The use of direct-fed microbials for mitigation of ruminant methane emissions: a review

Comparative effects of nisin and monensin supplementation on growth performance, rumen fermentation, nutrient digestion, and plasma metabolites of fattening Hu sheep

Introduction

This study was conducted to compare the effects of nisin (NIS) and ionophore antibiotic monensin (MON) on the growth performance, rumen fermentation, nutrient digestion and plasma metabolites of fattening Hu sheep.

Methods

Thirty-six male Hu sheep (23.5 ± 1.0 kg) were divided into two blocks based on BW (low BW and high BW). Sheep within each block were then allotted to 9 pens respectively (two sheep/pen). Pens within each block were randomly assigned to one of three dietary treatments: (1) basal diet (CON); (2) basal diet + 40 mg/kg DM of MON; (3) basal diet + 274.5 mg/kg DM of NIS. The study lasted 9 weeks, with the initial 2 weeks for adaptation and the subsequent 7 weeks for treatment.

Results

The results showed that both NIS and MON addition had no impacts on average daily gain (ADG), dry matter intake (DMI), and feed conservation rate (G:F) of sheep (p > 0.05). The digestibility of ether extract (EE) was lower in the MON-fed and NIS-fed sheep (p < 0.01) than in the CON group, whereas crude protein (CP) digestibility was higher in the MON-fed sheep compared to those fed NIS (p < 0.05). Both NIS and MON supplementation decreased acetate levels and acetate/propionate ratio in the rumen of Hu sheep (p < 0.05). Sheep fed MON exhibited higher total cholesterol concentrations (p < 0.05) compared to the CON and NIS groups. However, there were no significant differences in other plasma metabolites, including blood urea nitrogen (BUN), total bile acid, triglyceride, total protein, albumin, globulin, glucose, etc., among the three groups (p > 0.05).

Discussion

In conclusion, dietary addition of NIS and MON altered the rumen fermentation mode by reducing acetate levels, with no discernible effects on the growth performance of the fattening Hu sheep.

Microbiome and metabolome analyses of milk and feces from dairy cows with healthy, subclinical, and clinical mastitis

Mastitis is commonly recognized as a localized inflammatory udder disease induced by the infiltration of exogenous pathogens. In the present study, our objective was to discern fecal and milk variations in both microbiota composition and metabolite profiles among three distinct groups of cows: healthy cows, cows with subclinical mastitis and cows with clinical mastitis. The fecal microbial community of cows with clinical mastitis was significantly less rich and diverse than the one harbored by healthy cows. In parallel, mastitis caused a strong disturbance in milk microbiota. Metabolomic profiles showed that eleven and twenty-eight molecules exhibited significant differences among the three groups in feces and milk, respectively. Similarly, to microbiota profile, milk metabolome was affected by mastitis more extensively than fecal metabolome, with particular reference to amino acids and sugars. Pathway analysis revealed that amino acids metabolism and energy metabolism could be considered as the main pathways altered by mastitis. These findings underscore the notable distinctions of fecal and milk samples among groups, from microbiome and metabolomic points of view. This observation stands to enhance our comprehension of mastitis in dairy cows.

A meta-analysis of probiotic interventions to mitigate ruminal methane emissions in cattle: implications for sustainable livestock farming

In recent years, the significant impact of ruminants on methane emissions has garnered international attention. While dietary strategies have been implemented to solve this issue, probiotics gained the attention of researchers due to their sustainability. However, it is challenging to ascertain their effectiveness as an extensive range of strains and doses have been reported in the literature. Hence, the objective of this experiment was to perform a meta-analysis of probiotic interventions aiming to reduce ruminal methane emissions from cattle. From 362 articles retrieved from scientific databases, 85 articles were assessed independently by two reviewers, and 20 articles representing 49 comparisons were found eligible for meta-analysis. In each study, data such as mean, SD, and sample sizes of both the control and probiotic intervention groups were extracted. The outcomes of interest were methane emission, methane yield, and methane intensity. For the meta-analysis, effect sizes were pooled using a fixed effect or a random effect model depending on the heterogeneity. Afterward, sensitivity analyses were conducted to confirm the robustness of the findings. Overall pooled standardized mean differences (SMDs) with their confidence intervals (CIs) did not detect significant differences in methane emission (SMD = -0.04; 95% CI = -0.18-0.11; P = 0.632), methane yield (SMD = -0.08; 95% CI = -0.24-0.07; P = 0.291), and methane intensity (SMD = -0.22; 95% CI = -0.50-0.07; P = 0.129) between cattle supplemented with probiotics and the control group. However, subgroup analyses revealed that multiple-strain bacterial probiotics (SMD = -0.36; 95% CI = -0.62 to -0.11; P = 0.005), specifically the combination of bacteria involved in reductive acetogenesis and propionate production (SMD = -0.71; 95% CI = -1.04 to -0.36; P = 0.001), emerged as better interventions. Likewise, crossbreeds (SMD = -0.48; 95% CI = -0.78 to -0.18; P = 0.001) exhibited a more favorable response to the treatments. Furthermore, meta-regression demonstrated that longer periods of supplementation led to significant reductions in methane emissions (P = 0.001), yield (P = 0.032), and intensity (P = 0.012) effect sizes. Overall, the results of the current study suggest that cattle responses to probiotic interventions are highly dependent on the probiotic category. Therefore, extended trials performed with probiotics containing multiple bacterial strains are showing the most promising results. Ideally, further trials focusing on the use of probiotics to reduce ruminal methane in cattle should be conducted to complete the available literature.

Influence of BOVAMINE DEFEND Plus on growth performance, carcass characteristics, estimated dry matter digestibility, rumen fermentation characteristics, and immune function in finishing beef steers

One hundred and eighty crossbred beef steers (406.0 ± 2.2 kg) were used to determine the impact of a novel direct-fed microbial (DFM) on growth performance, carcass characteristics, rumen fermentation characteristics, and immune response in finishing beef cattle. Steers were blocked by body weight (BW) and randomly assigned, within block, to 1 of 2 treatments (3 replicates/treatment: 30 steers/replicate). Treatments included: (1) no DFM (control) and (2) DFM supplementation at 50 mg ∙ animal-1 ∙ d-1 (BOVAMINE DEFEND Plus). All steers were fed a high-concentrate finishing diet and individual feed intake was recorded daily via the GrowSafe system. BWs were collected every 28 d. On day 55, 10 steers per pen were injected with ovalbumin (OVA). Jugular blood samples were collected from each steer on days 0, 7, 14, and 21 post injection. On day 112, the same steers were injected again with OVA and intramuscularly with a pig red blood cell solution. Jugular blood samples were collected from each steer on days 0, 7, 14, and 21 post injection. On day 124, rumen fluid was collected from 3 steers per treatment and used to estimate in vitro rumen fermentation characteristics. Equal numbers of steers per treatment were transported to a commercial abattoir on days 145, 167, and 185 of the experiment, harvested, and carcass data were collected. Initial BW was similar across treatments. On days 28 and 55, steers receiving DFM had heavier BW (P < 0.01) compared to controls. The average daily gain was greater in DFM-supplemented steers from days 0 to 28 (P < 0.01) and days 0 to 55 (P < 0.01) of the experiment compared to controls. Overall dry matter intake (DMI) was greater (P < 0.04) and overall feed efficiency was similar in DFM-supplemented steers compared to controls. Dressing percentage (P < 0.02) was greater in steers receiving DFM compared to controls. Antibody titers to injected antigens were similar across treatments. However, red blood cell superoxide dismutase activity was greater (P < 0.05) in DFM-supplemented steers compared to controls. In vitro molar proportions of isobutyric and butyric acid were greater (P < 0.01) and dry matter (DM) digestibility tended (P < 0.07) to be greater in rumen fluid obtained from steers supplemented with DFM. These data suggest that BOVAMINE DEFEND Plus supplementation improves growth performance during the initial period of the finishing phase, increases overall DMI and dressing percentage, and may impact antioxidant status in beef cattle.

