Effect of slow-release urea on the composition of ruminal bacteria and fungi communities in yak

Linkages between rumen microbiome, host, and environment in yaks, and their implications for understanding animal production and management

Livestock on the Qinghai-Tibetan Plateau is of great importance for the livelihood of the local inhabitants and the ecosystem of the plateau. The natural, harsh environment has shaped the adaptations of local livestock while providing them with requisite eco-services. Over time, unique genes and metabolic mechanisms (nitrogen and energy) have evolved which enabled the yaks to adapt morphologically and physiologically to the Qinghai-Tibetan Plateau. The rumen microbiota has also co-evolved with the host and contributed to the host's adaptation to the environment. Understanding the complex linkages between the rumen microbiota, the host, and the environment is essential to optimizing the rumen function to meet the growing demands for animal products while minimizing the environmental impact of ruminant production. However, little is known about the mechanisms of host-rumen microbiome-environment linkages and how they ultimately benefit the animal in adapting to the environment. In this review, we pieced together the yak's adaptation to the Qinghai-Tibetan Plateau ecosystem by summarizing the natural selection and nutritional features of yaks and integrating the key aspects of its rumen microbiome with the host metabolic efficiency and homeostasis. We found that this homeostasis results in higher feed digestibility, higher rumen microbial protein production, higher short-chain fatty acid (SCFA) concentrations, and lower methane emissions in yaks when compared with other low-altitude ruminants. The rumen microbiome forms a multi-synergistic relationship among the rumen microbiota services, their communities, genes, and enzymes. The rumen microbial proteins and SCFAs act as precursors that directly impact the milk composition or adipose accumulation, improving the milk or meat quality, resulting in a higher protein and fat content in yak milk and a higher percentage of protein and abundant fatty acids in yak meat when compared to dairy cow or cattle. The hierarchical interactions between the climate, forage, rumen microorganisms, and host genes have reshaped the animal's survival and performance. In this review, an integrating and interactive understanding of the host-rumen microbiome environment was established. The understanding of these concepts is valuable for agriculture and our environment. It also contributes to a better understanding of microbial ecology and evolution in anaerobic ecosystems and the host-environment linkages to improve animal production.

Effect of Tea Saponins on Rumen Microbiota and Rumen Function in Qinchuan Beef Cattle

Antibiotics can promote livestock growth but have side effects, so the search for safe and effective alternatives to antibiotics is urgent. This study aimed to evaluate the effect of supplementing cattle feed with tea saponins on ruminal bacteria and fungi. Sixteen Qinchuan beef cattle with a live body weight of 250 ± 10 kg were divided into four groups (four animals in each group) using a completely randomized experimental design. Four different levels of tea saponins were provided to the Qinchuan cattle as treatments, including 0 g/cattle per day control, CON), 10 g/cattle per day (low-level, LT), 20 g/cattle per day (medium-level, MT) and 30 g/cattle per day (high-level, HT). The pre-feeding period was 10 days and the official period was 80 days in this experiment. After 90 days of feeding, the rumen fluid from sixteen Qinchuan beef cattle was collected using an oral stomach tube for evaluating changes in ruminal microbiota and rumen fermentation parameters. Results indicate that the total VFAs and proportions of propionate in the LT group was significantly higher than that in the CON and HT groups (p < 0.05). For ruminal bacteria, results indicate that the Chao1 index of the MT group was significantly lower than the CON and HT groups (p < 0.05). The phyla Bacteroidetes and Firmicutes were found to be the most abundant in all treatment groups, with the LT group having significantly increased relative abundances of Proteobacteria, Actinobacteria and Ascomycota at the phylum level (p < 0.05). The relative abundance of Bacteroides was found to be relatively lower in the LT, MT and HT treatment groups compared with the CON treatment group at the genus level (p < 0.05). For ruminal fungi, the LT treatment group was found to have higher relative abundances of Saccharomyces and Aspergillus, and lower relative abundances of Succiniclasticum and Bacteroides at the at the phylum level (p < 0.05). Compared with the CON treatment group, a significant increase in the relative abundance of Saccharomyces and Aspergillus were observed in the LT treatment group at the genus level (p < 0.05). PICRUSt analyses identified pathways associated with Xenobiotic biodegradation and metabolism and glycolysisIII to be significantly enriched in the LT and HT treatment groups (p < 0.05). These findings could provide insights on how tea saponins may influence ruminal bacteria and fungi, providing a theoretical basis for replacing antibiotics with tea saponins for promoting growth in cattle.

