Metagenomic analysis of the rumen microbial community following inhibition of methane formation by a halogenated methane analog

Characteristics of rumen microbiota and Prevotella isolates found in high propionate and low methane-producing dairy cows

Ruminal methane production is the main sink for metabolic hydrogen generated during rumen fermentation, and is a major contributor to greenhouse gas (GHG) emission. Individual ruminants exhibit varying methane production efficiency; therefore, understanding the microbial characteristics of low-methane-emitting animals could offer opportunities for mitigating enteric methane. Here, we investigated the association between rumen fermentation and rumen microbiota, focusing on methane production, and elucidated the physiological characteristics of bacteria found in low methane-producing cows. Thirteen Holstein cows in the late lactation stage were fed a corn silage-based total mixed ration (TMR), and feed digestion, milk production, rumen fermentation products, methane production, and rumen microbial composition were examined. Cows were classified into two ruminal fermentation groups using Principal component analysis: low and high methane-producing cows (36.9 vs. 43.2 L/DMI digested) with different ruminal short chain fatty acid ratio [(C2+C4)/C3] (3.54 vs. 5.03) and dry matter (DM) digestibility (67.7% vs. 65.3%). However, there were no significant differences in dry matter intake (DMI) and milk production between both groups. Additionally, there were differences in the abundance of OTUs assigned to uncultured Prevotella sp., Succinivibrio, and other 12 bacterial phylotypes between both groups. Specifically, a previously uncultured novel Prevotella sp. with lactate-producing phenotype was detected, with higher abundance in low methane-producing cows. These findings provide evidence that Prevotella may be associated with low methane and high propionate production. However, further research is required to improve the understanding of microbial relationships and metabolic processes involved in the mitigation of enteric methane.

The application of omics technologies for understanding tropical plants-based bioactive compounds in ruminants: a review

Finding out how diet impacts health and metabolism while concentrating on the functional qualities and bioactive components of food is the crucial scientific objective of nutritional research. The complex relationship between metabolism and nutrition could be investigated with cutting-edge "omics" and bioinformatics techniques. This review paper provides an overview of the use of omics technologies in nutritional research, with a particular emphasis on the new applications of transcriptomics, proteomics, metabolomics, and genomes in functional and biological activity research on ruminant livestock and products in the tropical regions. A wealth of knowledge has been uncovered regarding the regulation and use of numerous physiological and pathological processes by gene, mRNA, protein, and metabolite expressions under various physiological situations and guidelines. In particular, the components of meat and milk were assessed using omics research utilizing the various methods of transcriptomics, proteomics, metabolomics, and genomes. The goal of this review is to use omics technologies-which have been steadily gaining popularity as technological tools-to develop new nutritional, genetic, and leadership strategies to improve animal products and their quality control. We also present an overview of the new applications of omics technologies in cattle production and employ nutriomics and foodomics technologies to investigate the microbes in the rumen ecology. Thus, the application of state-of-the-art omics technology may aid in our understanding of how species and/or breeds adapt, and the sustainability of tropical animal production, in the long run, is becoming increasingly important as a means of mitigating the consequences of climate change.

Review: Biological consequences of the inhibition of rumen methanogenesis

Decreasing enteric CH4 emissions from ruminants is important for containing global warming to 1.5 °C and avoid the worst consequences of climate change. However, the objective of mitigating enteric CH4 emissions is difficult to reconcile with the forecasted increase in production of ruminant meat and milk, unless CH4 production per animal and per kilogram of animal product are decreased substantially. Chemical compound 3-nitrooxypropanol and bromoform-containing red algae Asparagopsis are currently the most potent inhibitors of rumen methanogenesis, but their average efficacy would have to be increased to mitigate enteric CH4 emissions to contain global warming to 1.5 °C, if the demand for ruminant products increases as predicted. We propose that it may be possible to enhance the efficacy of inhibitors of methanogenesis through understanding the mechanisms that cause variation in their efficacy across studies. We also propose that a more thorough understanding of the effects of inhibiting methanogenesis on rumen and postabsorptive metabolism may help improve feed efficiency and cost-effectiveness as co-benefits of the methanogenesis inhibition intervention. For enhancing efficacy, we examine herein how different inhibitors of methanogenesis affect the composition of the rumen microbial community and discuss some mechanisms that may explain dissimilar sensitivities among methanogens to different types of inhibitors. For improving feed efficiency and cost-effectiveness, we discuss the consequences of inhibiting methanogenesis on rumen fermentation, and how changes in rumen fermentation can in turn affect postabsorptive metabolism and animal performance. The objectives of this review are to identify knowledge gaps of the consequences of inhibiting methanogenesis on rumen microbiology and rumen and postabsorptive metabolism, propose research to address those knowledge gaps and discuss the implications that this research can have for the efficacy and adoption of inhibitors of methanogenesis. Depending on its outcomes, research on the microbiological, biochemical, and metabolic consequences of the inhibition of rumen methanogenesis could help the adoption of feed additives inhibitors of methanogenesis to mitigate enteric CH4 emissions from ruminants to ameliorate climate change.

Dynamic changes of rumen microbiota and serum metabolome revealed increases in meat quality and growth performances of sheep fed bio-fermented rice straw

BACKGROUND

Providing high-quality roughage is crucial for improvement of ruminant production because it is an essential component of their feed. Our previous study showed that feeding bio-fermented rice straw (BF) improved the feed intake and weight gain of sheep. However, it remains unclear why feeding BF to sheep increased their feed intake and weight gain. Therefore, the purposes of this research were to investigate how the rumen microbiota and serum metabolome are dynamically changing after feeding BF, as well as how their changes influence the feed intake, digestibility, nutrient transport, meat quality and growth performances of sheep. Twelve growing Hu sheep were allocated into 3 groups: alfalfa hay fed group (AH: positive control), rice straw fed group (RS: negative control) and BF fed group (BF: treatment). Samples of rumen content, blood, rumen epithelium, muscle, feed offered and refusals were collected for the subsequent analysis.

RESULTS

Feeding BF changed the microbial community and rumen fermentation, particularly increasing (P < 0.05) relative abundance of Prevotella and propionate production, and decreasing (P < 0.05) enteric methane yield. The histomorphology (height, width, area and thickness) of rumen papillae and gene expression for carbohydrate transport (MCT1), tight junction (claudin-1, claudin-4), and cell proliferation (CDK4, Cyclin A2, Cyclin E1) were improved (P < 0.05) in sheep fed BF. Additionally, serum metabolome was also dynamically changed, which led to up-regulating (P < 0.05) the primary bile acid biosynthesis and biosynthesis of unsaturated fatty acid in sheep fed BF. As a result, the higher (P < 0.05) feed intake, digestibility, growth rate, feed efficiency, meat quality and mono-unsaturated fatty acid concentration in muscle, and the lower (P < 0.05) feed cost per kg of live weight were achieved by feeding BF.

CONCLUSIONS

Feeding BF improved the growth performances and meat quality of sheep and reduced their feed cost. Therefore, bio-fermentation of rice straw could be an innovative way for improving ruminant production with minimizing production costs.

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

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

- Invited Review - Understanding the functionality of the rumen microbiota: searching for better opportunities for rumen microbial manipulation

Rumen microbiota play a central role in the digestive process of ruminants. Their remarkable ability to break down complex plant fibers and proteins, converting them into essential organic compounds that provide animals with energy and nutrition. Research on rumen microbiota not only contributes to improving animal production performance and enhancing feed utilization efficiency but also holds the potential to reduce methane emissions and environmental impact. Nevertheless, studies on rumen microbiota face numerous challenges, including complexity, difficulties in cultivation, and obstacles in functional analysis. This review provides an overview of microbial species involved in the degradation of macromolecules, the fermentation processes, and methane production in the rumen, all based on cultivation methods. Additionally, the review introduces the applications, advantages, and limitations of emerging omics technologies such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics, in investigating the functionality of rumen microbiota. Finally, the article offers a forward-looking perspective on the new horizons and technologies in the field of rumen microbiota functional research. These emerging technologies, with continuous refinement and mutual complementation, have deepened our understanding of rumen microbiota functionality, thereby enabling effective manipulation of the rumen microbial community.

- Invited Review - The role of rumen microbiota in enteric methane mitigation for sustainable ruminant production

Ruminal methane production functions as the main sink for metabolic hydrogen generated through rumen fermentation and is recognized as a considerable source of greenhouse gas emissions. Methane production is a complex trait affected by dry matter intake, feed composition, rumen microbiota and their fermentation, lactation stage, host genetics, and environmental factors. Various mitigation approaches have been proposed. Because individual ruminants exhibit different methane conversion efficiencies, the microbial characteristics of low-methane-emitting animals can be essential for successful rumen manipulation and environment-friendly methane mitigation. Several bacterial species, including Sharpea, uncharacterized Succinivibrionaceae, and certain Prevotella phylotypes have been listed as key players in low-methane-emitting sheep and cows. The functional characteristics of the unclassified bacteria remain unclear, as they are yet to be cultured. Here, we review ruminal methane production and mitigation strategies, focusing on rumen fermentation and the functional role of rumen microbiota, and describe the phylogenetic and physiological characteristics of a novel Prevotella species recently isolated from low methane-emitting and high propionate-producing cows. This review may help to provide a better understanding of the ruminal digestion process and rumen function to identify holistic and environmentally friendly methane mitigation approaches for sustainable ruminant production.

