Effect of dietary concentrate to forage ratios on ruminal bacterial and anaerobic fungal populations of cashmere goats

Exploring rumen fermentation and microbial populations in Dhofari goats fed a chitosan-added diet

The use of chitosan (CHI) in ruminant diets is a promising natural modifier for rumen fermentation, capable of modulating both the rumen pattern and microbial activities. The objective of this study was to explore the rumen fermentation and microbial populations in Dhofari goats fed a diet supplemented with CHI. A total of 24 Dhofari lactating goats (body weight, 27.32 ± 1.80 kg) were assigned randomly into three experimental groups (n = 8 ewes/group). Goats were fed a basal diet with either 0 (control), 180 (low), or 360 (high) mg CHI/kg of dietary dry matter (DM) for 45 days. Feeding high CHI linearly increased (p < 0.05) the propionate level and reduced the acetate, butyrate, and total protozoa count (p < 0.05). Ruminal ammonia nitrogen (NH3-N) concentrations and the acetate:propionate ratio decreased linearly when goats were fed CHI (p < 0.05). The abundances of both Spirochetes and Fibrobacteres phyla were reduced (p < 0.05) with both CHI doses relative to the control. Both low and high CHI reduced (p < 0.05) the relative abundances of Butyrivibrio hungatei, Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens, Selenomonas ruminantium and Neocallimastix californiae populations. Adding CHI significantly decreased (p < 0.05) the abundances of Ascomycota, Basidiomycota, and Bacillariophyta phyla compared to the control. Adding CHI to the diet reduces the abundance of fibrolytic-degrading bacteria, however, it increases the amylolytic-degrading bacteria. Application of 360 mg of CHI/kg DM modified the relative populations of ruminal microbes, which could enhance the rumen fermentation patterns in Dhofari goats.

Impact of methane mitigation strategies on the native ruminant microbiome: A protocol for a systematic review and meta-analysis

Recently, research has investigated the role of the ruminant native microbiome, and the role microbes play in methane (CH4) production and mitigation. However, the variation across microbiome studies makes implementing impactful strategies difficult. The first objective of this study is to identify, summarize, compile, and discuss the current literature on CH4 mitigation strategies and how they interact with the native ruminant microbiome. The second objective is to perform a meta-analysis on the identified16S rRNA sequencing data. A literature search using Web of Science, Scopus, AGRIS, and Google Scholar will be implemented. Eligible criteria will be defined using PICO (population, intervention, comparator, and outcomes) elements. Two independent reviewers will be utilized for both the literature search and data compilation. Risk of bias will be assessed using the Cochrane Risk Bias 2.0 tool. Publicly available 16S rRNA amplicon gene sequencing data will be downloaded from NCBI Sequence Read Archive, European Nucleotide Archive or similar database using appropriate extraction methods. Data processing will be performed using QIIME2 following a standardized protocol. Meta-analyses will be performed on both alpha and beta diversity as well as taxonomic analyses. Alpha diversity metrics will be tested using a Kruskal-Wallis test with a Benjamini-Hochberg multiple testing correction. Beta diversity will be statistically tested using PERMANOVA testing with multiple test corrections. Hedge's g standardized mean difference statistic will be used to calculate fixed and random effects model estimates using a 95% confidence interval. Heterogeneity between studies will be assessed using the I2 statistic. Potential publication bias will be further assessed using Begg's correlation test and Egger's regression test. The GRADE approach will be used to assess the certainty of evidence. The following protocol will be used to guide future research and meta-analyses for investigating CH4 mitigation strategies and ruminant microbial ecology. The future work could be used to enhance livestock management techniques for GHG control. This protocol is registered in Open Science Framework (https://osf.io/vt56c) and available in the Systematic Reviews for Animals and Food (https://www.syreaf.org/contact).

High concentrate diets altered the structure and function of rumen microbiome in goats

This study used metatranscriptomics to investigate the effects of concentrate diet level on rumen microbiome composition and function in goats. A total of 12 healthy 120-day-old Da'er goats were randomly allotted into two treatments: L group (low dietary concentrate level group, concentrate: forage ratio was 25: 75) and H group (high dietary concentrate level group, concentrate: forage ratio was 80: 20). The study included a 10-day pre-feeding period and a 60-day growth experiment. The results showed that compared with the L group, the average daily gain and the slaughter rate in the H group were increased, while the F/G was decreased; the concentration of lactate and ammonia nitrogen, and the proportion of butyrate and valerate in the rumen of the H group were increased, while the proportion of acetate, and the ratio of acetate to propionate were decreased (p < 0.05). Among rumen bacteria, compared with the L group, the H group significantly decreased the relative abundance of Firmicutes and Fibrobacteria at the phylum level, decreased the relative abundance of Bacteroidetes, Fibrobacter, and Sarcina and increased the relative abundance of Clostridium at the genus level, and decreased the relative abundance of Fibrobacter succinogenes, Sarcina sp. DSM 11001, Oscillibacter sp. KLE 1728, and Ruminococcus flavefaciens and increased the relative abundance of Clostridium sp. ND2 and Firmicutes bacteria CAG: 103 at the species level (p < 0.05). Among rumen fungi, the relative abundance of Basidiomycota, Neocallimastigomycota, Mortierella, Mortierella elongata, and Gonapodyna prolifera was lower in the H group than that in the L group (p < 0.05). Functional annotation results showed that the abundance of Glycoside hydrolases genes in rumen microbiome was significantly decreased in the H group compared to the L group (p < 0.05). The result of KEGG DEGs enrichment analysis showed that the gene expression of cellulose 1,4-β-cellobiosidase, acetyl-CoA hydrolase, lactate dehydrogenase, succinate-semialdehyde dehydrogenase, D-malate dehydrogenase and related genes in methane production pathways of rumen microbiome was decreased in the H group. In summary, feeding high concentrate diets improved the production performance of goats, altered the structure and composition of rumen microbiome and changed the function of rumen microbiome.