Supplementation with Astragalus Root Powder Promotes Rumen Microbiota Density and Metabolome Interactions in Lambs

The gut microbiota is highly symbiotic with the host, and the microbiota and its metabolites are essential for regulating host health and physiological functions. Astragalus, as a feed additive, can improve animal immunity. However, the effects of Astragalus root powder on the rumen microbiota and their metabolites in lambs are not apparent. In this study, thirty healthy Hu sheep lambs with similar body weights (17.42 ± 2.02 kg) were randomly selected for the feeding experiment. Lambs were fed diets supplemented with 0.3% Astragalus root powder, and the rumen microbiota density and metabolome were measured to determine the effects of Astragalus on the health of lambs in the rumen. The results showed that the relative abundance of Butyrivibrio fibrisolvens (Bf), Ruminococcus flavefaciens (Rf), Succiniclasticum (Su), and Prevotella (Pr) in the rumen was increased in the Astragalus group (p < 0.01), and metabolic profiling showed that the metabolites, such as L-lyrosine and L-leucine, were upregulated in the Astragalus group (p < 0.01). KEGG functional annotation revealed that upregulated metabolites were mainly enriched in the pathways of amino acid metabolism, lipid metabolism, fatty acid biosynthesis, and bile secretion in the Astragalus group, and downregulated metabolites were enriched in the pathways of methane metabolism and other pathways. Correlation analysis revealed that butyric acid was positively correlated with Roseburia and Blautia (p < 0.05) and negatively correlated with Desulfovibrio (p < 0.05). Thus, by analyzing the interactions of Astragalus root powder with the density of rumen microorganisms and their metabolites in lambs, it was shown that Astragalus root powder could improve the structure of rumen microbiota and their metabolites and then participate in the regulation of amino acid metabolism, lipid metabolism, immune metabolism, and other pathways to improve the efficiency of energy absorption of the lambs.

Recent Advances in Enteric Methane Mitigation and the Long Road to Sustainable Ruminant Production

Mitigation of methane emission, a potent greenhouse gas, is a worldwide priority to limit global warming. A substantial part of anthropogenic methane is emitted by the livestock sector, as methane is a normal product of ruminant digestion. We present the latest developments and challenges ahead of the main efficient mitigation strategies of enteric methane production in ruminants. Numerous mitigation strategies have been developed in the last decades, from dietary manipulation and breeding to targeting of methanogens, the microbes that produce methane. The most recent advances focus on specific inhibition of key enzymes involved in methanogenesis. But these inhibitors, although efficient, are not affordable and not adapted to the extensive farming systems prevalent in low- and middle-income countries. Effective global mitigation of methane emissions from livestock should be based not only on scientific progress but also on the feasibility and accessibility of mitigation strategies.

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

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

Supplementation of complex natural feed additive containing (C. militaris, probiotics and red ginseng by-product) on rumen-fermentation, growth performance and carcass characteristics in Korean native steers

This study evaluated the effects of a complex natural feed additive on rumen fermentation, carcass characteristics and growth performance in Korean-native steers. In this study, in vitro and in vivo experiment were conducted. Seven different levels of complex natural feed additive (CA) were added to the buffered rumen fluid using AnkomRF gas production system for 12, 24 and 48 h. All experimental data were analyzed by mixed procedure of SAS. Total gas production increased in the CA groups, with the highest response observed in the 0.06% group at 48 h of incubation (linear, p = 0.02; quadratic, p < 0.01). Regarding rumen fermentation parameters, the total volatile fatty acid (TVFA) tended to increase in all the CA groups (p = 0.07). The concentrations of butyrate, iso-butyrate, and iso-valerate significantly increased in all treatment groups (p < 0.05). In the in vivo experiment, 23 Korean-native steers were allocated to two groups: (1) Control and (2) Treatment; control +0.07% CA (DM basis), in a randomized complete-block design and blocked by body weight (ave. body weight = 641.96 kg ± 62.51 kg, p = 0.80) and feed intake (ave. feed intake = 13.96 kg ± 0.74 kg, p = 0.08) lasted for 252 days. Average daily gain decreased in the treatment group (p < 0.01). Backfat thickness significantly decreased in the CA group (p = 0.03), whereas meat color tended to increase (p = 0.07). In conclusion, in the in vitro experiment, the inclusion of complex natural feed additive decreased methane proportion and tended to increase TVFA production, but supplementation to Korean native steers decreased average daily gain and backfat thickness.

Effects of nisin on bacterial community and fermentation profiles, in vitro rumen fermentation, microbiota, and methane emission of alfalfa silage

BACKGROUND

Alfalfa (Medicago sativa L.) has been used widely in preparing silage. However, forage legumes are prone to contamination by spoilage bacteria during fermentation. Nisin has broad-spectrum antibacterial properties and has been applied as an inhibitor of rumen methane emissions. However, little research has been carried out on the application of nisin in silage. This study therefore aimed to investigate the impacts of different nisin concentrations on the bacterial community and fermentation dynamics, in vitro ruminal fermentation characteristics, microbiota, and methane emissions of alfalfa silage.

RESULTS

The detection limits of organic acid in nisin-treated silages were not reached in 0.09 g kg-1 nisin (0.09 level) from days 1 to 7 of ensiling. With increasing nisin concentrations, the silage dry matter increased linearly (P < 0.05), and dry matter loss decreased linearly (P < 0.05). Moreover, both the 0.06 g kg-1 nisin (0.06 level) and 0.09 level treatments increased the relative abundance of Pediococcus acidilactici during ensiling. Concurrently, as the nisin concentrations increased, ruminal methane production decreased linearly (P < 0.05), while the relative abundances of ruminal Succinivibrio, Fibrobacter succinogenes and Ruminobacter amylophilus increased linearly (P < 0.05). The populations of ruminal total bacteria, methanogens, protozoa, and fungi decreased linearly with increasing nisin concentrations (P < 0.05).

CONCLUSION

The addition of nisin delayed the fermentation process, preserved more nutrients in alfalfa silage, and promoted fermentation dominated by P. acidilactici in the late phase of ensiling. Moreover, nisin reduced in vitro rumen methane emissions without adverse effects on dry matter digestibility. © 2023 Society of Chemical Industry.

Review: Reducing enteric methane emissions improves energy metabolism in livestock: is the tenet right?

The production of enteric methane in the gastrointestinal tract of livestock is considered as an energy loss in the equations for estimating energy metabolism in feeding systems. Therefore, the spared energy resulting from specific inhibition of methane emissions should be re-equilibrated with other factors of the equation. And, it is commonly assumed that net energy from feeds increases, thus benefitting production functions, particularly in ruminants due to the important production of methane in the rumen. Notwithstanding, we confirm in this work that inhibition of emissions in ruminants does not transpose into consistent improvements in production. Theoretical calculations of energy flows using experimental data show that the expected improvement in net energy for production is small and difficult to detect under the prevailing, moderate inhibition of methane production (≈25%) obtained using feed additives inhibiting methanogenesis. Importantly, the calculation of energy partitioning using canonical models might not be adequate when methanogenesis is inhibited. There is a lack of information on various parameters that play a role in energy partitioning and that may be affected under provoked abatement of methane. The formula used to calculate heat production based on respiratory exchanges should be validated when methanogenesis is inhibited. Also, a better understanding is needed of the effects of inhibition on fermentation products, fermentation heat, and microbial biomass. Inhibition induces the accumulation of H2, the main substrate used to produce methane, that has no energetic value for the host, and it is not extensively used by the majority of rumen microbes. Currently, the fate of this excess of H2 and its consequences on the microbiota and the host are not well known. All this additional information will provide a better account of energy transactions in ruminants when enteric methanogenesis is inhibited. Based on the available information, it is concluded that the claim that enteric methane inhibition will translate into more feed-efficient animals is not warranted.

