alters the functional composition of rumen bacteria. However, there were differences in the functions of rumen bacteria between sheep breeds, with T-sheep showing a greater emphasis on energy metabolism-related functions, while H-sheep showed a greater emphasis on protein metabolism-related functions.

Discussion

These findings provide evidence of the special rumen microbial community that helps T-sheep efficiently obtain energy from low-protein and low-energy diets, enabling them to survive in the extreme environment of the Qinghai-Tibet Plateau.

A Review of Potential Feed Additives Intended for Carbon Footprint Reduction through Methane Abatement in Dairy Cattle

Eight rumen additives were chosen for an enteric methane-mitigating comparison study including garlic oil (GO), nitrate, Ascophyllum nodosum (AN), Asparagopsis (ASP), Lactobacillus plantarum (LAB), chitosan (CHI), essential oils (EOs) and 3-nitrooxypropanol (3-NOP). Dose-dependent analysis was carried out on selected feed additives using a meta-analysis approach to determine effectiveness in live subjects or potential efficacy in live animal trials with particular attention given to enteric gas, volatile fatty acid concentrations, and rumen microbial counts. All meta-analysis involving additives GO, nitrates, LAB, CHI, EOs, and 3-NOP revealed a reduction in methane production, while individual studies for AN and ASP displayed ruminal bacterial community improvement and a reduction in enteric CH4. Rumen protozoal depression was observed with GO and AN supplementation as well as an increase in propionate production with GO, LAB, ASP, CHI, and 3-NOP rumen fluid inoculation. GO, AN, ASP, and LAB demonstrated mechanisms in vitro as feed additives to improve rumen function and act as enteric methane mitigators. Enzyme inhibitor 3-NOP displays the greatest in vivo CH4 mitigating capabilities compared to essential oil commercial products. Furthermore, this meta-analysis study revealed that in vitro studies in general displayed a greater level of methane mitigation with these compounds than was seen in vivo, emphasising the importance of in vivo trials for final verification of use. While in vitro gas production systems predict in vivo methane production and fermentation trends with reasonable accuracy, it is necessary to confirm feed additive rumen influence in vivo before practical application.

Combined effects of nitrate and medium-chain fatty acids on methane production, rumen fermentation, and rumen bacterial populations in vitro

This study investigated the combined effects of nitrate (NT) and medium-chain fatty acids (MCFA), including C8, C10, C12, and C14, on methane (CH4) production, rumen fermentation characteristics, and rumen bacteria using a 24 h batch incubation technique. Four types of treatments were used: control (no nitrate, no MCFA), NT (nitrate at 3.65 mM), NT + MCFA (nitrate at 3.65 mM + one of the four MCFA at 500 mg/L), and NT + MCFA/MCFA (nitrate at 3.65 mM + a binary combination of MCFA at 250 and 250 mg/L). All treatments decreased (P < 0.001) methanogenesis (mL/g dry matter incubated) compared with the control, but their efficiency was dependent on the MCFA type. The most efficient CH4 inhibitor was the NT + C10 treatment (- 40%). The combinations containing C10 and C12 had the greatest effect on bacterial alpha and beta diversity and relative microbial abundance (P < 0.001). Next-generation sequencing showed that the family Succinivibrionaceae was favored in treatments with the greatest CH4 inhibition at the expense of Prevotella and Ruminococcaceae. Furthermore, the relative abundance of Archaea decreased (P < 0.05) in the NT + C10 and NT + C10/C12 treatments. These results confirm that the combination of NT with MCFA (C10 and C12 in particular) may effectively reduce CH4 production.

Effects of Sodium Nitrate and Coated Methionine on Lactation Performance, Rumen Fermentation Characteristics, Amino Acid Metabolism, and Microbial Communities in Lactating Buffaloes

Sodium nitrate is used as a non-protein nitrogen supplement while methionine is considered as a common methionine additive for ruminants. This study investigated the effects of sodium nitrate and coated methionine supplementation on milk yield, milk composition, rumen fermentation parameters, amino acid composition, and rumen microbial communities in lactating buffaloes. Forty mid-lactation multiparous Murrah buffaloes within the initial days in milk (DIM) = 180.83 ± 56.78 d, milk yield = 7.63 ± 0.19 kg, body weight = 645 ± 25 kg were selected and randomly allocated into four groups (N = 10). All of animals received the same total mixed ratio (TMR) diet. Furthermore, the groups were divided into the control group (CON), 70 g/d sodium nitrate group (SN), 15 g/d palmitate coated L-methionine group (MET), and 70 g/d sodium nitrate +15 g/d palmitate coated L-methionine group (SN+MET). The experiment lasted for six weeks, including two weeks of adaption. The results showed that most rumen-free amino acids, total essential amino acids, and total amino acids in Group SN increased (p < 0.05), while the dry matter intake (DMI) and rumen acetate, propionate, valerate, and total volatile fatty acids (TVFA) in Group MET decreased (p < 0.05). However, there was no significant difference in milk yield, milk protein, milk fat, lactose, total solid content, and sodium nitrate residue in milk among groups (p > 0.05). Group SN+MET had a decreased rumen propionate and valerate (p < 0.05), while increasing the Ace, Chao, and Simpson indices of alpha diversity of rumen bacteria. Proteobacteria and Actinobacteriota were significantly increased (p < 0.05) in Group SN+MET, but Bacteroidota, and Spirochaetota were decreased (p < 0.05). In addition, Group SN+MET also increased the relative abundance of Acinetobacter, Lactococcus, Microbacterium, Chryseobacterium, and Klebsiella, which were positively correlated with cysteine and negatively correlated with rumen acetate, propionate, valerate, and TVFA. Rikenellaceae_RC9_gut_group was identified as a biomarker in Group SN. Norank_f__UCG-011 was identified as a biomarker in Group MET. Acinetobacter, Kurthia, Bacillus, and Corynebacterium were identified as biomarkers in Group SN+MET. In conclusion, sodium nitrate increased rumen free amino acids, while methionine decreased dry matter intake (DMI) and rumen volatile fatty acids. The combined use of sodium nitrate and methionine enriched the species abundance of microorganisms in the rumen and affected the composition of microorganisms in the rumen. However, sodium nitrate, methionine, and their combination had no significant effect on the milk yield and milk composition. It was suggested that the combined use of sodium nitrate and methionine in buffalo production was more beneficial.

In vitro screening of anti-methanogenic additives for use in Australian grazing systems

Despite considerable effort to develop and optimise additives to reduce methane emissions from cattle, little information on additive effectiveness exists for cattle under grazing scenarios. As the majority of Australian cattle production occurs on grazing land it is pertinent to report on the use of additives under simulated conditions. The current study evaluated the addition of nine additives to Rhodes grass hay under in vitro conditions, to estimate their impact on methane (CH4), gas production, and rumen fermentation parameters (volatile fatty acids, rumen pH and in vitro dry matter digestibility [IVDMD]). Citral extract at 0.1% of rumen media decreased all CH4 production parameters, but reduced gas production and digestibility, compared to a 100% hay control. Similarly, Sandalwood essential oil decreased CH4 production at 48 h, IVDMD and gas production, compared to the control. Biochar + nitrates at 5 and 8% DM, and Biochar + Asparagopsis at 5% DM decreased cumulative CH4 production (15.6%, 25.9%, 23.8%, respectively; P &lt; 0.01), compared to the control. No changes in IVDMD and gas production were observed. As such, the biochar additives were considered the most promising additives from those evaluated with a substrate designed to replicate Australian grazing systems.