Yaks Are Dependent on Gut Microbiota for Survival in the Environment of the Qinghai Tibet Plateau

The yak (Poephagus grunniens) has evolved unique adaptations to survive the harsh environment of the Qinghai-Tibetan Plateau, while their gut microorganisms play a crucial role in maintaining the health of the animal. Gut microbes spread through the animal population not only by horizontal transmission but also vertically, which enhances microbial stability and inheritance between generations of the population. Homogenization of gut microbes in different animal species occurs in the same habitat, promoting interspecies coexistence. Using the yak as a model animal, this paper discusses the adaptive strategies under extreme environments, and how the gut microbes of the yak circulate throughout the Tibetan Plateau system, which not only affects other plateau animals such as plateau pikas, but can also have a profound impact on the health of people. By examining the relationships between yaks and their gut microbiota, this review offers new insights into the adaptation of yaks and their ecological niche on the Qinghai-Tibetan plateau.

Effect of the supplementation of exogenous complex non-starch polysaccharidases on the growth performance, rumen fermentation and microflora of fattening sheep

The objective of this study was to evaluate the effects of exogenous non-starch polysaccharidases (a mixture of cellulase, xylanase, β-glucanase and mannanase) on the growth performance and nutrient digestibility, rumen fermentation, and rumen microflora of sheep. The animal trial was conducted using 36 5-month-old female fattening hybrid sheep (Duolang♂ × Hu♀) who were randomly assigned into four groups comprising nine sheep per treatment: CON, T1, T2, and T3, with 0, 0.1, 0.3, and 0.5% NSPases/kg DM of TMR, respectively. This complex enzyme product was screened for optimal ratios based on previous in vitro tests and responded positively to the in vitro fermentation of the TMR. When treated with NSPases, there was a non-linear effect of average daily gain and feed conversion rate, with the greatest improvement observed in the T2 group. There were no significant differences (p > 0.05) in nutrient intake or apparent digestibility among the NSPase-supplemented groups. In addition, T2 group had a significantly higher acetate to propionate ratio and pH (p < 0.05) than the other groups, and NH3-N and microbial protein concentrations showed a quadratic curve. The results revealed that both immunoglobulins and serum hormones increased linearly with addition (p < 0.05). As the T2 group showed the best growth performance, the CON and T2 groups were subjected to rumen metagenomic analysis. The results showed higher abundance of bacteria and lower abundance of Viruses in the rumen microbiota of the T2 group compared to the CON group. In addition, Uroviricota and Proteobacteria abundance was significantly lower in the T2 group than in the CON group at the phylum level (p < 0.05). These results suggest that the supplementation of high-concentrate rations with NSPases enhance immunity, reduces virus abundance in the rumen, improves rumen health, and promotes rumen fermentation. Our findings provide novel insights for improving growth performance and alleviating inflammatory responses arising from high concentrate feeding patterns in ruminants. However, the biological mechanisms cannot be elucidated by exploring the composition of rumen microbe alone, and further studies are required.

Enhancing biogas generation from lignocellulosic biomass through biological pretreatment: Exploring the role of ruminant microbes and anaerobic fungi

Biogas production from Lignocellulosic Biomass (LB) via anaerobic digestion (AD) has gained attention for its potential in self-sustainability. However, the recalcitrance of LB cell walls pose a challenge to its degradability and biogas generation. Therefore, pretreatment of LB is necessary to enhance lignin removal and increase degradability. Among the different approaches, environmentally friendly biological pretreatment ispromising as it avoids the production of inhibitors. The ruminal microbial community, including anaerobic fungi, bacteria, and protozoa, has shown an ability to effectively degrade LB through biomechanical and microbial penetration of refractory cell structures. In this review, we provide an overview of ruminant microbes dominating LB's AD, their degradation mechanism, and the bioaugmentation of the rumen. We also explore the potential cultivation of anaerobic fungi from the rumen, their enzyme potential, and their role in AD. The rumen ecosystem, comprising both bacteria and fungi, plays a crucial role in enhancing AD. This comprehensive review delves into the intricacies of ruminant microorganisms' adhesion to plant cells, elucidates degradation mechanisms, and explores integrated pretreatment approaches for the effective utilization of LB, minimizing the impact of inhibitors. The discussion underscores the considerable potential of ruminant microbes in pretreating LB, paving the way for sustainable biogas production. Optimizing fungal colonization and ligninolytic enzyme production, such as manganese peroxidase and laccase, significantly enhances the efficiency of fungal pretreatment. Integrating anaerobic fungi through bioaugmentation during mainstream processing demonstrably increases methane production. This study opens promising avenues for further research and development of these microorganisms for bioenergy production.

