Shifts of Hydrogen Metabolism From Methanogenesis to Propionate Production in Response to Replacement of Forage Fiber With Non-forage Fiber Sources in Diets in vitro

Environmental impact of phytobiotic additives on greenhouse gas emission reduction, rumen fermentation manipulation, and performance in ruminants: an updated review

Ruminal fermentation is a natural process involving beneficial microorganisms that contribute to the production of valuable products and efficient nutrient conversion. However, it also leads to the emission of greenhouse gases, which have detrimental effects on the environment and animal productivity. Phytobiotic additives have emerged as a potential solution to these challenges, offering benefits in terms of rumen fermentation modulation, pollution reduction, and improved animal health and performance. This updated review aims to provide a comprehensive understanding of the specific benefits of phytobiotic additives in ruminant nutrition by summarizing existing studies. Phytobiotic additives, rich in secondary metabolites such as tannins, saponins, alkaloids, and essential oils, have demonstrated biological properties that positively influence rumen fermentation and enhance animal health and productivity. These additives contribute to environmental protection by effectively reducing nitrogen excretion and methane emissions from ruminants. Furthermore, they inhibit microbial respiration and nitrification in soil, thereby minimizing nitrous oxide emissions. In addition to their environmental impact, phytobiotic additives improve rumen manipulation, leading to increased ruminant productivity and improved quality of animal products. Their multifaceted properties, including anthelmintic, antioxidant, antimicrobial, and immunomodulatory effects, further contribute to the health and well-being of both animals and humans. The potential synergistic effects of combining phytobiotic additives with probiotics are also explored, highlighting the need for further research in this area. In conclusion, phytobiotic additives show great promise as sustainable and effective solutions for improving ruminant nutrition and addressing environmental challenges.

The effect of supplementation with rubber seed kernel pellet on in vitro rumen fermentation characteristics and fatty acid profiles in swamp buffalo

BACKGROUND

Rubber seed kernel is a by-product derived from rubber tree plantations. It is rich in C18 unsaturated fatty acids (UFA) and has the potential to be used as a protein source for ruminant diets. This investigation has been conducted to determine the influence of rubber seed kernel pellet (RUSKEP) supplementation on in vitro rumen fermentation characteristics and fatty acid profiles in swamp buffalo. Using a completely randomized design (CRD) and supplementation of RUSKEP at 0, 2, 4, 6, 8, and 10% dry matter (DM) of substrate.

RESULTS

The supplementation with RUSKEP had no effect on gas kinetics, cumulative gas production, or degradability. Ruminal pH decreased linearly (P < 0.01) and ammonia-nitrogen (NH3-N) concentration decreased quadratically (P < 0.01) by RUSKEP supplementation. The proportion of acetate (C2) decreased linearly (P < 0.01), but propionate (C3) and butyrate (C4) increased linearly (P < 0.01), resulting in a decrease in the acetate to propionate ratio (C2:C3) (P < 0.01) by RUSKEP supplementation. With an increasing level of dietary RUSKEP, there was a slight increase in UFA in the rumen by increasing the oleic acid (OA; C18:1 cis-9 + trans-9), linoleic acid (LA; C18:2 cis-9,12 + trans-9,12), and α-linolenic acid (ALA; C18:3 cis-9,12,15) concentrations (P < 0.01).

CONCLUSIONS

Adding up to 10% of RUSKEP could improve in vitro rumen fermentation and C18 unsaturated fatty acids, especially ALA, in swamp buffalo.

Microbial metabolites as modulators of host physiology

The gut microbiota is increasingly recognised as a key player in influencing human health and changes in the gut microbiota have been strongly linked with many non-communicable conditions in humans such as type 2 diabetes, obesity and cardiovascular disease. However, characterising the molecular mechanisms that underpin these associations remains an important challenge for researchers. The gut microbiota is a complex microbial community that acts as a metabolic interface to transform ingested food (and other xenobiotics) into metabolites that are detected in the host faeces, urine and blood. Many of these metabolites are only produced by microbes and there is accumulating evidence to suggest that these microbe-specific metabolites do act as effectors to influence human physiology. For example, the gut microbiota can digest dietary complex polysaccharides (such as fibre) into short-chain fatty acids (SCFA) such as acetate, propionate and butyrate that have a pervasive role in host physiology from nutrition to immune function. In this review we will outline our current understanding of the role of some key microbial metabolites, such as SCFA, indole and bile acids, in human health. Whilst many studies linking microbial metabolites with human health are correlative we will try to highlight examples where genetic evidence is available to support a specific role for a microbial metabolite in host health and well-being.

Composition of the rumen archaeal community of growing camels fed different concentrate levels

Understanding the rumen fermentation and methanogenic community in camels fed intensively is critical for optimizing rumen fermentation, improving feed efficiency, and lowering methane emissions. Using Illumina MiSeq sequencing, quantitative real-time PCR, and high-performance liquid chromatography, this study evaluates the influence of different concentrate supplement levels in the diet on rumen fermentation as well as the diversity and structure of the rumen methanogenic community for growing dromedary camels. Twelve growing camels were divided into three groups and given three levels of concentrate supplement, 0.7% (C1), 1% (C2), and 1.3% (C3) based on their body weight. All animals were fed alfalfa hay ad libitum. The levels of total volatile fatty acid, rumen ammonia, and methanogen copy number were unaffected by the supplementation level. Increasing the concentrate supplement level increased the proportion of propionic acid while decreasing the proportion of acetic acid. Increasing the level of concentrate in the diet had no effect on alpha diversity metrics or beta diversity of rumen methanogens. Methanobrevibacter and Methanosphaera predominated the methanogenic community and were declined as concentrate supplement level increased. This study sheds new light on the effect of concentrate supplement level in growing camels' diet on rumen fermentation and methanogenic community, which could help in the development of a strategy that aimed to reduce methane emissions and enhance feed efficiency.

