Shrub coverage alters the rumen bacterial community of yaks (Bos grunniens) grazing in alpine meadows

The Alpine ibex (Capra ibex) gut microbiome, seasonal dynamics, and potential application in lignocellulose bioconversion

Aiming to shed light on the biology of wild ruminants, we investigated the gut microbiome seasonal dynamics of the Alpine ibex (Capra ibex) from the Central Italian Alps. Feces were collected in spring, summer, and autumn during non-invasive sampling campaigns. Samples were analyzed by 16S rRNA amplicon sequencing, shotgun metagenomics, as well as targeted and untargeted metabolomics. Our findings revealed season-specific compositional and functional profiles of the ibex gut microbiome that may allow the host to adapt to seasonal changes in available forage, by fine-tuning the holobiont catabolic layout to fully exploit the available food. Besides confirming the importance of the host-associated microbiome in providing the phenotypic plasticity needed to buffer dietary changes, we obtained species-level genome bins and identified minimal gut microbiome community modules of 11-14 interacting strains as a possible microbiome-based solution for the bioconversion of lignocellulose to high-value compounds, such as volatile fatty acids.

Effects of Age in Fecal Microbiota and Correlations with Blood Parameters in Genetic Nucleus of Cattle

This study aimed to determine the impact of age on the fecal microbiota in the genetic nucleus of cattle, with a focus on microbial richness, composition, functional diversity, and correlations with blood parameters. Fecal and blood samples from 21 cattle were analyzed using 16S rRNA gene sequencing. Older cattle exhibited greater bacterial diversity and abundance, with significant changes in alpha diversity indices (p < 0.05). Beta diversity analysis revealed significant variations in microbial composition between age groups and the interaction of age and sex (p < 0.05). Correlations between alpha diversity, community composition, and hematological values highlighted the influence of microbiota on bovine health. Beneficial butyrate-producing bacteria, such as Ruminococcaceae, were more abundant in older cattle, suggesting a role in gut health. Functional diversity analysis indicated that younger cattle had significantly more abundant metabolic pathways in fermentation and anaerobic chemoheterotrophy. These findings suggest management strategies including tailored probiotic therapies, dietary adjustments, and targeted health monitoring to enhance livestock health and performance. Further research should include comprehensive metabolic analyses to better correlate microbiota changes with age-related variations, enhancing understanding of the complex interactions between microbiota, age, and reproductive status.

Unlocking the potential of sugarcane leaf waste for sustainable methane production: Insights from microbial pre-hydrolysis and reactor optimization

Sugarcane leaf waste, a byproduct of the growing global sugar industry, challenges agricultural waste management. This study explores its potential for methane production via anaerobic digestion. A microbial pre-hydrolysis, using lignocellulose-degrading bacteria, enhanced soluble chemical oxygen demand at an optimal initial substrate concentration of 40 g-volatile solid/L. Comparative analysis with untreated and bioaugmented leaves revealed the pre-hydrolyzed leaves achieved the highest methane production rate (MPR) at 14.0 ± 0.5 mL-CH4/L·d, surpassing others by 1.47 and 1.67 times. Two continuous stirred tank reactors were employed to assess the optimal hydraulic retention time (HRT). Results showed a stable methane production with an HRT of 25 days, yielding high MPRs: 88.70 ± 0.63 mL-CH4/L·d from pre-hydrolyzed sugarcane leaves and 82.57 ± 1.22 mL-CH4/L·d from microbial consortium-augmented leaves. A 25-day HRT fosters high microbial diversity with Bacteroidota, Firmicutes, Chloroflexi, and Verrucomicrobiota dominance, indicating favorable conditions. Conversely, a 20-day HRT results in lower diversity due to unfavorable factors like low pH during organic overloading, leading to increased concentrations of volatile fatty acids and lactic acid, with Firmicutes as the predominant phylum. This study highlights sugarcane leaf waste's potential as a valuable resource for sustainable methane production.

Ruminal microbiota and muscle metabolome characteristics of Tibetan plateau yaks fed different dietary protein levels

Introduction

The dietary protein level plays a crucial role in maintaining the equilibrium of rumen microbiota in yaks. To explore the association between dietary protein levels, rumen microbiota, and muscle metabolites, we examined the rumen microbiome and muscle metabolome characteristics in yaks subjected to varying dietary protein levels.

Methods

In this study, 36 yaks were randomly assigned to three groups (n = 12 per group): low dietary protein group (LP, 12% protein concentration), medium dietary protein group (MP, 14% protein concentration), and high dietary protein group (HP, 16% protein concentration).