Network analysis to evaluate complexities in relationships among fermentation variables measured within continuous culture experiments

The objective of this study was to leverage a frequentist (ELN) and Bayesian learning (BLN) network analyses to summarize quantitative associations among variables measured in 4 previously published dual-flow continuous culture fermentation experiments. Experiments were originally designed to evaluate effects of nitrate, defaunation, yeast, and/or physiological shifts associated with pH or solids passage rates on rumen conditions. Measurements from these experiments that were used as nodes within the networks included concentrations of individual volatile fatty acids, mM and nitrate, NO3-,%; outflows of non-ammonia nitrogen (NAN, g/d), bacterial N (BN, g/d), residual N (RN, g/d), and ammonia N (NH3-N, mg/dL); degradability of neutral detergent fiber (NDFd, %) and degradability of organic matter (OMd, %); dry matter intake (DMI, kg/d); urea in buffer (%); fluid passage rate (FF, L/d); total protozoa count (PZ, cells/mL); and methane production (CH4, mmol/d). A frequentist network (ELN) derived using a graphical LASSO (least absolute shrinkage and selection operator) technique with tuning parameters selected by Extended Bayesian Information Criteria (EBIC) and a BLN were constructed from these data. The illustrated associations in the ELN were unidirectional yet assisted in identifying prominent relationships within the rumen that were largely consistent with current understanding of fermentation mechanisms. Another advantage of the ELN approach was that it focused on understanding the role of individual nodes within the network. Such understanding may be critical in exploring candidates for biomarkers, indicator variables, model targets, or other measurement-focused explorations. As an example, acetate was highly central in the network suggesting it may be a strong candidate as a rumen biomarker. Alternatively, the major advantage of the BLN was its unique ability to imply causal directionality in relationships. Because the BLN identified directional, cascading relationships, this analytics approach was uniquely suited to exploring the edges within the network as a strategy to direct future work researching mechanisms of fermentation. For example, in the BLN acetate responded to treatment conditions such as the source of N used and the quantity of substrate provided, while acetate drove changes in the protozoal populations, non-NH3-N and residual N flows. In conclusion, the analyses exhibit complementary strengths in supporting inference on the connectedness and directionality of quantitative associations among fermentation variables that may be useful in driving future studies.

Effect of Hydrogen-Consuming Compounds on In Vitro Ruminal Fermentation, Fatty Acids Profile, and Microbial Community in Water Buffalo

The present study aimed to investigate the effect of hydrogen-consuming compounds on ruminal methane (CH4) production, in vitro fermentation parameters, fatty acids profile, and microbial community in water buffalo. Different sodium nitrate to disodium fumarate ratios [2:1 (F), 1:1 (S), 1:2 (T)] were studied in vitro by batch culture technique in the presence of linoleic acid. Results revealed that the dominant bacterial communities were not affected with sodium nitrate and disodium fumarate, whereas CH4 production and Verrucomicrobia, Succiniclasticum, norank_f__Muribaculaceae, and Prevotellaceae_UCG-003 were reduced (P < 0.05). However, ruminal pH, unsaturated fatty acids/saturated fatty acids (UFA/SFA) and Campilobacterota, Selenomonas, Succinivibrio, Oribacterium, Christensenellaceae_R-7_group, Campylobacter, Shuttleworthia, Schwartzia, and Prevotellaceae_YAB2003_group were increased (P < 0.05). Total volatile fatty acids (TVFA) and Spirochaetae, Fibrobacterota, Verrucomicrobia, Fibrobacter, Treponema, and Prevotellaceae were decreased in F (P < 0.05), but cis-9, trans-11CLA, acetate/propionate and Proteobacteria, Campilobacterota, Selenomonas, Succinivibrio, and Campylobacter were increased in F (P < 0.05). The highly selected bacterial genera in F were Campylobacter and Succinivibrio. The disodium fumarate, enhanced (P < 0.05) the TVFA, propionate, total bacteria, Butyrivibrio proteoclasticus, and Atypical butyrivibrio. The concentrations of C18:3n3, C20:3n6, C21:0, C22:2n6, and C22:1n9, as well as the populations of total fungi, protozoa, methanogens, Butyrivibrio hungatei in T were higher (P < 0.05). The highly selected bacterial genera in T were Fibrobacter and Treponema. Conclusively, the addition of sodium nitrate and disodium fumarate can reduce the CH4 production and optimize ruminal fatty acid composition. Furthermore, disodium fumarate can alleviate the adverse effect of sodium nitrate on the rumen fermentation.

Sodium nitrate has no detrimental effect on milk fatty acid profile and rumen bacterial population in water buffaloes

This study evaluated the influence of dietary sodium nitrate on ruminal fermentation profiles, milk production and composition, microbial populations and diversity in water buffaloes. Twenty-four female water buffaloes were randomly divided into four groups and fed with 0, 0.11, 0.22, 044 g sodium nitrate per kg body weight diets, respectively. Results showed that the concentration of acetate, propionate, butyrate and total VFA in all sodium nitrate–adapted water buffaloes were greater than the control group (P  < 0.05). Although the milk fatty acids value at 0.11 g sodium nitrate/kg/d were slightly lower than other treatments, no significant differences were observed among different treatments (P  > 0.05). Compared to the control group, the archaea richness (ace and chao1) and diversity (Shannon index) indices were increased by nitrate supplementation (P  < 0.05). Compared with the control group, sodium nitrate did not affect bacterial abundance at the phylum and genus level, but the relative abundance of the methanogen genera was greatly changed. There was a tendency for Methanobrevibacter to decrease in the sodium nitrate group (P  = 0.091). Comparisons of archaea communities by PCoA analysis showed significant separation between the control group and nitrate treatments (P  = 0.025). It was concluded that added 0.11–0.44 g sodium nitrate/kg of body weight increased the rumen VFA production and archaeal diversity of water buffaloes but had no detrimental effect on milk yield or composition, fatty acids profile, rumen methanogen or Butyrivibrio group population related to biohydrogenation.

Influence of nitrate supplementation on in-vitro methane emission, milk production, ruminal fermentation, and microbial methanotrophs in dairy cows fed at two forage levels

Modifying the chemical composition of a diet can be a good strategy for reducing methane emission in the rumen. However, this strategy can have adverse effects on the ruminal microbial flora. The aim of our study was to reduce methane without disturbing ruminal function by stimulating the growth and propagation of methanotrophs. In this study, we randomly divided twenty multiparous Holstein dairy cows into 4 groups in a 2×2 factorial design with two forage levels (40% and 60%) and two nitrate supplementation levels (3.5% and zero). We examined the effect of experimental diets on cow performance, ruminal fermentation, blood metabolites and changes of ruminal microbial flora throughout the experimental period (45-day). Additionally, in vitro methane emission was evaluated. Animals fed diet with 60% forage had greater dry matter intake (DMI) and milk fat content, but lower lactose and milk urea content compared with those fed 40% forage diet. Moreover, nitrate supplementation had no significant effect on DMI and milk yield. Furthermore, the interactions showed that nitrate reduces DMI and milk fat independently of forage levels. Our findings showed that nitrate can increase ammonia concentration, pH, nitrite, and acetate while reducing the total volatile fatty acids concentration, propionate, and butyrate in the rumen. With increasing nitrate, methane emission was considerably decreased possibly due to the stimulated growth of Fibrobacteria, Proteobacteria, type II Methanotrophs, and Methanoperedense nitroreducens, especially with high forage level. Overall, nitrate supplementation could potentially increase methane oxidizing microorganisms without adversely affecting cattle performance.

Changes in rumen microbial community composition in yak in response to seasonal variations

AIMS

Yak is a dominant ruminant, well adapted to grazing on pasture year around in the harsh climate of the 3000-meter-high Qinghai-Tibetan Plateau. The complex microbial community that resides within the yak rumen is responsible for fermentation and contributes to its climatic adaptation. This study aimed to characterize the rumen microbiota responses to wide seasonal variations, especially those necessary for survival in the cold seasons.

METHODS AND RESULTS

In the present study, we performed 16s rRNA gene sequencing to investigate the seasonal variations in microbiota composition, diversity and associated volatile fatty acids (VFAs) in yak rumen. The results showed that rumen microbiota were dominated by Bacteroides (72.13%-78.54%) and Firmicutes; the relative abundance of Firmicutes was higher in summer (17.44%) than in winter (10.67%; p < 0.05). The distribution of taxa differed among spring, summer and winter rumen communities (PERMANOVA, p = 0.001), whereas other taxa (e.g., Fibrobacter, Verrucomicrobia, Anaerostipes and Paludibacter), which could potentially help overcome harsh climate conditions were observed in higher abundance during the cold spring and winter seasons. The highest total VFA concentration in the yak rumen was obtained in summer (p < 0.05), followed by spring and winter, and both positive and negative correlations between VFAs and specific genera were revealed.

