Rumen Microbiome and Metabolome of Tibetan Sheep (Ovis aries) Reflect Animal Age and Nutritional Requirement

Potential Role of Lauric Acid in Milk Fat Synthesis in Chinese Holstein Cows Based on Integrated Analysis of Ruminal Microbiome and Metabolome

The composition and metabolic profile of the ruminal microbiome have an impact on milk composition. To unravel the ruminal microbiome and metabolome affecting milk fat synthesis in dairy cows, 16S rRNA and internal transcribed spacer (ITS) gene sequencing, as well as ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MS/MS) methods were used to investigate the significant differences in ruminal bacterial and fungal communities as well as metabolome among Chinese Holstein cows with contrasting milk fat contents under the same diet (H-MF 5.82 ± 0.41% vs. L-MF 3.60 ± 0.12%). Another objective was to culture bovine mammary epithelial cells (BMECs) to assess the effect of metabolites on lipid metabolism. Results showed that the acetate-to-propionate ratio and xylanase activity in ruminal fluid were both higher in H-MF. Microbiome sequencing identified 10 types of bacteria and four types of fungi differently abundant at the genus level. Metabolomics analysis indicated 11 different ruminal metabolites between the two groups, the majority of which were lipids and organic acids. Among these, lauric acid (LA) was enriched in fatty acid biosynthesis with its concentration in milk fat of H-MF cows being greater (217 vs. 156 mg per 100 g milk), thus, it was selected for an in vitro study with BMECs. Exogenous LA led to a marked increase in intracellular triglyceride (TG) content and lipid droplet formation, and it upregulated the mRNA abundance of fatty acid uptake and activation (CD36 and ACSL1), TG synthesis (DGAT1, DGAT2 and GPAM), and transcriptional regulation (SREBP1) genes. Taken together, the greater relative abundance of xylan-fermenting bacteria and fungi, and lower abundance of bacteria suppressing short-chain fatty acid-producing bacteria or participating in fatty acid hydrogenation altered lipids and organic acids in the rumen of dairy cows. In BMECs, LA altered the expression of genes involved in lipid metabolism in mammary cells, ultimately promoting milk fat synthesis. Thus, it appears that this fatty acid plays a key role in milk fat synthesis.

Multi-omics revealed rumen microbiota metabolism and host immune regulation in Tibetan sheep of different ages

The rumen microbiota and metabolites play an important role in energy metabolism and immune regulation of the host. However, the regulatory mechanism of rumen microbiota and metabolite interactions with host on Tibetan sheep's plateau adaptability is still unclear. We analyzed the ruminal microbiome and metabolome, host transcriptome and serum metabolome characteristics of Tibetan sheep at different ages. Biomarkers Butyrivibrio, Lachnospiraceae_XPB1014_group, Prevotella, and Rikenellaceae_RC9_gut_group were found in 4 months, 1.5 years, 3.5 years, and 6 years Tibetan sheep, respectively. The rumen microbial metabolites were mainly enriched in galactose metabolism, unsaturated fatty acid biosynthesis and fatty acid degradation pathways, and had significant correlation with microbiota. These metabolites further interact with mRNA, and are co-enriched in arginine and proline metabolism, metabolism of xenobiotics by cytochrome P450, propanoate metabolism, starch and sucrose metabolism, gap junction pathway. Meanwhile, serum metabolites also have a similar function, such as chemical carcinogenesis - reactive oxygen species, limonene and pinene degradation, and cutin, suberine and wax biosynthesis, thus participating in the regulation of the body's immune and energy-related metabolic processes. This study systematically revealed that rumen microbiota, metabolites, mRNA and serum metabolites of Tibetan sheep were involved in the regulation of fermentation metabolic function and immune level of Tibetan sheep at different ages, which provided a new perspective for plateau adaptability research of Tibetan sheep at different ages.