Effects of Varying Levels of Wheat Bran Dietary Fiber on Growth Performance, Fiber Digestibility and Gut Microbiota in Erhualian and Large White Pigs

To evaluate the tolerance of a high-fiber diet in Erhualian pigs (Er-HL), the present investigation systematically investigated the ramifications of varying wheat bran fiber levels, specified as total dietary fiber (TDF) values of 14.07%, 16.32%, 17.99%, and 18.85%, on growth performance, fiber digestibility and gut microbiota in Er-HL, large Large White pigs (L-LW, the same physiological stage as the Er-HL) and small Large White pigs (S-LW, the same body weight as the Er-HL). Our results revealed that fiber levels exerted no discernable impact on growth performance (average daily feed intake (ADFI), and average daily gain (ADG)) of Er-HL (p > 0.05). Conversely, L-LW exhibited a decrease in ADFI and ADG with increasing fiber levels (p < 0.05). Notably, the apparent total tract digestibility (ATTD) of various fiber components, including neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose, TDF and insoluble dietary fiber (IDF), in Er-HL were significantly higher than those in S-LW and L-LW irrespective of diets (p < 0.05). The ATTD of cellulose and hemicellulose in Er-HL significantly decreased with increasing fiber levels (p < 0.05), yet remained statistically indifferent when comparing the 7%-wheat-bran-replaced diet (7% WRB, TDF 16.32%) to the basal diet (TDF 14.07%) (p > 0.05). The cecal microbiota of Er-HL had higher richness estimators (Chao1 and ACE) than those of S-LW and L-LW irrespective of diets (p < 0.01). Breed serves as a pivotal determinant in shaping swine gut microbiota. Thirteen genera were selected as the key bacteria related to high fiber digestibility of Er-HL. Further functional examination of these key genera elucidated an enrichment of pathways pertinent to carbohydrate metabolism in Er-HL samples compared with S-LW and L-LW samples. In summary, Er-HL exhibited high-fiber tolerance both in terms of growth performance and fiber digestibility compared with Large White pigs. Specifically, the ATTD of NDF, ADF, hemicellulose, IDF and TDF were significantly higher in Er-HL compared with L-LW and S-LW, irrespective of diets. Fiber level exerted no discernable impact on growth performance (ADFI, ADG) and the ATTD of fiber (NDF, ADF, IDF and TDF) in Er-HL. The optimum fiber level of the Er-HL was identified as 7% WRB (TDF 16.32%). Thirteen genera were ascertained to significantly contribute to high fiber digestibility of Er-HL, correlating with an enhancement of carbohydrate metabolism pathways.

Winery by-products as a feed source with functional properties: dose-response effect of grape pomace, grape seed meal, and grape seed extract on rumen microbial community and their fermentation activity in RUSITEC

BACKGROUND

Grape and winery by-products have nutritional values for cattle and also contain functional compounds like phenols, which not only bind to protein but can also directly affect microbiota and their function in the rumen. We characterized the nutritional and functional effects of grape seed meal and grape pomace as well as an effective dosage of grape phenols on ruminal microbiota and fermentation characteristics using a rumen simulation technique.

RESULTS

Six diets (each n = 8) were compared including a control diet (CON, no by-product), a positive control diet (EXT, CON + 3.7% grape seed extract on a dry matter (DM) basis), two diets with grape seed meal at 5% (GS-low) and 10% (GS-high), and two diets with grape pomace: at 10% (GP-low) and 20% (GP-high), on a DM basis. The inclusion of the by-product supplied total phenols at 3.4%, 0.7%, 1.4%, 1.3%, and 2.7% of diet DM for EXT, GS-low, GS-high, GP-low, and GP-high, respectively. Diets were tested in four experimental runs. All treatments decreased ammonia concentrations and the disappearances of DM and OM (P < 0.05) compared to CON. EXT and GP-high lowered butyrate and odd- and branch-chain short-chain fatty acids while increased acetate compared to CON (P < 0.05). Treatments did not affect methane formation. EXT decreased the abundance of many bacterial genera including those belonging to the core microbiota. GP-high and EXT consistently decreased Olsenella and Anaerotipes while increased Ruminobacter abundances.

CONCLUSION

The data suggest that the inclusion of winery by-products or grape seed extract could be an option for reducing excessive ammonia production. Exposure to grape phenols at a high dosage in an extract form can alter the rumen microbial community. This, however, does not necessarily alter the effect of grape phenols on the microbial community function compared to feeding high levels of winery by-products. This suggests the dominant role of dosage over the form or source of the grape phenols in affecting ruminal microbial activity. In conclusion, supplementing grape phenols at about 3% of diet DM is an effective dosage tolerable to ruminal microbiota.

Effect of a garlic and citrus extract supplement on performance, rumen fermentation, methane production, and rumen microbiome of dairy cows

The aim of this trial was to determine the effect of a garlic and citrus extract supplement (GCE) on the performance, rumen fermentation, methane emissions, and rumen microbiome of dairy cows. Fourteen multiparous Nordic Red cows in mid-lactation from the research herd of Luke (Jokioinen, Finland) were allocated to 7 blocks in a complete randomized block design based on body weight, days in milk, dry matter intake (DMI), and milk yield. Animals within each block were randomly allocated to a diet with or without GCE. The experimental period for each block of cows (one for each of the control and GCE groups) consisted of 14 d of adaptation followed by 4 d of methane measurements inside the open circuit respiration chambers, with the first day being considered as acclimatization. Data were analyzed using the GLM procedure of SAS (SAS Institute Inc.). Methane production (g/d) and methane intensity (g/kg of energy-corrected milk) were lower by 10.3 and 11.7%, respectively, and methane yield (g/kg of DMI) tended to be lower by 9.7% in cows fed GCE compared with the control. Dry matter intake, milk production, and milk composition were similar between treatments. Rumen pH and total volatile fatty acid concentrations in rumen fluid were similar, whereas GCE tended to increase molar propionate concentration and decrease the molar ratio of acetate to propionate. Supplementation with GCE resulted in greater abundance of Succinivibrionaceae, which was associated with reduced methane. The relative abundance of the strict anaerobic Methanobrevibacter genus was reduced by GCE. The change in microbial community and rumen propionate proportion may explain the decrease in enteric methane emissions. In conclusion, feeding GCE to dairy cows for 18 d modified rumen fermentation and microbiota, leading to reduced methane production and intensity without compromising DMI or milk production in dairy cows. This could be an effective strategy for enteric methane mitigation of dairy cows.

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.

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.