Methane prediction equations including genera of rumen bacteria as predictor variables improve prediction accuracy

Methane (CH4) emissions from ruminants are of a significant environmental concern, necessitating accurate prediction for emission inventories. Existing models rely solely on dietary and host animal-related data, ignoring the predicting power of rumen microbiota, the source of CH4. To address this limitation, we developed novel CH4 prediction models incorporating rumen microbes as predictors, alongside animal- and feed-related predictors using four statistical/machine learning (ML) methods. These include random forest combined with boosting (RF-B), least absolute shrinkage and selection operator (LASSO), generalized linear mixed model with LASSO (glmmLasso), and smoothly clipped absolute deviation (SCAD) implemented on linear mixed models. With a sheep dataset (218 observations) of both animal data and rumen microbiota data (relative sequence abundance of 330 genera of rumen bacteria, archaea, protozoa, and fungi), we developed linear mixed models to predict CH4 production (g CH4/animal·d, ANIM-B models) and CH4 yield (g CH4/kg of dry matter intake, DMI-B models). We also developed models solely based on animal-related data. Prediction performance was evaluated 200 times with random data splits, while fitting performance was assessed without data splitting. The inclusion of microbial predictors improved the models, as indicated by decreased root mean square prediction error (RMSPE) and mean absolute error (MAE), and increased Lin's concordance correlation coefficient (CCC). Both glmmLasso and SCAD reduced the Akaike information criterion (AIC) and Bayesian information criterion (BIC) for both the ANIM-B and the DMI-B models, while the other two ML methods had mixed outcomes. By balancing prediction performance and fitting performance, we obtained one ANIM-B model (containing 10 genera of bacteria and 3 animal data) fitted using glmmLasso and one DMI-B model (5 genera of bacteria and 1 animal datum) fitted using SCAD. This study highlights the importance of incorporating rumen microbiota data in CH4 prediction models to enhance accuracy and robustness. Additionally, ML methods facilitate the selection of microbial predictors from high-dimensional metataxonomic data of the rumen microbiota without overfitting. Moreover, the identified microbial predictors can serve as biomarkers of CH4 emissions from sheep, providing valuable insights for future research and mitigation strategies.

Methane mitigation in ruminants with structural analogues and other chemical compounds targeting archaeal methanogenesis pathways

Ruminants are responsible for enteric methane production contributing significantly to the anthropogenic greenhouse gases in the atmosphere. Moreover, dietary energy is lost as methane gas without being available for animal use. Therefore, many mitigation strategies aiming at interventions at animals, diet, and microbiota have been explored by researchers. Specific chemical analogues targeting the enzymes of the methanogenic pathway appear to be more effective in specifically inhibiting the growth of methane-producing archaea without hampering another microbiome, particularly, cellulolytic microbiota. The targets of methanogenesis reactions that have been mainly investigated in ruminal fluid include methyl coenzyme M reductase (halogenated sulfonate and nitrooxy compounds), corrinoid enzymes (halogenated aliphatic compounds), formate dehydrogenase (nitro compounds, e.g., nitroethane and 2-nitroethanol), and deazaflavin (F420) (pterin and statin compounds). Many other potential metabolic reaction targets in methanogenic archaea have not been evaluated properly. The analogues are specifically effective inhibitors of methanogens, but their efficacy to lower methanogenesis over time reduces due to the metabolism of the compounds by other microbiota or the development of resistance mechanisms by methanogens. In this short review, methanogen populations inhabited in the rumen, methanogenesis pathways and methane analogues, and other chemical compounds specifically targeting the metabolic reactions in the pathways and methane production in ruminants have been discussed. Although many methane inhibitors have been evaluated in lowering methane emission in ruminants, advancement in unravelling the molecular mechanisms of specific methane inhibitors targeting the metabolic pathways in methanogens is very limited.

Tropical tree foliage supplementation in ruminants improves rumen fermentation and the bacterial profile and decreases methane production

The main of this study was to evaluate the effect of supplementation of tropical tree foliage in ruminant diets on the in vitro fermentation, bacterial population, volatile fatty acids (VFAs), and enteric CH4 production. Seven experimental diets were evaluated: a control treatment of Pennisetum purpureum (T7) and six treatments of P. purpureum supplemented (30%) with the foliage of Neomillspaughia emargiata (T1), Tabernaemontana amygdalifolia (T2), Caesalpinia gaumeri (T3), Piscidia piscipula (T4), Leucaena leucocephala (T5), and Havardia albicans (T6). The T2, T7, and T5 treatments had the highest (p < 0.05) digestibility of dry matter. Overall, supplementation increased (p < 0.05) the concentrations of propionic and butyric acid and decreased acetic acid. Methanogenic bacteria decreased (p < 0.05) in T1, T2, T5, and T6. Ruminococcus albus decreased in T1, T2, T3, and T5 and Selenomonas ruminiantum increased in T3. Fibrobacter succinogenes increased, except in T5. Methane production decreased (p < 0.05) in T1, T4, T5, and T6. The supplementation with Leucaena leucocephala, Tabernaemontana amygdalifolia, Neomillspaughia emargiata, Piscidia piscipula, Havardia albicans, and Caesalpinia gaumeri is a potential alternative nutritional strategy for ruminants that results in positive changes in VFAs profile, a decrease on CH4 production and methanogenic bacteria, and changes on fibrolytic and non-fibrolytic bacteria composition.HIGHLIGHTSTropical tree foliage supplementation increased propionic and butyric acid and decreased acetic acid concentrations.Fibrolytic, non-fibrolytic, and Methanogenic bacteria were selectively modulated with the supplementation of tropical tree foliage.The enteric methane (CH4) production decreased with the supplementation of tree foliage.The supplementation of Tabernaemontana amygdalifolia and Leucaena leucocephala had the highest digestibility and is a potential alternative nutritional strategy for ruminants.

Comparative analysis of rumen metagenome, metatranscriptome, fermentation and methane yield in cattle and buffaloes fed on the same diet

A study to compare the rumen microbial community composition, functional potential of the microbiota, methane (CH4) yield, and rumen fermentation was conducted in adult male cattle and buffaloes fed on the same diet. A total of 41 phyla, 169 orders, 374 families, and 1,376 microbial genera were identified in the study. Bacteroidetes and Firmicutes were the two most dominant bacterial phyla in both cattle and buffaloes. However, there was no difference in the abundance of Bacteroidetes and Firmicutes in the rumen metagenome of cattle and buffaloes. Based on the abundance, the Proteobacteria was the 3rd largest phylum in the metagenome, constituting 18-20% in both host species. Euryarchaeota was the most abundant phylum of the methanogens, whereas Methanobacteriales and Methanobrevibacter were the most abundant orders and genera in both species. The methanogen abundances were not different between the two host species. Like the metagenome, the difference between the compositional and functional abundances (metagenome vs. metatranscriptome) of the Bacteroidetes and Firmicutes was not significant, whereas the proteobacteria were functionally less active than their metagenomic composition. Contrary to the metagenome, the Euryarchaeota was the 3rd most functional phylum in the rumen and constituted ~15% of the metatranscriptome. Methanobacteriales were the most functional methanogens, accounting for more than 2/3rd of the total archaeal functionality. These results indicated that the methanogens from Euryarchaeota were functionally more active as compared to their compositional abundance. The CH4 yield (g/kg DMI), CH4 emission (g/kg DDM), dry matter (DM) intake, and rumen fermentation did not vary between the two host species. Overall, the study established a substantial difference between the compositional abundances and metabolic functionality of the rumen microbiota; however, feeding cattle and buffaloes on the same diet resulted in similar microbiota composition, metabolic functionality, and CH4 yield. Further studies are warranted to investigate the effect of different diets and environments on the composition and metabolic functionality of the rumen microbiota.

Rumen microbial degradation of bromoform from red seaweed (Asparagopsis taxiformis) and the impact on rumen fermentation and methanogenic archaea

BACKGROUND

The red macroalgae Asparagopsis is an effective methanogenesis inhibitor due to the presence of halogenated methane (CH4) analogues, primarily bromoform (CHBr3). This study aimed to investigate the degradation process of CHBr3 from A. taxiformis in the rumen and whether this process is diet-dependent. An in vitro batch culture system was used according to a 2 × 2 factorial design, assessing two A. taxiformis inclusion rates [0 (CTL) and 2% DM diet (AT)] and two diets [high-concentrate (HC) and high-forage diet (HF)]. Incubations lasted for 72 h and samples of headspace and fermentation liquid were taken at 0, 0.5, 1, 3, 6, 8, 12, 16, 24, 48 and 72 h to assess the pattern of degradation of CHBr3 into dibromomethane (CH2Br2) and fermentation parameters. Additionally, an in vitro experiment with pure cultures of seven methanogens strains (Methanobrevibacter smithii, Methanobrevibacter ruminantium, Methanosphaera stadtmanae, Methanosarcina barkeri, Methanobrevibacter millerae, Methanothermobacter wolfei and Methanobacterium mobile) was conducted to test the effects of increasing concentrations of CHBr3 (0.4, 2, 10 and 50 µmol/L).