Effects of excessive urea on rumen morphology and microbiota in Jianzhou Da'er goat (Capra hircus)

Urea is frequently used as a protein supplement in ruminant diets, but if used improperly, it can easily result in urea poisoning. The purpose of this study was to explore the effects of excessive urea feeding on rumen pathology and microbial diversity of the Jianzhou Da'er goat (Capra hircus). In this study, 9 male Jianzhou Da'er goats with an average weight of 22.9 kg were randomly divided into the control group (0% urea), 5% urea group and 10% urea group (dry matter basis, 3 goats per group). Morphological differences of rumen tissues were analyzed by Hematoxylin-Eosin staining and Prussian blue staining, and rumen microorganisms differences were analyzed by 16S rDNA sequencing on the Illumina Novaseq platform. Histopathological analysis showed that the length of rumen papilla in the 5% urea and 10% urea groups were shortened compared to the control group, and the thickness of the stratum corneum and muscular layer were significantly thinned (P < 0.05). 16S rRNA sequencing analysis indicated that microbial richness and diversity were significantly lower in goats fed on 5% urea or 10% urea, the abundance of Prevotella ruminicola was significantly decreased (P < 0.05), and the abundance of Ruminobacter amylophilus was significantly increased (P < 0.05), as compared with the control group. This study indicated that feeding 5% and 10% urea could damage rumen tissue morphology. Feeding 10% urea significantly reduced rumen microbial diversity and the abundance of Prevotella ruminicola, but increased the abundance of Ruminobacter amylophilus.

Effect of Clostridium butyricum Supplementation on in vitro Rumen Fermentation and Microbiota With High Grain Substrate Varying With Media pH Levels

Clostridium butyricum (C. butyricum) can survive at low pH, and it has been widely used as an alternative to antibiotics for the improvement of feed efficiency and animal health in monogastrics. A recent study suggested that the improved ruminal fermentation with supplementing C. butyricum is may be associated with increasing the abundance of rumen microbiota in Holstein heifers, as ruminal pH plays a key role in rumen microbiota and the probiotics are often active in a dose-dependent manner. The objective of this study was to determine the effects of increasing the doses of C. butyricum on gas production (GP) kinetics, dry matter disappearance (DMD), fermentation characteristics, and rumen microbiota using a high grain substrate in batch culture varying with media pH levels. The doses of C. butyricum were supplemented at 0 (control), 0.5 × 106, 1 × 106, and 2 × 106 CFU/bottle, respectively, at either media pH 6.0 or pH 6.6. The fermentation microbiota at 0 and 1 × 106 CFU/bottle were determined using the 16S rRNA high throughput sequencing technology. Overall, the GP, DMD, total volatile fatty acid (VFA) concentration, and the ratio of acetate:propionate were higher (P <0.01) at media pH 6.6 than at pH 6.0. However, there was interaction between pH × dose of C. butyricum for rate constant of GP (P = 0.01), average GP rate (P = 0.07), and volume of GP (P = 0.06); with the increase in C. butyricum supplementation, the GP kinetics were not changed at media pH 6.0, but the volume (P = 0.02), rate of GP (P = 0.01), and average GP rate (P = 0.01) were quadratically changed at media pH 6.6. The DMD was not affected by increasing the supplementation of C. butyricum. The molar proportions of propionate (P <0.09), butyrate (P <0.06), and NH3-N concentration (P = 0.02) were quadratically changed with increasing supplementation of C. butyricum regardless of media pH levels. The interactions between media pH level and dose of C. butyricum supplementation were noticed for alpha diversity indexes of Shannon (P = 0.02) and Evenness (P = 0.04). The alpha diversity indexes increased (P <0.05) except for Chao1 with supplementation of C. butyricum. The unweighted uniFrac analysis showed that the group of control at media pH 6.0 and control at media pH 6.6, and supplementation of C. butyricum and control at media pH 6.0 clustered separately from each other. At the phylum level, relative abundance (RA) of Bacteroidota was lower (P <0.01) and Firmicutes was higher (P <0.01) at media pH 6.6 than pH 6.0. Moreover, RA of Proteobacteria decreased (P <0.05) with supplemented C. butyricum at either media pH 6.6 or pH 6.0. At media pH 6.6, RA of Rikenellaceae_RC9_gut_group and Prevotella were decreased, and CAG-352 was increased (at genus level) compared to pH 6.0. Supplementation of C. butyricum decreased RA of Rikenellaceae_RC9_gut_group and increased CAG-352 at media pH 6.0. It could hence be concluded that manipulating media pH level and supplementation of C. butyricum effectively modulated in vitro rumen fermentation characteristics and microbiota but in a dose depending manner of C. butyricum addition.