Results

16S rDNA sequencing revealed that the HP group exhibited the highest Chao1 and Observed_species indices, while the LP group demonstrated the lowest. Shannon and Simpson indices were significantly elevated in the MP group relative to the LP group (P < 0.05). At the genus level, the relative abundance of Christensenellaceae_R-7_group in the HP group was notably greater than that in the LP and MP groups (P < 0.05). Conversely, the relative abundance of Rikenellaceae_RC9_gut_group displayed an increasing tendency with escalating feed protein levels. Muscle metabolism analysis revealed that the content of the metabolite Uric acid was significantly higher in the LP group compared to the MP group (P < 0.05). The content of the metabolite L-(+)-Arabinose was significantly increased in the MP group compared to the HP group (P < 0.05), while the content of D-(-)-Glutamine and L-arginine was significantly reduced in the LP group (P < 0.05). The levels of metabolites 13-HPODE, Decanoylcarnitine, Lauric acid, L-(+)-Arabinose, and Uric acid were significantly elevated in the LP group relative to the HP group (P < 0.05). Furthermore, our observations disclosed correlations between rumen microbes and muscle metabolites. The relative abundance of NK4A214_group was negatively correlated with Orlistat concentration; the relative abundance of Christensenellaceae_R-7_group was positively correlated with D-(-)-Glutamine and L-arginine concentrations.

Discussion

Our findings offer a foundation for comprehending the rumen microbiome of yaks subjected to different dietary protein levels and the intimately associated metabolic pathways of the yak muscle metabolome. Elucidating the rumen microbiome and muscle metabolome of yaks may facilitate the determination of dietary protein levels.

Fecal and vaginal microbiota of vaccinated and non-vaccinated pregnant elk challenged with Brucella abortus

Introduction

Brucella abortus is the causative agent of brucellosis in cattle and in humans, resulting in economic losses in the agricultural sector and representing a major threat to public health. Elk populations in the American Northwest are reservoirs for this bacterium and transmit the agent to domestic cattle herds. One potential strategy to mitigate the transmission of brucellosis by elk is vaccination of elk populations against B. abortus; however, elk appear to be immunologically distinct from cattle in their responses to current vaccination strategies. The differences in host response to B. abortus between cattle and elk could be attributed to differences between the cattle and elk innate and adaptive immune responses. Because species-specific interactions between the host microbiome and the immune system are also known to affect immunity, we sought to investigate interactions between the elk microbiome and B. abortus infection and vaccination.

Methods

We analyzed the fecal and vaginal microbial communities of B. abortus-vaccinated and unvaccinated elk which were challenged with B. abortus during the periparturient period.

Results

We observed that the elk fecal and vaginal microbiota are similar to those of other ruminants, and these microbial communities were affected both by time of sampling and by vaccination status. Notably, we observed that taxa representing ruminant reproductive tract pathogens tended to increase in abundance in the elk vaginal microbiome following parturition. Furthermore, many of these taxa differed significantly in abundance depending on vaccination status, indicating that vaccination against B. abortus affects the elk vaginal microbiota with potential implications for animal reproductive health.

Discussion

This study is the first to analyze the vaginal microbiota of any species of the genus Cervus and is also the first to assess the effects of B. abortus vaccination and challenge on the vaginal microbiome.

Effects of guanidinoacetic acid on in vitro rumen fermentation and microflora structure and predicted gene function

The fermentation substrate was supplemented with 0% guanidinoacetic acid (GAA) (control group, CON), 0.2% GAA (GAA02), 0.4% GAA (GAA04), 0.6% GAA (GAA06) and 0.8% GAA (GAA08) for 48 h of in vitro fermentation. Gas production was recorded at 2, 4, 6, 8, 12, 24, 36, and 48 h of fermentation. The gas was collected, and the proportions (%, v/v) of H2, CH4 and CO2 were determined. The rumen fermentation parameters, including pH, ammonia nitrogen (NH3-N), microbial protein (MCP) and volatile fatty acids (VFAs), were also determined. Furthermore, the bacterial community structure was analyzed through 16S rRNA high-throughput sequencing. The gene functions were predicted using PICRUSt1 according to the Kyoto Encyclopedia of Genes and Genomes (KEGG). The results showed that with the increase in GAA supplementation levels, the MCP and the concentration of rumen propionate were significantly increased, while the concentration of isovalerate was significantly decreased (p < 0.05). The results of microbial diversity and composition showed that the Shannon index was significantly decreased by supplementation with GAA at different levels (p < 0.05), but the relative abundance of norank_f_F082 and Papillibacter in the GAA06 group was significantly increased (p < 0.05). Especially in group GAA08, the relative abundances of Bacteroidota, Prevotella and Prevotellaceae_UCG-001 were significantly increased (p < 0.05). The results of gene function prediction showed that the relative abundances of the functions of flagellar assembly, bacterial chemotaxis, plant-pathogen interaction, mismatch repair and nucleotide excision repair were significantly decreased (p < 0.05), but the relative abundances of bile secretion and protein digestion and absorption were significantly increased (p < 0.05). In conclusion, supplementation with 0.8% GAA enhanced in vitro rumen fermentation parameters, increased the relative abundance of Prevotella and Prevotellaceae_UCG-001 in the rumen, and increased the metabolic pathways of bile secretion and protein digestion and absorption.

Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing

Asian elephant (Elephas maximus) is the national symbol of Thailand and linked to Thai history and culture for centuries. The elephant welfare improvement is one of the major components to achieve sustainable captive management. Microbiome inhabiting digestive tracts have been shown with symbiotic relations to host health. This work provided high-resolution microbiome profiles of 32 captive elephants at a species level by utilizing full-length 16S rRNA gene nanopore sequencing. Eleven common uncultured bacterial species were found across elephants fed with solid food including uncultured bacterium Rikenellaceae RC9 gut group, Kiritimatiellae WCHB1-41, Phascolarctobacterium, Oscillospiraceae NK4A214 group, Christensenellaceae R-7 group, Oribacterium, Oscillospirales UCG-010, Lachnospiraceae, Bacteroidales F082, uncultured rumen Rikenellaceae RC9 gut group, and Lachnospiraceae AC2044 group. We observed microbiome shifts along the age classes of baby (0-2 years), juvenile (2-10 years), and adult (> 10 years). Interestingly, we found distinct microbiome profiles among adult elephants fed with a local palm, Caryota urens, as a supplement. Potential beneficial microbes have been revealed according to the age classes and feed diets. The retrieved microbiome data could be provided as good baseline microbial profiles for monitoring elephant health, suggesting further studies towards dietary selection suitable for each age class and the use of local supplementary diets.

Cassava Foliage Effects on Antioxidant Capacity, Growth, Immunity, and Ruminal Microbial Metabolism in Hainan Black Goats

Cassava (Manihot esculenta Crantz) foliage is a byproduct of cassava production characterized by high biomass and nutrient content. In this study, we investigated the effects of cassava foliage on antioxidant capacity, growth performance, and immunity status in goats, as well as rumen fermentation and microbial metabolism. Twenty-five Hainan black goats were randomly divided into five groups (n = 5 per group) and accepted five treatments: 0% (T1), 25% (T2), 50% (T3), 75% (T4), and 100% (T5) of the cassava foliage silage replaced king grass, respectively. The feeding experiment lasted for 70 d (including 10 d adaptation period and 60 d treatment period). Feeding a diet containing 50% cassava foliage resulted in beneficial effects for goat growth and health, as reflected by the higher average daily feed intake (ADFI), average daily gain (ADG) and better feed conversion rate (FCR), as well as by the reduced serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), creatinine (CRE), and triglycerides (TG). Meanwhile, cassava foliage improved antioxidant activity by increasing the level of glutathion peroxidase (GSH-Px), superoxide dismutase (SOD), and total antioxidant capacity (T-AOC) and lowering malondialdehyde (MDA). Moreover, feeding cassava foliage was also beneficial to immunity status by enhancing complement 3 (C3), complement 4 (C4), immunoglobulin A (IgA), immunoglobulin G (IgG), and immunoglobulin M (IgM). Furthermore, the addition of dietary cassava foliage also altered rumen fermentation, rumen bacterial community composition, and metabolism. The abundance of Butyrivibrio_2 and Prevotella_1 was elevated, as were the concentrations of beneficial metabolites such as butyric acid; there was a concomitant decline in metabolites that hindered nutrient metabolism and harmed host health. In summary, goats fed a diet containing 50% cassava foliage silage demonstrated a greater abundance of Butyrivibrio_2, which enhanced the production of butyric acid; these changes led to greater antioxidant capacity, growth performance, and immunity in the goats.

Effect of a High-Starch or a High-Fat Diet on the Milk Performance, Apparent Nutrient Digestibility, Hindgut Fermentation Parameters and Microbiota of Lactating Cows