Responses of Fermentation Characteristics and Microbial Communities to Vitamin B12 Supplementation in In Vitro Ruminal Cultures

Vitamin B12, an important cofactor involved in propionate formation, is synthesized exclusively by bacteria and archaebacteria. Humans need to intake vitamin B12 through food, and dairy products are generally the best source of vitamin B12. In the present study, the effects of vitamin B12 supplementation in diets on in vitro ruminal fermentation characteristics and microbial communities were investigated to provide a reference for increasing the vitamin B12 content in milk by dietary supplementation. A completely randomized design was carried out using the in vitro rumen culture technique, and 5 vitamin B12 dose levels (0, 0.5, 1.0, 2.0, and 4 mg/g of dry matter) were used. The results showed that vitamin B12 supplementation in diets decreased acetate: propionate ratio and butyrate concentration. The change in the acetate: propionate ratio can be attributed to the increased relative abundances of the Proteobacteria phylum and the Negativicutes class, both of which are involved in propionate metabolism. The decrease in butyrate concentration can likely be attributed to a reduction in relative abundance of species belonging to the Clostridia class, which are known as the predominant butyrate producers in the mammalian intestine. In addition, vitamin B12 supplementation in diets reduced the CH4 production by altering the species composition of the archaeal community. In conclusion, dietary supplementation of vitamin B12 resulted in rumen perturbation. In vivo studies should be conducted cautiously when evaluating the effects of vitamin B12 supplementation on the synthesis and absorption of it, as well as its content in milk.

Stool and Ruminal Microbiome Components Associated With Methane Emission and Feed Efficiency in Nelore Beef Cattle

Background: The impact of extreme changes in weather patterns on the economy and human welfare is one of the biggest challenges our civilization faces. From anthropogenic contributions to climate change, reducing the impact of farming activities is a priority since it is responsible for up to 18% of global greenhouse gas emissions. To this end, we tested whether ruminal and stool microbiome components could be used as biomarkers for methane emission and feed efficiency in bovine by studying 52 Brazilian Nelore bulls belonging to two feed intervention treatment groups, that is, conventional and by-product-based diets.

Results: We identified a total of 5,693 amplicon sequence variants (ASVs) in the Nelore bulls’ microbiomes. A Differential abundance analysis with the ANCOM approach identified 30 bacterial and 15 archaeal ASVs as differentially abundant (DA) among treatment groups. An association analysis using Maaslin2 software and a linear mixed model indicated that bacterial ASVs are linked to the host’s residual methane emission (RCH₄) and residual feed intake (RFI) phenotype variation, suggesting their potential as targets for interventions or biomarkers.

Conclusion: The feed composition induced significant differences in both abundance and richness of ruminal and stool microbial populations in ruminants of the Nelore breed. The industrial by-product-based dietary treatment applied to our experimental groups influenced the microbiome diversity of bacteria and archaea but not of protozoa. ASVs were associated with RCH₄ emission and RFI in ruminal and stool microbiomes. While ruminal ASVs were expected to influence CH₄ emission and RFI, the relationship of stool taxa, such as Alistipes and Rikenellaceae (gut group RC9), with these traits was not reported before and might be associated with host health due to their link to anti-inflammatory compounds. Overall, the ASVs associated here have the potential to be used as biomarkers for these complex phenotypes.

The Fibrolytic Enzyme Profiles and the Composition of Fungal Communities in Donkey Cecum-Colon Ecosystem

Simple Summary

The donkey hindgut is a microbial-rich ecosystem in which caecum and colon fungi play an important role in dietary fiber degradation. In addition, the fibrolytic enzymes produced by hindgut microorganisms are key to the ability of equines to hydrolysis plant fiber. In the present study, the fibrolytic enzyme activities within donkey caecum and colon were firstly measured by spectrophotometry. The dorsal colon presented a higher fibrolytic enzyme activity in comparison with caecum. The fungal community composition along donkey caecum and colon was determined by sequencing an internal transcribed spacer region (ITS) using Illumina MiSeq. The predominant fungi at phylum level were Ascomycota, Basidiomycota, and Neocallimastigomycota. The Aspergillus, Wallemia, Phanerochaete, Fusarium, and Penicillium were detected as the dominant genera, but their metabolic and functional significance in donkey cecum-colon ecosystem need further investigation. In terms of the anaerobic fungi Neocallimastigomycota, its abundance was greater in donkey colon than in caecum. The relative abundance of enzymes related to plant cell wall breakdown were also predicted by PICRUSt, and they were also greater in donkey colon than in caecum. The present study provided new information about fibrolytic enzyme profiles and fungal communities in donkey hindgut. The findings could therefore contribute to the further understanding of the fungal taxa and their dietary fiber degradation mechanisms in donkey hindgut ecosystem.

Abstract

The fibrolytic enzymes and the hindgut fungi in donkey cecum-colon ecosystem play an important role in dietary fiber digestion. A better understanding of the fibrolytic enzyme profiles and the fungal community along donkey caecum and colon is key for optimizing hindgut function. In the present study, the fibrolytic enzyme activities within donkey caecum and colon were firstly measured by spectrophotometry. Activities of carboxymethyl cellulase, avicelase, xylanase, and acetyl esterase were greater in donkey dorsal colon than in caecum, indicating that the colon microorganisms may be more efficient in producing fibrolytic enzymes compared to caecum microbes. The fungal community composition along donkey hindgut was determined by sequencing ITS region using Illumina MiSeq. Three fungal phyla were identified by sequence comparison: Ascomycota (66.8%–74.4%), Basidiomycota (21.6%–30.9%), and Neocallimastigomycota (0.9%–3.3%). The Aspergillus, Wallemia, Phanerochaete, Fusarium, and Penicillium were detected as the dominant genera, but their metabolic and functional significance in donkey cecum-colon ecosystem need further investigation. In terms of the anaerobic fungi Neocallimastigomycota, its abundance was greater in donkey colon than in caecum (p < 0.05), indicating that the donkey hindgut region was associated with differences in fungal community composition. Moreover, the relative abundance of enzymes related to plant cell wall degradation were predicted by PICRUSt, and they were also lower in caecum than in colon. The present study provided new information about fibrolytic enzyme profiles and fungal composition in donkey hindgut ecosystem.

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.