Comfrey polysaccharides modulate the gut microbiota and its metabolites SCFAs and affect the production performance of laying hens

Effects of dietary supplementation of comfrey polysaccharides (CPs) on production performance, egg quality, and microbial composition of cecum in laying hens were evaluated. A total of 240 laying hens were allocated into 4 groups with 6 replicates per group. The laying hens were fed diets containing CPs at levels of 0, 0.5, 1.0, and 1.5 %, respectively. The results showed that the egg production rate increased by 5.97 %, the egg mass improved by 6.71 %, and the feed conversion rate reduced by 5.43 % in the 1.0 % supplementation group of CPs compared with those in the control group. The digestibility of ash, crude fat, and phosphorus was notably improved by the addition of CPs at 1.0 % (P < 0.05). The relative abundances of Bacteroidetes at the phylum level, Bacteroidaceae, Rikenellaceae, and Prevotellaceae at the family level were increased by CPs (P < 0.05). The relative abundances of Bacteroides, Megamonas, Rikenellaceae_RC9_gut_group, [Ruminococcus]_torques_group, Methanobrevibacter, Desulfovibrio, Romboutsia, Alistipes, and Intestinimonas at the genus level were increased by CPs (P < 0.05). Dietary supplementation of CPs could enhance the production performance of laying hens, which might be related to the improvement of nutrient digestibility and microbial community modulations in the cecum. Therefore, CPs have potential application value as prebiotics in laying hens.

Effect of commercial slow-release urea product on in vitro rumen fermentation and ruminal microbial community using RUSITEC technique

Background

The objectives of this study were to determine the effect of commercial slow-release urea (SRU) on in vitro fermentation characteristics, nutrient digestibility, gas production, microbial protein synthesis and bacterial community using a rumen simulation technique (RUSITEC). The experiment was a completely randomized design with four treatments and four replications of each treatment. Treatments were: control diet (no SRU addition), control diet plus 0.28% SRU (U28), or plus 0.56% SRU (U56), and control diet that was modified substituting a part of soybean meal equivalent to 0.35% SRU (MU35; dry matter [DM] basis). The experiment consisted of 8 d of adaptation and 7 d of data and sample collection. Rumen inoculum was obtained from three ruminally fistulated Angus cows fed the same diet to the substrate incubated.

Results

Digestibility of DM, organic matter (OM), crude protein (CP), fibre and starch was not affected, but daily production of gas (P < 0.07) and methane (P < 0.05) was quadratically increased with increasing SRU supplementation. The increase of SRU addition did not affect fermentation pH and total volatile fatty acid (VFA) production, whereas linearly (P < 0.01) decreased proportion of propionate, and linearly (P < 0.01) increased acetate to propionate ratio and ammonia nitrogen (N) concentration. The microbial N efficiency was also linearly (P < 0.03) improved with increasing supplementation of SRU. In comparison with control diet, the dietary substitution of SRU for part of soybean meal increased (P < 0.05) the digestibility of DM, OM and CP and decreased (P < 0.02) the total gas production. The total VFA production and acetate to propionate ratio did not differ between control and MU35, whereas the proportion of butyrate was lower (P < 0.05) and that of branched-chain VFA was greater (P < 0.05) with MU35 than control diet. Total and liquid-associated microbial N production as well as ammonia N concentration were greater (P < 0.03) with MU35 than control diet. Observed operational taxonomic units (OTUs), Shannon diversity index, and beta diversity of the microbial community did not differ among treatments. Taxonomic analysis revealed no effect of adding SRU on the relative abundance of bacteria at the phylum level, while at the genus level, the beneficial impact of SRU on relative abundance of Rikenellaceae and Prevotellaceae in feed particle-associated bacteria, and the abundance of Roseburia in liquid associate bacteria was greater (P < 0.05) with MU35.