RESULTS

The addition of AT significantly decreased CH4 production (P = 0.002) and the acetate:propionate ratio (P = 0.003) during a 72-h incubation. The concentrations of CHBr3 showed a rapid decrease with nearly 90% degraded within the first 3 h of incubation. On the contrary, CH2Br2 concentration quickly increased during the first 6 h and then gradually decreased towards the end of the incubation. Neither CHBr3 degradation nor CH2Br2 synthesis were affected by the type of diet used as substrate, suggesting that the fermentation rate is not a driving factor involved in CHBr3 degradation. The in vitro culture of methanogens showed a dose-response effect of CHBr3 by inhibiting the growth of M. smithii, M. ruminantium, M. stadtmanae, M. barkeri, M. millerae, M. wolfei, and M. mobile.

CONCLUSIONS

The present work demonstrated that CHBr3 from A. taxiformis is quickly degraded to CH2Br2 in the rumen and that the fermentation rate promoted by different diets is not a driving factor involved in CHBr3 degradation.

Effect of grape pomace supplement on growth performance, gastrointestinal microbiota, and methane production in Tan lambs

Grape pomace (GP), a by-product in wine production, is nutritious and can be used as a feed ingredient for ruminants; however, its role in shaping sheep gastrointestinal tract (GIT) microbiota is unclear. We conducted a controlled trial using a randomized block design with 10 Tan lambs fed a control diet (CD) and 10 Tan lambs fed a pelleted diet containing 8% GP (dry matter basis) for 46 days. Rumen, jejunum, cecum, and colon bacterial and archaeal composition were identified by 16S rRNA gene sequencing. Dry matter intake (DMI) was greater (p < 0.05) in the GP than CD group; however, there was no difference in average daily gain (ADG, p < 0.05) and feed conversion ratio (FCR, p < 0.05) between the two groups. The GP group had a greater abundance of Prevotella 1 and Prevotella 7 in the rumen; of Sharpe, Ruminococcaceae 2, and [Ruminococcus] gauvreauii group in the jejunum; of Ruminococcaceae UCG-014 and Romboutsia in the cecum, and Prevotella UCG-001 in the colon; but lesser Rikenellaceae RC9 gut group in the rumen and cecum, and Ruminococcaceae UCG-005 and Ruminococcaceae UCG-010 in the colon than the CD group. The pathways of carbohydrate metabolism, such as L-rhamnose degradation in the rumen, starch and glycogen degradation in the jejunum, galactose degradation in the cecum, and mixed acid fermentation and mannan degradation in the colon were up-graded; whereas, the pathways of tricarboxylic acid (TCA) cycle VIII, and pyruvate fermentation to acetone in the rumen and colon were down-graded with GP. The archaeal incomplete reductive TCA cycle was enriched in the rumen, jejunum, and colon; whereas, the methanogenesis from H2 and CO2, the cofactors of methanogenesis, including coenzyme M, coenzyme B, and factor 420 biosynthesis were decreased in the colon. The study concluded that a diet including GP at 8% DM did not affect ADG or FCR in Tan lambs. However, there were some potential benefits, such as enhancing propionate production by microbiota and pathways in the GIT, promoting B-vitamin production in the rumen, facilitating starch degradation and amino acid biosynthesis in the jejunum, and reducing methanogenesis in the colon.

Effects of rearing mode on gastro-intestinal microbiota and development, immunocompetence, sanitary status and growth performance of lambs from birth to two months of age

BACKGROUND

Artificial rearing system, commonly used in prolific sheep breeds, is associated to increased mortality and morbidity rates before weaning, which might be linked to perturbations in digestive tract maturation, including microbiota colonization. This study evaluated the effect of rearing mode (mothered or artificially reared) on the establishment of the rumen and intestinal microbiome of lambs from birth to weaning. We also measured immunological and zootechnical parameters to assess lambs' growth and health. GIT anatomy as well as rumen and intestinal epithelium gene expression were also analysed on weaned animals to assess possible long-term effects of the rearing practice.

RESULTS

Total VFA concentrations were higher in mothered lambs at 2 months of age, while artificially-reared lambs had lower average daily gain, a more degraded sanitary status and lower serum IgG concentration in the early growth phase. Metataxonomic analysis revealed higher richness of bacterial and eukaryote populations in mothered vs. artificially-reared lambs in both Rumen and Feces. Beta diversity analysis indicated an evolution of rumen and fecal bacterial communities in mothered lambs with age, not observed in artificially-reared lambs. Important functional microorganisms such as the cellulolytic bacterium Fibrobacter succinogenes and rumen protozoa did not establish correctly before weaning in artificially-reared lambs. Enterobacteriaceae and Escherichia coli were dominant in the fecal microbiota of mothered lambs, but main E. coli virulence genes were not found differential between the two groups, suggesting they are commensal bacteria which could exert a protective effect against pathogens. The fecal microbiota of artificially-reared lambs had a high proportion of lactic acid bacteria taxa. No difference was observed in mucosa gene expression in the two lamb groups after weaning.

CONCLUSIONS

The rearing mode influences gastrointestinal microbiota and health-associated parameters in offspring in early life: rumen maturation was impaired in artificially-reared lambs which also presented altered sanitary status and higher risk of gut dysbiosis. The first month of age is thus a critical period where the gastrointestinal tract environment and microbiota are particularly unstable and special care should be taken in the management of artificially fed newborn ruminants.

Invited review: Rumen modifiers in today's dairy rations

Our aim was to review feed additives that have a potential ruminal mechanism of action when fed to dairy cattle. We discuss how additives can influence ruminal fermentation stoichiometry through electron transfer mechanisms, particularly the production and usage of dihydrogen. Lactate accumulation should be avoided, especially when acidogenic conditions suppress ruminal neutral detergent fiber digestibility or lead to subclinical acidosis. Yeast products and other probiotics are purported to influence lactate uptake, but growing evidence also supports that yeast products influence expression of gut epithelial genes promoting barrier function and resulting inflammatory responses by the host to various stresses. We also have summarized methane-suppressing additives for potential usage in dairy rations. We focused on those with potential to decrease methane production without decreasing fiber digestibility or milk production. We identified some mitigating factors that need to be addressed more fully in future research. Growth factors such as branched-chain volatile fatty acids also are part of crucial cross-feeding among groups of microbes, particularly to optimize fiber digestibility in the rumen. Our developments of mechanisms of action for various rumen-active modifiers should help nutrition advisors anticipate when a benefit in field conditions is more likely.

Could propionate formation be used to reduce enteric methane emission in ruminants?

To meet the increasing demand for meat and milk, the livestock industry has to increase its production. Without improving its efficiency, increased livestock, especially ruminant animals, will worsen the environmental damage, mainly from enteric CH₄ emission. Enteric CH₄ emission from ruminants not only exacerbates the global greenhouse effect but also reduces feed energy efficiency for the animals. The rumen disposes of metabolic hydrogen ([H]) primarily through methanogenesis and propionate formation. Theoretically, redirecting [H] from methanogenesis to propionate formation to reduce CH₄ production could be a promising method for reducing greenhouse gas emission from ruminants, and may also increase animal productivity. However, the feasibility of such a shifting has never been synthetically discussed. Thus, the objectives of this review are to provide a brief overview of the biochemical pathways for disposal of H₂ in the rumen, to analyze current feeding strategies that potentially promote propionate formation and their effects on methanogenesis, and to deliberate the challenge and opportunity associated with propionate formation as a sink to store the [H] shifting from enteric CH₄ inhibition.

Long-Read Metagenomics and CAZyme Discovery

Microorganisms play a primary role in regulating biogeochemical cycles and are a valuable source of enzymes that have biotechnological applications, such as carbohydrate-active enzymes (CAZymes). However, the inability to culture the majority of microorganisms that exist in natural ecosystems restricts access to potentially novel bacteria and beneficial CAZymes. While commonplace molecular-based culture-independent methods such as metagenomics enable researchers to study microbial communities directly from environmental samples, recent progress in long-read sequencing technologies are advancing the field. We outline key methodological stages that are required as well as describe specific protocols that are currently used for long-read metagenomic projects dedicated to CAZyme discovery.

Prevotella: A Key Player in Ruminal Metabolism

Ruminants are foregut fermenters that have the remarkable ability of converting plant polymers that are indigestible to humans into assimilable comestibles like meat and milk, which are cornerstones of human nutrition. Ruminants establish a symbiotic relationship with their microbiome, and the latter is the workhorse of carbohydrate fermentation. On the other hand, during carbohydrate fermentation, synthesis of propionate sequesters H, thus reducing its availability for the ultimate production of methane (CH4) by methanogenic archaea. Biochemically, methane is the simplest alkane and represents a downturn in energetic efficiency in ruminants; environmentally, it constitutes a potent greenhouse gas that negatively affects climate change. Prevotella is a very versatile microbe capable of processing a wide range of proteins and polysaccharides, and one of its fermentation products is propionate, a trait that appears conspicuous in P. ruminicola strain 23. Since propionate, but not acetate or butyrate, constitutes an H sink, propionate-producing microbes have the potential to reduce methane production. Accordingly, numerous studies suggest that members of the genus Prevotella have the ability to divert the hydrogen flow in glycolysis away from methanogenesis and in favor of propionic acid production. Intended for a broad audience in microbiology, our review summarizes the biochemistry of carbohydrate fermentation and subsequently discusses the evidence supporting the essential role of Prevotella in lignocellulose processing and its association with reduced methane emissions. We hope this article will serve as an introduction to novice Prevotella researchers and as an update to others more conversant with the topic.