The Effect of a Bacillus Probiotic and Essential Oils Compared to an Ionophore on the Rumen Microbiome Composition of Feedlot Cattle

The rising concern of antibiotic growth promoter use in livestock has necessitated the investigation into alternative feed additives. The effect of a probiotic and essential oils to an ionophore on the rumen microbiome composition of Bonsmara bulls raised under feedlot conditions was compared. Forty-eight Bonsmara weaners were allocated to four groups: a group with basal diet (CON) and three groups supplemented with monensin (MON), probiotic (PRO), and essential oils (EO). During the 120 days feeding period, rumen content was collected from four animals per group within each phase via a stomach tube for 16S rRNA and internal transcribed spacer (ITS) sequencing as well as volatile fatty acid analysis. In the starter phase, MON had a significantly lower acetate to propionate ratio and a higher Succinivibrionaceae abundance. The abundance of Lachnospiraceae was significantly higher in EO compared to MON. In the finisher phase, PRO had a significantly higher bacterial diversity. The alpha diversity did not differ between the fungal populations of the groups. The abundance of Proteobacteria was the lowest in PRO compared to the other groups. Limited variation was observed between the rumen microbiome composition of monensin compared to the other treatment groups, indicating that these alternatives can be considered.

Effects of adding Sophora alopecuroides to high concentrate diet on rumen fermentation parameters and microbial diversity of sheep

Objective

The purpose of this study was to investigate the effects of different doses of Sophora alopecuroides (SA) on the rumen fermentation and microbial diversity of sheep.

Methods

A total of 32 healthy Dumont crossbred male lambs weighing 25.73 ± 2.17 kg were randomly assigned to 4 treatment groups with 8 replicates each: a control group (CG) fed a basal diet with a concentrate-to-forage ratio of 7:3 and three experimental groups - the 0.1% group(TG1), 0.3% group (TG2), and 0.5% group (TG3), which were fed the same basal diet but supplemented with increasing doses of SA.

Results

(1) Increasing the SA dose led to a significant linear increase (p-< 0.05) in acetate, propionate, butyrate, and total volatile fatty acid (TVFA) concentrations in the rumen, as well as a significant quadratic effect (p-< 0.05) on the propionate concentration. In contrast, there was a significant linear decrease (p-< 0.05) in the NH3-N concentration in the rumen. (2) At the level of rumen bacterial phyla, the abundance of Bacteroidetes in the rumen increased, and that of Firmicutes decreased (p = 0.08). At the genus level, the rumen abundances of Ruminococcus and Phocaeicola of sheep in the three experimental groups were significantly higher than in the control group (p-< 0.05), and the abundances of Clostridiales and Candidatus-Hepatincola were significantly increased in the 0.1% and 0.3% groups (p < 0.05). (3) Regarding rumen anaerobic fungi, the differences between the control group and experimental groups at the phylum level and genus level were not significant (p > 0.05), but the relative abundances of Neocallimastigomycota and Piromyces in the 0.1% group were significantly higher than that in the control group.

Conclusion

SA addition to a high grain diet could increase the VFA concentration and pH in the sheep rumen, reduce the NH3-N concentration in the rumen and improve rumen fermentation function. Although there was no significant change in rumen bacterial or fungal diversity, SA addition increased the rumen abundances of Bacteroidetes, Ruminococcus, Phocaeicola, Clostridiales, Neocallimastigomycota and Piromyces, decreased the rumen abundance of Firmicutes, and had a positive effect on the rumen microbiota to improve sheep health.

Transmission of fungi and protozoa under grazing conditions from lactating yaks to sucking yak calves in early life

Microbiota from mothers is an essential source of microbes in early-life rumen microbiota, but the contribution of microbiota from different maternal sites to the rumen microbiota establishment in neonates needs more data. To fill this gap, we collected samples from the mouth, teat skin, and rumen of lactating yaks and from the rumen of sucking calves concomitantly on seven occasions between days 7 and 180 after birth under grazing conditions. We observed that the eukaryotic communities clustered based on sample sites, except for the protozoal community in the teat skin, with negative correlations between fungal and protozoal diversities in the rumen of calves. Furthermore, fungi in the dam's mouth, which is the greatest source of the calf's rumen fungi, accounted for only 0.1%, and the contribution of the dam's rumen to the calf's rumen fungi decreased with age and even disappeared after day 60. In contrast, the average contribution of the dam's rumen protozoa to the calf's rumen protozoa was 3.7%, and the contributions from the dam's teat skin (from 0.7 to 2.7%) and mouth (from 0.4 to 3.3%) increased with age. Thus, the divergence in dam-to-calf transmissibility between fungi and protozoa indicates that the foundation of these eukaryotic communities is shaped by different rules. This study provides the first measurements of the maternal contribution to the fungal and protozoal establishment in the rumen of sucking and grazing yak calves in early life, which could be beneficial for future microbiota manipulation in neonatal ruminants. KEY POINTS: • Dam to calf transfer of rumen eukaryotes occurs from multiple body sites. • A minor proportion of rumen fungi in calves originated from maternal sites. • The inter-generation transmission between rumen fungi and protozoa differs.