Effects of inoculating feruloyl esterase-producing Lactiplantibacillus plantarum A1 on ensiling characteristics, in vitro ruminal fermentation and microbiota of alfalfa silage

BACKGROUND

Ferulic acid esterase (FAE)-secreting Lactiplantibacillus plantarum A1 (Lp A1) is a promising silage inoculant due to the FAE's ability to alter the plant cell wall structure during ensiling, an action that is expected to improve forage digestibility. However, little is known regarding the impacts of Lp A1 on rumen microbiota. Our research assessed the influences of Lp A1 in comparison to a widely adopted commercial inoculant Lp MTD/1 on alfalfa's ensilage, in vitro rumen incubation and microbiota.

RESULTS

Samples of fresh and ensiled alfalfa treated with (either Lp A1 or Lp MTD/1) or without additives (as control; CON) and ensiled for 30, 60 and 90 d were used for fermentation quality, in vitro digestibility and batch culture study. Inoculants treated silage had lower (P < 0.001) pH, acetic acid concentration and dry matter (DM) loss, but higher (P = 0.001) lactic acid concentration than the CON during ensiling. Compared to the CON and Lp MTD/1, silage treated with Lp A1 had lower (P < 0.001) aNDF, ADF, ADL, hemicellulose, and cellulose contents and higher (P < 0.001) free ferulic acid concentration. Compared silage treated with Lp MTD/1, silage treated with Lp A1 had significantly (P < 0.01) improved ruminal gas production and digestibility, which were equivalent to those of fresh alfalfa. Real-time PCR analysis indicated that Lp A1 inoculation improved the relative abundances of rumen's total bacteria, fungi, Ruminococcus albus and Ruminococcus flavefaciens, while the relative abundance of methanogens was reduced by Lp MTD/1 compared with CON. Principal component analysis of rumen bacterial 16S rRNA gene amplicons showed a clear distinction between CON and inoculated treatments without noticeable distinction between Lp A1 and Lp MTD/1 treatments. Comparison analysis revealed differences in the relative abundance of some bacteria in different taxa between Lp A1 and Lp MTD/1 treatments. Silage treated with Lp A1 exhibited improved rumen fermentation characteristics due to the inoculant effects on the rumen microbial populations and bacterial community.

CONCLUSIONS

Our findings suggest that silage inoculation of the FAE-producing Lp A1 could be effective in improving silage quality and digestibility, and modulating the rumen fermentation to improve feed utilization.

The Effect of Direct-Fed Lactobacillus Species on Milk Production and Methane Emissions of Dairy Cows

Using direct-fed microbials to mitigate enteric methane emissions could be sustainable and acceptable to both consumers and producers. Forty lactating, multiparous, Holstein-Friesian cows were randomly allocated one of two treatments: (1) a base of ad libitum vetch (Vicia sativa) hay and 7.0 kg DM/d of a grain mix, or (2) the basal diet plus 10 mL of MYLO® (Terragen Biotech Pty Ltd., Coolum Beach, Queensland, Australia) delivering 4.17 × 108 cfu of Lactobacillus per mL. Neither feed intake (25.4 kg/d vs. 24.8 kg/d) nor milk yield (29.9 vs. 30.3 kg/d) were affected by treatment. Feed conversion efficiency was not affected by treatment when expressed on an energy-corrected milk basis (1.15 vs. 1.18 kg/kg DMI). Neither methane yield (31.6 vs. 31.1 g/kg DMI) nor methane intensity (27.1 vs. 25.2 g/kg energy corrected milk) were affected by treatments. While these results are contrary to our expectations and not significant, all were numerically in a favorable direction. Given there are reports that diet and dose rate may impact the size of any effect, we recommend a dose–response study be undertaken using a basal diet that is commonly used in pasture-based dairy systems.

Shift of Feeding Strategies from Grazing to Different Forage Feeds Reshapes the Rumen Microbiota To Improve the Ability of Tibetan Sheep (Ovis aries) To Adapt to the Cold Season

The dynamics of ruminant-rumen microbiome symbiosis associated with feeding strategies in the cold season were examined. Twelve pure-grazing adult Tibetan sheep (Ovis aries) (18 months old; body weight, 40 ± 0.23 kg) were transferred from natural pasture to two indoor feedlots and fed either a native-pasture diet (NPF group) or an oat hay diet (OHF group) (n = 6 per treatment), and then the flexibility of rumen microbiomes to adapt to these compositionally different feeding strategies was examined. Principal-coordinate analysis and similarity analysis indicated that the rumen bacterial composition correlated with altered feeding strategies. Microbial diversity was higher in the grazing group than in those fed with native pasture and an oat hay diet (P < 0.05). The dominant microbial phyla were Bacteroidetes and Firmicutes, and the core bacterial taxa comprised mostly (42.49% of shared operational taxonomic units [OTUs]) Ruminococcaceae (408 taxa), Lachnospiraceae (333 taxa), and Prevotellaceae (195 taxa), which were relatively stable across different treatments. Greater relative abundances of Tenericutes at the phylum level, Pseudomonadales at the order level, Mollicutes at the class level, and Pseudomonas at the genus level were observed in a grazing period than in the other two treatments (NPF and OHF) (P < 0.05). In the OHF group, due to the high nutritional quality of the forage, Tibetan sheep can produce high concentrations of short-chain fatty acids (SCFAs) and NH3-N by increasing the relative abundances of key bacteria in the rumen, such as Lentisphaerae, Negativicutes, Selenomonadales, Veillonellaceae, Ruminococcus 2, Quinella, Bacteroidales RF16 group, and Prevotella 1, to aid in nutrients degradation and energy utilization. The levels of beneficial bacteria were increased by the oat hay diet; these microbiotas are likely to help improve and maintain host health and metabolic ability in Tibetan sheep to adapt to cold environments. The rumen fermentation parameters were significantly influenced by feeding strategy in the cold season (P < 0.05). Overall, the results of this study demonstrate the strong effect of feeding strategies on the rumen microbiota of Tibetan sheep, which provided a new idea for the nutrition regulation of Tibetan sheep grazing in the cold season on the Qinghai-Tibetan Plateau. IMPORTANCE During the cold season, like other high-altitude mammals, Tibetan sheep have to adapt their physiological and nutritional strategies, as well as the structure and function of their rumen microbial community, to the seasonal variation of lower food availability and quality. This study focused on the changes and adaptability in the rumen microbiota of Tibetan sheep when they adapted from grazing to a high-efficiency feeding strategy during the cold season by analyzing the rumen microbiota of Tibetan sheep raised under the different management systems, and it shows the linkages among the rumen core and pan-bacteriomes, nutrient utilization, and rumen short-chain fatty acids. The findings from this study suggest that the feeding strategies potentially contribute to variations in the pan-rumen bacteriome, together with the core bacteriome. Fundamental knowledge on the rumen microbiomes and their roles in nutrient utilization furthers our understanding of how rumen microbial adaptation to harsh environments may function in hosts. The facts obtained from the present trial clarified the possible mechanisms of the positive effects of feeding strategy on nutrient utilization and rumen fermentation in harsh environments.