Characterizing Effects of Ingredients Differing in Ruminally Degradable Protein and Fiber Supplies on the Ovine Rumen Microbiome Using Next-Generation Sequencing

The ratio of concentrate to forage within diets is known to alter rumen microbial profiles, but comparatively less information is available on the effect of differing sources of individual nutrients on the microbiome. The objective of this study was to investigate rumen microbial responses to diets composed of protein and fiber sources expected to vary in nutrient degradability. The responses of interest included relative abundances of bacterial taxa as well as estimations of community richness and diversity. Ten ruminally cannulated wethers (Suffolk, Dorset, or Suffolk × Dorset) received four diet treatments consisting of either beet pulp or timothy hay and soybean meal (SBM) or heat-treated soybean meal (HSBM) in a partially replicated 4 × 4 Latin square experiment for 21 days. Timothy hay and beet pulp were expected to provide differing rumen degradabilities of neutral detergent fiber (NDF) while the soybean meals were expected to provide differing rumen degradabilities of crude protein (CP). Solid and liquid samples of rumen contents were collected for microbial DNA isolation and Next-Generation sequencing. Numerous rumen bacterial population shifts were observed due to change in fiber source, with increased abundances (P &lt; 0.05) of fibrolytic populations associated with timothy hay diets compared with beet pulp diets. Conversely, populations of the pectin-degrading genera, Treponema and Lachnospira, increased on the beet pulp treatment (P = 0.015 and P = 0.0049, respectively). Limited impact on bacterial taxa was observed between diets differing in protein source. The Paraprevotellaceae genus YRC22 was observed to increase in abundance on HSBM diets (P = 0.023) and the phylum Spirochaetes tended to be more abundant on SBM than HSBM diets (P = 0.071). Beet pulp decreased rumen bacterial diversity (P = 0.0027) and tended to decrease bacterial species richness (P = 0.051) compared to timothy hay. Our results serve to further underscore the sensitivity of rumen microbes to changes in their preferred substrates, particularly of those associated with fiber degradation.

Microbiome and Metabolic Changes of Milk in Response to Dietary Supplementation With Bamboo Leaf Extract in Dairy Cows

Bamboo leaf extracts, with high content of flavonoids and diverse biological activities, are used in animal husbandry. Increasing evidence has suggested an association between the bovine physiology and the udder microbiome, yet whether the microbiota and the metabolites of milk affect the mammary gland health or the milk quality remains unknown. In this study, we provide a potential mechanism for the effects of bamboo leaf extracts on milk microbiota and metabolites of dairy cows. Twelve multiparous lactating Chinese Holstein dairy cows were randomly separated into two groups: basal diet as the control group (CON, n = 6) and a diet supplemented with 30 g/d bamboo leaf extract per head as antioxidants of bamboo leaf (AOB) group (AOB, n = 6) for 7 weeks (2-week adaptation, 5-week treatment). Milk samples were collected at the end of the trial (week 7) for microbiome and associated metabolic analysis by 16S ribosomal RNA (rRNA) gene sequencing and liquid chromatography-mass spectrometry (LC-MS). The results showed that the milk protein was increased (p < 0.0001) and somatic cell count (SCC) showed a tendency to decrease (p = 0.09) with AOB supplementation. The relative abundance of Firmicutes was significantly decreased (p = 0.04) while a higher relative abundance of Probacteria (p = 0.01) was seen in the group receiving AOB compared to the CON group. The AOB group had a significantly lower relative abundance of Corynebacterium_1 (p = 0.01), Aerococcus (p = 0.01), and Staphylococcus (p = 0.02). There were 64 different types of metabolites significantly upregulated, namely, glycerophospholipids and fatty acyls, and 15 significantly downregulated metabolites, such as moracetin, sphinganine, and lactulose in the AOB group. Metabolic pathway analysis of the different metabolites revealed that the sphingolipid signaling pathway was significantly enriched, together with glycerophospholipid metabolism, sphingolipid metabolism, and necroptosis in response to AOB supplementation. Several typical metabolites were highly correlated with specific ruminal bacteria, demonstrating a functional correlation between the milk microbiome and the associated metabolites. These insights into the complex mechanism and corresponding biological responses highlight the potential function of AOB, warranting further investigation into the regulatory role of specific pathways in the metabolism.

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.

Effects of supplementation of nonforage fiber source in diets with different starch levels on growth performance, rumen fermentation, nutrient digestion, and microbial flora of Hu lambs

The objectives were to evaluate the effects of fiber source and dietary starch level on growth performance, nutrient digestion, rumen parameters, and rumen bacteria in fattening Hu lambs. A total of 360 Hu lambs (BW = 24.72 ± 0.14 kg, 2 months old) were subjected to a 2 × 3 factorial arrangement. Lambs randomly assigned 6 treatments with 6 repetitions (10 lambs per repetition) of each treatment. Six treatments were formulated to include the fiber sources with three starch levels. The experiment lasted a 63 d. The amount of feed, orts, and total feces were sampled on the 42nd day of the experiment. Rumen fluid samples were collected after 2 h of morning feeding on day 56. Rumen contents were collected last day after the selected lambs were slaughtered. Increasing the starch content decreased the digestibility of neutral detergent fiber (NDF, P = 0.005). Increasing the starch level increased the proportions of propionate (P = 0.002) and valerate (P = 0.001) and decreased the proportion of acetate (P < 0.001) and the ratio of acetate to propionate (P = 0.005). The abundance of Fibrobacter succinogenes was affected by an interaction between the fiber source and the starch level (P < 0.001). Fibrobacter succinogenes tended to be greater in lambs fed SH than in lambs fed BP (P = 0.091), which was greater in lambs fed high starch levels than in lambs fed low starch levels (P = 0.014). Increasing the starch level increased Streptococcus bovis abundance (P = 0.029) and decreased total bacteria (P = 0.025). At the genus level, increasing the starch level reduced the abundance of Butyrivibrio_2 (P = 0.020). Nevertheless, the final body weight (BW) and acid detergent fiber (ADF) digestibility were greater (P < 0.01) in lambs fed soybean hull (SH) than in lambs fed BP. The proportion of butyrate was greater (P = 0.005), while the rumen pH was lower (P = 0.001) in lambs fed beet pulp (BP) than in those fed SH. The abundances of Succiniclasticum, Candidatus_Saccharimonas, Ruminococcus_1, and Christensenellaceae_R-7 were greater in lambs fed SH than in those fed BP (P < 0.050), whereas the abundance of Fibrobacter was lower (P = 0.011). The predominant microbial phyla in all of the groups were Firmicutes, Bacteroidetes, and Fibrobacteres. Changing the starch level for fiber sources mainly changed the rumen community in terms of the phylum and genus abundances. Lambs fed SH with low starch level increased the final BW without affecting total volatile fatty acids (TVFA) concentrations.