Influence of Cuticular Waxes from Triticale on Rumen Fermentation: A Metabolomic and Microbiome Profiling Study

Cuticular wax, a critical defense layer for plants, remains a relatively unexplored factor in rumen fermentation. We investigated the impact of cuticular wax on rumen fermentation using triticale as a model. In total, six wax classes were identified, including fatty acids, aldehydes, alkane, primary alcohol, alkyresorcinol, and β-diketone, with low-bloom lines predominated by 46.05% of primary alcohols and high-bloom lines by 35.64% of β-diketone. Low-wax addition (2.5 g/kg DM) increased the gas production by 19.25% (P < 0.05) and total volatile fatty acids by 6.34% (P > 0.05), and enriched key carbohydrate-fermenting rumen microbes like Saccharofermentans, Ruminococcus, and Prevotellaceae, when compared to non-wax groups. Metabolites linked to nucleotide metabolism, purine metabolism, and protein/fat digestion in the rumen showed a positive correlation with low-wax, benefiting rumen microbes. This study highlights the intricate interplay among cuticular wax, rumen microbiota, fermentation, and metabolomics in forage digestion, providing insights into livestock nutrition and forage utilization.

The impact of different levels of wheat diets on hepatic oxidative stress, immune response, and lipid metabolism in Tibetan sheep (Ovis aries)

BACKGROUND

Compared with corn, wheat contains higher crude protein, amino acids concentration. However, wheat contains a mass of anti-nutritional factors, resulting in increased of the digesta viscosity and impaired the intestinal function in ruminant.

OBJECTIVE

This study aimed to investigate the effects of substitution of different amounts of wheat for corn on hepatic metabolism in the Tibetan lamb.

METHODS

Ninety Tibetan lambs (Body weight = 12.37 ± 0.92 kg) were randomly assigned to three groups: 0% wheat diet (Control), 10% wheat diet (Low group), and 15% wheat diet (High group). The feeding trial lasted for 130 d, including a 10 d adaption period. Hepatic gene expression profiling was performed via RNA sequencing after the conclusion of the feeding trials.

RESULTS

Results showed that greater level of glutathione peroxidase levels in L group compared with those of the C and H groups (P < 0.05). The immune indexes, including interleukin-1β (IL-1β), immunoglobulin A (IgA), and IgM were also elevated in L group compared with the other groups (P < 0.05). Compared with H group, the hepatocytes were arranged radially, and hepatic plates anastomosed with each other to form a labyrinth-like structure in L group. Transcriptomic analysis showed 872 differentially expressed genes (DEG) between H and L group, of which 755 were down-regulated and 117 were up-regulated. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, 32 pathways were significantly enriched (Q-value < 0.05), such as the cAMP signaling pathway, Th1 and Th2 cell differentiation, leukocyte transendothelial migration, platelet activation and adipocytokine signaling pathway. Additionally, the expression of comment DEGs were verified via quantitative reverse-transcription polymerase chain reaction.

CONCLUSION

In summary, our findings suggest that wheat can be supplemented up to 10% in Tibetan sheep, contributing to improve the hepatic oxidative stress, immune response and lipid metabolism through regulating the expression of related genes.

Effects of Dietary Protein Levels on Sheep Gut Metabolite Profiles during the Lactating Stage