CONCLUSIONS

Microbiota in yak rumen appear to be highly responsive to seasonal variations. Considering environmental factors, we suggest that seasonal adaptation by microbial communities in rumen enables their hosts to survive seasonal scarcity and cold stress in the spring and winter.

SIGNIFICANCE AND IMPACT OF STUDY

The present study furthers our understanding of how microbial adaptation to seasonal variations in nutrient availability and climate may function in high plateau ruminants, providing insights into the tripartite relationship between the environment, host and microbiota.

Effect of Methionine Supplementation on Rumen Microbiota, Fermentation, and Amino Acid Metabolism in In Vitro Cultures Containing Nitrate

This study evaluated the effect of methionine on in vitro methane (CH₄) production, rumen fermentation, amino acid (AA) metabolism, and rumen microbiota in a low protein diet. We evaluated three levels of methionine (M0, 0%; M1, 0.28%; and M2, 1.12%) of in the presence of sodium nitrate (1%) in a diet containing elephant grass (90%) and concentrate (10%). We used an in vitro batch culture technique by using rumen fluid from cannulated buffaloes. Total gas and CH₄ production were measured in each fermentation bottle at 3, 6, 9, 12, 24, 48, 72 h of incubation. Results revealed that M0 decreased (p < 0.001) the total gas and CH₄ production, but methionine exhibited no effect on these parameters. M0 decreased (p < 0.05) the individual and total volatile fatty acids (VFAs), while increasing (p < 0.05) the ruminal pH, acetate to propionate ratio, and microbial protein content. Methionine did not affect ruminal AA contents except asparagine, which substantially increased (p = 0.003). M2 increased the protozoa counts, but both M0 and M1 decreased (p < 0.05) the relative abundance of Firmicutes while increasing (p < 0.05) the Campilobacterota and Proteobacteria. However, Prevotella and γ-Proteobacteria were identified as biomarkers in the nitrate group. Our findings indicate that methionine can increase ruminal asparagine content and the population of Compylobactor.

Late Gestation Maternal Feed Restriction Decreases Microbial Diversity of the Placenta While Mineral Supplementation Improves Richness of the Fetal Gut Microbiome in Cattle

Feed intake restriction impacts both humans and ruminants in late gestation, although it is unknown whether this adverse maternal environment influences the microbiome of the reproductive tract, and through it, the colonization of the fetal gut. A 2 × 2 factorial design including a 70% feed intake restriction (feed restricted 'FR' or control diets 'CON') and mineral supplementation (unsupplemented 'S-' or supplemented 'S+') was used to analyze these effects in multiparous cows (n = 27). Vaginal swabs were obtained 60, 30, and 10 days prior to the estimated calving date, along with neonatal rumen fluid and meconium. Placental tissues and efficiency measurements were collected. Microbial DNA was extracted for 16S sequencing of the V4 region. Feed restriction decreased the diversity of the placental microbiome, but not the vagina, while mineral supplementation had little impact on these microbial communities. Mineral supplementation did improve the richness and diversity of the fetal gut microbiomes in relation to reproductive microbes. These differences within the placental microbiome may influence individual health and performance. Adequate maternal nutrition and supplementation yielded the greatest placental efficiency, which may aid in the establishment of a healthy placental microbiome and fetal microbial colonization.

Nitrate supplementation at two forage levels in dairy cows feeding: milk production and composition, fatty acid profiles, blood metabolites, ruminal fermentation, and hydrogen sink

Nitrate may reduce the ruminal methane emission by competing methanogenesis to achieve more hydrogen. For this purpose, twenty Holstein lactating cows were examined using a 2×2 factorial design in 4 groups for 60 days with two forage levels (40% and 60%) and supplemental nitrate 0% (F40 and F60) and 3.5% (F40N and F60N) of diet dry matter (DM). Then, the effect of nitrate and forage levels on cow performance, ruminal fermentation, methane emission, and metabolic hydrogen sink were evaluated. The nitrate supplementation did not significantly affect milk yield and ECM/DMI while, milk urea nitrogen was increased. Lowest quantity of milk vitamins (A and E) was observed in nitrate groups. The nitrate supplementation increased c9-C18:1, unsaturated fatty acids, and n-6/n-3 contents of the milk. Blood parameters were affected by nitrate supplementation. Blood met-Hb concentration was increased, while blood glucose was decreased in nitrate groups. High forage and nitrate fed animals (F60N) had higher ruminal acetate and lower propionate concentration, and higher acetate+butyrate to propionate ratio than other groups. Nitrite and NH3-N concentrations were higher in the rumen of nitrate fed animals. Nitrate supplementation inhibited gas volume and methane emission without affecting volatile fatty acids at 12 and 24 h of incubation. The H2 balance, H2 production and consumption, and recovery percentage were significantly lower in F60N group. In conclusion, nitrate supplementation can be employed as an alternative strategy for improving ruminal fermentation, milk quality and methane inhibition.

Active Rumen Bacterial and Protozoal Communities Revealed by RNA-Based Amplicon Sequencing on Dairy Cows Fed Different Diets at Three Physiological Stages

Seven Italian Simmental cows were monitored during three different physiological stages, namely late lactation (LL), dry period (DP), and postpartum (PP), to evaluate modifications in their metabolically-active rumen bacterial and protozoal communities using the RNA-based amplicon sequencing method. The bacterial community was dominated by seven phyla: Proteobacteria, Bacteroidetes, Firmicutes, Spirochaetes, Fibrobacteres, Verrucomicrobia, and Tenericutes. The relative abundance of the phylum Proteobacteria decreased from 47.60 to 28.15% from LL to DP and then increased to 33.24% in PP. An opposite pattern in LL, DP, and PP stages was observed for phyla Verrucomicrobia (from 0.96 to 4.30 to 1.69%), Elusimicrobia (from 0.32 to 2.84 to 0.25%), and SR1 (from 0.50 to 2.08 to 0.79%). The relative abundance of families Succinivibrionaceae and Prevotellaceae decreased in the DP, while Ruminococcaceae increased. Bacterial genera Prevotella and Treponema were least abundant in the DP as compared to LL and PP, while Ruminobacter and Succinimonas were most abundant in the DP. The rumen eukaryotic community was dominated by protozoal phylum Ciliophora, which showed a significant decrease in relative abundance from 97.6 to 93.9 to 92.6 in LL, DP, and PP, respectively. In conclusion, the physiological stage-dependent dietary changes resulted in a clear shift in metabolically-active rumen microbial communities.

Effects of bismuth subsalicylate and encapsulated calcium ammonium nitrate on ruminal fermentation of beef cattle