Conclusions

Supplementation of a dairy cow diet with SRU showed potential of increase in ammonia N concentration and microbial protein production, and change fermentation pattern to more acetate production. Adding SRU in dairy cow diet also showed beneficial effect on improving digestibility of OM and fibre. The results suggest that SRU can partially substitute soybean meal in dairy cow diet to increase microbial protein production without impairing rumen fermentation.

Amino acids metabolism by rumen microorganisms: Nutrition and ecology strategies to reduce nitrogen emissions from the inside to the outside

For the ruminant animal industry, the emission of nitrogenous substances, such as nitrous oxide (N₂O) and ammonia (NH₃), not only challenges environmental sustainability but also restricts its development. The metabolism of proteins and amino acids by rumen microorganisms is a key factor affecting nitrogen (N) excretion in ruminant animals. Rumen microorganisms that affect N excretion mainly include three types: proteolytic and peptidolytic bacteria (PPB), ureolytic bacteria (UB), and hyper-ammonia-producing bacteria (HAB). Microbes residing in the rumen, however, are influenced by several complex factors, such as diet, which results in fluctuations in the rumen metabolism of proteins and amino acids and ultimately affects N emission. Combining feed nutrition strategies (including ingredient adjustment and feed additives) and ecological mitigation strategies of N₂O and NH₃ in industrial practice can reduce the emission of nitrogenous pollutants from the ruminant breeding industry. In this review, the characteristics of the rumen microbial community related to N metabolism in ruminants were used as the metabolic basis. Furthermore, an effective strategy to increase N utilisation efficiency in combination with nutrition and ecology was reviewed to provide an inside-out approach to reduce N emissions from ruminants.

Meta-analysis and sustainability of feeding slow-release urea in dairy production

Slow-release urea (SRU) is a coated non-protein nitrogen (NPN) source for providing rumen degradable protein in ruminant nutrition. A meta-analysis was conducted to evaluate the effects of replacing vegetable protein sources with SRU (Optigen^®, Alltech Inc., USA) on the production performance of dairy cows. Additionally, the impact of SRU supplementation on dairy sustainability was examined by quantifying the carbon footprint (CFP) of feed use for milk production and manure nitrogen (N) excretion of dairy cows. Data on diet composition and performance variables were extracted from 17 experiments with 44 dietary comparisons (control vs. SRU). A linear mixed model and linear regression were applied to statistically analyse the effect of SRU on feed intake and production performance. Feeding SRU decreased (P < 0.05) dry matter intake (DMI, -500 g/d) and N intake (NI, -20 g/d). There was no significant effect (P > 0.05) on milk yield, fat-corrected milk, energy-corrected milk, and milk fat and protein composition. However, SRU supplementation improved (P < 0.05) feed efficiency (+3%) and N use efficiency (NUE, +4%). Regression analyses revealed that increasing SRU inclusion level decreased DMI and NI whereas increasing dietary crude protein (CP) increased both parameters. However, milk yield and feed efficiency increased in response to increasing levels of SRU inclusion and dietary CP. The NUE had a positive relationship with SRU level whereas NUE decreased with increasing dietary CP. The inclusion of SRU in dairy diets reduced the CFP of feed use for milk production (-14.5%; 373.13 vs. 319.15 g CO₂ equivalent/kg milk). Moreover, feeding SRU decreased manure N excretion by 2.7% to 3.1% (-12 to -13 g/cow/d) and N excretion intensity by 3.6% to 4.0% (-0.50 to -0.53 g N/kg milk). In conclusion, feeding SRU can contribute to sustainable dairy production through improvement in production efficiency and reduction in environmental impacts.