Diet-associated characteristics such as dietary protein levels can modulate the gut's primary or secondary metabolites, leading to effects on the productive performance and overall health of animals. Whereas fecal metabolite changes are closely associated with gut metabolome, this study aimed to see changes in the rumen metabolite profile of lactating ewes fed different dietary protein levels. For this, eighteen lactating ewes (approximately 2 years old, averaging 38.52 ± 1.57 kg in their initial body weight) were divided into three groups (n = 6 ewes/group) by following the complete randomized design, and each group was assigned to one of three low-protein (D_I), medium-protein (D_m), and high-protein (D_h) diets containing 8.58%, 10.34%, and 13.93% crude protein contents on a dry basis, respectively. The fecal samples were subjected to untargeted metabolomics using ultra-performance liquid chromatography (UPLC). The metabolomes of the sheep fed to the high-protein-diet group were distinguished as per principal-component analysis from the medium- and low-protein diets. Fecal metabolite concentrations as well as their patterns were changed by feeding different dietary protein levels. The discriminating metabolites between groups of nursing sheep fed different protein levels were identified using partial least-squares discriminant analysis. The pathway enrichment revealed that dietary protein levels mainly influenced the metabolism-associated pathways (n = 63 and 39 in positive as well as negative ionic modes, respectively) followed by protein (n = 15 and 8 in positive as well as negative ionic modes, respectively) and amino-acid (n = 14 and 7 in positive as well as negative ionic modes, respectively) synthesis. Multivariate and univariate analyses showed comparative changes in the fecal concentrations of metabolites in both positive and negative ionic modes. Major changes were observed in protein metabolism, organic-acid biosynthesis, and fatty-acid oxidation. Pairwise analysis and PCA reveal a higher degree of aggregation within the D-h group than all other pairs. In both the PCA and PLS-DA plots, the comparative separation among the D_h/D_m, D_h/D_I, and D_m/D_I groups was superior in positive as well as negative ionic modes, which indicated that sheep fed higher protein levels had alterations in the levels of the metabolites. These metabolic findings provide insights into potentiated biomarker changes in the metabolism influenced by dietary protein levels. The target identification may further increase our knowledge of sheep gut metabolome, particularly regarding how dietary protein levels influence the molecular mechanisms of nutritional metabolism, growth performance, and milk synthesis of sheep.

Ruminal and feces metabolites associated with feed efficiency, water intake and methane emission in Nelore bulls

The objectives of this study were twofold: (1) to identify potential differences in the ruminal and fecal metabolite profiles of Nelore bulls under different nutritional interventions; and (2) to identify metabolites associated with cattle sustainability related-traits. We used different nutritional interventions in the feedlot: conventional (Conv; n = 26), and by-product (ByPr, n = 26). Thirty-eight ruminal fluid and 27 fecal metabolites were significantly different (P < 0.05) between the ByPr and Conv groups. Individual dry matter intake (DMI), residual feed intake (RFI), observed water intake (OWI), predicted water intake (WI), and residual water intake (RWI) phenotypes were lower (P < 0.05) in the Conv group, while the ByPr group exhibited lower methane emission (ME) (P < 0.05). Ruminal fluid dimethylamine was significantly associated (P < 0.05) with DMI, RFI, FE (feed efficiency), OWI and WI. Aspartate was associated (P < 0.05) with DMI, RFI, FE and WI. Fecal C22:1n9 was significantly associated with OWI and RWI (P < 0.05). Fatty acid C14:0 and hypoxanthine were significantly associated with DMI and RFI (P < 0.05). The results demonstrated that different nutritional interventions alter ruminal and fecal metabolites and provided new insights into the relationship of these metabolites with feed efficiency and water intake traits in Nelore bulls.

Seasonal dietary shifts alter the gut microbiota of a frugivorous lizard Teratoscincus roborowskii (Squamata, Sphaerodactylidae)

Seasonal dietary shifts in animals are important strategies for ecological adaptation. An increasing number of studies have shown that seasonal dietary shifts can influence or even determine the composition of gut microbiota. The Turpan wonder gecko, Teratoscincus roborowskii, lives in extreme desert environments and has a flexible dietary shift to fruit-eating in warm seasons. However, the effect of such shifts on the gut microbiota is poorly understood. In this study, 16S rRNA sequencing and LC-MS metabolomics were used to examine changes in the gut microbiota composition and metabolic patterns of T. roborowskii. The results demonstrated that the gut microbes of T. roborowskii underwent significant seasonal changes, and the abundance of phylum level in autumn was significantly higher than spring, but meanwhile, the diversity was lower. At the family level, the abundance and diversity of the gut microbiota were both higher in autumn. Firmicutes, Bacteroidetes, and Proteobacteria were the dominant gut microbes of T. roborowskii. Verrucomicrobia and Proteobacteria exhibited dynamic ebb and flow patterns between spring and autumn. Metabolomic profiling also revealed differences mainly related to the formation of secondary bile acids. The pantothenate and CoA biosynthesis, and lysine degradation pathways identified by KEGG enrichment symbolize the exuberant metabolic capacity of T. roborowskii. Furthermore, strong correlations were detected between metabolite types and bacteria, and this correlation may be an important adaptation of T. roborowskii to cope with dietary shifts and improve energy acquisition. Our study provides a theoretical basis for exploring the adaptive evolution of the special frugivorous behavior of T. roborowskii, which is an important progress in the study of gut microbes in desert lizards.