Yeast Products Mediated Ruminal Subenvironmental Microbiota, and Abnormal Metabolites and Digestive Enzymes Regulated Rumen Fermentation Function in Sheep

Yeast products (YP) are commonly used as rumen regulators, but their mechanisms of action are still unclear. Based on our previous studies, we questioned whether yeast products would have an impact on rumen solid-associated (SA) and liquid-associated (LA) microorganisms and alter rumen fermentation patterns. Thirty 3-month-old male sheep weighing 19.27 ± 0.45 kg were selected and randomized into three groups for 60 days: (1) basal diet group (CON group), (2) basal diet add 20 g YP per day (low YP, LYP group) and (3) basal diet add 40 g YP per day (high YP, HYP group). The results demonstrated that the addition of YP increased rumen cellulase activity, butyrate and total volatile fatty acid (TVFA) concentrations (p < 0.05), while it decreased rumen amylase activity and abnormal metabolites, such as lactate, lipopolysaccharides (LPS) and histamine (HIS) (p < 0.05). Metagenomic analysis of rumen microorganisms in three groups revealed that YP mainly influenced the microbial profiles of the SA system. YP increased the relative abundance of R. flavefaciens and decreased methanogens in the SA system (p < 0.05). With the addition of YP, the abundance of only a few lactate-producing bacteria increased in the SA system, including Streptococcus and Lactobacillus (p < 0.05). However, almost all lactate-utilizing bacteria increased in the LA system, including Megasphaera, Selenomonas, Fusobacterium and Veillonella (p < 0.05). In addition, YP increased the abundance of certain GHs family members, including GH43 and GH98 (p < 0.05), but decreased the abundance of some KEGG metabolic pathways involved in starch and sucrose metabolism, biosynthesis of antibiotics and purine metabolism, among others. In conclusion, the addition of YP to high-concentrate diets can change the abundance of major functional microbiota in the rumen, especially in the solid fraction, which in turn affects rumen fermentation patterns and improves rumen digestibility.

Garlic and Its Bioactive Compounds: Implications for Methane Emissions and Ruminant Nutrition

Methane (CH4) emission from enteric fermentation of ruminant livestock is a source of greenhouse gases (GHG) and has become a significant concern for global warming. Enteric methane emission is also associated with poor feed efficiency. Therefore, research has focused on identifying dietary mitigation strategies to decrease CH4 emissions from ruminants. In recent years, plant-derived bioactive compounds have been investigated for their potential to reduce CH4 emissions from ruminant livestock. The organosulphur compounds of garlic have been observed to decrease CH4 emission and increase propionate concentration in anaerobic fermentations (in vitro) and in the rumen (in vivo). However, the mode of action of CH4 reduction is not completely clear, and the response in vivo is inconsistent. It might be affected by variations in the concentration and effect of individual substances in garlic. The composition of the diet that is being fed to the animal may also contribute to these differences. This review provides a summary of the effect of garlic and its bioactive compounds on CH4 emissions by ruminants. Additionally, this review aims to provide insight into garlic and its bioactive compounds in terms of enteric CH4 mitigation efficacy, consistency in afficacy, possible mode of action, and safety deriving data from both in vivo and in vitro studies.

Effect of Sodium Nitrate and Cysteamine on In Vitro Ruminal Fermentation, Amino Acid Metabolism and Microbiota in Buffalo

Nitrate is used as a methane inhibitor while cysteamine is considered as a growth promoter in ruminants. The present study evaluated the effect of sodium nitrate and cysteamine on methane (CH4) production, rumen fermentation, amino acid (AA) metabolism, and rumen microbiota in a low protein diet. Four treatments containing a 0.5 g of substrate were supplemented with 1 mg/mL sodium nitrate (SN), 100 ppm cysteamine hydrochloride (CS), and a combination of SN 1 mg/mL and CS 100 ppm (CS+SN), and a control (no additive) were applied in a completely randomized design. Each treatment group had five replicates. Two experimental runs using in vitro batch culture technique were performed for two consecutive weeks. Total gas and CH4 production were measured in each fermentation bottle at 3, 6, 9, 12, 24, 48, and 72 h of incubation. The results showed that SN and CS+SN reduced the production of total gas and CH4, increased the rumen pH, acetate, acetate to propionate ratio (A/P), and microbial protein (MCP) contents (p < 0.05), but decreased other volatile fatty acids (VFA) and total VFA (p = 0.001). The CS had no effect on CH4 production and rumen fermentation parameters except for increasing A/P. The CSN increased the populations of total bacteria, fungi, and methanogens but decreased the diversity and richness of rumen microorganisms. In conclusion, CS+SN exhibited a positive effect on rumen fermentation by increasing the number of fiber degrading and hydrogen-utilizing bacteria, with a desirable impact on rumen fermentation while reducing total gas and CH4 production.

Effects of acetate, propionate, and pH on volatile fatty acid thermodynamics in continuous cultures of ruminal contents

To investigate the effects of acetate, propionate, and pH on thermodynamics of volatile fatty acids (VFA) in the rumen, a dual-flow continuous culture study was conducted to quantify production of major VFA, interconversions among the VFA, and H₂ and CH₄ emissions in a 4 × 4 Latin square design. The 4 treatments were (1) control: pH buffered to an average of 6.75; (2) control plus 20 mmol/d of infused acetate (InfAc); (3) control plus 7 mmol/d of infused propionate (InfPr); and (4) a 0.5-unit decline in pH elicited by adjustment of the buffer (LowpH). All fermentors were fed 40 g of a pelleted diet containing whole alfalfa pellets and concentrate mix pellets (50:50) once daily. After 7 d of treatment, sequential, continuous infusions of [2-¹³C] sodium acetate (3.5 mmol/d), [U-¹³C] sodium propionate (2.9 mmol/d), and [1-¹³C] sodium butyrate (0.22 mmol/d) were carried out from 12 h before feeding for 36 h. Filtered liquid effluent (4 mL) was sampled at 0, 2, 4, 6, 8, 12, 16, and 22 h after feeding, and assessed for VFA concentrations, with another filtered sample (20 mL) used to quantify aqueous concentrations of CH₄ and H₂. Headspace CH₄ and H₂ gases were monitored continuously. Ruminal microbes were isolated from the mixed effluent samples, and the microbial community structure was analyzed using the 16S rRNA amplicon sequencing technique. The digestibility of neutral detergent fiber, acid detergent fiber, and starch and microbial C sequestrated from VFA were not affected by treatments. The LowpH treatment increased net propionate production and decreased H₂ and CH₄ headspace emissions, primarily due to shifts in metabolic pathways of VFA formation, likely due to the observed changes in bacterial community structure. Significant interconversions occurred between acetate and butyrate, whereas interconversions of other VFA with propionate were relatively small. The InfAc and InfPr treatments increased net acetate and propionate production, respectively; however, interconversions among VFA were not affected by pH, acetate, or propionate treatments, suggesting that thermodynamics might not be a primary influencer of metabolic pathways used for VFA formation.

Methane Reduction Potential of Brown Seaweeds and Their Influence on Nutrient Degradation and Microbiota Composition in a Rumen Simulation Technique

This study aimed to investigate the effects of two brown Icelandic seaweed samples (Ascophyllum nodosum and Fucus vesiculosus) on in vitro methane production, nutrient degradation, and microbiota composition. A total mixed ration (TMR) was incubated alone as control or together with each seaweed at two inclusion levels (2.5 and 5.0% on a dry matter basis) in a long-term rumen simulation technique (Rusitec) experiment. The incubation period lasted 14 days, with 7 days of adaptation and sampling. The methane concentration of total gas produced was decreased at the 5% inclusion level of A. nodosum and F. vesiculosus by 8.9 and 3.6%, respectively (P < 0.001). The total gas production was reduced by all seaweeds, with a greater reduction for the 5% seaweed inclusion level (P < 0.001). Feed nutrient degradation and the production of volatile fatty acids and ammonia in the effluent were also reduced, mostly with a bigger effect for the 5% inclusion level of both seaweeds, indicating a reduced overall fermentation (all P ≤ 0.001). Microbiota composition was analyzed by sequencing 16S rRNA amplicons from the rumen content of the donor cows, fermenter liquid and effluent at days 7 and 13, and feed residues at day 13. Relative abundances of the most abundant methanogens varied between the rumen fluid used for the start of incubation and the samples taken at day 7, as well as between days 7 and 13 in both fermenter liquid and effluent (P < 0.05). According to the differential abundance analysis with q2-ALDEx2, in effluent and fermenter liquid samples, archaeal and bacterial amplicon sequence variants were separated into two groups (P < 0.05). One was more abundant in samples taken from the treatment without seaweed supplementation, while the other one prevailed in seaweed supplemented treatments. This group also showed a dose-dependent response to seaweed inclusion, with a greater number of differentially abundant members between a 5% inclusion level and unsupplemented samples than between a 2.5% inclusion level and TMR. Although supplementation of both seaweeds at a 5% inclusion level decreased methane concentration in the total gas due to the high iodine content in the seaweeds tested, the application of practical feeding should be done with caution.

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.