A replicated 5 × 5 Latin square design with a 2 × 2 + 1 factorial arrangement of treatments was used to determine the effects of bismuth subsalicylate (BSS) and encapsulated calcium ammonium nitrate (eCAN) on ruminal fermentation of beef cattle consuming bahiagrass hay (Paspalum notatum) and sugarcane molasses. Ten ruminally cannulated steers (n = 8; 461 ± 148 kg of body weight [BW]; average BW ± SD) and heifers (n = 2; 337 ± 74 kg of BW) were randomly assigned to one of five treatments as follows: 1) 2.7 g/kg of BW of molasses (NCTRL), 2) NCTRL + 182 mg/kg of BW of urea (U), 3) U + 58.4 mg/kg of BW of BSS (UB), 4) NCTRL + 538 mg/kg of BW of eCAN (NIT), and 5) NIT + 58.4 mg/kg of BW of BSS (NITB). With the exception of NCTRL, all treatments were isonitrogenous. Beginning on day 14 of each period, ruminal fluid was collected and rectal temperature was recorded 4× per day for 3 d to determine ruminal changes every 2 h from 0 to 22 h post-feeding. Ruminal gas cap samples were collected at 0, 3, 6, 9, and 12 h on day 0 of each period followed by 0 h on days 1, 2, 3, and 14. Microbial N flow was determined using Cr-Ethylenediaminetetraacetic acid, YbCl3, and indigestible neutral detergent fiber for liquid, small particle, and large particle phases, respectively. Data were analyzed using the MIXED procedure of SAS. Orthogonal contrasts were used to evaluate the effects of nonprotein nitrogen (NPN) inclusion, NPN source, BSS, and NPN source × BSS. There was no treatment effect (P > 0.05) on concentrations of H2S on day 0, 1, 2, or 14; however, on day 3, concentrations of H2S were reduced (P = 0.018) when NPN was provided. No effect of treatment (P = 0.864) occurred for ruminal pH. There was an effect of NPN source on total concentrations of VFA (P = 0.011), where a 6% reduction occurred when eCAN was provided. There were effects of NPN (P = 0.001) and NPN source (P = 0.009) on the concentration of NH3-N, where cattle consuming NPN had a greater concentration than those not consuming NPN, and eCAN reduced the concentration compared with urea. Total concentrations of VFA and NH3-N were not affected (P > 0.05) by BSS. There was an effect of BSS (P = 0.009) on rectal temperature, where cattle not consuming BSS had greater temperatures than those receiving BSS. No differences for NPN, NPN source, nor BSS (P > 0.05) were observed for microbial N flow. In conclusion, eCAN does not appear to deliver equivalent ruminal fermentation parameters compared with urea, and BSS has limited effects on fermentation.

Effect of Aging Time on Meat Quality of Longissimus Dorsi from Yunling Cattle: A New Hybrid Beef Cattle

Simple Summary

Beef is in great demand in many countries. Consumers are more inclined to buy beef with good tenderness, color, flavor, and healthy fatty acid composition. Beef that has been aged is often more suitable for cooking and processing. A research gap exists regarding the analysis of meat quality during the aging process in Yunling cattle, a new hybrid beef cattle bred by Chinese researchers. This study measured a set of indicators of Yunling beef and other two breeds as controls (Simmental cattle, an excellent beef cattle breed used around the world, and Wenshan cattle, a local beef cattle breed in southern China), including the pH, water loss rate, cooking loss, Warner-Bratzler shear force, myofibrillar fragmentation index, inosine 5′-monophosphate, color, and fatty acid profiles. In addition, some growth performance and carcass characteristics were determined. The results showed that the pH, water holding capacity, growth performance, and carcass traits of Yunling and Simmental cattle were basically the same and better, respectively, than those of Wenshan cattle. Aging time had no effect on beef fatty acid composition, with Yunling beef showing a healthier fatty acid profile versus the other two breeds. With increased aging time, the tenderness and color of Yunling beef became more suitable for cooking and sensory characteristics. Therefore, this study suggests that Yunling beef should be used for cooking and processing after aging.

Abstract

The beef aging process is essential for compliance with certain major requisites, such as sensory characteristics for cooking and meat processing. Meat quality analysis of Yunling cattle, a new hybrid beef cattle bred by Chinese researchers, during the aging process, represents a major research gap. To explore Yunling beef initially, indicators associated with meat quality during the aging process of Yunling, Simmental, and Wenshan cattle were measured. In addition, some important economic traits were detected in the three breeds, including growth performance and carcass characteristics. The results showed that the growth performance, carcass traits, pH, and water holding capacity of Yunling and Simmental cattle were basically the same and better, respectively, than those of Wenshan cattle. The proportions of individual fatty acids in Yunling beef were healthier than in the other two breeds. Aging time did not affect the fatty acid profiles of the beef (p > 0.05). The contents of certain fatty acids in the three beef types displayed some differences in terms of days of aging (p < 0.05). The tenderness and meat color were better in the Yunling beef as the aging time increased, indicating that Yunling beef aged for 7 days was more suitable for cooking, exhibiting better sensory characteristics. Thus, a 7-day short-term aging process is very effective in improving the quality of Yunling beef. Our study attempted to fill a gap in the Yunling beef quality analysis during aging, providing further evidence for Yunling beef improvement.

Microbial community successions and their dynamic functions during harmful cyanobacterial blooms in a freshwater lake

The current study reports the community succession of different toxin and non-toxin producing cyanobacteria at different stages of cyanobacterial harmful algal blooms (CyanoHABs) and their connectivity with nitrogen and phosphorus cycles in a freshwater lake using an ecogenomics framework. Comprehensive high throughput DNA sequencing, water quality parameter measurements, and functional gene expressions over temporal and spatial scales were employed. Among the cyanobacterial community, the lake was initially dominated by Cyanobium during the months of May, June, and early July, and later primarily by Aphanizomenon and Dolichospermum depicting functional redundancy. Finally, Planktothrix appeared in late August and then the dominance switched to Planktothrix in September. Microcystis aeruginosa and Microcystis panniformis; two species responsible for cyanotoxin production, were also present in August and September, but in significantly smaller relative abundance. MC-LR (0.06-1.32 µg/L) and MC-RR (0.01-0.26 µg/L) were two major types of cyanotoxins detected. The presence of MC-LR and MC-RR were significantly correlated with the Microcystis-related genes (16SMic/mcyA/mcyG) and their expressions (r = 0.33 to 0.8, p < 0.05). The metabolic analyses further linked the presence of different cyanobacterial groups with distinct functions. The nitrogen metabolisms detected a relatively higher abundance of nitrite/nitrate reductase in early summer, indicating significant denitrification activity and the activation of N-fixation in the blooms dominated by Aphanizomenon/Dolichospermum (community richness) during nutrient-limited conditions. The phosphorus and carbohydrate metabolisms detected a trend to initiate a nutrient starvation alert and store nutrients from early summer, while utilizing the stored polyphosphate and carbohydrate (PPX and F6PPK) during the extreme ortho-P scarcity period, mostly in August or September. Specifically, the abundance of Aphanizomenon and Dolichospermum was positively correlated with the nitrogen-fixing nif gene and (p < 0.001) and the PPX enzyme for the stored polyphosphate utilization (r = 0.77, p < 0.001). Interestingly, the lake experienced a longer N-fixing period (2-3 months) before non-fixing cyanobacteria (Planktothrix) dominated the entire lake in late summer. The Provo Bay site, which is known to be nutrient-rich historically, had early episodes of filamentous cyanobacteria blooms compared to the rest of the lake.

Brisket Disease Is Associated with Lower Volatile Fatty Acid Production and Altered Rumen Microbiome in Holstein Heifers

Simple Summary

Development of the dairy industry in the high-altitude plateau environment through incorporation of Holstein cows is complicated by the risk of brisket disease. While the physiological effects of brisket disease are well-studied, its effects on rumen function and microbial community composition are not. There are clear shifts in volatile fatty acids production and rumen microbial community composition in Holstein heifers suffering from brisket disease. Observed shifts reveal key genera associated with healthy and disease states and suggest that bovine brisket disease is associated with impaired rumen functioning. This work supports further understanding of the roles of key rumen taxa in bovine brisket disease, with particular focus on candidate rumen biomarkers in healthy animals that may be able to reduce economic losses for farmers.

Abstract

Brisket disease is heritable but is also associated with non-genetic risk factors and effects of the disease on the rumen microbiome are unknown. Ten Holstein heifers were exposed to the plateau environment for three months and divided into two groups according to the index of brisket disease, the mean pulmonary arterial pressure (mPAP): brisket disease group (BD, n = 5, mPAP > 63 mmHg) and healthy heifer group (HH, n = 5, mPAP < 41 mmHg). Rumen fluid was collected for analysis of the concentrations of volatile fatty acids (VFAs). Extracted DNA from rumen contents was analyzed using Illumina MiSeq 16S rRNA sequencing technology. The concentration of total VFA and alpha-diversity metrics were significantly lower in BD group (p < 0.05). Ruminococcus and Treponema were significantly decreased in BD heifers (p < 0.05). Correlation analysis indicated that 10 genera were related to the mPAP (p < 0.05). Genera of Anaerofustis, Campylobacter, and Catonella were negatively correlated with total VFA and acetic acid (R < −0.7, p < 0.05), while genera of Blautia, YRC22, Ruminococcus, and Treponema were positively related to total VFA and acetic acid (R > 0.7; p < 0.05). Our findings may be a useful biomarker in future brisket disease work.