Mutations in FGFR1 were associated with growth traits in sheep (Ovis aries)

For its role in the mediation of myoblast proliferation, fibroblast growth factor receptor 1 (FGFR1) was considered a functional candidate gene for growth performance in Tibetan sheep. Via the polymerase chain reaction-restriction fragment length polymorphism (PCR-PFLP) approach, four single nucleotide polymorphisms (SNPs) including g.14752C > T (intron 1), g.45361A > G (intron 7), g.49400A > G (3'UTR region) and g.49587A > T (3'UTR region), were identified in 422 ewes. The association analysis demonstrated that individuals carrying the AA genotype of g.49400A > G had significantly greater withers height, length than those with GG genotype (p < 0.05). Individuals with genotype AA of g.49587A > T had significantly greater weight and chest circumference than those with genotype TT (p < 0.01). Additionally, the individuals with Hap1/1 diplotypes (CAAA-CAAA) were highly significantly associated with weight and chest circumference than Hap1/2 diplotypes (CAAA-CAAT) (p < 0.05). The quantitative real-time polymerase chain reaction (qPCR) analysis revealed that the FGFR1 was detectable expressed in muscle tissues within three different age stage. Remarkably higher mRNA expression was detected at fetal lamb stage as compared with adult ewes (p < 0.01). The outcome of this research confirmed that both g.49400A > G and g.49587A > T of FGFR1 were involved in growth-related traits, which may be considered to be genetic markers for improving the growth traits of Tibetan sheep.

Effects of altitude on the gut microbiome and metabolomics of Sanhe heifers

Introduction

Extreme environments at high altitudes pose a significant physiological challenge to animals. We evaluated the gut microbiome and fecal metabolism in Sanhe heifers from different altitudes.

Methods

Twenty Sanhe heifers (body weight: 334.82 ± 13.22 kg, 15-month-old) selected from two regions of China: the Xiertala Cattle Breeding Farm in Hulunbeier, Inner Mongolia [119°57' E, 47°17' N; approximately 700 m altitude, low altitude (LA)] and Zhizhao Dairy Cow Farm in Lhasa, Tibet [91°06' E, 29°36' N; approximately 3,650 m altitude, high altitude (HA)], were used in this study. Fecal samples were collected and differences in the gut microbiota and metabolomics of Sanhe heifers were determined using 16S rRNA gene sequencing and metabolome analysis.

Results and discussion

The results showed that altitude did not significantly affect the concentrations of fecal volatile fatty acids, including acetate, propionate, butyrate, and total volatile fatty acids (p > 0.05). However, 16S rRNA gene sequencing showed that altitude significantly affected gut microbial composition. Principal coordinate analysis based on Bray-Curtis dissimilarity analysis revealed a significant difference between the two groups (p = 0.001). At the family level, the relative abundances of Peptostreptococcaceae, Christensenellaceae, Erysipelotrichaceae, and Family_XIII were significantly lower (p < 0.05) in LA heifers than in HA heifers. In addition, the relative abundances of Lachnospiraceae, Domibacillus, Bacteroidales_S24-7_group, Bacteroidales_RF16_group, Porphyromonadaceae, and Spirochaetaceae were significantly higher in HA heifers than in LA heifers (p < 0.05). Metabolomic analysis revealed the enrichment of 10 metabolic pathways, including organismal systems, metabolism, environmental information processing, genetic information processing, and disease induction. The genera Romboutsia, Paeniclostridium, and g_unclassified_f_Lachnospiraceae were strongly associated with the 28 differential metabolites. This study is the first to analyze the differences in the gut microbiome and metabolome of Sanhe heifers reared at different altitudes and provides insights into the adaptation mechanism of Sanhe heifers to high-altitude areas.