Astragalus root extract improved average daily gain, immunity, antioxidant status and ruminal microbiota of early weaned yak calves

BACKGROUND

Early weaning in yak calves is being attempted to improve yak reproduction rate. However, this has to be done with caution because of the high mortality rate of calves due to the lack of nutrients and the harsh environmental conditions. Twenty-four weaned male yak calves were used in a 60 day feeding trial in which astragalus root extract (ARE) was supplemented. They were assigned randomly to one of four dietary treatments (n = six per treatment) that differed in ARE level: 0 g kg^-1 (control), ARE₀ ; 20 g kg^-1 , ARE₂₀ ; 50 g kg^-1 , ARE_50; and 80 g kg^-1 dry matter intake (DMI), ARE₈₀ .

RESULTS

Final bodyweight and average daily gain (ADG) were significantly higher and the DMI/ADG ratio was significantly lower in calves with ARE supplementation than control (ARE₀ ) calves. Ruminal concentrations of acetate and propionate and serum concentration of superoxide dismutase in ARE₈₀ calves were higher than in the other groups and serum concentration of insulin was higher in ARE₈₀ calves than in ARE₂₀ calves. Serum immunoglobulin G (IgG) and interleukin-2 (IL-2) concentrations in ARE-fed calves were higher than in controls. Serum tumor necrosis factor (TNF-α) concentration was higher in ARE₅₀ and ARE₈₀ groups than ARE₀ calves and serum interleukin-6 (IL-6) concentration was higher in ARE₈₀ than in ARE₀ calves. Serum immunoglobulin A (IgA), IgG and immunoglobulin M (IgM) concentrations increased with age in ARE-fed calves. ARE supplementation increased the abundance of fiber degrading bacteria.

CONCLUSION

ARE at a dosage of 5% to 8% DMI can be supplemented to early weaned yak calves to improve growth performance, antioxidant capacity and immunity. © 2020 Society of Chemical Industry.

Insight into the mechanism of urea inhibit ovalbumin-glucose glycation by conventional spectrometry and liquid chromatography-high resolution mass spectrometry

The inhibition effect of urea on ovalbumin (OVA) glycation was investigated, and the mechanism was evaluated through the changes in protein structure as well as glycation sites and average degree of substitution per peptide molecule (DSP) by conventional spectrometry and liquid chromatography-high resolution mass spectrometry (LC-HRMS). A urea concentration of 3 M was chosen as the optimum condition. Ultraviolet and fluorescence spectra suggested that both glycation and urea treatment could unfold the OVA, but urea inhibited the glycation-induced protein unfolding. Circular dichroism spectra showed that urea treatment could increase the β-sheet content and reduce the α-helix content of OVA. LC-HRMS indicated that the number of glycation sites was reduced from 15 to 3, and DSP values decreased with urea treatment. In conclusion, urea could significantly inhibit the OVA-glucose glycation, and the sites competition as well as structure unfolding inhibition resulted from urea could be the main factors.

Influence of probiotics on biofilm formation and diversity of bacteria colonising crop sorghum ensiled with unsalable vegetables

The objective of this study was to characterise in situ digestion kinetics and bacterial colonisation of crop sorghum ensiled with unsalable carrot or pumpkin at 0, 20 or 40% dry matter (DM). Silages with or without the application of a commercial probiotic were incubated in situ for 0, 3, 6, 9, 24 and 48 h. Calculation of in situ digestion kinetics was conducted for DM, organic matter and neutral detergent fibre (aNDF). The V4 region of the 16S rRNA gene was sequenced to determine the composition and diversity of bacteria colonising the silage. Organic matter and DM digestion kinetics indicated that greater vegetable inclusion increased (P < 0.05) the soluble fraction and effective degradability. Bacterial richness at 48 h incubation was greater (P = 0.02) in 20% carrot and 40% pumpkin treatments, compared with the control. An effect of level × probiotic was observed with increased Shannon diversity (P = 0.01) for 40% carrot and 20% pumpkin probiotic treatments, respectively. Primary colonising bacteria were members of the Prevotella genus, dominating after 3 and 6 h of incubation. The abundance of Prevotella increased by 4.1% at 3 h (P < 0.01) and by 4.7% at 9 h incubation with probiotics, compared with the control. Secondary biofilm colonisers included members of Treponema, Saccharofermentans, Fibrobacter, Ruminobacter and Anaerosporobacter genera, dominant from 9 h incubation onward. This study demonstrated that including unsalable vegetables at 20 or 40% DM increases the soluble fraction and effective degradability of sorghum silage during in situ digestion and increases diversity of bacteria colonising ensiled vegetables within the rumen. KEY POINTS: • Ensiling unsalable vegetables is a viable strategy to reduce food waste. • Ensiled vegetables increased in situ soluble fraction and effective degradability. • Bacterial richness at 48 h incubation improved with 20% carrot or 40% pumpkin. • Diversity of colonising rumen bacteria increased with carrot or pumpkin inclusion.