Metabolomic Analysis of Multiple Biological Specimens (Feces, Serum, and Urine) by 1H-NMR Spectroscopy from Dairy Cows with Clinical Mastitis

Due to huge economic losses to the dairy industry worldwide, mastitis can be considered as one of the most common diseases in dairy cows. This work aimed to study this disease by comparing multiple biological specimens (feces, serum, and urine) from individuals with or without clinical mastitis. This was performed by a single analytical platform, namely ¹H-NMR, through a multi-matrix strategy. Thanks to the high reproducibility of ¹H-NMR, we could characterize 120 molecules across dairy cow feces, serum, and urine. Among them, 23 molecules were in common across the three biofluids. By integrating the results of multi-matrix metabolomics, several pathways pertaining to energy metabolism and amino acid metabolism appeared to be affected by clinical mastitis. The present work wished to deepen the understanding of dairy cow mastitis in its clinical form. Simultaneous analysis of metabolome changes across several key biofluids could facilitate knowledge discovery and the reliable identification of potential biomarkers, which could be, in turn, used to shed light on the early diagnosis of dairy cow mastitis in its subclinical form.

Effect of supplementation with ruminal probiotics on growth performance, carcass characteristics, plasma metabolites, methane emissions, and the associated rumen microbiome changes in beef cattle

To evaluate the effect of supplementing beef cattle with a ruminal probiotic consisting of native rumen microbes (NRM; Chordicoccus furentiruminis, Prevotella albensis, and Succinivibrio dextrinosolvens) on methane (CH4) emissions, growth performance, carcass characteristics, and plasma metabolites, Angus × SimAngus-crossbred steers (n = 32; 8 per pen) and heifers (n = 48; 12 per pen) with an initial body weight (BW) of 353 ± 64 kg were used in randomized complete block design. Cattle were blocked by sex and BW and randomly assigned to 1 of 2 treatments (2 pens per treatment). Treatments consisted of diets offered for ad libitum intake with (NRM) or without (CON) the inclusion of the ruminal probiotic. Cattle were fed a growing diet for 49 d followed by a ground corn-based diet for 124 ± 27 d until reaching the targeted final BW (635 kg for steers and 590 kg for heifers). Methane emissions were estimated using the GreenFeed system (n = 12 per treatment) prior to trial commencement (baseline; period 1), and on three (2, 3, and 4), and two (5 and 6) different sampling periods throughout the growing and finishing stage, respectively. All data were analyzed using the PROC MIXED procedure of SAS. For CH4 production (g/d), there was a tendency for an NRM supplementation × period interaction (P = 0.07) where cattle-fed diets with NRM had lower production of methane in periods 3 and 4. Including NRM in the diet decreased CH4 yield (g/kg of dry matter intake (DMI)) by 20%. For CH4 emission intensity (g/kg of average daily gain (ADG)), an interaction (P < 0.01) of NRM supplementation × period occurred. In periods 2 and 3, cattle-fed diets with NRM inclusion had lower CH4 emission intensity than CON cattle. During the 84-d period when all cattle were still on the finishing diet, feeding NRM increased (P = 0.02) ADG and tended to increase (P = 0.10) DMI. At the end of the 84-d period, cattle-fed NRM tended to be heavier (P = 0.06) than CON cattle. Cattle supplemented with NRM required less (P = 0.04) days on feed to reach the targeted final BW. No differences (P ≤ 0.11) were detected for gain-to-feed ratio and carcass characteristics. Cattle-fed NRM had greater abundance of uncultured rumen bacteria that may improve rumen digestion when fed a high grain diet and potentially promote the reduction of enteric CH4 production. Results from this study suggest that daily administration of NRM may be a strategy to mitigate methanogenesis and improve the growth performance of beef cattle.

A newly developed bacteriocin like substance to replace monensin in diets of lactating ewes

The aim of the present experiment was to evaluate the effect of feeding a newly produced bacteriocin-like substance (BLS) as a replacement for monensin in the diets of lactating ewes. In Experiment 1, the effects of BLS or monensin at 0.5, 1, 1.5, and 2 g/kg diet on in vitro ruminal fermentation were compared. In Experiment 2, 30 multiparous Barki ewes were divided into three treatments in a complete randomized design for 90 days. The ewes were fed a basal diet without supplementation or supplemented with monensin or BLS at 0.5 g/kg DM diet. In Experiment 1, the highest levels of BLS and monensin decreased gas production, while all levels of additives linearly decreased methane production. In Experiment 2, BLS increased nutrient digestibility. Additives increased ruminal total and individual volatile fatty acids and decreased ruminal ammonia-N. The BLS increased serum albumin and decreased the concentrations of serum liver enzymes, while both additives increased serum glucose and decreased urea-N. Additives increased daily production of milk, while the BLS treatment increased the feed efficiency. It is concluded that dietary inclusion of BLS at 0.5 g/kg DM for lactating ewes is recommended to replace monensin.

Glucogenic and lipogenic diets affect in vitro ruminal microbiota and metabolites differently

This study was conducted to evaluate the effects of two glucogenic diets (C: ground corn and corn silage; S: steam-flaked corn and corn silage) and a lipogenic diet (L: sugar beet pulp and alfalfa silage) on the ruminal bacterial and archaeal structures, the metabolomic products, and gas production after 48 h in vitro fermentation with rumen fluid of dairy cows. Compared to the C and S diets, the L dietary treatment leaded to a lower dry matter digestibility (DMD), lower propionate production and ammonia-nitrogen concentration. The two glucogenic diets performed worse in controlling methane and lactic acid production compared to the L diet. The S diet produced the greatest cumulative gas volume at any time points during incubation compared to the C and L diet. The metabolomics analysis revealed that the lipid digestion especially the fatty acid metabolism was improved, but the amino acid digestion was weakened in the L treatment than in other treatments. Differences in rumen fermentation characteristics were associated with (or resulting from) changes in the relative abundance of bacterial and archaeal genera. The rumen fluid fermented with L diet had a significantly higher number of cellulolytic bacteria, including the genera of Ruminococcus, Butyrivibrio, Eubacterium, Lachnospira, unclassified Lachnospiraceae, and unclassified Ruminococcaceae. The relative abundances of amylolytic bacteria genera including Selenomonas_1, Ruminobacter, and Succinivibrionaceae_UCG-002 were higher in samples for diets C and S. The results indicated that the two glucogenic diets leaded to a higher relative abundance of bacteria which functions in succinate pathway resulting in a higher propionate production. The steam-flaked corn diet had a higher gas production and lower level of metabolites in fatty acids and amino acids. Most highly abundant bacteria were observed to be not sensitive to dietary alterations of starch and fiber, except for several amylolytic bacteria and cellulolytic bacteria. These finding offered new insights on the digesting preference of ruminal bacteria, which can assist to improve the rumen functioning.

Management of Enteric Methane Emissions in Ruminants Using Feed Additives: A Review

In ruminants' metabolism, a surplus of hydrogen is removed from the reduction reaction of NAD⁺ (nicotinamide adenine dinucleotide) by the formation of methane by methanogenic bacteria and archaea methanogens. The balance of calculations between VFA (volatile fatty acids), CO₂, and CH₄ indicates that acetate and butyrate play a role in methane production, while the formation of propionate maintains hydrogen and therefore reduces methane production. CH₄ formation in ruminant livestock is not desired because it reduces feed efficiency and contributes to global warming. Therefore, numerous strategies have been investigated to mitigate methane production in ruminants. This review focuses on feed additives which have the capability of reducing methane emissions in ruminants. Due to the environmental importance of methane emissions, such studies are needed to make milk and meat production more sustainable. Additionally, the additives which have no adverse effects on rumen microbial population and where the reduction effects are a result of their hydrogen sink property, are the best reduction methods. Methane inhibitors have shown such a property in most cases. More work is needed to bring methane-reducing agents in ruminant diets to full market maturity, so that farmers can reap feed cost savings and simultaneously achieve environmental benefits.