Starch-protein interaction in the rumen of weaned dairy calves

The objectives of this study were to investigate the effect of starch and protein interaction on rumen environment, in situ digestion, and total-tract digestibility of nutrients in weaned dairy calves between 8 and 16 wk of age. Sixteen rumen-cannulated calves were randomly divided into 4 dietary treatment groups with 4 calves fed in each treatment. The treatment diets had 2 levels of starch [18%, low starch (LS), or 38%, high starch (HS)] and 2 levels of protein [16%, low protein (LP), or 22%, high protein (HP)] on a dry matter (DM) basis in calf grower: (1) LPLS, (2) LPHS, (3) HPLS, and (4) HPHS. Calves were fed for ad libitum intake (95% assigned grower and 5% grass hay), and refusals were collected weekly. Total-tract digestibility collection and in situ digestibility procedures were performed for each calf at 11 and 15 wk. Samples for in situ digestibility, grass hay (GH), soybean hulls (SBH), wheat middlings (WM), ground corn (GrC), and soybean meal (SBM) were incubated for 9 and 24 h. There was no starch and protein interaction on total-tract digestibility of calves. Total-tract DM, neutral detergent fiber (NDF) and acid detergent fiber (ADF) digestibility, and feed efficiency were affected by both protein and starch inclusion level in calf diet. Total-tract starch digestibility was lower for LS diets. Dry matter digestibility and feed efficiency were greater in calves fed HP and HS diets compared with calves fed LP and LS diets, respectively. Fiber digestibility (NDF and ADF) was less in calves fed HS diets compared with calves fed LS diets but was greater in calves fed HP diets compared with calves fed LP diets. Level of protein did not affect in situ DM and NDF disappearance of GH, but HP increased in situ DM and NDF disappearance of SBH. High-starch diets decreased DM and NDF disappearance of both GH and SBH. At 20 h after feeding, ruminal pH was 0.51 unit higher in calves fed HPHS compared with calves fed LPHS. Total ruminal VFA and proportion of propionate was greater with HS versus LS, whereas proportion of acetate was greater with LS versus HS. The DM disappearance of SBM and WM and NDF disappearance of WM was greater for calves fed HPHS compared with calves fed LPHS at 11 wk of age. In our study, when HP was fed with HS, rumen pH, in situ digestion of WM and SBM, and total-tract digestion of DM, NDF, and ADF increased. This provides evidence for starch-protein interaction in the rumen of recently weaned dairy calves. Improvements in total-tract and in situ digestibility suggest that both protein and starch levels are important for 8- to 16-wk-old calves.

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 propylene glycol on in vitro ruminal fermentation, methanogenesis, and microbial community structure

We evaluated the effects of propylene glycol (PG) on in vitro ruminal fermentation, methanogenesis, and microbial community structure. A completely randomized design was conducted in the in vitro incubation, and 4 culture PG dose levels (0, 7.5, 15, and 22.5 μL/g of dry matter) were used in the trial. Based on the fermentation results, the control group (0 μL/g of dry matter, CON) and the second treatment group (15.0 μL/g of dry matter, TRT) were chosen for further analysis to explore the effects of PG on the bacterial and archaeal community structure. The concentrations of propanol, propanal, and succinate increased linearly, whereas the concentration of l-lactate decreased linearly as PG doses increased. The molar proportion of propionate demonstrated a linear increase with increasing PG doses. In contrast with propionate, the molar proportion of acetate and butyrate, and acetate-to-propionate ratio decreased linearly with increasing PG doses. The addition of PG markedly decreased methane production without negative effects on nutrient degradability. In the archaeal level, the relative abundance of Methanobrevibacter tended to decrease, but that of Methanomassiliicoccus significantly increased in TRT group. At the bacterial level, the relative abundance of Bacteroidetes and Prevotella in TRT group was numerically higher than that in CON group. The analysis of the Negativicutes class showed that the relative abundance of Succiniclasticum tended to increase, whereas that of Selenomonas tended to decrease in TRT group. These results demonstrated that PG might be used as an inhibitor to mitigate methane emission. However, the small decrease in methane production will limit the application of PG as a methane inhibitor in production practices. Further research is needed to determine whether use together with other inhibitors may improve the effects of PG on the utilization of reducing equivalents ([H]) and methane production.

Comparative analysis of the metabolically active microbial communities in the rumen of dromedary camels under different feeding systems using total rRNA sequencing

Breakdown of plant biomass in rumen depends on interactions between bacteria, archaea, fungi, and protozoa; however, the majority of studies of the microbiome of ruminants, including the few studies of the rumen of camels, only studied one of these microbial groups. In this study, we applied total rRNA sequencing to identify active microbial communities in 22 solid and liquid rumen samples from 11 camels. These camels were reared at three stations that use different feeding systems: clover, hay and wheat straw (G1), fresh clover (G2), and wheat straw (G3). Bacteria dominated the libraries of sequence reads generated from all rumen samples, followed by protozoa, archaea, and fungi respectively. Firmicutes, Thermoplasmatales, Diplodinium, and Neocallimastix dominated bacterial, archaeal, protozoal and fungal communities, respectively in all samples. Libraries generated from camels reared at facility G2, where they were fed fresh clover, showed the highest alpha diversity. Principal co-ordinate analysis and linear discriminate analysis showed clusters associated with facility/feed and the relative abundance of microbes varied between liquid and solid fractions. This provides preliminary evidence that bacteria dominate the microbial communities of the camel rumen and these communities differ significantly between populations of domesticated camels.