Exploring the temporal dynamics of rumen bacterial and fungal communities in yaks (Bos grunniens) from 5 days after birth to adulthood by full-length 16S and 18S rRNA sequencing

The rumen of ruminants is inhabited by complex and diverse microorganisms. Young animals are exposed to a variety of microorganisms from their mother and the environment, and a few colonize and survive in their digestive tracts, forming specific microflora as the young animals grow and develop. In this study, we conducted full-length sequencing of bacterial and fungal communities in the rumen of pastured yaks of different ages (from 5  days after birth to adulthood) using amplified sequencing technology. The results showed that the rumen microflora of Zhongdian yaks changed gradually from 5 to 180  days after birth and tended to stabilize at 2  years of age. The rumen of adult yaks was the most suitable for the growth and reproduction of most bacteria. Bactria diversity of the yak rumen increased gradually from 5  days after birth to adulthood. With the growth of yaks, different dominated bacteria were enriched in different groups, but Prevotella remained highly abundant in all groups. The yak rumen at 90  days of age was the most suitable for the growth and reproduction of most fungi, and 90 days of age could be a cut-off point for the distribution of fungal communities. Fungal Thelebolus was the firstly reported in yak rumen and was enriched in the yak rumen of 90  days after birth. The most abundant and balanced fungal genera were found in adult yaks, and most of them were only detected in adult yaks. Our study reported on the rumen bacterial and fungal communities of Zhongdian yaks grazed at different ages and provided insights into the dynamic changes of dominant microflora with yak growth.

Metagenomic analysis reveals the efficient digestion mechanism of corn stover in Angus bull rumen: Microbial community succession, CAZyme composition and functional gene expression

Ruminant rumen is a biological fermentation system that can efficiently degrade lignocellulosic biomass. The knowledge about mechanisms of efficient lignocellulose degradation with rumen microorganisms is still limited. In this study, composition and succession of bacteria and fungi, carbohydrate-active enzymes (CAZymes), and functional genes involved in hydrolysis and acidogenesis were revealed during fermentation in Angus bull rumen via metagenomic sequencing. Results showed that degradation efficiency of hemicellulose and cellulose reached 61.2% and 50.4% at 72 h fermentation, respectively. Main bacterial genera were composed of Prevotella, Butyrivibrio, Ruminococcus, Eubacterium, and Fibrobacter, and main fungal genera were composed of Piromyces, Neocallimastix, Anaeromyces, Aspergillus, and Orpinomyces. Principal coordinates analysis indicated that community structure of bacteria and fungi dynamically changed during 72 h fermentation. Bacterial networks with higher complexity had stronger stability than fungal networks. Most CAZyme families showed a significant decrease trend after 48 h fermentation. Functional genes related to hydrolysis decreased at 72 h, while functional genes involved in acidogenesis did not change significantly. These findings provide a in-depth understanding of mechanisms of lignocellulose degradation in Angus bull rumen, and may guide the construction and enrichment of rumen microorganisms in anaerobic fermentation of waste biomass.

Effects of ensiling sugarcane tops with bacteria-enzyme inoculants on growth performance, nutrient digestibility, and the associated rumen microbiome in beef cattle