Red seaweed extracts reduce methane production by altering rumen fermentation and microbial composition in vitro

A series of in vitro batch culture incubations were carried out to investigate changes in rumen fermentation characteristics, methane (CH4) production, and microbial composition in response to supplementation with five different red seaweed species (Amphiroa anceps, AANC; Asparagopsis taxiformis, ATAX; Chondracanthus tenellus, CTEN; Grateloupia elliptica, GELL; and Gracilaria parvispora, GPAR). Prior to the incubations, the total flavonoid and polyphenol content of the red seaweed extracts was quantified. The incubated substrate consisted of timothy hay and corn grain [60:40 dry matter (DM) basis]. Treatments were substrate mixtures without seaweed extract (CON) or substrate mixtures supplemented with 0.25 mg/mL of red seaweed extract. Samples were incubated for 6, 12, 24, 36, and 48 h. Each sample was incubated in triplicates in three separate runs. In vitro DM degradability, fermentation parameters (i.e., pH, volatile fatty acids, and ammonia nitrogen), total gas production, and CH4 production were analyzed for all time points. Microbial composition was analyzed using 16S rRNA amplicon sequencing after 24 h of incubation. The highest CH4 reduction (mL/g DM, mL/g digested DM, and % of total gas production) was observed in ATAX (51.3, 50.1, and 51.5%, respectively, compared to CON; P < 0.001) after 12 h of incubation. The other red seaweed extracts reduced the CH4 production (mL/g DM; P < 0.001) in the range of 4.6-35.0% compared to CON after 24 h of incubation. After 24 h of incubation, supplementation with red seaweed extracts tended to increase the molar proportion of propionate (P = 0.057) and decreased the acetate to propionate ratio (P = 0.033) compared to the CON. Abundances of the genus Methanobrevibacter and total methanogens were reduced (P = 0.050 and P = 0.016) by red seaweed extract supplementation. The linear discriminant analysis effect size (P < 0.05, LDA ≥ 2.0) showed that UG Succinivibrionaceae, Anaeroplasma, and UG Ruminococcaceae, which are associated with higher propionate production, starch degradation, and amylase activity were relatively more abundant in red seaweed extracts than in the CON. Our results suggest that supplementation with red seaweed extracts altered the microbiota, leading to the acceleration of propionate production and reduction in CH4 production.

Bacteria and Methanogens in the Human Microbiome: a Review of Syntrophic Interactions

Methanogens are microorganisms belonging to the Archaea domain and represent the primary source of biotic methane. Methanogens encode a series of enzymes which can convert secondary substrates into methane following three major methanogenesis pathways. Initially recognized as environmental microorganisms, methanogens have more recently been acknowledged as host-associated microorganisms after their detection and initial isolation in ruminants in the 1950s. Methanogens have also been co-detected with bacteria in various pathological situations, bringing their role as pathogens into question. Here, we review reported associations between methanogens and bacteria in physiological and pathological situations in order to understand the metabolic interactions explaining these associations. To do so, we describe the origin of the metabolites used for methanogenesis and highlight the central role of methanogens in the syntrophic process during carbon cycling. We then focus on the metabolic abilities of co-detected bacterial species described in the literature and infer from their genomes the probable mechanisms of their association with methanogens. The syntrophic interactions between bacteria and methanogens are paramount to gut homeostasis. Therefore, any dysbiosis affecting methanogens might impact human health. Thus, the monitoring of methanogens may be used as a bio-indicator of dysbiosis. Moreover, new therapeutic approaches can be developed based on their administration as probiotics. We thus insist on the importance of investigating methanogens in clinical microbiology.

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.

Hydrogen and formate production and utilisation in the rumen and the human colon

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

Metagenomics reveals differences in microbial composition and metabolic functions in the rumen of dairy cows with different residual feed intake

Background

Rumen microbial composition and functions have vital roles in feed digestion and fermentation and are linked to feed efficiency in cattle. This study selected Holstein cows, which are high in both milk protein content and milk yield, to analyse the relationship between the rumen microbiota and residual feed intake (RFI). Eighteen multiparous lactating cows were divided into low RFI (LRFI, high efficiency, n = 9) and high RFI (HRFI, low efficiency, n = 9) groups to investigate the differences in microbial composition and functions.

Results

The relative abundances of butyrate producers, including the Clostridium, Butyrivibrio, Eubacterium and Blautia genera, were higher in HRFI cows than in LRFI cows (P < 0.05). Four carbohydrate metabolic pathways (glycolysis/gluconeogenesis, pentose phosphate pathway, fructose and mannose metabolism, and butanoate metabolism) and one energy metabolism pathway (methane metabolism), were more abundant in HRFI animals (P < 0.05). Quorum sensing and DNA replication pathways were more abundant in HRFI cows. For CAZyme profiles, 14 out of 19 genes encoding carbohydrates-deconstructing enzymes were more abundant in HRFI cows (P < 0.05). Seven Lachnospiraceae species associated with carbohydrate metabolism and quorum sensing may contribute to the difference in feed efficiency. Moreover, the LRFI cows had lower abundances of Methanosphaera (P < 0.01), Methanobrevibacter ruminantium (P = 0.09) and methanogenesis functions (P = 0.04).

Conclusions

The rumen microbiota of low-efficiency cows has stronger abilities to degrade carbohydrates and produce methane, and quorum sensing pathways could also be associated with differences in feed efficiency. This study provides a deeper understanding of the microbial ecology of dairy cows with different feed efficiencies and highlights the possibility of modulating the rumen microbiome or microbial functions to improve the feed efficiency of dairy cows.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00170-3.

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.

Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan

The rumen contains a complex microbial ecosystem that degrades plant materials, such as cellulose and hemicellulose. We herein reconstructed 146 nonredundant, rumen-specific metagenome-assembled genomes (MAGs), with ≥50% completeness and <10% contamination, from cattle in Japan. The majority of MAGs were potentially novel strains, encoding various enzymes related to plant biomass degradation and volatile fatty acid production. The MAGs identified in the present study may be valuable resources to enhance the resolution of future taxonomical and functional studies based on metagenomes and metatranscriptomes.

Carryover effect of direct-fed microbial supplementation and early weaning on the growth performance and carcass characteristics of growing Najdi lambs

Growing Najdi lambs were randomly selected from lambs weaned at 30, 45, and 60 days old which were treated with 3 doses of direct-fed microbial (DFM) at 5, 10, and 15 days old to investigate the carryover effect of early weaning and DFM supplementation on their growth performance and carcass characteristics. Ten lambs from each group were transferred to individual pens for a feeding trial using the total mixed ration (Wafi). Lambs treated with DFM and weaned at 60 days old showed numerically higher body weight and average daily gains compared to other groups. Concerning the carcass and meat quality, there were significant differences between all groups in all carcass and tissue measurements, except for the back-fat and body wall thickness. In conclusion, treatment did not have any significant negative effect on body weight, feed intake, and conversion ratio compared with the control, but positively affected Zn and Cu absorption. DFM also played an important role in fat metabolism, which affects fat deposits in carcasses. The most important finding was that early weaning can be performed using DFM supplementation without any negative effect on the lambs’ performance during growth.