Effects of dietary crude protein levels in the concentrate supplement after grazing on rumen microbiota and metabolites by using metagenomics and metabolomics in Jersey-yak

Introduction

The crude protein level in the diet will affect the fermentation parameters, microflora, and metabolites in the rumen of ruminants. It is of great significance to study the effect of crude protein levels in supplementary diet on microbial community and metabolites for improving animal growth performance. At present, the effects of crude protein level in supplementary diet on rumen fermentation parameters, microbial community, and metabolites of Jersey-Yak (JY) are still unclear.

Methods

The purpose of this experiment was to study the appropriate crude protein level in the diet of JY. The rumen fermentation indexes (volatile fatty acids and pH) were determined by supplementary diets with crude protein levels of 15.16 and 17.90%, respectively, and the microbial community and metabolites of JYs were analyzed by non-target metabonomics and metagenome sequencing technology, and the changes of rumen fermentation parameters, microbial flora, and metabolites in the three groups and their interactions were studied.

Results and Discussion

The crude protein level in the supplementary diet had significant effects on pH, valeric acid, and the ratio of acetic acid to propionic acid (p < 0.05). The protein level had no significant effect on the dominant microflora at the phylum level (p > 0.05), and all three groups were Bacteroides and Firmicutes. The results of metabolite analysis showed that the crude protein level of supplementary diet significantly affected the metabolic pathways such as Bile secretion and styrene degradation (p < 0.05), and there were different metabolites between the LP group and HP group, and these different metabolites were related to the dominant microbial to some extent. To sum up, in this experiment, the effects of crude protein level in supplementary diet on rumen microorganisms and metabolites of JY and their relationship were studied, which provided the theoretical basis for formulating a more scientific and reasonable supplementary diet in the future.

Contribution of gut microbiomes and their metabolomes to the performance of Dorper and Tan sheep

BACKGROUND

Livestock is an excellent source of high nutritional value protein for humans; breeding livestock is focused on improving meat productivity and quality. Dorper sheep is a distinguished breed with an excellent growth performance, while Tan sheep is a Chinese local breed famous for its delicious meat. Several studies have demonstrated that the composition of gut microbiome and metabolome modulate host phenotype.

METHODS

In the present study, we performed 16S amplicon sequencing and metabolomic analyses of the rumen and hindgut microbiome of 8-month-old Dorper and Tan sheep, raised under identical feeding and management conditions, to explore the potential effects of gut microbiome and its metabolites on growth performance and meat quality.

RESULTS

Our study identified Lactobacillus, a marker genus in the rumen, to be significantly associated with the levels of fumaric acid, nicotinic acid, and 2-deoxyadenosine (P-value < 0.05). Statistical analysis showed that nicotinic acid was significantly negatively correlated with body weight (P-value < 0.01), while 2-deoxyadenosine was significantly positively correlated with fatty acids content (P-value < 0.05). There was a biologically significant negative correlation between Phascolarctobacterium and deoxycytidine levels in the hindgut. Deoxycytidine was significantly positively correlated with body weight, protein, and amino acid content. Differences in rumen fermentation patterns that are distinctive among breeds were identified. Tan sheep mainly used Lactobacillus and fumaric acid-mediated pyruvic acid for energy supply, while Dorper sheep utilize glycogenic amino acids. The difference of iron metabolism in the hindgut of Dorper sheep affects lipid production, while Phascolarctobacterium in Tan sheep is related to roughage tolerance. The accumulation of nucleosides promotes the growth performance of Dorper sheep.

CONCLUSION

These findings provide insights into how the microbiome-metabolome-dependent mechanisms contribute to growth rate and fat contents in different breeds. This fundamental research is vital to identifying the dominant traits of breeds, improving growth rate and meat quality, and establishing principles for precision feeding.