Major challenges when ensiling sugarcane tops include fermentation that results in high quantities of alcohol and decrease in nutrient digestibility due to the accumulation of fiber components. Increased efforts to apply bacteria-enzyme inoculants in silage have the potential to improve nutrient digestibility. This study aimed to evaluate the effects of ensiling sugarcane tops with bacteria-enzyme inoculants or mixed bacterial inoculants on growth performance, nutrient digestibility, and rumen microbiome in beef cattle. Chopped sugarcane tops were ensiled in plastic bags for 60 d after application of 1) no inoculant (control check, CK); 2) bacteria-enzyme inoculants containing Pediococcus acidilactici, Saccharomyces cerevisiae, cellulase, and xylanase (T1, viable colony-forming units of each bacterial strain ≥108 CFU/g; enzyme activity of each enzyme ≥200 U/g); or 3) mixed bacterial inoculants containing Lactobacillus plantarum, Bacillus subtilis, and Aspergillus oryzae (T2, viable colony-forming units of each bacterial strain ≥107 CFU/g). Silages were fed to eighteen Holstein bull calves (n = 6/treatment) weighing 163.83 ± 7.13 kg to determine intake in a 49-d experimental period. The results showed that beef cattle-fed T1 silage or T2 silage had a significantly higher (P < 0.05) average daily gain than those fed CK silage, but the difference in dry matter intake was not significant (P > 0.05). The apparent digestibility of crude protein (CP) and acid detergent fiber (ADF) were higher (P < 0.05) for beef cattle-fed T1 silage or T2 silage than for those fed CK silage. The rumen bacterial community of beef cattle-fed T1 silage or T2 silage had a tendency to increase (P > 0.05) abundance of Firmicutes and Rikenellaceae_RC9_gut_group than those fed CK silage. Rumen fungal communities of beef cattle-fed T1 or T2 silage had a tendency to increase (P > 0.05) abundance of Mortierellomycota and of Mortierella than those fed CK silage. Spearman's rank correlation coefficient showed that the apparent digestibility of ADF for beef cattle was positively correlated with unclassified_p_Ascomycota of the fungal genera (P < 0.05). Neocalimastigomycota of the fungal phyla was strongly positively correlated with the apparent digestibility of neutral detergent fiber (NDF) (P < 0.05). Ruminococcus was positively correlated with the apparent digestibility of CP (P < 0.05). It was concluded that both T1 and T2 improved the growth performance of beef cattle by improving the ruminal apparent digestibility of CP and ADF, and had no significant impact on major rumen microbial communities in beef cattle.

Dynamic alterations in yak (Bos grunniens) rumen microbiome in response to seasonal variations in diet

Rumen microorganisms play important roles in the healthy growth of yaks. This study investigated changes in yak rumen microbiome during natural grazing at the warm seasons and supplementary feeding at cold seasons. High-throughput sequencing of 16S rRNA and metagenome analysis were conducted to investigate the structures and functions of yak rumen microbial communities. The results indicated that Bacteroidetes and Firmicutes were the most abundant phyla. In addition, Bacteroidetes might play a more important role than Firmicutes during the supplementary feeding stage (spring and winter), but less during natural grazing stage (summer and autumn). KEGG analysis showed that the amino sugar and nucleotide sugar metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, starch and sucrose metabolism, and fructose and mannose metabolism were the main pathways in the microbial community, which were significantly different between seasons. The carbohydrate-active enzymes (CAZyme) annotation revealed that cellulose was an important carbon source for microorganisms in yak rumen. Glycoside hydrolases (GHs) were the most abundant class of CAZymes, followed by glycosyl transferases (GTs), which were important to digestion of oil, cellulose, and hemicellulose in food. These results contribute to the understanding of microbial components and functions in yak rumen.

The Response of Ruminal Microbiota and Metabolites to Different Dietary Protein Levels in Tibetan Sheep on the Qinghai-Tibetan Plateau

Ruminal microbiota and metabolites play crucial roles in animal health and productivity. Exploring the dynamic changes and interactions between microbial community composition and metabolites is important for understanding ruminal nutrition and metabolism. Tibetan sheep (Ovis aries) are an important livestock resource on the Qinghai-Tibetan Plateau (QTP), and the effects of various dietary protein levels on ruminal microbiota and metabolites are still unknown. The aim of this study was to investigate the response of ruminal microbiota and metabolites to different levels of dietary protein in Tibetan sheep. Three diets with different protein levels (low protein 10.1%, medium protein 12.1%, and high protein 14.1%) were fed to Tibetan sheep. 16S rRNA gene sequencing and gas chromatography coupled with time-of-flight mass spectrometry (GC-TOF-MS) were used to study the profile changes in each group of ruminal microbes and metabolites, as well as the potential interaction between them. The rumen microbiota in all groups was dominated by the phyla Bacteroidetes and Firmicutes regardless of the dietary protein level. At the genus level, Prevotella_1, Rikenellaceae_RC9_gut_group and Prevotellaceae_UCG-001 were dominant. Under the same forage-to-concentrate ratio condition, the difference in the dietary protein levels had no significant impact on the bacterial alpha diversity index and relative abundance of the major phyla and genera in Tibetan sheep. Rumen metabolomics analysis revealed that dietary protein levels altered the concentrations of ruminal amino acids, carbohydrates and organic acids, and significantly affected tryptophan metabolism (p < 0.05). Correlation analysis of the microbiota and metabolites revealed positive and negative regulatory mechanisms. Overall, this study provides detailed information on rumen microorganisms and ruminal metabolites under different levels of dietary protein, which could be helpful in subsequent research for regulating animal nutrition and metabolism through nutritional interventions.