Dietary Supplementation with Sodium Sulfate Improves Rumen Fermentation, Fiber Digestibility, and the Plasma Metabolome through Modulation of Rumen Bacterial Communities in Steers

Six steers were used to study the effects of dietary supplementation with sodium sulfate (Na₂SO₄) on rumen fermentation, nutrient digestion, rumen microbiota, and plasma metabolites. The animals were fed a basal ration with Na₂SO₄ added at 0 g/day (sulfur [S] content of 0.115% dry matter [DM]), 20 g/day (S at 0.185% DM), or 40 g/day (S at 0.255% DM) in a replicate 3-by-3 Latin square design. The results indicated that supplementing with Na₂SO₄ increased the ruminal concentration of total volatile fatty acids, the molar proportions of acetate and butyrate, the ruminal concentrations of microbial protein, SO₄ ^2--S, and S^2--S, and the digestibility of fiber, while it decreased the molar proportion of propionate and the ruminal concentration of ammonia nitrogen. Supplementing with Na₂SO₄ increased the diversity and the richness of rumen microbiota and the relative abundances of the phylum Firmicutes and genera Ruminococcus 2, Rikenellaceae RC9 gut group, and Desulfovibrio, whereas it decreased the relative abundances of the phylum Bacteroidetes and genera Prevotella 1, Prevotellaceae UCG-001, and Treponema 2 Supplementing with Na₂SO₄ also increased the plasma concentrations of amino acids (l-arginine, l-methionine, l-cysteine, and l-lysine), purine derivatives (xanthine and hypoxanthine), vitamins (thiamine and biotin), and lipids (acetylcarnitine and l-carnitine). It was concluded that supplementing the steer ration with Na₂SO₄ was beneficial for improving the rumen fermentation, fiber digestibility, and nutrient metabolism through modulating the rumen microbial community.IMPORTANCE Essential elements like nitrogen and sulfur greatly affect rumen fermentation and metabolism in ruminants. However, little knowledge is available on the effects of sulfur on the rumen microbiota and plasma metabolome. The results of the present trial demonstrated that supplementing the steer ration with sodium sulfate markedly improved rumen fermentation, fiber digestibility, and metabolism of amino acids, purine derivatives, and vitamins through effects on the ruminal microbiome. The facts obtained from the present trial clarified the possible mechanisms of the positive effects of sulfur on rumen fermentation and nutrient utilization.

Steam Explosion Pretreatment Changes Ruminal Fermentation in vitro of Corn Stover by Shifting Archaeal and Bacterial Community Structure

Steam explosion is an environment-friendly pretreatment method to improve the subsequent hydrolysis process of lignocellulosic biomass. Steam explosion pretreatment improved ruminal fermentation and changed fermentation pattern of corn stover during ruminal fermentation in vitro. The study gave a comprehensive insight into how stream explosion pretreatment shifted archaeal and bacterial community structure to change ruminal fermentation in vitro of corn stover. Results showed that steam explosion pretreatment dramatically improved the apparent disappearance of dry matter (DM), neutral detergent fiber (NDF), and acid detergent fiber (ADF). Steam explosion pretreatment significantly increased the molar proportion of propionate and decreased the ratio of acetate to propionate. At archaeal level, steam explosion pretreatment significantly increased the relative abundance of Methanobrevibacter, which can effectively remove metabolic hydrogen to keep the fermentation continuing. At bacterial level, the shift in fermentation was achieved by increasing the relative abundance of cellulolytic bacteria and propionate-related bacteria, including Spirochaetes, Elusimicrobia, Fibrobacteres, Prevotella, Treponema, Ruminococcus, and Fibrobacter.

Physicochemical stressors and mixed alkaloid supplementation modulate ruminal microbiota and fermentation in vitro

The drop of ruminal pH and heat are common physicochemical stressors challenging ruminal microbiota, nutrient digestion and cattle performance. We characterized the ruminal microbiota and digestive activity in response to different pH (6.0 and 6.6) and temperature (39.5 and 42 °C), as well as established the effective dose of alkaloid supplementation (0, 0.088 and 0.175% of feedstock DM) to modulate ruminal fermentation under these conditions. The acidotic condition decreased microbial diversity and abundances of minor bacterial families whereas most of the highly abundant families like Lactobacillaceae, Prevotellaceae, and Bifidobacteriaceae thrived under the stress. Abundances of all three methanogenic archaea taxa detected increased with heat, as did methane production. However, while Methanomassiliicoccaceae benefited from the low pH, Methanomicrobiaceae diminished and methane production decreased. The low dose of alkaloid addition shifted the fermentation to more propionate and less acetate and the high dose decreased methane and ammonia concentration under the low pH. In conclusion, physicochemical stressors shape the microbial community and function. Mixed alkaloid supplementation facilitates the activity of rumen microbial community under acidotic stress.

Microbiome and metabolic changes in milk in response to artemisinin supplementation in dairy cows

This study aimed to explore the effects of artemisinin (ART) on the milk microbiome and metabolites of dairy cow. A total of 12 mid-lactation Holstein dairy cows with similar parity, days in milk were randomly divided into 2 groups receiving either a total mixed ration (TMR) as the control group or this TMR and 120 g/d/head ART as the ART group. The milk samples were collected weekly to determine the contents, and end-of-trial (week 8) milk samples were used to identify microbial species and metabolite profiles by 16S rRNA sequencing and LC–MS analyses, respectively. We observed that the milk fat content significantly increased by ART treatment (P < 0.05). The bacterial community richness was significantly lower in the ART group (P < 0.05), while the diversity showed no difference (P > 0.05). Compared with its abundance in the control (CON) group, Firmicutes was significantly decreased, whereas Proteobacteria was significantly increased. Furthermore, in the ART group, the relative abundances of the genera Aerococcus, Staphylococcus, Corynebacterium_1 and Facklamia were significantly lower (P < 0.01). Metabolomics analysis revealed that ART significantly increasing the concentrations of glycerophospholipids, glycerolipids and flavonoids compared with those in the CON group. An enrichment analysis of the different metabolites showed that ART mainly affected glycerophospholipid metabolism and the pantothenate and CoA biosynthesis pathways. These findings revealed that ART supplementation could affect the milk microbiota and metabolites, that glycerophospholipids and glycerolipids could be potential biomarkers in the milk response to ART feed in dairy cows, and that ART changes substances in milk by maintaining lipid metabolism in the mammary gland.