Depicting Fecal Microbiota Characteristic in Yak, Cattle, Yak-Cattle Hybrid and Tibetan Sheep in Different Eco-Regions of Qinghai-Tibetan Plateau

The gut microbiota is closely associated with the health and production performance of livestock. Partial studies on ruminant microbiota are already in progress in the Qinghai-Tibetan Plateau Area (QTPA) in China, but large-scale and representative profiles for the QTPA are still lacking. Here, 16S rRNA sequencing was used to analyze 340 samples from yak, cattle, yak-cattle hybrids, and Tibetan sheep, which lived in a shared environment from 4 eco-regions of the QTPA during the same season, and aimed to investigate the fecal microbiota community composition, diversity, and potential function. All samples were clustered into 2 enterotypes, which were derived from the genera Ruminococcaceae UCG-005 and Acinetobacter, respectively. Environment, human activity, species, and parasitization all affected the fecal microbiota. By assessing the relationship between the fecal microbiota and the above variables, we identified a scattered pattern of fecal microbiota dissimilarity based more significantly on diet over other factors. Additionally, gastrointestinal nematode infection could reduce the capacity of the bacterial community for biosynthesis of other secondary metabolites, carbohydrate metabolism, and nucleotide metabolism. Ultimately, this study provided a fecal microbiota profile for ruminants living in 4 eco-regions of the QTPA and its potential future applications in developing animal husbandry regimes. IMPORTANCE Cattle, yak, and sheep reside as the main ruminants distributed throughout most regions of Qinghai-Tibetan Plateau Area (QTPA) in China. However, there is a lack of large-scale research in the QTPA on their fecal microbiota, which can regulate and reflect host health as an internalized "microbial organ." Our study depicted the fecal microbiota community composition and diversity of yak, cattle, yak-cattle hybrids, and Tibetan sheep from 4 eco-regions of the QTPA. Additionally, our results demonstrated here that the ruminant samples could be clustered into 2 enterotypes and that diet outweighed other factors in shaping fecal microbiota in the QTPA. This study provided a basis for understanding the microbiota characteristic of ruminants and its possible applications for livestock production in the QTPA.

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.

Rumen Bacteria Abundance and Fermentation Profile during Subacute Ruminal Acidosis and Its Modulation by Aspergillus oryzae Culture in RUSITEC System

This study aimed at characterizing changes in rumen bacteria abundance and fermentation profiles by artificial saliva (AS) pH, and at evaluating the potential modulatory role of Aspergillus oryzae culture (AOC) in a rumen simulation technique (RUSITEC) system. The treatment included high AS pH (pH 6.8) or low AS pH (pH 5.5) according to the McDougall’s method, and low AS pH was sustained by changing the composition of the AS (NaHCO3 from 9.8 to 1.96 g/L, Na2HPO4 from 9.3 to 1.86 g/L). In low AS pH condition, the diets contained either 0% AOC, 1.25% AOC, or 2.5% AOC. Therefore, there are four treatments: (1) high AS pH, 0% AOC (HASP); (2) low AS pH, 0% AOC (AOC0); (3) low AS pH, 1.25% AOC (AOC1); (4) low AS pH, 2.5% AOC (AOC2), respectively. The experimental diets were supplemented with 16 g basic diets with the forage to concentrate ratio of 40:60. The experiments were conducted two independent 13 days, with 9 days adaption periods and 4 days sample collection. The results showed that low AS pH decreased the degradabilites of dry matter (DM), organic matter (OM), crude protein (CP), neutral detergent fiber (NDF), and acid detergent fiber (ADF) (p < 0.05), which occurred due to a decreased abundance of fibrolytic Ruminococcus albus (p < 0.001). The total concentration of volatile fatty acid (VFA) and proportion of propionate were decreased in the low AS pH (p = 0.026) and tended to increase the molar proportion of butyrate (p = 0.086) and the ratio of acetate to propionate (p = 0.088). The abundances of phylum Firmicutes (p = 0.065) and Proteobacteria (p = 0.063) tended to be greater in low AS pH group than high AS pH group. Low AS pH increased the abundance of phylum Actinobacteria (p = 0.002) compared to the high AS pH and decreased the abundances of phylum Spirochaetes (p = 0.032). Compared with the high AS pH, low AS pH increased the abundances of Prevotella (p = 0.003), Pseudoscardovia (p = 0.001), Mitsuokella (p = 0.005), and Dialister (p = 0.047), and decreased the abundances of Olivibacter (p = 0.026), Ruminobacter (p = 0.025), Treponema (p = 0.037), and Sphaerochaeta (p = 0.027) at genus level. Under a severe SARA in RUSITEC, supplementation of 2.5% AOC increased OM degradability, the copy numbers of Selenomonas ruminantium and Fibrobacter succinogenes. These findings indicate that the reduction AS pH at 5.5 caused a strong shift in bacterial composition in rumen. In addition, the addition of AOC in diets increased the growth rate of certain rumen bacteria that digest fiber or utilize lactate under SARA condition in RUSITEC system.