Effect of whole-plant corn silage treated with lignocellulose-degrading bacteria on growth performance, rumen fermentation, and rumen microflora in sheep

Lignification of cellulose limits the effective utilisation of fibre in plant cell wall. Lignocellulose-degrading bacteria secrete enzymes that decompose lignin and have the potential to improve fibre digestibility. Therefore, this study aimed to investigate the effect of whole-plant corn silage inoculated with lignocellulose-degrading bacteria on the growth performance, rumen fermentation, and rumen microbiome in sheep. Twelve 2-month-old male hybrid sheep (Dorper ♂ × small-tailed Han ♀) were randomly assigned into two dietary groups (n = 6): (1) untreated whole-plant corn silage (WPCS) and (2) WPCS inoculated with bacterial inoculant (WPCSB). Whole-plant corn silage inoculated with bacterial inoculant had higher in situ NDF digestibility than WPCS. Sheep in the WPCSB group had significantly higher average daily gain, DM intake, and feed conversion rate than those in the WPCS group (P < 0.05). Furthermore, higher volatile fatty acid concentrations were detected in WPCSB rumen samples, leading to lower ruminal pH (P < 0.05). The WPCSB group showed higher abundance of Bacteroidetes and lower abundance of Firmicutes in the rumen microbiome than the WPCS group (P < 0.05). Multiple differential genera were identified, with Prevotella being the most dominant genus and more abundant in WPCSB samples. Moreover, the enriched functional attributes, including those associated with glycolysis/gluconeogenesis and citrate cycle, were more actively expressed in the WPCSB samples than in the WPCS samples. Additionally, certain glucoside hydrolases that hydrolyse the side chains of hemicelluloses and pectins were also actively expressed in the WPCSB microbiome. These findings suggested that WPCSB increased NDF digestibility in three ways: (1) by increasing the relative abundance of the most abundant genera, (2) by recruiting more functional features involved in glycolysis/gluconeogenesis and citrate cycle pathways, and (3) by increasing the relative abundance and/or expression activity of the glucoside hydrolases involved in hemicellulose and pectin metabolism. Our findings provide novel insights into the microbial mechanisms underlying improvement in the growth performance of sheep/ruminants. However, the biological mechanisms cannot be fully elucidated using only metagenomics tools; therefore, a combined multi-omics approach will be used in subsequent studies.

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.

The Remodeling Effects of High-Concentrate Diets on Microbial Composition and Function in the Hindgut of Dairy Cows

At present, research on high-concentrate (HC) diets mostly focused on the rumen, and there is a paucity of information on the hindgut microbiota of dairy cows. In the present study, a 2 × 2 crossover design with four healthy Holstein cows was used, and the metagenomics approach was adopted to reveal the remodeling effects of HC diets on hindgut microbiota and their metabolic functions. Results showed that, compared with the low-concentrate (LC) diets, HC diets have markedly decreased (p < 0.05) the abundance of cellulolytic bacteria (such as Fibrobacter, Ruminococcus, and Ruminiclostridium) and methanogens (such as Methanobrevibacter, Methanosarcina, and Methanosphaera); and correspondingly, HC diets have significantly reduced (p < 0.05) the abundance of carbohydrate-active enzymes (CAZy) related to hemicellulases (GH10, GH11, and GH54) and cellulases (GH1, GH44, and GH45) and increased the abundance of one oligosaccharide-degrading enzyme (GH32). Furthermore, 62 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of hindgut microbiota were affected (p < 0.05) by different dietary treatments, and the major pathways altered by HC diets were “Methane metabolism” (enriched in the LC group), “Lipid metabolism” (enriched in the HC group), and several sub-pathways in “Amino acid metabolism” (such as Phenylalanine metabolism, and Phenylalanine, tyrosine, and tryptophan biosynthesis). Also, the microbial genes involved in the pathways “Methane metabolism” (except 1 gene), “Tryptophan metabolism”, and “Phenylalanine metabolism” were all decreased (p < 0.05) in the present study. These findings suggested that HC diets caused the remodeling of hindgut microbiota and its potential functions, and these results may benefit in gaining a deeper understanding of the impact of HC diets on the hindgut microbiota of dairy cows.

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.

The Present Role and New Potentials of Anaerobic Fungi in Ruminant Nutrition

The ruminal microbiota allows ruminants to utilize fibrous feeds and is in the limelight of ruminant nutrition research for many years. However, the overwhelming majority of investigations have focused on bacteria, whereas anaerobic fungi (AF) have been widely neglected by ruminant nutritionists. Anaerobic fungi are not only crucial fiber degraders but also important nutrient sources for the host. This review summarizes the current findings on AF and, most importantly, discusses their new application potentials in modern ruminant nutrition. Available data suggest AF can be applied as direct-fed microbials to enhance ruminal fiber degradation, which is indeed of interest for high-yielding dairy cows that often show depressed ruminal fibrolysis in response to high-grain feeding. Moreover, these microorganisms have relevance for the nutrient supply and reduction of methane emissions. However, to reach AF-related improvements in ruminal fiber breakdown and animal performance, obstacles in large-scale AF cultivation and applicable administration options need to be overcome. At feedstuff level, silage production may benefit from the application of fungal enzymes that cleave lignocellulosic structures and consequently enable higher energy exploitation from forages in the rumen. Concluding, AF hold several potentials in improving ruminant feeding and future research efforts are called for to harness these potentials.