Dynamic Variations in Rumen Fermentation Characteristics and Bacterial Community Composition during In Vitro Fermentation

This study aimed to explore the dynamic variations of rumen fermentation characteristics and bacterial community composition during a 24 h in vitro fermentation. A total of twenty-three samples were collected from original rumen fluid (ORF, n = 3), fermentation at 12 h (R12, n = 10), and fermentation at 24 h (R24, n = 10). Results showed that gas production, concentrations of microbial crude protein, ammonia nitrogen, and individual volatile fatty acids (VFA), as well as total VFA and branched-chain VFA concentrations, were higher in R24 when compared with R12 (p < 0.05). However, no significant differences were observed in acetate to propionate ratio and fermentation efficiency between R12 and R24 (p > 0.05). Bacterial diversity analysis found that Shannon index and Simpson index were higher in R24 (p < 0.05), and obvious clusters were observed in rumen bacterial community between R12 and R24. Taxonomic analysis at the phylum level showed that the abundances of Proteobacteria and Fibrobacteres were higher in R12 than that in R24, and inverse results were observed in Bacteroidetes, Firmicutes, Cyanobacteria, Verrucomicrobia, Lentisphaerae, and Synergistetes abundances. Taxonomic analysis at the genus level revealed that the abundances of Rikenellaceae RC9 gut group, Succiniclasticum, Prevotellaceae UCG-003, Christensenellaceae R-7 group, Ruminococcaceae UCG-002, Veillonellaceae UCG-001, and Ruminococcaceae NK4A214 group were higher in R24, whereas higher abundances of Succinivibrionaceae UCG-002, Ruminobacter, and Fibrobacter, were found in R12. Correlation analysis revealed the negative associations between gas production and abundances of Proteobacteria, Succinivibrionaceae UCG-002, and Ruminobacter. Moreover, the abundances of Firmicutes, Rikenellaceae RC9 gut group, Christensenellaceae R-7 group, and Ruminococcaceae UCG-002 positively correlated with VFA production. These results indicate that both rumen fermentation characteristics and bacterial community composition were dynamic during in vitro fermentation, whereas the fermentation pattern, efficiency, and bacterial richness remained similar. This study provide insight into the dynamics of rumen fermentation characteristics and bacterial composition during in vitro fermentation. This study may also provide a reference for decision-making for the sampling time point when conducting an in vitro fermentation for bacterial community investigation.

Differences in the Composition of the Rumen Microbiota of Finishing Beef Cattle Divergently Ranked for Residual Methane Emissions

With the advent of high throughput technology, it is now feasible to study the complex relationship of the rumen microbiota with methanogenesis in large populations of ruminant livestock divergently ranked for enteric emissions. Recently, the residual methane emissions (RME) concept has been identified as the optimal phenotype for assessing the methanogenic potential of ruminant livestock due to the trait's independence from animal productivity but strong correlation with daily methane emissions. However, there is currently a dearth of data available on the bacterial and archaeal microbial communities residing in the rumens of animals divergently ranked for RME. Therefore, the objective of this study was to investigate the relationship between the rumen microbiota and RME in a population of finishing beef cattle. Methane emissions were estimated from individual animals using the GreenFeed Emissions Monitoring system for 21 days over a mean feed intake measurement period of 91 days. Residual methane emissions were calculated for 282 crossbred finishing beef cattle, following which a ∼30% difference in all expressions of methane emissions was observed between high and low RME ranked animals. Rumen fluid samples were successfully obtained from 268 animals during the final week of the methane measurement period using a trans-oesophageal sampling device. Rumen microbial DNA was extracted and subjected to 16S rRNA amplicon sequencing. Animals ranked as low RME had the highest relative abundances (P < 0.05) of lactic-acid-producing bacteria (Intestinibaculum, Sharpea, and Olsenella) and Selenomonas, and the lowest (P < 0.05) proportions of Pseudobutyrivibrio, Butyrivibrio, and Mogibacterium. Within the rumen methanogen community, an increased abundance (P < 0.05) of the genus Methanosphaera and Methanobrevibacter RO clade was observed in low RME animals. The relative abundances of both Intestinibaculum and Olsenella were negatively correlated (P < 0.05) with RME and positively correlated with ruminal propionate. A similar relationship was observed for the abundance of Methanosphaera and the Methanobrevibacter RO clade. Findings from this study highlight the ruminal abundance of bacterial genera associated with the synthesis of propionate via the acrylate pathway, as well as the methanogens Methanosphaera and members of the Methanobrevibacter RO clade as potential microbial biomarkers of the methanogenic potential of beef cattle.

The microbiome of the buffalo digestive tract

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

Synergistic effects of 3-nitrooxypropanol with fumarate in the regulation of propionate formation and methanogenesis in dairy cows in vitro

3-nitrooxypropanol (3-NOP) is effective in reducing ruminal methane emission in ruminants. But it also causes a drastic increase in hydrogen accumulation, resulting in a feed energy waste. Fumarate is a key precursor for propionate formation and plays an important role in rumen hydrogen metabolism. Therefore, this study examined the effects of 3-NOP combined with fumarate on volatile fatty acids, methanogenesis and microbial community structures in dairy cows in vitro . The in vitro culture experiment was performed using a 2 × 2 factorial design: two 3-NOP levels (0 or 2 mg/g DM) and two fumarate levels (0 or 100 mg/g DM), including 3 runs × 4 treatments × 4 replicates and 4 blanks only containing inoculum. Rumen fluid was collected from three lactating Holstein cows with permanent ruminal fistulas. The combination of 3-NOP and fumarate reduced methane emission by 11.48% without affecting dry matter degradebility. Propionate concentration increased and acetate/propionate ratio decreased significantly. In terms of bacteria, the combination of 3-NOP and fumarate reduced the abundance of Ruminococcus and Lachnospiraceae_NK3A20_group and increased the abundance of Prevotella and Succiniclasticum. For archaea, the combination of 3-NOP and fumarate significantly increased the abundance of Methanobrevibacter_sp._AbM4, while the abundance of OTU581 (belongs to strain uncultured_rumen_methanogen_g__Methanobrevibacter) was significantly decreased. These results indecated that the combination of 3-NOP with fumarate could alleviate the accumulation of hydrogen and enhance the inhibition of methanogenesis compared with 3-NOP only in dairy cows. IMPORTANCE The global problem of climate change and the greenhouse effect has become increasingly severe, and the abatement of greenhouse gases has received great attention from the international community. Methane produced by ruminants during digestion not only aggravates the greenhouse effect, but also causes a waste of feed energy. As a methane inhibitor, 3-nitrooxypropanol can effectively reduce methane emission from ruminants. However, when it inhibits methane emission, the emission of hydrogen increases sharply, resulting in the waste of feed resources. Fumarate is a propionic acid precursor, which can promote the metabolism of hydrogen to propionic acid in animals. Therefore, we studied the effects of the combined addition of 3-nitrooxypropanol and fumarate on methanogenesis, rumen fermentation and rumen flora. It is of great significance to inhibit methane emission from ruminants and slow down the greenhouse effect.

Alternative pathways for hydrogen sink originated from the ruminal fermentation of carbohydrates: Which microorganisms are involved in lowering methane emission?

Agriculture is responsible for a great share of the anthropogenic sources of greenhouse gases that, by warming the earth, threaten its biodiversity. Among greenhouse gas emissions, enteric CH4 from livestock is an important target to slow down climate changes. The CH4 is originated from rumen fermentation and its concentration is affected by several factors, including genetics and nutrition. Ruminants have an extraordinary symbiosis with microorganisms (bacteria, fungi, and protozoa) that ferment otherwise indigestible carbohydrates, from which they obtain energy to grow and continue actively producing, among other products, volatile fatty acids, CO2 and H2. Detrimental ruminal accumulation of H2 is avoided by methanogenesis carried out by Archaea methanogens. Importantly, methanogenesis is not the only H2 sink pathway. In fact, other bacteria can reduce substrates using metabolic hydrogen formed during carbohydrate fermentation, namely propionate production and reductive acetogenesis, thus lowering the CH4 produced. Although the complexity of rumen poses challenges to mitigate CH4 production, the emergence of sequencing techniques that allow the study of microbial communities, gene expression, and metabolome are largely contributing to unravel pathways and key players in the rumen. Indeed, it is now recognized that in vivo emissions of CH4 are correlated to microbial communities, and particularly with the abundance of methanogens, several bacterial groups, and  their genes. The goal of CH4 mitigation is to work in favor of the natural processes, without compromising rumen function, animal health, and productivity. Notwithstanding, the major challenge continues to be the feasibility and affordability of the proposed solutions.