Inhibition of methanogenesis by nitrate, with or without defaunation, in continuous culture

Within the rumen, nitrate can serve as an alternative sink for aqueous hydrogen [H₂(aq)] accumulating during fermentation, producing nitrite, which ideally is further reduced to ammonium but can accumulate under conditions not yet explained. Defaunation has also been associated with decreased methanogenesis in meta-analyses because protozoa contribute significantly to H₂ production. In the present study, we applied a 2 × 2 factorial treatment arrangement in a 4 × 4 Latin square design to dual-flow continuous culture fermentors (n = 4). Treatments were control without nitrate (-NO₃^-) versus with nitrate (+NO₃^-; 1.5% of diet dry matter), factorialized with normal protozoa (faunated, FAUN) versus defaunation (DEF) by decreasing the temperature moderately and changing filters over the first 4 d of incubation. We detected no main effects of DEF or interaction of faunation status with +NO₃^-. The main effect of +NO₃^- increased H₂(aq) by 11.0 µM (+117%) compared with -NO₃^-. The main effect of +NO₃^- also decreased daily CH₄ production by 8.17 mmol CH₄/d (31%) compared with -NO₃^-. Because there were no treatment effects on neutral detergent fiber digestibility, the main effect of +NO₃^- also decreased CH₄ production by 1.43 mmol of CH₄/g of neutral detergent fiber degraded compared with -NO₃^-. There were no effects of treatment on other nutrient digestibilities, N flow, or microbial N flow per gram of nutrient digested. The spike in H₂(aq) after feeding NO₃^- provides evidence that methanogenesis is inhibited by substrate access rather than concentration, regardless of defaunation, or by direct inhibition of NO₂^-. Methanogens were not decreased by defaunation, suggesting a compensatory increase in non-protozoa-associated methanogens or an insignificant contribution of protozoa-associated methanogens. Despite adaptive reduction of NO₃^- to NH₄⁺ and methane inhibition in continuous culture, practical considerations such as potential to depress dry matter intake and on-farm ration variability should be addressed before considering NO₃^- as an avenue for greater sustainability of greenhouse gas emissions in US dairy production.

Insights into Metatranscriptome, and CAZymes of Buffalo Rumen Supplemented with Blend of Essential Oils

The aim of this study was to investigate the rumen microbial diversity and functionality in buffaloes fed with a blend of essential oils (BEO) using LSD switch over design. The BEO consisting of blend of Trachyspermum copticum (Ajwain) oil, Cymbopogon citratus (lemon grass) oil and Syzygium aromaticum (clove bud) oleoresin mixed in equal proportion, was fed at the rate of 0, 0.75 and 1.5 ml/100 kg of body weight in 0 (control), 0.75 and 1.5 groups, respectively. The metatranscriptomic libraries of the rumen microbiome were represented by 7 domains, 84 phyla, 64 archeal genera and 663 bacterial genera with Bacteroidetes and Firmicutes constituting 80% of phyla abundance irrespective of feeding regime. Methanogenic archaea was represented by 22 phyla with Methanobrevibacter as the major genus. BEO feeding reduced the abundance of Methanococcus and Thermoplasma (P < 0.05) at all levels. The results revealed that the feeding of BEO shifted the archeal and bacterial population at very low magnitude. The study explored the vast diversity of buffalo rumen bacteria and archaea, and the diverse wealth of rumen enzymes (CAZymes), which revealed that a major part of CAZymes comes from the less known rumen microbes indicating alternative paths of fiber degradation along with the very well known ones.

A meta-analysis of the bovine gastrointestinal tract microbiota

The bovine gastrointestinal (GI) tract microbiota has important influences on animal health and production. Presently, a large number of studies have used high-throughput sequencing of the archaeal and bacteria 16S rRNA gene to characterize these microbiota under various experimental parameters. By aggregating publically available archaeal and bacterial 16S rRNA gene datasets from 52 studies we were able to determine taxa that are common to nearly all microbiota samples from the bovine GI tract as well as taxa that are strongly linked to either the rumen or feces. The methanogenic genera Methanobrevibacter and Methanosphaera were identified in nearly all fecal and rumen samples (> 99.1%), as were the bacterial genera Prevotella and Ruminococcus (≥ 92.9%). Bacterial genera such as Alistipes, Bacteroides, Clostridium, Faecalibacterium and Escherichia/Shigella were associated with feces and Fibrobacter, Prevotella, Ruminococcus and Succiniclasticum with the rumen. As expected, individual study strongly affected the bacterial community structure, however, fecal and rumen samples did appear separated from each other. This meta-analysis provides the first comparison of high-throughput sequencing 16S rRNA gene datasets generated from the bovine GI tract by multiple studies and may serve as a foundation for improving future microbial community research with cattle.

Encapsulated nitrate replacing soybean meal changes in vitro ruminal fermentation and methane production in diets differing in concentrate to forage ratio

The objective of this study was to evaluate the effects of using encapsulated nitrate product (ENP) replacing soybean meal in diets differing in concentrate to forage ratio on ruminal fermentation and methane production in vitro using a semi-automatic gas production technique. Eight treatments were used in a randomized complete design with a 2 × 4 factorial arrangement: two diet (20C:80F and 80C:20F concentrate to forage ratio) and four levels of ENP addition (0%, 1.5%, 3.0%, and 4.5% of DM) replacing soybean meal. There was a diet × ENP interaction (p = 0.02) for methane production. According to ENP addition, diets with 80C:20F showed more intense reduction on methane production that 20C:80F. A negative linear effect was observed for propionate production with ENP addition in diet with 80C:20F and to the relative abundance of methanogens Archaea, in both diet. The replacement of soybean meal by ENP in levels up to 3% of DM inhibited methane production due to a reduction in the methanogens community without affecting the organic matter degradability. However, ENP at 4.5% of DM level affected fiber degradability, abundance of cellulolytic bacteria, and propionic acid production, indicating that this level of inclusion is not recommended for ruminant production.

Immediate Effects of Ammonia Shock on Transcription and Composition of a Biogas Reactor Microbiome

The biotechnological process of biogas production from organic material is carried out by a diverse microbial community under anaerobic conditions. However, the complex and sensitive microbial network present in anaerobic degradation of organic material can be disturbed by increased ammonia concentration introduced into the system by protein-rich substrates and imbalanced feeding. Here, we report on a simulated increase of ammonia concentration in a fed batch lab-scale biogas reactor experiment. Two treatment conditions were used simulating total ammonia nitrogen concentrations of 4.9 and 8.0 g/L with four replicate reactors. Each reactor was monitored concerning methane generation and microbial composition using 16S rRNA gene amplicon sequencing, while the transcriptional activity of the overall process was investigated by metatranscriptomic analysis. This allowed investigating the response of the microbial community in terms of species composition and transcriptional activity to a rapid upshift to high ammonia conditions. Clostridia and Methanomicrobiales dominated the microbial community throughout the entire experiment under both experimental conditions, while Methanosarcinales were only present in minor abundance. Transcription analysis demonstrated clostridial dominance with respect to genes encoding for enzymes of the hydrolysis step (cellulase, EC 3.2.1.4) as well as dominance of key genes for enzymes of the methanogenic pathway (methyl-CoM reductase, EC 2.8.4.1; heterodisulfide reductase, EC 1.8.98.1). Upon ammonia shock, the selected marker genes showed significant changes in transcriptional activity. Cellulose hydrolysis as well as methanogenesis were significantly reduced at high ammonia concentrations as indicated by reduced transcription levels of the corresponding genes. Based on these experiments we concluded that, apart from the methanogenic archaea, hydrolytic cellulose-degrading microorganisms are negatively affected by high ammonia concentrations. Further, Acholeplasma and Erysipelotrichia showed lower abundance under increased ammonia concentrations and thus might serve as indicator species for an earlier detection in order to counteract against ammonia crises.