Replacing Barley and Soybean Meal With By-products, in a Pasture Based Diet, Alters Daily Methane Output and the Rumen Microbial Community in vitro Using the Rumen Simulation Technique (RUSITEC)

Plant based by-products (BP) produced from food and bioethanol industries are human inedible, but can be recycled into the global food chain by ruminant livestock. However, limited data is available on the methanogenesis potential associated with supplementing a solely BP formulated concentrate to a pastoral based diet. Therefore the objective of this in vitro study was to investigate the effects of BP inclusion rate (in a formulated concentrate) to a pasture based diet on dietary digestibility, rumen fermentation patterns, methane production and the prokaryotic microbial community composition. Diets consisted of perennial ryegrass and one of two supplementary concentrates, formulated to be isonitrogenous (16% CP) and isoenergetic (12.0 MJ/ME/kg), containing either 35% BP, barley and soybean meal (BP35) or 95% BP (BP95) offered on a 50:50 basis, however, starch, NDF and fat content varied. The BPs, included in equal proportions on a DM basis, were soyhulls, palm kernel expeller and maize dried distillers grains. The BP35 diet had greater (P < 0.05) digestibility of the chemical constituents DM, OM, CP, NDF, ADF. Greater total VFA production was seen in the BP35 diet (P < 0.05). Daily methane production (mmol/day; +22.7%) and methane output per unit of total organic matter digested (MPOMD; +20.8%) were greatest in the BP35 diet (P < 0.01). Dietary treatment influenced microbial composition (PERMANOVA; P = 0.023) with a greater relative abundance of Firmicutes (adj P < 0.01) observed in the BP35. The Firmicutes:Bacteroidetes ratio was significantly reduced in the BP95 diet (P < 0.01). The relative proportions of Proteobacteria (adj P < 0.01), Succinivibrionaceae (adj P < 0.03) and Succinivibrio (adj P = 0.053) increased in the BP95 diet. The abundance of Proteobacteria was found to be negatively associated with daily methane production (r_s, −0.71; P < 0.01) and MPOMD (r_s, −0.65; P < 0.01). Within Proteobacteria, the relationship of methane production was maintained with the mean abundance of Succinivibrio (r_s, −0.69; P < 0.01). The abundance of the Firmicutes phyla was found to be positively correlated with both daily methane production (r_s, 0.79; P < 0.001) and MPOMD (r_s, 0.75; P < 0.01). Based on in vitro rumen simulation data, supplementation of an exclusively BP formulated concentrate was shown to reduce daily methane output by promoting a favorable alteration to the rumen prokaryotic community.

Bayesian modeling reveals host genetics associated with rumen microbiota jointly influence methane emission in dairy cows

Reducing methane emissions from livestock production is of great importance for the sustainable management of the Earth’s environment. Rumen microbiota play an important role in producing biogenic methane. However, knowledge of how host genetics influences variation in ruminal microbiota and their joint effects on methane emission is limited. We analyzed data from 750 dairy cows, using a Bayesian model to simultaneously assess the impact of host genetics and microbiota on host methane emission. We estimated that host genetics and microbiota explained 24% and 7%, respectively, of variation in host methane levels. In this Bayesian model, one bacterial genus explained up to 1.6% of the total microbiota variance. Further analysis was performed by a mixed linear model to estimate variance explained by host genomics in abundances of microbial genera and operational taxonomic units (OTU). Highest estimates were observed for a bacterial OTU with 33%, for an archaeal OTU with 26%, and for a microbial genus with 41% heritability. However, after multiple testing correction for the number of genera and OTUs modeled, none of the effects remained significant. We also used a mixed linear model to test effects of individual host genetic markers on microbial genera and OTUs. In this analysis, genetic markers inside host genes ABS4 and DNAJC10 were found associated with microbiota composition. We show that a Bayesian model can be utilized to model complex structure and relationship between microbiota simultaneously and their interaction with host genetics on methane emission. The host genome explains a significant fraction of between-individual variation in microbial abundance. Individual microbial taxonomic groups each only explain a small amount of variation in methane emissions. The identification of genes and genetic markers suggests that it is possible to design strategies for breeding cows with desired microbiota composition associated with phenotypes.

Anaerobic co-digestion of Pennisetum hybrid and pig manure: A comparative study of performance and microbial community at different mixture ratio and organic loading rate

To investigate how the changes in performance and the microbial community of the co-digestion system of Pennisetum hybrid and pig manure, two co-digestion systems in a semi-continuous mode were established at different grass:manure mixture ratios (50:50 and 75:25), and at variable organic loading rates (OLRs). The two reactors were in a steady-state at the OLRs of 2.0-5.0 g VS/(L·d), with the specific and volumetric biogas yields of 383.86 ± 65.13 to 574.28 ± 72.04 mL/g VS and 0.87 ± 0.07 to 2.36 ± 0.13 m³/(m³·d), respectively. The co-digestion system with a mixture ratio of 75:25 failed at an OLR of 5.5 g VS/(L⋅d). This failure could be attributed to the accumulation of volatile fatty acids (VFAs) owing to the imbalance between acid-production and -oxidation bacteria. By contrast, the co-digestion system with mixture ratio of 50:50 failed at an OLR of 7.0 g VS/(L⋅d), which was likely due to mechanical issues or improper reactor configuration. The genus Proteiniphilum contributed to the increase in total ammonia nitrogen. These findings provide useful guidance for optimizing co-digestion system, enhancing reactor performance and improving the wastes treatment.

The effects of dietary medium-chain fatty acids on ruminal methanogenesis and fermentation in vitro and in vivo: A meta-analysis

The efficacy of methane (CH₄ ) suppression using medium-chain fatty acids (MCFA) remains inconclusive, despite a number of studies on this topic are available. We thus carried out a meta-analysis to integrate the published data on different concentrations and types of MCFA such as lauric acid and myristic acid, which investigated ruminal methanogenesis and fermentation in in vitro and in vivo experiments. In vitro MCFA sources were classified either as pure MCFA (lauric acid, myristic acid and their combinations) or as natural MCFA-rich oils (canola oil enriched with lauric acids, coconut oil, krabok oil and palm kernel oil). The MCFA sources used in the in vivo studies were coconut oil, lauric acid, myristic acid and the combination of lauric and myristic acids. A total of 41 studies (20 in vitro and 21 in vivo studies) were compiled in our database, which included the data on CH₄ emission, digestibility, ruminal fermentation products and microbial populations. The results showed that the amount of CH₄ production per unit of digested organic matter decreased linearly under in vitro conditions (p < .01) and tended to decrease quadratically under in vivo conditions (p < .07) with increasing doses of MCFA. Populations of protozoa (p < .01) in both in vitro and in vivo responded negatively in a linear manner, whereas Archaea population diminished quadratically (p = .04) only in the in vitro conditions with increasing doses of MCFA. Increasing dietary MCFA concentrations also reduced the fibre digestibility linearly (p < .05) in both in vitro and in vivo conditions. CH₄ production for different sources of MCFA decreased in following order: coconut oil > lauric acid > myristic acid > mixed lauric and myristic acids > palm kernel oil > canola oil enriched with lauric acids > krabok oil. It can be concluded that the effect of MCFA on ruminal methanogenesis depends on the amount and type of MCFA.