Fleece rot and dermatophilosis (lumpy wool) in sheep: opportunities and challenges for new vaccines

During prolonged wetting of the fleece, proliferation of bacterial flora often dominated by Pseudomonas aeruginosa or Dermatophilus congolensis can induce dermatitis and fleece damage termed fleece rot and dermatophilosis respectively, which predispose sheep to blowfly strike. A large research effort in the 1980s and 1990s on vaccines to control fleece rot and dermatophilosis met with limited success. This review examines theoretical and technological advances in microbial ecology, pathogenesis, immunology, vaccine development and the characterisation of microbial virulence factors that create new opportunities for development of vaccines against these diseases. Genomic technologies have now created new opportunities for examining microbial dynamics and pathogen virulence in dermatitis. An effective vaccine requires the combination of appropriate antigens with an adjuvant that elicits a protective immune response that ideally provides long-lasting protection in the field. A clinical goal informed by epidemiological, economic and animal welfare values is needed as a measure of vaccine efficacy. Due to dependence of fleece rot and dermatophilosis on sporadic wet conditions for their expression, vaccine development would be expedited by in vitro correlates of immune protection. The efficacy of vaccines is influenced by genetic and phenotypic characteristics of the animal. Advances in understanding vaccine responsiveness, immune defence in skin and immune competence in sheep should also inform any renewed efforts to develop new fleece rot and dermatophilosis vaccines. The commercial imperatives for new vaccines are likely to continue to increase as the animal welfare expectations of society intensify and reliance on pharmacotherapeutics decrease due to chemical resistance, market pressures and societal influences. Vaccines should be considered part of an integrated disease control strategy, in combination with genetic selection for general immune competence and resistance to specific diseases, as well as management practices that minimise stress and opportunities for disease transmission. The strategy could help preserve the efficacy of pharmacotherapeutics as tactical interventions to alleviate compromised welfare when adverse environmental conditions lead to a break down in integrated strategic disease control. P. aeruginosa and D. congolensis are formidable pathogens and development of effective vaccines remains a substantial challenge.

Characterization of microbial communities from rumen and large intestine of lactating creole goats grazing in arid plant communities

Arid plant communities provide variable diets that can affect digestive microbial communities of free-foraging ruminants. Thus, we used next-generation sequencing of 16S and 18S rDNA to characterize microbial communities in the rumen (regurgitated digesta) and large intestine (faeces) and diet composition of lactating creole goats from five flocks grazing in native plant communities in the Sonoran Desert in the rainy season. The bacterial communities in the rumen and large intestine of the five flocks had similar alpha diversity (Chao1, Shannon, and Simpson indices). However, bacterial community compositions were different: a bacterial community dominated by Proteobacteria in the rumen transitioned to a community dominated by Firmicutes in the large intestine. Bacterial communities of rumen were similar across flocks; similarly occurred with large-intestine communities. Archaea had a minimum presence in the goat digestive tract. We detected phylum Basidiomycota, Ascomycota, and Apicomplexa as the main fungi and protozoa. Analyses suggested different diet compositions; forbs and grasses composed the bulk of plants in the rumen and forbs and shrubs in faeces. Therefore, lactating goats consuming different diets in the Sonoran Desert in the rainy season share a similar core bacterial community in the rumen and another in the large intestine and present low archaeal communities.

Using genome comparisons of wild-type and resistant mutants of Methanococcus maripaludis to help understand mechanisms of resistance to methane inhibitors

Methane emissions from enteric fermentation in the ruminant digestive system generated by methanogenic archaea are a significant contributor to anthropogenic greenhouse gas emissions. Additionally, methane produced as an end-product of enteric fermentation is an energy loss from digested feed. To control the methane emissions from ruminants, extensive research in the last decades has been focused on developing viable enteric methane mitigation practices, particularly, using methanogen-specific inhibitors. We report here the utilization of two known inhibitors of methanogenic archaea, neomycin and chloroform, together with a recently identified inhibitor, echinomycin, to produce resistant mutants of Methanococcus maripaludis S2 and S0001. Whole-genome sequencing at high coverage (> 100-fold) was performed subsequently to investigate the potential targets of these inhibitors at the genomic level. Upon analysis of the whole-genome sequencing data, we identified mutations in a number of genetic loci pointing to potential mechanisms of inhibitor action and their underlying mechanisms of resistance.

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

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

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.

Inhibited Methanogenesis in the Rumen of Cattle: Microbial Metabolism in Response to Supplemental 3-Nitrooxypropanol and Nitrate

3-Nitrooxypropanol (3-NOP) supplementation to cattle diets mitigates enteric CH₄ emissions and may also be economically beneficial at farm level. However, the wider rumen metabolic response to methanogenic inhibition by 3-NOP and the NO2- intermediary metabolite requires further exploration. Furthermore, NO3- supplementation potently decreases CH₄ emissions from cattle. The reduction of NO3- utilizes H₂ and yields NO2-, the latter of which may also inhibit rumen methanogens, although a different mode of action than for 3-NOP and its NO2- derivative was hypothesized. Our objective was to explore potential responses of the fermentative and methanogenic metabolism in the rumen to 3-NOP, NO3- and their metabolic derivatives using a dynamic mechanistic modeling approach. An extant mechanistic rumen fermentation model with state variables for carbohydrate substrates, bacteria and protozoa, gaseous and dissolved fermentation end products and methanogens was extended with a state variable of either 3-NOP or NO3-. Both new models were further extended with a NO2- state variable, with NO2- exerting methanogenic inhibition, although the modes of action of 3-NOP-derived and NO3--derived NO2- are different. Feed composition and intake rate (twice daily feeding regime), and supplement inclusion were used as model inputs. Model parameters were estimated to experimental data collected from the literature. The extended 3-NOP and NO3- models both predicted a marked peak in H₂ emission shortly after feeding, the magnitude of which increased with higher doses of supplement inclusion. The H₂ emission rate appeared positively related to decreased acetate proportions and increased propionate and butyrate proportions. A decreased CH₄ emission rate was associated with 3-NOP and NO3- supplementation. Omission of the NO2- state variable from the 3-NOP model did not change the overall dynamics of H₂ and CH₄ emission and other metabolites. However, omitting the NO2- state variable from the NO3- model did substantially change the dynamics of H₂ and CH₄ emissions indicated by a decrease in both H₂ and CH₄ emission after feeding. Simulations do not point to a strong relationship between methanogenic inhibition and the rate of NO3- and NO2- formation upon 3-NOP supplementation, whereas the metabolic response to NO3- supplementation may largely depend on methanogenic inhibition by NO2-.

Accessing Dietary Effects on the Rumen Microbiome: Different Sequencing Methods Tell Different Stories

The current study employed both amplicon and shotgun sequencing to examine and compare the rumen microbiome in Angus bulls fed with either a backgrounding diet (BCK) or finishing diet (HG), to assess if both methods produce comparable results. Rumen digesta samples from 16 bulls were subjected for microbial profiling. Distinctive microbial profiles were revealed by the two methods, indicating that choice of sequencing approach may be a critical facet in studies of the rumen microbiome. Shotgun-sequencing identified the presence of 303 bacterial genera and 171 archaeal species, several of which exhibited differential abundance. Amplicon-sequencing identified 48 bacterial genera, 4 archaeal species, and 9 protozoal species. Among them, 20 bacterial genera and 5 protozoal species were differentially abundant between the two diets. Overall, amplicon-sequencing showed a more drastic diet-derived effect on the ruminal microbial profile compared to shotgun-sequencing. While both methods detected dietary differences at various taxonomic levels, few consistent patterns were evident. Opposite results were seen for the phyla Firmicutes and Bacteroidetes, and the genus Selenomonas. This study showcases the importance of sequencing platform choice and suggests a need for integrative methods that allow robust comparisons of microbial data drawn from various omic approaches, allowing for comprehensive comparisons across studies.

Conditions stimulating neutral detergent fiber degradation by dosing branched-chain volatile fatty acids. III: Relation with solid passage rate and pH on prokaryotic fatty acid profile and community in continuous culture

Our objectives were to evaluate potential interactions in culture conditions that influence how exogenously dosed branched-chain VFA (BCVFA) would be recovered as elongated fatty acids (FA) or would affect bacterial populations. A 2 × 2 × 2 factorial arrangement of treatments evaluated 3 factors: (1) without versus with BCVFA (0 vs. 2 mmol/d each of isobutyrate, isovalerate, and 2-methylbutyrate; each dose was partially substituted with ¹³C-enriched tracers before and during the collection period); (2) high versus low pH (ranging diurnally from 6.3 to 6.8 vs. 5.7 to 6.2); and (3) low versus high particulate-phase passage rate (k_p; 2.5 vs. 5.0%/h) in continuous cultures administered a 50:50 forage:concentrate diet twice daily. Samples of effluent were collected and composited before harvesting bacteria from which FA and DNA were extracted. Profiles and enrichments of FA in bacteria were evaluated by gas chromatography and isotope-ratio mass spectrometry. The ¹³C enrichment in bacterial FA was calculated as percentage recovery of dosed ¹³C-labeled BCVFA. Dosing BCVFA increased the even-chain iso-FA, preventing the reduced concentration at higher k_p and potentially as a physiological response to decreased pH. However, decreasing pH decreased recovery of ¹³C in these even-chain FA, suggesting greater reliance on isobutyrate produced from degradation of dietary valine. The iso-FA were decreased, whereas anteiso-FA and 16:0 increased with decreasing pH. Thus, 2-methylbutyrate still appeared to be important as a precursor for anteiso-FA to counter the increased rigidity of bacterial membranes that had more saturated straight-chain FA when pH decreased. Provision of BCVFA stimulated the relative sequence abundance of Fibrobacter and Treponema, both of which require isobutyrate and 2-methylbutyrate. Numerous bacterial community members were shifted by low pH, including increased Prevotella and genera within the phylum Proteobacteria, at the expense of members within phylum Firmicutes. Because of relatively few interactions with pH and k_p, supplementation of BCVFA can stimulate neutral detergent fiber degradability via key fibrolytic bacteria across a range of conditions. Decreasing pH shifted bacterial populations and their FA composition, suggesting that further research is needed to distinguish pH from dietary changes.