A comparative analysis of carcass and meat traits, and rumen bacteria between Chinese Mongolian sheep and Dorper × Chinese Mongolian crossbred sheep

Mutton is one of the most widely consumed meats globally. The Chinese Mongolian sheep (MS) breed is an indigenous breed of sheep characterised by high-quality meat and strong adaptability. Dorper × Chinese Mongolian crossbred sheep (DS) is an improved breed with a rapid growth rate and high mutton yield found in parts of China. The rumen microbiota is known to play a key role in shaping host nutrition and health. However, the carcass traits and meat nutritional qualities of DS and MS remain poorly defined, as does how rumen microbes affect these characteristics. The objective of this study was to compare carcass profiles, rumen bacterial communities, and meat nutritional qualities between MS and DS and clarify the associations between rumen microbiota and meat nutritional composition. We found that DS had a faster growth rate and better carcass traits than MS, including BW, carcass weight, meat weight, and loin-eye area. We further found that metabolite and rumen bacterial community composition differed between the two sheep breeds. First, compared with MS, DS had lower contents of some sweet amino acids, monounsaturated fatty acids, n-3 polyunsaturated fatty acids, and beneficial metabolites. Secondly, MS and DS had distinct rumen bacterial compositions, and these differential bacteria were related to carcass traits as well as to contents of meat amino acids, free fatty acids, and other metabolites. Taken together, our data showed that DS had better carcass characteristics but lower meat nutritional quality, parameters that were associated with differences in rumen bacterial community composition. These findings may benefit future breeding strategies aimed at improving sheep carcass performance and meat quality worldwide.

Biotechnological potential of rumen microbiota for sustainable bioconversion of lignocellulosic waste to biofuels and value-added products

Lignocellulosic biomass is an abundant resource with untapped potential for biofuel, enzymes, and chemical production. Its complex recalcitrant structure obstructs its bioconversion into biofuels and other value-added products. For improving its bioconversion efficiency, it is important to deconstruct its complex structure. In natural systems like rumen, diverse microbial communities carry out hydrolysis, acidogenesis, acetogenesis, and methanogenesis of lignocellulosic biomass through physical penetration, synergistic and enzymatic actions enhancing lignocellulose degradation activity. This review article aims to discuss comprehensively the rumen microbial ecosystem, their interactions, enzyme production, and applications for efficient bioconversion of lignocellulosic waste to biofuels. Furthermore, meta 'omics' approaches to elucidate the structure and functions of rumen microorganisms, fermentation mechanisms, microbe-microbe interactions, and host-microbe interactions have been discussed thoroughly. Additionally, feed additives' role in improving ruminal fermentation efficiency and reducing environmental nitrogen losses has been discussed. Finally, the current status of rumen microbiota applications and future perspectives for the development of rumen mimic bioreactors for efficient bioconversion of lignocellulosic wastes to biofuels and chemicals have been highlighted.

Functional Diversity within Gut Microbiomes: Implications for Conserving Biodiversity

Conservation research has historically been conducted at the macro level, focusing on animals and plants and their role in the wider ecosystem. However, there is a growing appreciation of the importance of microbial communities in conservation. Most microbiome research in conservation thus far has used amplicon sequencing methods to assess the taxonomic composition of microbial communities and inferred functional capabilities from these data. However, as manipulation of the microbiome as a conservation tool becomes more and more feasible, there is a growing need to understand the direct functional consequences of shifts in microbiome composition. This review outlines the latest advances in microbiome research from a functional perspective and how these data can be used to inform conservation strategies. This review will also consider some of the challenges faced when studying the microbiomes of wild animals and how they can be overcome by careful study design and sampling methods. Environmental changes brought about by climate change or direct human actions have the potential to alter the taxonomic composition of microbiomes in wild populations. Understanding how taxonomic shifts affect the function of microbial communities is important for identifying species most threatened by potential disruption to their microbiome. Preservation or even restoration of these functions has the potential to be a powerful tool in conservation biology and a shift towards functional characterisation of gut microbiome diversity will be an important first step.