Inulin improves the egg production performance and affects the cecum microbiota of laying hens

Egg production performance, egg quality, nutrient digestibility, and microbial composition as affected by dietary inulin supplementation were evaluated in laying hens. A total of 300 laying hens were divided into 5 groups and fed diets containing inulin at levels of 0 (control), 5, 10, 15 and 20 g/kg, respectively. The results showed that the 15 g/kg inulin supplementation level improved average egg weight by 2.54%, egg mass by 5.76%, and laying rate by 3.09%, and decreased the feed conversion ratio by 3.61% compared to those of the control during feeding weeks 1 to 8. Dietary inulin supplementation improved eggshell thickness, nutrient digestibility and cecum Bacteroidales_S24-7_ group abundance in the laying hens. In conclusion, dietary inulin supplementation, particularly at the level of 15 g/kg, improved the egg production performance and eggshell thickness of laying hens, mainly due to increased nutrient digestibility and selective modulations of the cecum microbial communities.

Survey of rumen microbiota of domestic grazing yak during different growth stages revealed novel maturation patterns of four key microbial groups and their dynamic interactions

BACKGROUND

The development and maturation of rumen microbiota across the lifetime of grazing yaks remain unexplored due to the varied lifestyles and feed types of yaks as well as the challenges of obtaining samples. In addition, the interactions among four different rumen microbial groups (bacteria, archaea, fungi and protozoa) in the rumen of yak are not well defined. In this study, the rumen microbiota of full-grazing yaks aged 7 days to 12 years old was assessed to determine the maturation patterns of these four microbial groups and the dynamic interactions among them during different growth stages.

RESULTS

The rumen microbial groups (bacteria, archaea, protozoa and fungi) varied through the growth of yaks from neonatal (7 days) to adult (12 years), and the bacterial and archaeal groups were more sensitive to changes in growth stages compared to the two eukaryotic microbial groups. The age-discriminatory taxa within each microbial group were identified with the random forest model. Among them, Olsenella (bacteria), Group 10 sp., belonging to the family Methanomassiliicoccaceae (archaea), Orpinomyces (fungi), and Dasytricha (protozoa) contributed the most to discriminating the age of the rumen microbiota. Moreover, we found that the rumen archaea reached full maturation at 5 approximately years of age, and the other microbial groups matured between 5 and 8 years of age. The intra-interactions patterns and keystone species within each microbial group were identified by network analysis, and the inter-interactions among the four microbial groups changed with growth stage. Regarding the inter-interactions among the four microbial groups, taxa from bacteria and protozoa, including Christensenellaceae R-7 group, Prevotella 1, Trichostomatia, Ruminococcaceae UCG-014 and Lachnospiraceae, were the keystone species in the network based on betweenness centrality scores.

CONCLUSIONS

This study depicted a comprehensive view of rumen microbiota changes in different growth stages of grazing yaks. The results revealed the unique microbiota maturation trajectory and the intra- and inter-interactions among bacteria, archaea, fungi and protozoa in the rumen of grazing yaks across the lifetime of yaks. The information obtained in this study is vital for the future development of strategies to manipulate rumen microbiota in grazing yaks for better growth and performance in the harsh Qinghai-Tibetan Plateau ecosystem.