The Efficacy of Plant-Based Bioactives Supplementation to Different Proportion of Concentrate Diets on Methane Production and Rumen Fermentation Characteristics In Vitro

Simple Summary

Using natural feed additives to mitigate methane emissions from ruminants is a promising strategy. Many antimethanogenic compounds have been used to alter rumen fermentation, yet their potential to reduce methane production effectively is not consistent across different kinds of feeding styles (forage:concentrate ratios). Consequently, in the current study we investigated the efficacy of plant-bioactives extract (PE) (a novel phytogenic mixture of garlic and citrus extracts) on rumen fermentation characteristics and methane production in different kinds of feeding styles. The current In Vitro study showed that PE was effective in reducing methane production in all feeding styles without exhibiting any adverse effect on nutrient digestibility. Furthermore, PE supplementation was able to improve the rumen fermentation through increasing the production of total volatile fatty acids. Therefore, PE mixture could be used as a dietary supplement to reduce the methane production from ruminants.

Abstract

This In Vitro study was conducted to investigate the impact of plant-bioactives extract (PE), a combination of garlic powder and bitter orange extract, on methane production, rumen fermentation, and digestibility in different feeding models. The dietary treatments were 1000 g grass/kg ration + 0 g concentrate/kg ration (100:0), 80:20, 60:40, 40:60, and 20:80. The PE was supplemented at 200 g/kg of the feed. Each group consisted of 6 replicates. The experiment was performed as an In Vitro batch culture for 24 h at 39 °C. This procedure was repeated in three consecutive runs. The results of this experiment showed that supplementation with PE strongly reduced methane production in all kinds of feeding models (p < 0.001). Its efficacy in reducing methane/digestible dry matter was 44% in the 100:0 diet, and this reduction power increased up to a 69.2% with the inclusion of concentrate in the 20:80 diet. The PE application significantly increased gas and carbon dioxide production and the concentration of ammonia-nitrogen, but decreased the pH (p < 0.001). In contrast, it did not interfere with organic matter and fiber digestibility. Supplementation with PE was effective in altering rumen fermentation toward less acetate and more propionate and butyrate (p < 0.001). Additionally, it improved the production of total volatile fatty acids in all feeding models (p < 0.001). In conclusion, the PE combination showed effective methane reduction by improving rumen fermentation characteristics without exhibiting adverse effects on fiber digestibility. Thus, PE could be used with all kinds of feeding models to effectively mitigate methane emissions from ruminants.

Red seaweed (Asparagopsis taxiformis) supplementation reduces enteric methane by over 80 percent in beef steers

The red macroalgae (seaweed) Asparagopsis spp. has shown to reduce ruminant enteric methane (CH₄) production up to 99% in vitro. The objective of this study was to determine the effect of Asparagopsis taxiformis on CH₄ production (g/day per animal), yield (g CH₄/kg dry matter intake (DMI)), and intensity (g CH₄/kg ADG); average daily gain (ADG; kg gain/day), feed conversion efficiency (FCE; kg ADG/kg DMI), and carcass and meat quality in growing beef steers. Twenty-one Angus-Hereford beef steers were randomly allocated to one of three treatment groups: 0% (Control), 0.25% (Low), and 0.5% (High) A. taxiformis inclusion based on organic matter intake. Steers were fed 3 diets: high, medium, and low forage total mixed ration (TMR) representing life-stage diets of growing beef steers. The Low and High treatments over 147 days reduced enteric CH₄ yield 45 and 68%, respectively. However, there was an interaction between TMR type and the magnitude of CH₄ yield reduction. Supplementing low forage TMR reduced CH₄ yield 69.8% (P <0.01) for Low and 80% (P <0.01) for High treatments. Hydrogen (H₂) yield (g H₂/DMI) increased (P <0.01) 336 and 590% compared to Control for the Low and High treatments, respectively. Carbon dioxide (CO₂) yield (g CO₂/DMI) increased 13.7% between Control and High treatments (P = 0.03). No differences were found in ADG, carcass quality, strip loin proximate analysis and shear force, or consumer taste preferences. DMI tended to decrease 8% (P = 0.08) in the Low treatment and DMI decreased 14% (P <0.01) in the High treatment. Conversely, FCE tended to increase 7% in Low (P = 0.06) and increased 14% in High (P <0.01) treatment compared to Control. The persistent reduction of CH₄ by A. taxiformis supplementation suggests that this is a viable feed additive to significantly decrease the carbon footprint of ruminant livestock and potentially increase production efficiency.

Examining the Variables Leading to Apparent Incongruity between Antimethanogenic Potential of Tannins and Their Observed Effects in Ruminants—A Review

In recent years, several secondary plant metabolites have been identified that possess antimethanogenic properties. Tannin-rich forages have the potential to reduce methane emissions in ruminants while also increasing their nutrient use efficiency and promoting overall animal health. However, results have been highly inconclusive to date, with their antimethanogenic potential and effects on both animal performance and nutrition being highly variable even within a plant species. This variability is attributed to the structural characteristics of the tannins, many of which have been linked to an increased antimethanogenic potential. However, these characteristics are seldom considered in ruminant nutrition studies—often because the analytical techniques are inadequate to identify tannin structure and the focus is mostly on total tannin concentrations. Hence, in this article, we (i) review previous research that illustrate the variability of the antimethanogenic potential of forages; (ii) identify the source of inconsistencies behind these results; and (iii) discuss how these could be optimized to generate comparable and repeatable results. By adhering to this roadmap, we propose that there are clear links between plant metabolome and physiology and their antimethanogenic potential that can be established with the ultimate goal of improving the sustainable intensification of livestock.

Impacts of Mootral on Methane Production, Rumen Fermentation, and Microbial Community in an in vitro Study

Methane mitigation strategies have a two-sided benefit for both environment and efficient livestock production. This preliminary short-term in vitro trial using Mootral (garlic and citrus extracts), a novel natural feed supplement, was conducted to evaluate its efficacy on rumen fermentation characteristics, methane production, and the bacterial and archaeal community. The experiment was performed as a batch culture using rumen fluid collected from sheep, and Mootral was supplemented in three concentrations: 0% (Control), 10%, and 20% of the substrate (50% Grass:50% Concentrate). The rumen fermentation data and alpha diversity of microbial community were analyzed by ordinary one-way analysis of variance. The relative abundance and statistical significance of families and operational taxonomic units (OTUs) among the groups were compared by Kruskal–Wallis H test using Calypso software. After 24-h incubation at 39°C, Mootral in a dose-dependent manner improved the production of total volatile fatty acids and propionate while it reduced the acetate proportion and acetate/propionate ratio. The total produced gas was two times higher in the Mootral-supplemented groups than control (P < 0.01), while the proportion of methane in the produced gas was reduced by 22% (P < 0.05) and 54% (P < 0.01) for 10 and 20% Mootral, respectively. Mootral did not change pH, digestibility, and ammonia-nitrogen. Microbial community analyses showed that Mootral effectively changed the ruminal microbiome. The bacterial community showed an increase of the relative abundance of the propionate-producing family such as Prevotellaceae (P = 0.014) and Veillonellaceae (P = 0.030), while there was a decrease in the relative abundance of some hydrogen-producing bacteria by Mootral supplementation. In the archaeal community, Methanobacteriaceae was decreased by Mootral supplementation compared with control (P = 0.032), while the Methanomassiliicoccaceae family increased in a dose-dependent effect (P = 0.038). The results of the study showed the efficacy of the new mixture to alter the ruminal microbial community, produce more propionate, and reduce microbial groups associated with methane production, thus suggesting that Mootral is a promising natural mixture for methane reduction from ruminants.

Effects of brewers' spent grain protein hydrolysates on gas production, ruminal fermentation characteristics, microbial protein synthesis and microbial community in an artificial rumen fed a high grain diet

Background

Brewers’ spent grain (BSG) typically contains 20% – 29% crude protein (CP) with high concentrations of glutamine, proline and hydrophobic and non-polar amino acid, making it an ideal material for producing value-added products like bioactive peptides which have antioxidant properties. For this study, protein was extracted from BSG, hydrolyzed with 1% alcalase and flavourzyme, with the generated protein hydrolysates (AlcH and FlaH) showing antioxidant activities. This study evaluated the effects of AlcH and FlaH on gas production, ruminal fermentation characteristics, nutrient disappearance, microbial protein synthesis and microbial community using an artificial rumen system (RUSITEC) fed a high-grain diet.

Results

As compared to the control of grain only, supplementation of FlaH decreased (P < 0.01) disappearances of dry matter (DM), organic matter (OM), CP and starch, without affecting fibre disappearances; while AlcH had no effect on nutrient disappearance. Neither AlcH nor FlaH affected gas production or VFA profiles, however they increased (P < 0.01) NH₃-N and decreased (P < 0.01) H₂ production. Supplementation of FlaH decreased (P < 0.01) the percentage of CH₄ in total gas and dissolved-CH₄ (dCH₄) in dissolved gas. Addition of monensin reduced (P < 0.01) disappearance of nutrients, improved fermentation efficiency and reduced CH₄ and H₂ emissions. Total microbial nitrogen production was decreased (P < 0.05) but the proportion of feed particle associated (FPA) bacteria was increased with FlaH and monensin supplementation. Numbers of OTUs and Shannon diversity indices of FPA microbial community were unaffected by AlcH and FlaH; whereas both indices were reduced (P < 0.05) by monensin. Taxonomic analysis revealed no effect of AlcH and FlaH on the relative abundance (RA) of bacteria at phylum level, whereas monensin reduced (P < 0.05) the RA of Firmicutes and Bacteroidetes and enhanced Proteobacteria. Supplementation of FlaH enhanced (P < 0.05) the RA of genus Prevotella, reduced Selenomonas, Shuttleworthia, Bifidobacterium and Dialister as compared to control; monensin reduced (P < 0.05) RA of genus Prevotella but enhaced Succinivibrio.