Changes in Rumen Microbiota Affect Metabolites, Immune Responses and Antioxidant Enzyme Activities of Sheep under Cold Stimulation

Simple Summary

Under a cold environment, the animal’s weight is reduced and even health is affected. As we all know, microbiota is beneficial to animal health. It can produce metabolites to improve animal immunity and avoid damage. Therefore, we aimed to understand the self-protection mechanisms of sheep under cold stress. To investigate this mechanism, we designed two experiments to explore the effects of low temperature and wind speed on sheep phenotypes, rumen microbes, immune cytokines and oxidative stress. Our results identified that the sheep remained healthy in a cold environment. This may be due to the enrichment of Lachnospiraceae in the rumen. A large amount of propionate may enter into the gluconeogenesis reaction, resulting in a decrease in the content of propionate in the rumen, thereby reducing animal’s immunity. In summary, the increase of Lachnospiraceae and propionate in the rumen may help sheep live in a cold environment. Our experiments provide some direction for the healthy feeding of animals in cold environments.

Abstract

Low-temperature environments can strongly affect the normal growth and health of livestock. In winter, cold weather can be accompanied by strong winds that aggravate the effects of cold on livestock. In this study, two experiments were conducted to investigate the effect of low temperature and/or wind speed on physiological indices, rumen microbiota, immune responses and oxidative stress in sheep. When sheep were exposed to cold temperature and/or stronger wind speeds, the average daily gain (ADG) decreased (p < 0.05), and the abundance of Lachnospiraceae was significantly higher (p < 0.05). The acetate and propionate contents and the proportion of propionate in the rumen also significantly reduced (p < 0.05). The immunoglobulin G (IgG) and TH1-related cytokines in the blood were significantly lower (p < 0.05). However, antioxidant enzyme contents were significantly increased and the concentration of malondialdehyde (MDA) was reduced (p < 0.05). In a cold environment, the abundance of Lachnospiraceae in the rumen of sheep was highly enriched, and the decreasing of propionate might be one of the factors affecting the immunity of the animals, the sheep did not suffer from oxidative damage during the experiment.

Alterations in Rumen Bacterial Community and Metabolome Characteristics of Cashmere Goats in Response to Dietary Nutrient Density

This study was conducted to investigate the impacts of dietary energy and protein on rumen bacterial composition and ruminal metabolites. A total of 12 ruminal samples were collected from Shaanbei white cashmere goats which were divided into two groups, including high-energy and high-protein (Group H; crude protein, CP: 9.37% in dry matter; metabolic energy, ME: 9.24 MJ/kg) and control (Group C; CP: 8.73%; ME: 8.60 MJ/kg) groups. Thereby, 16S rRNA gene sequencing and a quantitative polymerase chain reaction were performed to identify the rumen bacterial community. Metabolomics analysis was done to investigate the rumen metabolites and the related metabolic pathways in Groups C and H. The high-energy and high-protein diets increased the relative abundance of phylum Bacteroidetes and genera Prevotella_1 and Succiniclasticum, while decreasing the number of Proteobacteria (p < 0.05). The dominant differential metabolites were amino acids, peptides, and analogs. Tyrosine metabolism played an important role among the nine main metabolic pathways. Correlation analysis revealed that both Prevotella_1 (r = 0.608, p < 0.05) and Ruminococcus_2 (r = 0.613, p < 0.05) showed a positive correlation with catechol. Our findings revealed that the diets with high energy and protein levels in Group H significantly altered the composition of ruminal bacteria and metabolites, which can help to improve the dietary energy and protein use efficiency in goats.

Cosubstrate strategy for enhancing lignocellulose degradation during rumen fermentation in vitro: Characteristics and microorganism composition

To enhance the degradation of wheat straw (WS) and corn straw (CS) in rumen fermentation, characterization of degradation and ruminal microorganisms of monosubstrate (WS/CS) groups and a cosubstrate strategy with food waste (FW) group was performed. The cellulose, hemicellulose, and lignin degradation efficiency of WS and CS; soluble chemical oxygen demand; volatile fatty acid yields; and activity of ligninolytic, cellulolytic, and hemicellulolytic enzymes for the cosubstrate group were improved compared with those for the corresponding monosubstrate groups. An accurate and a good of fit of the Weibull kinetic model, decreased crystallinity index values, and characteristic absorbance bands in the Fourier transform-infrared spectra further confirmed that cosubstrate addition with FW decreased the resistance of cellulose and hemicellulose to biodegradation. High-throughput sequencing results suggested that the bacterial diversity in CS rumen fermentation and fungal diversity and richness in WS rumen fermentation were promoted with FW as a cosubstrate. The cosubstrate addition with FW significantly affected the composition of the ruminal bacteria and fungi in rumen fermentation. The relative abundances (RAs) of rumen bacteria were increased in the cosubstrate CS/WS and FW fermentation conditions, and the enhancement of CS degradation with FW supplementation was stronger than that of WS rumen fermentation with FW supplementation. The RAs of the ruminal fungal genera Ustilago and Fusarium were promoted in CS and WS fermentation with FW, respectively. Moreover, the fermentation properties and rumen flora in the FW rumen fermentation also provided some evidence to suggest an enhancement of the cosubstrate strategy compared with the monosubstrate strategy.