Application of Metabolomics in Diagnosis of Cow Mastitis: A Review

Cow mastitis, with high incidence rate and complex cause of disease, is one of the main diseases that affect the development of dairy industry in the world. Clinical mastitis and subclinical mastitis caused by Staphylococcus aureus, Escherichia coli, Streptococcus, and other pathogens have a huge potential safety hazard to food safety and the rapid development of animal husbandry. The economic loss caused by cow mastitis is billions of dollars every year in the world. In recent years, the omics technology has been widely used in animal husbandry with the continuous breakthrough of sequencing technology and the continuous reduction of sequencing cost. For dairy cow mastitis, the traditional diagnostic technique, such as histopathological screening, somatic cell count, milk pH test, milk conductivity test, enzyme activity test, and infrared thermography, are difficult to fully and comprehensively clarify its pathogenesis due to their own limitations. Metabolomics technology is an important part of system biology, which can simultaneously analyze all low molecular weight metabolites such as amino acids, lipids, carbohydrates under the action of complex factors including internal and external environment and in a specific physiological period accurately and efficiently, and then clarify the related metabolic pathways. Metabolomics, as the most downstream of gene expression, can amplify the small changes of gene and protein expression at the level of metabolites, which can more fully reflect the cell function. The application of metabolomics technology in cow mastitis can analyze the hetero metabolites, identify the related biomarkers, and reveal the physiological and pathological changes of cow mammary gland, so as to provide valuable reference for the prediction, diagnosis, and treatment of mastitis. The research progress of metabolomics technology in cow mastitis in recent years was reviewed, in order to provide guidance for the development of cow health and dairy industry safety in this manuscript.

Cattle, climate and complexity: food security, quality and sustainability of the Australian cattle industries

BACKGROUND

Marked increases in atmospheric CO₂ concentrations are largely associated with the release of sequestered carbon in fossil fuels. While emissions of green-house gasses (GHG) from cattle have significant global warming potential, these are biogenic sources and substantially involve carbon in natural cycles, rather than fossil fuel. Cattle use human inedible feeds and by-products of human food production to produce nutrient-dense foods of great value to humans.

INTERVENTIONS TO REDUCE GHG PRODUCTION

Reductions in land clearing and burning of grasslands and increased carbon sequestration in soils and trees have potential to substantially reduce GHG emissions. Increased efficiencies of production through intensified feeding and enteric modification have markedly reduced intensity of GHG emissions for cattle in Australia. Genetic selection for lower emissions has modest, but cumulative potential to reduce GHG (mostly CH₄ ) emissions and intensity. Improved reproductive performance can reduce intensity of GHG emissions, especially in beef production. Feeds and technologies that reduce GHG production and intensity include improved pastures, grain feeding, dietary lipids, nitrates, ionophores, seaweed, 3-NOP, hormonal growth promotants in beef, and improved diets for peri-parturient dairy cattle. There is considerable potential to further reduce emissions from cattle using the technologies reviewed.

INTERVENTIONS TO REDUCE HEAT STRESS

Cattle are susceptible to heat stress and ameliorating interventions include tree and shelter belts, shade, housing, cooling with fans and water and dietary manipulations.

CONCLUSIONS

Numerous interventions can reduce GHG emissions and intensity from cattle. There are opportunities to increase carbon capture and maintain biodiversity in Australia's extensive rangelands, but these require quantification and application. We can reduce the intensity of CH₄ emissions for cattle in Australia and simultaneously improve their well-being.

Research progress on the application of feed additives in ruminal methane emission reduction: a review

BACKGROUND

Ruminal methane (CH4) emissions from ruminants not only pollute the environment and exacerbate the greenhouse effect, but also cause animal energy losses and low production efficiency. Consequently, it is necessary to find ways of reducing methane emissions in ruminants. Studies have reported that feed additives such as nitrogen-containing compounds, probiotics, prebiotics, and plant extracts significantly reduce ruminant methane; however, systematic reviews of such studies are lacking. The present article summarizes research over the past five years on the effects of nitrogen-containing compounds, probiotics, probiotics, and plant extracts on methane emissions in ruminants. The paper could provide theoretical support and guide future research in animal production and global warming mitigation.

METHODS

This review uses the Web of Science database to search keywords related to ruminants and methane reduction in the past five years, and uses Sci-Hub, PubMed, etc. as auxiliary searchers. Read, filter, list, and summarize all the retrieved documents, and finally complete this article.

RESULTS

Most of the extracts can not only significantly reduce CH4 greenhouse gas emissions, but they will not cause negative effects on animal and human health either. Therefore, this article reviews the mechanisms of CH4 production in ruminants and the application and effects of N-containing compounds, probiotics, prebiotics, and plant extracts on CH4 emission reduction in ruminants based on published studies over the past 5 years.

CONCLUSION

Our review provides a theoretical basis for future research and the application of feed additives in ruminant CH4 emission reduction activities.

Influence of three microbial feed additives of Megasphaera elsdenii, Saccharomyces cerevisiae and Lactobacillus sp. on ruminal methane and carbon dioxide production, and biofermentation kinetics

AIMS

This study was performed to investigate the effects of Megasphaera elsdenii (Me), Saccharomyces cerevisiae (SC) and lactic acid bacteria (FP-Lactobacillus fermentum plus Lactobacillus plantarum) alone or in combination on biogas production and ruminal biofermentation parameter in a heterofermenter system.

METHODS AND RESULTS

Eight treatments were evaluated; (i) control (without additive; CON); (ii) Me; (iii) SC; (iv) FP; (v) Me plus SC (MSC); (vi) Me plus FP (MFP); (vii) SC plus FP (SCFP) and (viii) Me plus SC plus FP (MSCFP). Doses of FP, Me and SC were 1·5 × 10⁸ (CFU per ml), 1·5 × 10⁸ (CFU per ml) and 1·4 × 10⁷ (CFU 0·002^-1  g), respectively. Biogas production in all time increased (P < 0·05) by MSCFP than CON additive. The proportional methane (CH₄ ) decreased (P < 0·05) in MSCFP and FP, while carbon dioxide (CO₂ ) was decreased (P < 0·05) by SC compared MSCFP and MSC. The proportional CO₂ decreased (P < 0·05) by MSCFP and FP additive. The mean concentration of NH₃ -N was not affected by treatments. Concentration of total volatile fatty acids and the percent of acetate and propionate was not affected by treatments. The highest (P < 0·05) percent of butyrate and valerate were observed in MSCFP additive. The experiment showed that microbial additives of FP, SCFP and MSCFP reduced proportional CH₄ and CO₂ .

CONCLUSIONS

Microbial additives of MFP and MSCFP had a sustainable positive efficiency on pH and volatile fatty acids and mitigate CH₄ and CO₂ .

SIGNIFICANCE AND IMPACT OF THE STUDY

The use of microbial additives control on the ruminal pH (MFP) and improve VFA such as butyrate (MSC, MSCFP) and valerate (MSCFP) and reduce the greenhouse gases production showed a reduced risk of ruminal acidosis.

Effect of different glucogenic to lipogenic nutrient ratios on rumen fermentation and bacterial community in vitro

Aims

This study was to investigate the effect of different ratios of glucogenic to lipogenic nutrients on rumen fermentation and the corresponding ruminal bacterial communities.

Methods and Results

Four diets, including glucogenic diet (G), lipogenic diet (L), two mixed diets: GL1 (G: L = 2 : 1) and GL2 (G:L = 1 : 2), served as substrates and were incubated with rumen fluid in vitro. The results revealed that the gas production, dry matter digestibility and propionate proportion were significantly increased by the G diet than others. The G diet increased the bacterial genera of Succinivibrionaceae_UCG_002, Succinivibrio, Selenomonas_1 and Ruminobacter but decreased some cellulolytic bacteria including the Eubacterium and several genera in family Ruminococcaceae than others.

Conclusions

When the glucogenic nutrient was above 1/3 of the dietary energy source among the four diets, the in vitro incubation had a higher feed digestibility and lower acetate to propionate ratio. Bacterial genera, including Selenomonas, Succinivibrio, Ruminobacter, certain genera in Ruminococcaceae, Christensenellaceae_R‐7_group and Eubacterium, were more sensitive to the glucogenic to lipogenic nutrients ratio.

Significance and Impact of the Study

The present study provides a new perspective about the effect of dietary glucogenic to lipogenic ingredient ratios on rumen metabolism by comparing end‐products, gas production and bacterial composition via an in vitro technique.