Conclusions

The supplementation of FlaH in high-grain diets may potentially protect CP and starch from ruminal degradation, without adversely affecting fibre degradation and VFA profiles. It also showed promising effects on reducing CH₄ production by suppressing H₂ production. Protein enzymatic hydrolysates from BSG using flavourzyme showed potential application to high value-added bio-products.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-020-00531-5.

The application of omics in ruminant production: a review in the tropical and sub-tropical animal production context

The demand for animal products (e.g. dairy and beef) in tropical regions is expected to increase in parallel with the public demand for sustainable practices, due to factors such as population growth and climate change. The necessity to increase animal production output must be achieved with better management and production technologies. For this to happen, novel research methodologies, animal selection and postgenomic tools play a pivotal role. Indeed, improving breeder selection programs, the quality of meat and dairy products as well as animal health will contribute to higher sustainability and productivity. This would surely benefit regions where resource quality and quantity are increasingly unstable, and research is still very incipient, which is the case of many regions in the tropics. The purpose of this review is to demonstrate how omics-based approaches play a major role in animal science, particularly concerning ruminant production systems and research associated to the tropics and developing countries. SIGNIFICANCE: Environmental conditions in the tropics make livestock production harder, compared to temperate regions. Due to global warming, the sustainability of livestock production will become increasingly problematic. The use of novel omics technologies could generate useful information to understand adaptation mechanisms of resilient breeds and/or species. The application of omics to tropical animal production is still residual in the currently available literature. With this review, we aim to summarize the most notable results in the field whilst encouraging further research to deal with the future challenges that animal production in the tropics will need to face.

The effect of a diet based on rice straw co-fermented with probiotics and enzymes versus a fresh corn Stover-based diet on the rumen bacterial community and metabolites of beef cattle

Improvement of the food value of rice straw is urgently required in rice crop growing areas to mitigate pollution caused by rice straw burning and enhance the supply of high-quality forages for ruminants. The aims of the present study were to compare the effects of fresh corn Stover and rice straw co-fermented with probiotics and enzymes on rumen fermentation and establish the feasibility of increasing the rice straw content in ruminant diets and, by extension, reducing air pollution caused by burning rice straw. Twenty Simmental hybrid beef cattle were randomly allotted to two groups with ten cattle per group. They were fed diets based either on rice straw co-fermented with probiotics and enzymes or fresh corn Stover for 90 days. Rumen fluid was sampled with an esophageal tube vacuum pump device from each animal on the mornings of days 30, 60, and 90. Bacterial diversity was evaluated by sequencing the V4–V5 region of the 16S rRNA gene. Metabolomes were analyzed by gas chromatography/time-of-flight mass spectrometry (GC–TOF/MS). Compared to cattle fed fresh corn Stover, those fed rice straw co-fermented with probiotics and enzymes had higher (P < 0.05) levels of acetic acid and propionate in rumen liquid at d 60 and d 90 respectively, higher (P < 0.05) abundances of the phyla Bacteroidetes and Fibrobacteres and the genera Ruminococcus, Saccharofermentans, Pseudobutyrivibrio, Treponema, Lachnoclostridium, and Ruminobacter, and higher (P < 0.05) concentrations of metabolites involved in metabolisms of amino acid, carbohydrate, and cofactors and vitamins. Relative to fresh corn Stover, rice straw co-fermented with probiotics and enzymes resulted in higher VFA concentrations, numbers of complex carbohydrate-decomposing and H₂-utilizing bacteria, and feed energy conversion efficiency in the rumen.

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.

Associative effects of wet distiller's grains plus solubles and tannin-rich peanut skin supplementation on in vitro rumen fermentation, greenhouse gas emissions, and microbial changes1

Two sets of in vitro rumen fermentation experiments were conducted to determine effects of diets that included wet distiller's grains plus solubles (WDGS) and tannin-rich peanut skin (PS) on the in vitro digestibility, greenhouse gas (GHG) and other gas emissions, fermentation rate, and microbial changes. The objectives were to assess associative effects of various levels of PS or WDGS on the in vitro digestibility, GHG and other gas emissions, fermentation rate, and microbial changes in the rumen. All gases were collected using an ANKOM Gas Production system for methane (CH4), carbon dioxide (CO2), nitrous oxide (N2O), and hydrogen sulfide (H2S) analyses. Cumulative ruminal gas production was determined using 250 mL ANKOM sampling bottles containing 50 mL of ruminal fluid (pH 5.8), 40 mL of artificial saliva (pH 6.8), and 6 g of mixed diets after a maximum of 24 h of incubation. Fermenters were flushed with CO2 gas and held at 39 °C in a shaking incubator for 24 h. Triplicate quantitative real-time polymerase chain reaction (qPCR) analyses were conducted to determine microbial diversity. When WDGS was supplied in the diet, in the absence of PS, cumulative CH4 production increased (P < 0.05) with 40% WDGS. In the presence of PS, production of CH4 was reduced but the reduction was less at 40% WDGS. In the presence of PS, ruminal lactate, succinate, and acetate/propionate (A/P) ratio tended to be less with a WDGS interaction (P < 0.01). In the presence of PS and with 40% WDGS, average populations of Bacteroidetes, total methanogens, Methanobrevibacter sp. AbM4, and total protozoa were less. The population of total methanogens (R2 = 0.57; P < 0.01), Firmicutes (R2 = 0.46: P < 0.05), and Firmicutes/Bacteroidetes (F/B) ratio (R2 = 0.46; P < 0.03) were strongly correlated with ruminal CH4 production. Therefore, there was an associative effect of tannin-rich PS and WDGS, which suppressed methanogenesis both directly and indirectly by modifying populations of ruminal methanogens.

Recent insight and future techniques to enhance rumen fermentation in dairy goats

Recent development of novel techniques in systems biology have been used to improve and manipulate the rumen microbial ecosystem and gain a deeper understanding of its physiological and microbiological interactions and relationships. This provided a deeper insight and understanding of the relationship and interactions between the rumen microbiome and the host animal. New high-throughput techniques have revealed that the dominance of Proteobacteria in the neonatal gut might be derived from the maternal placenta through fetal swallowing of amniotic fluid in utero, which gradually decreases in the reticulum, omasum, and abomasum with increasing age after birth. Multi "omics" technologies have also enhanced rumen fermentation and production efficiency of dairy goats using dietary interventions through greater knowledge of the links between nutrition, metabolism, and the rumen microbiome and their effect in the environment. For example, supplementation of dietary lipid, such as linseed, affects rumen fermentation by favoring the accumulation of α-linolenic acid biohydrogenation with a high correlation to the relative abundance of Fibrobacteriaceae. This provides greater resolution of the interlinkages among nutritional strategies, rumen microbes, and metabolism of the host animal that can set the foundation for new advancements in ruminant nutrition using multi 'omics' technologies.

Comparison of Bacterial Populations in the Ceca of Swine at Two Different Stages and their Functional Annotations

The microbial composition in the cecum of pig influences host health, immunity, nutrient digestion, and feeding requirements significantly. Advancements in metagenome sequencing technologies such as 16S rRNAs have made it possible to explore cecum microbial population. In this study, we performed a comparative analysis of cecum microbiota of crossbred Korean native pigs at two different growth stages (stage L = 10 weeks, and stage LD = 26 weeks) using 16S rRNA sequencing technology. Our results revealed remarkable differences in microbial composition, α and β diversity, and differential abundance between the two stages. Phylum composition analysis with respect to SILVA132 database showed Firmicutes to be present at 51.87% and 48.76% in stages L and LD, respectively. Similarly, Bacteroidetes were present at 37.28% and 45.98% in L and LD, respectively. The genera Prevotella, Anaerovibrio, Succinivibrio, Megasphaera were differentially enriched in stage L, whereas Clostridium, Terrisporobacter, Rikenellaceae were enriched in stage LD. Functional annotation of microbiome by level-three KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis revealed that glycine, serine, threonine, valine, leucine, isoleucine arginine, proline, and tryptophan metabolism were differentially enriched in stage L, whereas alanine, aspartate, glutamate, cysteine, methionine, phenylalanine, tyrosine, and tryptophan biosynthesis metabolism were differentially enriched in stage LD. Through machine-learning approaches such as LEfSe (linear discriminant analysis effect size), random forest, and Pearson's correlation, we found pathways such as amino acid metabolism, transport systems, and genetic regulation of metabolism are commonly enriched in both stages. Our findings suggest that the bacterial compositions in cecum content of pigs are heavily involved in their nutrient digestion process. This study may help to meet the demand of human food and can play significant roles in medicinal application.