Diversity and Composition of Rumen Bacteria, Fungi, and Protozoa in Goats and Sheep Living in the Same High-Altitude Pasture

Simple Summary

Tibetan goats and sheep graze together but have different growth performances, immune responses, and feeding preferences in the Tibetan pasture. Rumen microbiota composed of bacteria, fungi, and protozoa are necessary for a healthy ruminant. Therefore, in this study, we comprehensively describe composition and diversity of bacteria, fungi, and protozoa in the high- altitude rumen. Compared with sheep, the bacteria that degrade crude protein and produce volatile fatty acids (VFA) were increased in the rumen of goats (Saccharofermentans and Lachnospiraceae_XPB1014) (p < 0.05). In addition, when compared with goats, the fungi and protozoa that degrade fiber were increased in rumen of sheep (Neocallimastigaceae and Metadinium) (p < 0.05). Furthermore, VFA were significantly increased in the rumen of goats compared with sheep (p < 0.05). The VFA level was consistent with differences in the microbiota composition in the rumen between goats and sheep. Under mixed grazing conditions, goats tend to select a high-crude protein diet that is good for growth, whereas sheep tend to select a high-lignin diet that is difficult to digest. Therefore, the different microbiota in the rumen of goats and sheep may be explained by dietary preference.

Abstract

Environmental adaptation of ruminants was highly related to microbiota in the rumen. To investigate the diversity and composition of bacteria, fungi, and protozoa in the rumen of high-altitude animals, amplicon gene sequencing was performed using rumen fluid samples derived from both Tibetan goats and sheep at the same pasture in a highland (altitude > 4800 m). Between these two species, the ruminal bacteria and fungi were significantly different at multiple taxonomic levels. The alpha diversity of bacteria was significantly high in goats (p < 0.05). One hundred and sixty-four and 29 Operational Taxonomy Units (OTUs) with significant differences were detected in bacteria and fungi, respectively. The abundance of bacteria, fungi, and protozoa in the rumen was characterized at multiple taxonomic levels, and we determined that Firmicutes, Bacteroidetes, Neocallimastigomycota, and Ciliophora were the most abundant bacteria, fungi, and protozoa. The family Neocallimastigaceae and the genus Metadinium had cellulose degradation capacity in the rumen with high abundance, thereby, suggesting that fungi and protozoa played an essential role in rumen fermentation. In addition, by comparing microbiota in the rumen of goats and sheep it was found, that the fiber-degrading fungi genus (Cyllamyces) was increased in the rumen of sheep (p < 0.05) whereas VFA-producing bacteria (Saccharofermentans and Lachnospiraceae_XPB1014) were increased in the rumen of goats (p < 0.05). Interestingly, in the rumen, no differences in protozoa were observed between goats and sheep (p > 0.05). Furthermore, when compared to sheep, level of acetic acid, propionic acid, and total volatile fatty acid (TVFA) were significantly increased in the rumen of goats (p < 0.05). Taken together, these results suggested microbiota in the rumen drive goats to better adapt to high-altitude grazing conditions.

Characterization of Anaerobic Rumen Fungal Community Composition in Yak, Tibetan Sheep and Small Tail Han Sheep Grazing on the Qinghai-Tibetan Plateau

Simple Summary

Anaerobic rumen fungi play a vital role in fiber degradation. The objective of this study was to compare the anaerobic rumen fungal communities of full grazing ruminants in the Qinghai-Tibetan Plateau. Our results showed that the anaerobic rumen fungal community was affected by host species and the dynamic associations of them were host specific. This is the first study exploring the anaerobic rumen fungi in the full-grazing ruminants, which could lay a solid foundation to really identify fiber degradation fungal taxa using culture-dependent techniques in the future.

Abstract

The anaerobic rumen fungal community play a critical role in fibrous material degradation. However, there is a lack of data describing the composition of anaerobic rumen fungal community of full grazing ruminants in the Qinghai-Tibetan Plateau. For this reason, we employed the next-generation sequencing technique to elucidate the rumen fungal structure composition and evaluate the effects of host species on fungal communities. Community comparisons (Bray–Curtis index) between yak and Tibetan sheep revealed that the rumen fungal community was affected by host species (p < 0.05). The alpha diversity indices in the yak were significantly higher than in the Tibetan sheep and Small Tail Han sheep. Neocallimastigomycota was predominant regardless of host species. Within this phylum, unidentified genus of Neocallimastigaceae was the most dominant in all samples, followed by Piromyces and Orpinomyces. Moreover, the shared and unique OTUs in the rumen were identified and most of them belonged to the Orpinomyces. Co-occurrence network analysis identified that each animal species had their own keystone species and most of them were non-dominant flora. Our data indicate that host breeds override living environment as the key factor that determines fungal community in the rumen of grazing ruminants in the Qinghai-Tibetan Plateau.