Calcium salts of long-chain fatty acids from linseed oil decrease methane production by altering the rumen microbiome in vitro

Calcium salts of long-chain fatty acids (CSFA) from linseed oil have the potential to reduce methane (CH4) production from ruminants; however, there is little information on the effect of supplementary CSFA on rumen microbiome as well as CH4 production. The aim of the present study was to evaluate the effects of supplementary CSFA on ruminal fermentation, digestibility, CH4 production, and rumen microbiome in vitro. We compared five treatments: three CSFA concentrations-0% (CON), 2.25% (FAL) and 4.50% (FAH) on a dry matter (DM) basis-15 mM of fumarate (FUM), and 20 mg/kg DM of monensin (MON). The results showed that the proportions of propionate in FAL, FAH, FUM, and MON were increased, compared with CON (P < 0.05). Although DM and neutral detergent fiber expressed exclusive of residual ash (NDFom) digestibility decreased in FAL and FAH compared to those in CON (P < 0.05), DM digestibility-adjusted CH4 production in FAL and FAH was reduced by 38.2% and 63.0%, respectively, compared with that in CON (P < 0.05). The genera Ruminobacter, Succinivibrio, Succiniclasticum, Streptococcus, Selenomonas.1, and Megasphaera, which are related to propionate production, were increased (P < 0.05), while Methanobrevibacter and protozoa counts, which are associated with CH4 production, were decreased in FAH, compared with CON (P < 0.05). The results suggested that the inclusion of CSFA significantly changed the rumen microbiome, leading to the acceleration of propionate production and the reduction of CH4 production. In conclusion, although further in vivo study is needed to evaluate the reduction effect on rumen CH4 production, CSFA may be a promising candidate for reduction of CH4 emission from ruminants.

Effect of microbial feed additives on growth performance, microbial protein synthesis, and rumen microbial population in growing lambs

Arabi lambs (n =28; body weight = 24 ± 3.7 kg; average age = 120 ± 8 days) were used to investigate the effect of microbial additives on growth performance, microbial protein synthesis and rumen microbial population of fattening lamb based on completely randomized design. Four treatments were studied: (1) control (without additive; CON); (2) Lactobacillus fermentum and L. plantarum (FP); (3) Saccharomyces cerevisiae (SC) plus FP (SCFP); and (4) Megasphaera elsdenii plus SCFP (MSCFP). Lambs were inoculated before morning feeding (daily oral dosed) with a 50 mL microbial suspension as follows: FP, 50 mL bacterial suspension containing 4.5 × 10⁸ colony-forming unit per day (cfu/d) of L. plantarum and L. fermentum (in ratio 50:50); SCFP, 50 mL microbial suspension containing 4.5 × 10⁸ cfu/d FP and 1.4 × 10¹⁰ cfu/d SC; MSCFP, 50 mL microbial suspension containing 4.5 × 10⁸ cfu/d Me, 4.5 × 10⁸ cfu/d FP and 1.4 × 10¹⁰ cfu/d SC. Feed intake and body weight of lambs were not affected by microbial additives. Average daily gain and feed efficiency were increased on day 0 to 21. The highest concentration of uric acid, total excreted purine derivatives (PD), microbial N, microbial CP, and metabolizable protein were in MSCFP lambs. The ruminal population of Ruminococcus albus and Ruminococcus flavefaciens was higher in MSCFP and SCFP than CON and FP lambs. The highest and the lowest abundance of M. elsdenii and methanogen respectively was observed in lambs fed on microbial additives. The tendency to improve growth performance vs. CON may be due to improvements in microbial protein synthesis and microbial populations, especially fiber-degrading bacteria. The decrease in the population of methanogens as a result of the use of microbial additives is another positive result.

Anaerobic Fungi: Past, Present, and Future

Anaerobic fungi (AF) play an essential role in feed conversion due to their potent fiber degrading enzymes and invasive growth. Much has been learned about this unusual fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he characterized the first AF. Molecular approaches targeting specific phylogenetic marker genes have facilitated taxonomic classification of AF, which had been previously been complicated by the complex life cycles and associated morphologies. Although we now have a much better understanding of their diversity, it is believed that there are still numerous genera of AF that remain to be described in gut ecosystems. Recent marker-gene based studies have shown that fungal diversity in the herbivore gut is much like the bacterial population, driven by host phylogeny, host genetics and diet. Since AF are major contributors to the degradation of plant material ingested by the host animal, it is understandable that there has been great interest in exploring the enzymatic repertoire of these microorganisms in order to establish a better understanding of how AF, and their enzymes, can be used to improve host health and performance, while simultaneously reducing the ecological footprint of the livestock industry. A detailed understanding of AF and their interaction with other gut microbes as well as the host animal is essential, especially when production of affordable high-quality protein and other animal-based products needs to meet the demands of an increasing human population. Such a mechanistic understanding, leading to more sustainable livestock practices, will be possible with recently developed -omics technologies that have already provided first insights into the different contributions of the fungal and bacterial population in the rumen during plant cell wall hydrolysis.

Multi-omics reveals functional genomic and metabolic mechanisms of milk production and quality in dairy cows

MOTIVATION

Enhancing the utilization of human-inedible crop by-products by ruminants to produce high-quality milk for human consumption is an emerging global task. We performed a multi-omics-based study to decipher the regulatory biological processes of milk production when cows fed low-quality crop by-products with the aim to improve their utilization.

RESULTS

Seven types of different high-throughput omics data were generated across three central organs [rumen, liver and mammary gland (MG)] and biofluids (rumen fluid and blood) that involved in milk production. The integrated multi-omics analysis including metabolomics, metagenomics and transcriptomics showed altered microbiome at compositional and functional levels, microbial metabolites in the rumen, down-regulated genes and associated functions in liver and MG. These changes simultaneously contributed to down-regulated three key metabolic nodes (propionate, glucose and amino acid) across these organs and biofluids that led to lowered milk yield and quality when cows consumed corn stover (CS). Hippuric acid was identified as a biomarker that led to low milk production in CS-fed cows, suggesting a future evaluation parameter related to the metabolic mechanism of low-quality forage utilization. This study unveils the milk production-related biological mechanism across different biofluids and tissues under a low-quality forage diet, which provides a novel understanding and potential improvement strategies for future crop by-products utilization and sustainable ruminant production.

AVAILABILITY AND IMPLEMENTATION

The raw files of metagenomics, metabolomics, and transcriptomics data can be accessed at NCBI SRA (No. SRR5028206), EMBI-EBI (No. MTBLS411), and GEO (NO. GSE78524) databases respectively.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Inhibition of enteric methanogenesis in dairy cows induces changes in plasma metabolome highlighting metabolic shifts and potential markers of emission

There is scarce information on whether inhibition of rumen methanogenesis induces metabolic changes on the host ruminant. Understanding these possible changes is important for the acceptance of methane-reducing practices by producers. In this study we explored the changes in plasma profiles associated with the reduction of methane emissions. Plasma samples were collected from lactating primiparous Holstein cows fed the same diet with (Treated, n = 12) or without (Control, n = 13) an anti-methanogenic feed additive for six weeks. Daily methane emissions (CH₄, g/d) were reduced by 23% in the Treated group with no changes in milk production, feed intake, body weight, and biochemical indicators of health status. Plasma metabolome analyses were performed using untargeted [nuclear magnetic resonance (NMR) and liquid chromatography-mass spectrometry (LC–MS)] and targeted (LC–MS/MS) approaches. We identified 48 discriminant metabolites. Some metabolites mainly of microbial origin such as dimethylsulfone, formic acid and metabolites containing methylated groups like stachydrine, can be related to rumen methanogenesis and can potentially be used as markers. The other discriminant metabolites are produced by the host or have a mixed microbial-host origin. These metabolites, which increased in treated cows, belong to general pathways of amino acids and energy metabolism suggesting a systemic non-negative effect on the animal.