Dietary Bioactive Lipid Compounds Rich in Menthol Alter Interactions Among Members of Ruminal Microbiota in Sheep

This study aimed to investigate the effects of two practically relevant doses of menthol-rich plant bioactive lipid compounds (PBLC) on fermentation, microbial community composition, and their interactions in sheep rumen. Twenty-four growing Suffolk sheep were divided into three treatments and were fed hay ad libitum plus 600 g/d of concentrate containing no PBLC (Control) or PBLC at low dose (80 mg/d; PBLC-L) or high dose (160 mg/d; PBLC-H). After 4 weeks on the diets, samples of ruminal digesta were collected and analyzed for short-chain fatty acid (SCFA), ammonia, and microbiota; microbiota being analyzed in the solid and the liquid digesta fractions separately. Ruminal SCFA and ammonia concentrations were not affected by the PBLC treatments. The microbiota in the solid fraction was more diverse than that in the liquid fraction, and the relative abundance of most taxa differed between these two fractions. In the solid fraction, phylogenetic diversity increased linearly with increased PBLC doses, whereas evenness (lowest in PBLC-L) and Simpson diversity index (greatest in PBLC-H) changed quadratically. In the liquid fraction, however, the PBLC supplementation did not affect any of the microbial diversity measurements. Among phyla, Chloroflexi (highest in PBLC-L) and unclassified_bacteria (lowest in PBLC-L) were altered quadratically by PBLC. Lachnospiraceae, Bacteroidaceae (increased linearly), BS11 (increased in PBLC-L), Christensenellaceae (decreased in PBLC treatments), and Porphyromonadaceae (increased in PBLC treatments) were affected at the family level. Among genera, Butyrivibrio increased linearly in the solid fraction, YRC22 increased linearly in the liquid fraction, whereas Paludibacter increased and BF311 increased linearly with increasing doses of PBLC in both fractions. The PBLC treatments also lowered methanogens within the classes Thermoplasmata and Euryarchaeota. Correlation network analysis revealed positive and negative correlations among many microbial taxa. Differential network analysis showed that PBLC supplementation changed the correlation between some microbial taxa and SCFA. The majority of the predicted functional features were different between the solid and the liquid digesta fractions, whereas the PBLC treatments altered few of the predicted functional gene categories. Overall, dietary PBLC treatments had little influence on the ruminal fermentation and microbiota but affected the associations among some microbial taxa and SCFA.

Rumen bacterial community responses to DPA, EPA and DHA in cattle and sheep: A comparative in vitro study

The role of marine lipids as modulators of ruminal biohydrogenation of dietary unsaturated fatty acids may be explained by the effects of their n-3 polyunsaturated fatty acids (PUFA) on the bacterial community. However, the impact of individual PUFA has barely been examined, and it is uncertain which bacteria are truly involved in biohydrogenation. In addition, despite interspecies differences in rumen bacterial composition, we are not aware of any direct comparison of bovine and ovine responses to dietary PUFA. Therefore, rumen fluid from cannulated cattle and sheep were used as inocula to examine in vitro the effect of 20:5n-3 (EPA), 22:5n-3 (DPA), and 22:6n-3 (DHA) on the bacterial community. Amplicon 16 S rRNA sequencing suggested that EPA and DHA had a greater contribution to the action of marine lipids than DPA both in cattle and sheep. Certain effects were exclusive to each ruminant species, which underlines the complexity of rumen microbial responses to dietary fatty acids. Based on changes in bacterial abundance, Barnesiella, Prevotella, Paraprevotella, Hallela, Anaerovorax, Succiniclasticum, Ruminococcus and Ruminobacter may be involved in the ruminal response in biohydrogenation to the addition of marine lipids, but further research is necessary to confirm their actual role in ruminal lipid metabolism.

Age-based dynamic changes of phylogenetic composition and interaction networks of health pig gut microbiome feeding in a uniformed condition

Background

The gut microbiota impacts on a range of host biological processes, and the imbalances in its composition are associated with pathology. Though the understanding of contribution of the many factors, e.g. gender, diet and age, in the development of gut microbiota has been well established, the dynamic changes of the phylogenetic composition and the interaction networks along with the age remain unclear in pigs.

Results

Here we applied 16S ribosomal RNA gene sequencing, enterotype-like clustering (Classification of the gut microbiome into distinct types) and phylogenetic co-occurrence network to explore the dynamic changes of pig gut microbiome following the ages with a successive investigation at four ages in a cohort of 953 pigs. We found that Firmicutes and Bacteroidetes are two predominant phyla throughout the experimental period. The richness of gut microbiota was significantly increased from 25 to 240 days of age. Principal coordinates analysis showed a clear difference in the gut microbial community compositions between pre-weaning piglets and the pigs at the other three age groups. The gut microbiota of pre-weaning piglets was clearly classified into two enterotypes, which were dominated by Fusobacterium and p-75-a5, respectively. However, Prevotella and Treponema were the main drivers of the enterotypes for pigs at the age of 80, 120 and 240 days. Besides the piglets, even some adult pigs switched putative enterotypes between ages. We confirmed that the topological features of phylogenetic co-occurrence networks, including scale, stability and complexity were increased along with the age. The biological significance for modules in the network of piglets were mainly associated with the utilization of simple carbohydrate and lactose, whereas the sub-networks identified at the ages of 80, 120 and 240 days may be involved in the digestion of complex dietary polysaccharide. The modules related to the metabolism of protein and amino acids could be identified in the networks at 120 and 240 days. This dynamic change of the functional capacities of gut microbiome was further supported by functional prediction analysis.

Conclusions

The present study provided meaningful biological insights into the age-based dynamic shifts of ecological community of porcine gut microbiota.

Electronic supplementary material

The online version of this article (10.1186/s12917-019-1918-5) contains supplementary material, which is available to authorized users.

Potential roles of nitrate and live yeast culture in suppressing methane emission and influencing ruminal fermentation, digestibility, and milk production in lactating Jersey cows

Concern over the carbon footprint of the dairy industry has led to various dietary approaches to mitigate enteric CH₄ production. One approach is feeding the electron acceptor NO₃^-, thus outcompeting methanogens for aqueous H₂. We hypothesized that a live yeast culture (LYC; Saccharomyces cerevisiae from Yea-Sacc 1026, Alltech Inc., Nicholasville, KY) would stimulate the complete reduction of NO₃^- to NH₃ by selenomonads, thus decreasing the quantity of CH₄ emissions per unit of energy-corrected milk production while decreasing blood methemoglobin concentration resulting from the absorbed intermediate, NO₂^-. Twelve lactating Jersey cows (8 multiparous and noncannulated; 4 primiparous and ruminally cannulated) were used in a replicated 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments. Cattle were fed diets containing 1.5% NO₃^- (from calcium ammonium nitrate) or an isonitrogenous control diet (containing additional urea) and given a top-dress of ground corn without or with LYC, with the fourth week used for data collection. Noncannulated cows were spot measured for CH₄ emission by mouth using GreenFeed (C-Lock Inc., Rapid City, SD). The main effect of NO₃^- decreased CH₄ by 17% but decreased dry matter intake by 10% (from 19.8 to 17.8 kg/d) such that CH₄:dry matter intake numerically decreased by 8% and CH₄:milk net energy for lactation production was unaffected by treatment. Milk and milk fat production were not affected, but NO₃^- decreased milk protein from 758 to 689 g/d. Ruminal pH decreased more sharply after feeding for cows fed diets without NO₃^-. Acetate:propionate was greater for cows fed NO₃^-, particularly when combined with LYC (interaction effect). Blood methemoglobin was higher for cattle fed NO₃^- than for those fed the control diet but was low for both treatments (1.5 vs. 0.5%, respectively; only one measurement exceeded 5%), indicating minimal risk for NO₂^- accumulation at our feeding level of NO₃^-. Although neither apparent organic matter nor neutral detergent fiber digestibilities were affected, apparent N digestibility had an interaction for NO₃^- × LYC such that apparent N digestibility was numerically lowest for diets containing both NO₃^- and LYC compared with the other 3 diets. Under the conditions of this study, NO₃^- mitigated ruminal methanogenesis but also depressed dry matter intake and milk protein yield. Based on the fact that few interactions were detected, LYC had a minimal role in attenuating negative cow responses to NO₃^- supplementation.