Compositional analysis of ruminal bacteria from ewes selected for somatic cell score and milk persistency

Ruminants are dependent on their rumen microbiota to obtain energy from plants. The composition of the microbiome was well-known to be associated with health status, and production traits, but published results are difficult to reproduce due to large sources of variation. The objectives of this study were to evaluate the associations of ruminal microbiota and its association with genetic lines selected by somatic cell score (SCS) or milk persistency (PERS), as well as milk production, somatic cell score, fat and protein contents, and fatty acids and proteins of milk, using the principles of compositional data. A large sample of 700 Lacaune dairy ewes from INRAE La Fage feeding the same diet and belonging to two divergent genetic lines selected for SCS or PERS was used. The ruminal bacterial metagenome was sequenced using the 16S rRNA gene, resulting in 2,059 operational taxonomic units affiliated with 112 genera. The abundance data were centred log-transformed after the replacement of zeros with the geometric Bayesian method. Discriminant analysis of the SCS showed differences between SCS+ and SCS- ewes, while for PERS no difference was obtained. Milk traits as fat content, protein content, saturated fatty acids and caseins of milk were negatively associated with Prevotella (R = [-0.08;-0.16]), Suttonella (R = [-0.09;-0.16]) and Ruminococcus (R = [-0.08;-0.16]), and positively associated with Lachnospiraceae (R = [0.09;0.16]) and Christensenellaceae (R = [0.09;0.16]). Our findings provide an understanding of the application of compositional data to microbiome analysis, and the potential association of Prevotella, Suttonella, Ruminococcaceae and Lachnospiraceae with milk production traits such as milk fatty acids and proteins in dairy sheep.

Untargeted and Targeted Metabolomics Profiling of Muscle Reveals Enhanced Meat Quality in Artificial Pasture Grazing Tan Lambs via Rescheduling the Rumen Bacterial Community

Tan is a local fat-tail sheep that is famous for its great eating quality but with little attention to its meat metabolome. The aim of this study was to investigate Tan-lamb meat metabolome as well as the key rumen bacteria related to the beneficial compound deposition in the muscle using untargeted and targeted metabolomics under different feeding regimes: indoor feeding (F), artificial pasture grazing with indoor feeding (GF), and pure artificial pasture grazing (G). The untargeted metabolome was detected by ultraperformance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry. Ruminal bacterial communities were detected by 16S rRNA sequencing. Using untargeted metabolomics, the main three altered metabolic pathways in the lamb, including amino acid, lipid, and nucleotide metabolisms, were found in the G group compared to the GF and F groups. Increased N-acetyl-l-aspartic acid, N-acetylaspartylglutamate, acetylcarnitine, and l-carnitine, but decreased carnosine and creatinine, were the main newly found G group-associated metabolites, which might contribute to the improved lamb meat functional quality. Compared to the F group, the G group feeding increased the contents of sweet amino acids (e.g., glycine, alanine, serine, and threonine) and umami amino acids (e.g., glutamic acid and aspartic acid) in the muscle, and G and GF groups increased the level of meat polyunsaturated fatty acid (PUFA), especially the concentration of n3 PUFA, and reduced n6/n3 in the muscle by targeted metabolomics. The abundance of ruminal Moryella was decreased, and Schwartzia and Anaeroplasma were increased in the G group, which were both strongly correlated with the n3 PUFA and other functional compounds in the muscle of lambs. In conclusion, artificial pasture grazing modified the meat amino acid and fatty acid composition as well as the related biological pathways through rescheduling the rumen bacterial community, which would be a better selection for production of healthier lamb meat products.