Effects of dietary replacement of soybean meal with dried distillers grains with solubles on the microbiota occupying different ecological niches in the rumen of growing Hu lambs

Background

Diet has a profound impact on the rumen microbiota, and the impact can vary among the different rumen ecological niches (REN). This study investigated the effects of dietary replacement of soybean meal (SBM) with dried distillers grains with solubles (DDGS) on the rumen microbiota occupying different REN of growing Hu lambs. After a 9-week feeding trial, 6 lambs from each dietary treatment (SBM vs. DDGS-based diets) were slaughtered for sample collection. The microbiota of the rumen solid, liquid, and epithelium fractions was examined using amplicon sequencing analysis of bacterial 16S rRNA gene, functional prediction, and qPCR.

Results

No interaction of dietary protein source (PS) and REN were detected for virtually all the measurements made in this study. The DDGS substitution resulted in very limited influence on bacterial community structure. However, the metabolic pathways predicted from 16S rRNA gene sequences varied greatly between SBM- and DDGS-based diets. The populations of rumen total bacteria, fungi, sulfate-reducing bacteria (SRB), and methanogens were not influenced by DDGS substitution, but the population of protozoa was reduced. The bacterial communities in rumen solid (RS) and liquid (RL) were similar in taxonomic composition but were different in relative abundance of some taxa. In contrast, the bacterial composition and relative abundance of rumen epithelium (RE) were greatly distinct from those of the RS and the RL. In alignment with the bacterial relative abundance, the metabolic pathways predicted from 16S rRNA genes also varied greatly among the different REN. The populations of total bacteria, protozoa, and methanogens attached to the RE were smaller than those in the RS and RL, and the fungal population on the rumen epithelium was smaller than that in the RS but similar to that in the RL. On the contrary, the SRB population on the RE was greater than that in the RS and RL.

Conclusions

Substitution of SBM with DDGS had greater impact to the protozoa than to the other microbes, and the microbial community structure and functions at different REN are distinct and niche-adapted.

Changes in the host transcriptome and microbial metatranscriptome of the ileum of dairy calves subjected to artificial dosing of exogenous rumen contents

Development of a properly functioning gastrointestinal tract (GIT) at an early age is critical for the wellbeing and lifetime productivity of dairy cattle. The role of early microbial colonization on GIT development in neonatal cattle and the associated molecular changes remain largely unknown, particularly for the small intestine. In this study, we performed artificial dosing of exogenous rumen fluid during the early life of the calf, starting at birth through the weaning transition at 8 wk. Six calves were included in this study. At 8 wk of age, tissue from the ileum was collected and subjected to host transcriptome and microbial metatranscriptome analysis using RNA sequencing. A total of 333 genes showed significant differential expression (DE) (fold-change ≥2; adjusted P < 0.1, mean read-count ≥10) between the treated and control calves. Gene ontology analysis indicated that these DE genes are predominantly associated with processes related to the host immune response (P < 0.0001). Association analysis between the host gene expression and the microbial genus abundance identified 57 genes as having significant correlation with the ileum microbial genera (P < 0.0001). Of these, three genes showed significant association with six microbial genera: lysozyme 2 (LYZ2), fatty acid binding protein 5 (FABP5), and fucosyltransferase (FUT1). Specifically, the profound increase in expression of LYZ2 in treated calves suggests the initiation of antibacterial activity and innate response from the host. Despite the limitation of a relatively small sample size, this study sheds light on the potential impact of early introduction of microbes on the small intestine of calves.

Effects of Dietary Energy Levels on Rumen Fermentation, Microbial Diversity, and Feed Efficiency of Yaks (Bos grunniens)

The microbial community of the yak (Bos grunniens) rumen plays an important role in surviving the harsh Tibetan environment where seasonal dynamic changes in pasture cause nutrient supply imbalances, resulting in weight loss in yaks during the cold season. A better understanding of rumen microbiota under different feeding regimes is critical for exploiting the microbiota to enhance feed efficiency and growth performance. This study explored the impact of different dietary energy levels on feed efficiency, rumen fermentation, bacterial community, and abundance of volatile fatty acid (VFA) transporter transcripts in the rumen epithelium of yaks. Fifteen healthy castrated male yaks were divided into three groups and fed with low (YL), medium (YM), and high energy (YH) levels diet having different NEg of 5.5, 6.2, and 6.9 MJ/kg, respectively. The increase in feed efficiency was recorded with an increase in dietary energy levels. The increase in dietary energy levels decreased the pH and increased the concentrations of acetate, propionate, butyrate, and valerate in yak rumens. The increase in the mRNA abundance of VFA transporter genes (MCT1, DRA, PAT1, and AE2) in the rumen epithelium of yaks was recorded as dietary energy level increased. High relative abundances of Firmicutes and Bacteroidetes were recorded with the increase in dietary energy levels. Significant population shifts at the genus level were recorded among the three treatments. This study provides new insights into the dietary energy-derived variations in rumen microbial community.

Metabolic Hydrogen Flows in Rumen Fermentation: Principles and Possibilities of Interventions

Rumen fermentation affects ruminants productivity and the environmental impact of ruminant production. The release to the atmosphere of methane produced in the rumen is a loss of energy and a cause of climate change, and the profile of volatile fatty acids produced in the rumen affects the post-absorptive metabolism of the host animal. Rumen fermentation is shaped by intracellular and intercellular flows of metabolic hydrogen centered on the production, interspecies transfer, and incorporation of dihydrogen into competing pathways. Factors that affect the growth of methanogens and the rate of feed fermentation impact dihydrogen concentration in the rumen, which in turn controls the balance between pathways that produce and incorporate metabolic hydrogen, determining methane production and the profile of volatile fatty acids. A basic kinetic model of competition for dihydrogen is presented, and possibilities for intervention to redirect metabolic hydrogen from methanogenesis toward alternative useful electron sinks are discussed. The flows of metabolic hydrogen toward nutritionally beneficial sinks could be enhanced by adding to the rumen fermentation electron acceptors or direct fed microbials. It is proposed to screen hydrogenotrophs for dihydrogen thresholds and affinities, as well as identifying and studying microorganisms that produce and utilize intercellular electron carriers other than dihydrogen. These approaches can allow identifying potential microbial additives to compete with methanogens for metabolic hydrogen. The combination of adequate microbial additives or electron acceptors with inhibitors of methanogenesis can be effective approaches to decrease methane production and simultaneously redirect metabolic hydrogen toward end products of fermentation with a nutritional value for the host animal. The design of strategies to redirect metabolic hydrogen from methane to other sinks should be based on knowledge of the physicochemical control of rumen fermentation pathways. The application of new –omics techniques together with classical biochemistry methods and mechanistic modeling can lead to exciting developments in the understanding and manipulation of the flows of metabolic hydrogen in rumen fermentation.

Manipulating the rumen microbiome to address challenges facing Australasian dairy farming

As dairy production systems expand globally, there is an increasing need to reduce the impact of dairy wastes on the environment by decreasing urinary N output and reducing emissions of green-house gasses (GHG). An understanding of rumen microbiome composition can result in the development of strategies that reduce methane emissions and nitrogen leakage, ultimately lowering the impact of dairying on the environment, while improving animal productivity. The strongest driver of the composition of the rumen microbiome was found to be the diet of the host animal. Thus, dietary manipulation offers a viable solution to alter the microbiome to address present-day challenges faced by the dairy industry. In the present review, we discuss such strategies and provide insight into rumen microbiome changes that have resulted in reduced GHG emissions and improved animal productivity.