Dietary Energy Level Promotes Rumen Microbial Protein Synthesis by Improving the Energy Productivity of the Ruminal Microbiome

Improving the yield of rumen microbial protein (MCP) has significant importance in the promotion of animal performance and the reduction of protein feed waste. The amount of energy supplied to rumen microorganisms is an important factor affecting the amount of protein nitrogen incorporated into rumen MCP. Substrate-level phosphorylation (SLP) and electron transport phosphorylation (ETP) are two major mechanisms of energy generation within microbial cells. However, the way that energy and protein levels in the diet impact the energy productivity of the ruminal microbiome and, thereafter, rumen MCP yields is not known yet. In present study, we have investigated, by animal experiments and metagenome shotgun sequencing, the effects of energy-rich and protein-rich diets on rumen MCP yields, as well as SLP-coupled and ETP-coupled energy productivity of the ruminal microbiome. We have found that an energy-rich diet induces a significant increase in rumen MCP yield, whereas a protein-rich diet has no significant impacts on it. Based on 10 reconstructed pathways related to the energy metabolism of the ruminal microbiome, we have determined that the energy-rich diet induces significant increases in the total abundance of SLP enzymes coupled to the nicotinamide adenine dinucleotide (NADH) oxidation in the glucose fermentation and F-type ATPase of the electron transporter chain, whereas the protein-rich diet has no significant impact in the abundance of these enzymes. At the species level, the energy-rich diet induces significant increases in the total abundance of 15 ETP-related genera and 40 genera that have SLP-coupled fermentation pathways, whereas the protein-rich diet has no significant impact on the total abundance of these genera. Our results suggest that an increase in dietary energy levels promotes rumen energy productivity and MCP yield by improving levels of ETP and SLP coupled to glucose fermentation in the ruminal microbiome. But, an increase in dietary protein level has no such effects.

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

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

Long-Term Encapsulated Nitrate Supplementation Modulates Rumen Microbial Diversity and Rumen Fermentation to Reduce Methane Emission in Grazing Steers

This study investigated the long-term effects (13 months) of encapsulated nitrate supplementation (ENS) on enteric methane emissions, rumen fermentation parameters, ruminal bacteria, and diversity of archaea in grazing beef cattle. We used a total of thirty-two Nellore steers (initial BW of 197 ± 15.3 kg), 12 of which were fitted with rumen cannulas. For 13 months, the animals were maintained in 12 paddocks and fed a concentrate of ground corn, soybean meals, mineral supplements, and urea (URS) or encapsulated nitrate (EN) containing 70 g of EN/100 kg of BW (corresponding to 47 g NO₃^-/100 kg BW). Encapsulated nitrate supplementation resulted in similar forage, supplement and total DMI values as URS (P > 0.05), but ENS tended to increase (+48 g/d; P = 0.055) average daily weight gain. Daily reductions in methane emissions (-9.54 g or 18.5%) were observed with ENS when expressed as g of CH₄/kg of forage dry matter intake (fDMI) (P = 0.037). Lower concentrations of NH₃-N and a higher ruminal pH were observed in ENS groups 6 h after supplementation (P < 0.05). Total VFA rumen concentration 6 h (P = 0.009) and 12 h after supplementation with EN resulted in lower acetate concentrations in the rumen (P = 0.041). Steers supplemented with EN had a greater ruminal abundance of Bacteroides, Barnesiella, Lactobacillus, Selenomonas, Veillonella, Succinimonas, Succinivibrio, and Duganella sp. (P < 0.05), but a lower abundance of Methanobrevibacter sp. (P = 0.007). Strong negative correlations were found between daily methane emissions and Proteobacteria, Erysipelotrichaceae, Prevotellaceae, and Roseburia, Kandleria, Selenomonas, Veillonella, and Succinivibrio sp. (P < 0.05) in the rumen of ENS steers. Encapsulated nitrate is a feed additive that persistently affects enteric methane emission in grazing steers, thereby decreasing Methanobrevibacter abundance in the rumen. In addition, ENS can promote fumarate-reducer and lactate-producer bacteria, thereby reducing acetate production during rumen fermentation.

Rumen microbial responses to supplemental nitrate. II. Potential interactions with live yeast culture on the prokaryotic community and methanogenesis in continuous culture

Nitrates have been fed to ruminants, including dairy cows, as an electron sink to mitigate CH₄ emissions. In the NO₃^- reduction process, NO₂^- can accumulate, which could directly inhibit methanogens and possibly other microbes in the rumen. Saccharomyces cerevisiae yeast was hypothesized to decrease NO₂^- through direct reduction or indirectly by stimulating the bacterium Selenomonas ruminantium, which is among the ruminal bacteria most well characterized to reduce both NO₃^- and NO₂^-. Ruminal fluid was incubated in continuous cultures fed diets without or with NaNO₃ (1.5% of diet dry matter; i.e., 1.09% NO₃^-) and without or with live yeast culture (LYC) fed at a recommended 0.010 g/d (scaled from cattle to fermentor intakes) in a 2 × 2 factorial arrangement of treatments. Treatments with LYC had increased NDF digestibility and acetate:propionate by increasing acetate molar proportion but tended to decrease total VFA production. The main effect of NO₃^- increased acetate:propionate by increasing acetate molar proportion; NO₃^- also decreased molar proportions of isobutyrate and butyrate. Both NO₃^- and LYC shifted bacterial community composition (based on relative sequence abundance of 16S rRNA genes). An interaction occurred such that NO₃^- decreased valerate molar proportion only when no LYC was added. Nitrate decreased daily CH₄ emissions by 29%. However, treatment × time interactions were present for both CH₄ and H₂ emission from the headspace; CH₄ was decreased by the main effect of NO₃^- until 6 h postfeeding, but NO₃^- and LYC decreased H₂ emission up to 4 h postfeeding. As expected, NO₃^- decreased methane emissions in continuous cultures; however, contrary to expectations, LYC did not attenuate NO₂^- accumulation.

Effects of nitrate supplementation and forage level on gas production, nitrogen balance and dry-matter degradation in sheep

The present study was conducted to evaluate the effect of nitrate supplementation on dry-matter (DM) degradation and ruminal fermentation parameters by using in vitro gas production and in situ technique. In vitro gas production and in situ DM degradation in the presence or absence of nitrate were recorded at all incubation times. At all incubation times, diets incubated with nitrate gave a significantly lower gas production than did the other diets, except at 2-h incubation. Ruminal DM degradation did not differ among the experimental treatments. Furthermore, at most incubation times, total volatile fatty acids in diets containing nitrate were lower than those in the other treatments. Nitrate supplementation considerably increased gas production from the insoluble fraction, whereas it decreased gas production from the quickly soluble fraction, and potential gas production. Moreover, in all incubations, there were significant correlations between gas production and in situ DM-degradation parameters. The control diet had the greatest retained nitrogen content, but the diets containing nitrate had the greatest faecal nitrogen. The results showed that nitrate addition resulted in a lower gas production and volatile fatty acid production in in vitro assay. It was concluded that considering the strong posetive relationship between the two methodologies, the degradability parameters can be predicted from obtained gas production.

Different dietary protein sources in low protein diets regulate colonic microbiota and barrier function in a piglet model

Protein fermentation has an adverse effect on colonic health; high-quality proteins and reducing the protein level (protein restriction) can effectively decrease the amount of proteins flowing into the colon for microbial protein fermentation.