Effects of oregano essential oil on in vitro ruminal fermentation, methane production, and ruminal microbial community

Different inclusion rates of oregano essential oil (OEO) were investigated for their effects on ruminal in vitro fermentation parameters, total gas, methane production, and bacterial communities. Treatments were (1) control, 0 mg/L of OEO (CON); 13 mg/L (OEO1); 52 mg/L (OEO2); 91 mg/L (OEO3); and 130 mg/L (OEO4), each incubated with 150 mL of buffered rumen fluid and 1,200 mg of substrate for 24 h using the Ankom in vitro gas production system (Ankom Technology Corp., Fairport, NY). Treatment responses were statistically analyzed using polynomial contrasts. Digestibility of DM, NDF, and ADF increased quadratically with increasing OEO inclusion rates. Digestibility of DM and NDF were highest for OEO2, whereas ADF digestibility was highest for OEO3, compared with CON, with the remaining treatments being intermediate and similar. Ammonia nitrogen concentrations decreased from CON at a quadratic rate with increasing OEO inclusion rates, and OEO2 had the lowest concentration compared with the other groups. Total VFA, acetate, propionate, butyrate, valerate, and isovalerate concentrations linearly decreased with increasing OEO inclusion rates. Total gas production levels by CON and OEO4 were greater than those of OEO1, OEO2, and OEO3 in a quadratic response, and methane production linearly decreased from CON, compared with OEO4, at a decreasing rate with OEO inclusion rates. As determined by 16S rRNA sequencing, the α biodiversity of ruminal bacteria was similar among OEO inclusion rates. Increasing OEO inclusion rates linearly increased the relative abundance of Prevotella and Dialister bacteria. Several bacteria demonstrated different polynomial responses, whereas several bacteria were similar among increasing OEO inclusion rates. These results suggested that OEO supplementation can modify ruminal fermentation to alter VFA concentrations and reduce methane emissions by extensively altering the ruminal bacterial community, suggesting an optimal feeding rate for future animal studies of approximately 52 mg/L for mature ruminants.

A comparative study of the effects of microbial agents and anaerobic sludge on microalgal biotransformation into organic fertilizer

The effects of Lactobacillus bulgaricus, Rhodopseudomonas palustris, Issatchenkia orientalis and anaerobic sludge on anaerobic digestion of microalgae to organic fertilizer were studied. High-throughput sequencing was used to analyze characteristics of microbial community structure during anaerobic digestion of microalgae using different inocula. Lactobacillales and Saccharomycetales were more likely to become dominant bacteria and eukaryotes. The relative abundance of Lactobacillales was 98.15%, 88.61% and 81.73% of total bacteria at the beginning, middle and end of the experiment, respectively. Meanwhile, the relative abundance of Saccharomycetales was 90.91%, 98.41% and 98.8% of eukaryotes at the beginning, middle and end of the experiment, respectively. At the end of digestion, the microcystin content in the reactor inoculated with Issatchenkia orientalis decreased to 0.71 μg/kg, which met drinking water standards. Rhodopseudomonas palustris did not become a dominant microorganism and had the most negative impact on the atmosphere. Volatile organic compounds were 11.92 mg/kg while the odor concentration reached 97,724 ou/m³. The organic matter content in reactors inoculated with specific groups of microbial agents, which was higher than the standard required for bio-organic fertilizer, occupying over 96% dry weight. In addition, the effective microorganism counts of Issatchenkia orientalis and Lactobacillus bulgaricus in fermentation products reached 1.8E+09 colony-forming units (cfu)/g and 1.6E+09 cfu/g, respectively, which are suitable values for microbial fertilizer.