Replacement of forage fiber with non-forage fiber sources in dairy cow diets changes milk extracellular vesicle-miRNA expression

Milk is a dynamic source of nutrients and bioactive factors, varying with the nutrition status of the cattle. We partly replaced alfalfa hay with whole cotton seed and soybean hull (non-forage fiber source, NFFS) in the feed formula of treated cows and evaluated the effects on milk extracellular vesicles (EVs). The NFFS supplement did not affect the shape of milk EVs observed using a transmission electron microscope. Nanoparticle tracking analysis revealed that the EV concentration increased significantly in treated cows (P = 0.019), with the peak diameter unaffected by the treatment. The EV-RNA concentration and small RNA content, particularly rRNAs and tRNAs, significantly increased in the treated cows (P < 0.05). The other small RNAs, i.e. miRNAs, cis-regulatory elements, snRNAs, and other Rfam RNAs showed no significant difference between the two groups. Totally 276 milk EV-miRNAs were identified. Thirteen miRNAs, accounting for 76%, in the highly expressed top 20, were immune-related. In addition, 9 differently expressed miRNAs (4 up-regulated and 5 down-regulated) were identified (P < 0.05). Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the differently expressed miRNAs were related to the citrate cycle, fat digestion and absorption process, taurine and hypo-taurine metabolism, and glycosphingolipid biosynthesis. This study documents the milk nutrition assessment from macromolecules, especially EVs.

Microbiome and Metabolome Analyses of Milk From Dairy Cows With Subclinical Streptococcus agalactiae Mastitis-Potential Biomarkers

The microbial ecosystem in the udders of dairy cows directly influences the flavor and quality of milk. However, to our knowledge, no published research has analyzed the complex relationship between the udder microbiome and its associated metabolism in animals with subclinical mastitis. We identified the bacterial species and measured relative population numbers in the milk of cows with subclinical Streptococcus agalactiae mastitis (GBS) and compared this information to that from the milk of healthy cows. Metabolite profiles were determined to investigate correlations between the milk microbiota and metabolic factors in healthy vs. GBS dairy cows. Six milk samples from GBS cows and six from healthy cows were subjected to 16S rRNA gene sequencing to identify the microbial species using a MiSeq high-throughput sequencing apparatus. The metabolites present in the milk were identified by gas chromatography time-of-flight mass spectrometry. Both principal component analysis and orthogonal partial least squares discriminant analysis indicated that the metabolites were well-separated from each other in the milk samples from the two groups. GBS dramatically altered microbial diversity, and the GBS group had significantly fewer Proteobacteria, Actinobacteria, and Acidobacteria than the CON group, with greater relative abundance of Firmicutes (p < 0.01). Several bacterial genera, such as Streptococcus, were significantly more abundant in milk from the GBS group than in milk from the CON group, and there was a tendency for greater abundance of Turicibacter (p = 0.07) and Enterococcus spp. (p = 0.07) in the GBS group. The levels of five milk metabolites were significantly higher in the GBS group than in the CON group: phenylpyruvic acid, the homogentisic acid: 4-hydroxyphenylpyruvic acid ratio, the xanthine: guanine ratio, uridine and glycerol. Metabolic pathway analysis of the different metabolites revealed that the following were enriched in both groups: galactose metabolism; pentose and glucuronate interconversion; starch and sucrose metabolism; alanine, aspartate and glutamate metabolism; arginine biosynthesis; citrate cycle (TCA cycle); D-glutamine and D-glutamate metabolism; and the neomycin, kanamycin, and gentamicin biosynthesis pathways. Several typical metabolites were highly correlated with specific ruminal bacteria, such as Streptococcaceae, Lachnospiraceae, Lactobacillaceae and Corynebacteriaceae, demonstrating the functional correlations between the milk microbiome and associated metabolites. These findings revealed that the milk microbiota and metabolite profiles were significantly different between the two groups of cows, raising the question of whether the microbiota associated with the bovine mammary gland could be related to mammary gland health. There was also a relationship between milk quality and the presence of spoilage bacteria. Other bacterial taxa should be investigated, as related information may provide insights into how perturbations in milk metabolomics profiles relate to differences in milk synthesis between healthy cows and those with subclinical mastitis.

Illumina MiSeq sequencing reveals the effects of grape seed procyanidin on rumen archaeal communities in vitro

Objective

The present study explored the effects of grape seed procyanidin extract (GSPE) on rumen fermentation, methane production and archaeal communities in vitro.

Methods

A completely randomized experiment was conducted with in vitro incubation in a control group (CON, no GSPE addition; n = 9) and the treatment group (GSPE, 1 mg/bottle GSPE, 2 g/kg dry matter; n = 9). The methane and volatile fatty acid concentrations were determined using gas chromatography. To explore methane inhibition after fermentation and the response of the ruminal microbiota to GSPE, archaeal 16S rRNA genes were sequenced by MiSeq high-throughput sequencing.

Results

The results showed that supplementation with GSPE could significantly inhibit gas production and methane production. In addition, GSPE treatment significantly increased the proportion of propionate, while the acetate/propionate ratio was significantly decreased. At the genus level, the relative abundance of Methanomassiliicoccus was significantly increased, while the relative abundance of Methanobrevibacter decreased significantly in the GSPE group.

Conclusion

In conclusion, GSPE is a plant extract that can reduce methane production by affecting the structures of archaeal communities, which was achieved by a substitution of Methanobrevibacter with Methanomassiliicoccus.