A rapid shift to high-grain diet results in dynamic changes in rumen epimural microbiome in sheep

The rapid shift to high-grain (HG) diets in ruminants can affect the function of the rumen epithelium, but the dynamic changes in the composition of the epithelium-associated (epimural) bacterial community in sheep still needs further investigation. Twenty male lambs were randomly allocated to four groups (n = 5). Animals of the first group received hay diet and represented a control group (CON). Simultaneously, animals in the other three groups (HG groups) were rapidly shifted to an HG diet (60% concentrate)which continued for 7 (HG7), 14 (HG14) and 28 (HG28) days, correspondingly. Results showed that ruminal pH dramatically decreased due to the rapid shift to the HG diet (P <0.001), while, the concentrations of butyrate (P <0.001), lactate (P = 0.001), valerate (P = 0.008) and total volatile fatty acids (P = 0.001) increased. Diversity estimators showed a dramatic decrease after the shift without recovering as the HG feeding continued. The principal coordinates analysis showed that CON group clustered separately from all HG groups with the presence of significant difference only between HG7 and HG28 (P = 0.034). The non-parametric multivariate analysis (npmv R-package) deduced that the primary significant differences in phyla and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt)-predicted Kyoto Encyclopedia of Genes and Genomes (KEGGs) was attributed mainly to the diet composition (P <0.001, P = 0.001) compared to its application period (P = 0.140, 0.545) which showed a significant effect only on the genus (P = 0.001) and the operational taxonomic units (OTUs) level (P = 0.011). The Kruskal-Wallis test deduced that six phyla showed a significant effect due to the shift in diet composition. At the genus level, HG feeding altered the abundance of 12 taxa, four of which showed a significant variation due to the duration of the HG diet application. Similarly, we found that 21 OTUs showed significant variations due to the duration of the HG diet application. Furthermore, the genes abundance predicted by PICRUSt revealed that the HG feeding significantly affected seven metabolic pathways identified in the KEGG. Particularly, the abundance of gene families associated with carbohydrates metabolism were significantly higher in HG feeding groups (P = 0.027). Collectively, these results revealed that the rapid transition to an HG diet causes dramatic alterations in ruminal fermentation and the composition and function of ruminal epithelium-associated microbiome in sheep, while, the duration of the HG diet application causes drastic alterations to the abundance of some species.

Substrate-Induced Response in Biogas Process Performance and Microbial Community Relates Back to Inoculum Source

This study investigated whether biogas reactor performance, including microbial community development, in response to a change in substrate composition is influenced by initial inoculum source. For the study, reactors previously operated with the same grass–manure mixture for more than 120 days and started with two different inocula were used. These reactors initially showed great differences depending on inoculum source, but eventually showed similar performance and overall microbial community structure. At the start of the present experiment, the substrate was complemented with milled feed wheat, added all at once or divided into two portions. The starting hypothesis was that process performance depends on initial inoculum source and microbial diversity, and thus that reactor performance is influenced by the feeding regime. In response to the substrate change, all reactors showed increases and decreases in volumetric and specific methane production, respectively. However, specific methane yield and development of the microbial community showed differences related to the initial inoculum source, confirming the hypothesis. However, the different feeding regimes had only minor effects on process performance and overall community structure, but still induced differences in the cellulose-degrading community and in cellulose degradation.

Nitrate decreases ruminal methane production with slight changes to ruminal methanogen composition of nitrate-adapted steers

BACKGROUND

This study was conducted to examine effects of nitrate on ruminal methane production, methanogen abundance, and composition. Six rumen-fistulated Limousin×Jinnan steers were fed diets supplemented with either 0% (0NR), 1% (1NR), or 2% (2NR) nitrate (dry matter basis) regimens in succession. Rumen fluid was taken after two-week adaptation for evaluation of in vitro methane production, methanogen abundance, and composition measurements.

RESULTS

Results showed that nitrate significantly decreased in vitro ruminal methane production at 6 h, 12 h, and 24 h (P < 0.01; P < 0.01; P = 0.01). The 1NR and 2NR regimens numerically reduced the methanogen population by 4.47% and 25.82% respectively. However, there was no significant difference observed between treatments. The alpha and beta diversity of the methanogen community was not significantly changed by nitrate either. However, the relative abundance of the methanogen genera was greatly changed. Methanosphaera (P_L = 0.0033) and Methanimicrococcus (P_L = 0.0113) abundance increased linearly commensurate with increasing nitration levels, while Methanoplanus abundance was significantly decreased (P_L = 0.0013). The population of Methanoculleus, the least frequently identified genus in this study, exhibited quadratic growth from 0% to 2% when nitrate was added (P_Q = 0.0140).

CONCLUSIONS

Correlation analysis found that methane reduction was significantly related to Methanobrevibacter and Methanoplanus abundance, and negatively correlated with Methanosphaera and Methanimicrococcus abundance.

Effect of urea-supplemented diets on the ruminal bacterial and archaeal community composition of finishing bulls

In this study, we evaluated the effects of urea-supplemented diets on the ruminal bacterial and archaeal communities of finishing bulls using sequencing technology. Eighteen bulls were fed a total mixed ration based on maize silage and concentrate (40:60) and randomly allocated to one of three experimental diets: a basal diet with no urea (UC, 0%), a basal diet supplemented with low urea levels (UL, 0.8% dry matter (DM) basis), and a basal diet supplemented with high urea levels (UH, 2% DM basis). All treatments were iso-nitrogenous (14% crude protein, DM basis) and iso-metabolic energetic (ME = 11.3 MJ/kg, DM basis). After a 12-week feeding trial, DNA was isolated from ruminal samples and used for 16S rRNA gene amplicon sequencing. For bacteria, the most abundant phyla were Firmicutes (44.47%) and Bacteroidetes (41.83%), and the dominant genera were Prevotella (13.17%), Succiniclasticum (4.24%), Butyrivibrio (2.36%), and Ruminococcus (1.93%). Urea supplementation had no effect on most phyla (P > 0.05), while there was a decreasing tendency in phylum TM7 with increasing urea levels (P = 0.0914). Compared to UC, UH had lower abundance of genera Butyrivibrio and Coprococcus (P = 0.0092 and P = 0.0222, respectively). For archaea, the most abundant phylum was Euryarchaeota (99.81% of the sequence reads), and the most abundant genus was Methanobrevibacter (90.87% of the sequence reads). UH increased the abundance of genus Methanobrevibacter and Methanobacterium (P = 0.0299 and P = 0.0007, respectively) and decreased the abundance of vadinCA11 (P = 0.0151). These findings suggest that urea-supplemented diets were associated with a shift in archaeal biodiversity and changes in the bacterial community in the rumen.

The Structural and Functional Capacity of Ruminal and Cecal Microbiota in Growing Cattle Was Unaffected by Dietary Supplementation of Linseed Oil and Nitrate

Microorganisms in the digestive tract of ruminants differ in their functionality and ability to use feed constituents. While cecal microbiota play an important role in post-rumen fermentation of residual substrates undigested in the rumen, limited knowledge exists regarding its structure and function. In this trial we investigated the effect of dietary supplementation with linseed oil and nitrate on methane emissions and on the structure of ruminal and cecal microbiota of growing bulls. Animals were allocated to either a CTL (control) or LINNIT (CTL supplemented with 1.9% linseed and 1.0% nitrates) diet. Methane emissions were measured using the GreenFeed system. Microbial diversity was assessed using amplicon sequencing of microbial genomic DNA. Additionally, total RNA was extracted from ruminal contents and functional mcrA and mtt genes were targeted in amplicon sequencing approach to explore the diversity of functional gene expression in methanogens. LINNIT had no effect on methane yield (g/kg DMI) even though it decreased methane production by 9% (g/day; P < 0.05). Methanobrevibacter- and Methanomassiliicoccaceae-related OTUs were more abundant in cecum (72 and 24%) compared to rumen (60 and 11%) irrespective of the diet (P < 0.05). Feeding LINNIT reduced the relative abundance of Methanomassiliicoccaceae mcrA cDNA reads in the rumen. Principal component analysis revealed significant differences in taxonomic composition and abundance of bacterial communities between rumen and cecum. Treatment decreased the relative abundance of a few Ruminococcaceae genera, without affecting global bacterial community structure. Our research confirms a high level of heterogeneity in species composition of microbial consortia in the main gastrointestinal compartments where feed is fermented in ruminants. There was a parallel between the lack of effect of LINNIT on ruminal and cecal microbial community structure and functions on one side and methane emission changes on the other. These results suggest that the sequencing strategy used here to study microbial diversity and function accurately reflected the absence of effect on methane phenotypes in bulls treated with linseed plus nitrate.