The Effects of Different Concentrate-to-Forage Ratio Diets on Rumen Bacterial Microbiota and the Structures of Holstein Cows During the Feeding Cycle

The objectives of this study were to investigate the ruminal bacterial changes during the feeding cycle. Six ruminally cannulated Holstein cows were used in this experiment. The high-forage (HF) and high-concentrate (HC) diets contained 70% and 30% dietary forage, respectively. Dairy cows were fed their respective diets for at least 28 days, then samples were collected at 0, 2, 4, 9, 12, 16 and 20 h post-feeding. The results showed that pH, the concentration of (total volatile fatty acids) TVFAs and the percentages of acetate, propionate and butyrate were significantly affected by diet and time interactions. The diversity of rumen microbiota in HF dietary treatments was significantly higher than that in the HC dietary treatments. ACE (Abundance-based Coverage Estimator) and Chao 1 indices peak at 12 h post-feeding and then decline over the next 8 h. The rumen microbiota was mainly composed of the phyla Firmicutes, Bacteroidetes and Proteobacteria without considering the diet and time. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional profile prediction indicated that the carbohydrate metabolism was different at 9, 12 and 20 h post-feeding time, which revealed that the soluble carbohydrates were enough for microbial fermentation shortly after feeding. This research gave a further explanation of the interactions among rumen microorganisms, which could further help manipulate the rumen metabolism.

Characterization of the Rumen Microbiota and Volatile Fatty Acid Profiles of Weaned Goat Kids under Shrub-Grassland Grazing and Indoor Feeding

In this study, we conducted comparative analyses to characterize the rumen microbiota and volatile fatty acid (VFA) profiles of weaned Nanjiang Yellow goat kids under shrub-grassland grazing (GR), shrub-grassland grazing and supplementary feeding (SF), and indoor feeding (IF) systems. We observed significant differences (p < 0.05) in the concentrations of total VFA and the proportions of acetate and butyrate in the rumen fluid among the three groups, whereas the proportions of propionate and the acetate/propionate ratio did not differ substantially. Alpha diversity of the rumen bacterial and archaeal populations in the GR and SF kids was significantly higher (p < 0.05) than that in the IF goat kids, and significant differences (p < 0.05) in similarity were observed in the comparisons of GR vs. IF and SF vs. IF. The most predominant bacterial phyla were Bacteroidetes and Firmicutes across the three groups, and the archaeal community was mainly composed of Euryarchaeota. At the genus and species levels, the cellulose-degrading bacteria, including Lachnospiraceae, Ruminococcaceae and Butyrivibrio fibrisolvens, were abundant in the GR and SF groups. Furthermore, 27 bacterial and 11 unique archaeal taxa, such as Lachnospiraceae, Butyrivibrio fibrisolvens, and Methanobrevibacter ruminantium, were identified as biomarkers, and showed significantly different (p < 0.05) abundances among the three groups. Significant Spearman correlations (p < 0.05), between the abundances of several microbial biomarkers and the concentrations of VFAs, were further observed. In summary, our results demonstrated that the adaptation to grazing required more rumen bacterial populations due to complex forage types in shrub-grassland, although the rumen fermentation pattern did not change substantially among the three feeding systems. Some microbial taxa could be used as biomarkers for different feeding systems, particularly cellulose-degrading bacteria associated with grazing.

The Composition of Fungal Communities in the Rumen of Gayals (Bos frontalis), Yaks (Bos grunniens), and Yunnan and Tibetan Yellow Cattle (Bos taurs)

The rumen is a microbial-rich ecosystem in which rumen fungi play an important role in the feed digestion of ruminants. The composition of rumen fungi in free-range ruminants such as gayals, yaks, Tibetan yellow cattle, and the domesticated Yunnan yellow cattle was investigated by sequencing an internal transcribed spacer region 1 (ITS1) using Illumina MiSeq. A total of 285 092 optimized sequences and 904 operational taxonomic units (OTUs) were obtained from the four cattle breeds. The rumen fungi abundance and Chao and Simpson indexes were all higher in free-range ruminants than in domesticated ruminants. Three fungal phyla were identified by sequence comparison: Neocallimastigomycota, Basidiomycota, and Ascomycota. Basidiomycota and Ascomycota have very low abundance in the rumen of four breeds cattle but anaerobic fungi (AF) Neocallimastigomycota occurred in a high abundance. In Neocallimastigomycota, the dominant genera were Piromyces, Anaeromyces, Cyllamyces, Neocallimastix, and Orpionmyces in four cattle breeds. The composition of the major genera of Neocallimastigaceae varied greatly among the four cattle breeds. The unclassified genera were unequally distributed in gayals, yaks, Tibetan and Yunnan yellow cattle, accounting for 90.63%, 98.52%, 97.79%, and 27.01% respectively. It appears that free-range ruminants have more unknown rumen fungi than domesticated ruminants and the cattle breeds and animal diets had an impact on the diversity of rumen fungi.