In this study, changes in milk performance, nutrient digestibility, hindgut fermentation parameters and microflora were observed by inducing milk fat depression (MFD) in dairy cows fed with a high-starch or a high-fat diet. Eight Holstein cows were paired in a completely randomized cross-over design within two 35 d periods (18 d control period and 17d induction period). During the control period, all cows were fed the low-starch and low-fat diet (CON), and at the induction period, four of the cows were fed a high-starch diet with crushed wheat (IS), and the other cows were fed a high-fat diet with sunflower fat (IO). The results showed that, compared to when the cows were fed the CON diet, when cows were fed the IS or IO diet, they had lower milk fat concentrations, energy corrected milk, 3.5% fat-corrected milk yield, feed efficiency and apparent digestibility of NDF and ADF. However, cows fed the IO diet had a lower apparent digestibility of ether extracts. In addition, we observed that when cows were fed the high-starch (IS) or high-fat (IO) diet, they had a higher fecal concentration of propionate and acetate, and a lower NH3-N. Compared to when the cows were fed the CON diet, cows fed the IS diet had a lower pH, and cows fed the IO diet had a lower concentration of valerate in feces. In the hindgut microbiota, the relative abundance of Oscillospiraceae_UCG-005 was increased, while the Verrucomicrobiota and Lachnospiraceae_AC2044_group were decreased when cows were fed the IO diet. The relative abundance of Prevotellaceae_UCG-003 was increased, while the Alistipes and Verrucomicrobiota decreased, and the Treponema, Spirochaetota and Lachnospiraceae_AC2044_group showed a decreasing trend when cows were fed the IS diet. In summary, this study suggested that high-starch or high-fat feeding could induce MFD in dairy cows, and the high-fat diet had the greatest effect on milk fat; the high-starch or high-fat diet affected hindgut fermentation and apparent fiber digestibility. The changes in hindgut flora suggested that hindgut microbiota may be associated with MFD in cows.

Supplementation with Antimicrobial Peptides or a Tannic Acid Can Effectively Replace the Pharmacological Effects of Zinc Oxide in the Early Stages of Weaning Piglets

Zinc oxide (ZnO) harms the environment and can potentially increase the number of drug-resistant bacteria. Therefore, there is an urgent need to find safe and effective alternatives to improve gut health and reduce the incidence of diarrhea in weaned piglets. This study conducted an antibacterial test of ZnO, antibacterial peptides (AMPs), and tannic acid (TA) in vitro. Thirty piglets were randomly allotted to one of the following three dietary treatments: ZnO (2000 mg/kg ZnO diet), AMPs (700 mg/kg AMPs diet), and TA (1000 mg/kg TA diet). The results showed that the minimum inhibitory concentrations of ZnO and TA against Escherichia coli and Salmonella were lower than those of AMPs, and the minimum inhibitory concentrations of ZnO, AMPs, and TA against Staphylococcus aureus were the same. Compared to ZnO, AMPs increased the digestibility of dry, organic matter and the crude fat. Additionally, TA significantly (p < 0.05) increased the digestibility of dry and organic matter. On experimental day 14, the plasma interleukin-6 (IL-6) content of piglets supplemented with AMPs and TA was increased significantly (p < 0.05). On experimental day 28, alanine aminotransferase activity in the plasma of weaned piglets in the ZnO and TA groups was significantly (p < 0.05) higher than in piglets in the AMPs group. The levels of plasma IL-6 and immunoglobulin M (IgM) were significantly higher (p < 0.05) in the ZnO and AMPs groups than in the TA group. On experimental days 14 and 28, no significant differences were observed in the antioxidant capacity among the three experimental groups. Intestinal microbial diversity analysis showed that the Chao1 and ACE indices of piglets in the AMPs group were significantly higher (p < 0.05) than those in the ZnO and TA groups. At the genus level, the relative abundance of Treponema_2 was higher in the feces of piglets fed a diet supplemented with TA than in those fed diet supplemented with ZnO (p < 0.05). The relative abundance of Lachnospiraceae was higher in the feces of piglets fed a diet supplemented with AMPs than in those fed diet supplemented with ZnO or TA. Overall, AMPs and TA could be added to feed as substitutes for ZnO to reduce diarrhea, improve nutrient digestibility and immunity, and increase the abundance of beneficial intestinal bacteria in weaned piglets.

Shift of Feeding Strategies from Grazing to Different Forage Feeds Reshapes the Rumen Microbiota To Improve the Ability of Tibetan Sheep (Ovis aries) To Adapt to the Cold Season

The dynamics of ruminant-rumen microbiome symbiosis associated with feeding strategies in the cold season were examined. Twelve pure-grazing adult Tibetan sheep (Ovis aries) (18 months old; body weight, 40 ± 0.23 kg) were transferred from natural pasture to two indoor feedlots and fed either a native-pasture diet (NPF group) or an oat hay diet (OHF group) (n = 6 per treatment), and then the flexibility of rumen microbiomes to adapt to these compositionally different feeding strategies was examined. Principal-coordinate analysis and similarity analysis indicated that the rumen bacterial composition correlated with altered feeding strategies. Microbial diversity was higher in the grazing group than in those fed with native pasture and an oat hay diet (P < 0.05). The dominant microbial phyla were Bacteroidetes and Firmicutes, and the core bacterial taxa comprised mostly (42.49% of shared operational taxonomic units [OTUs]) Ruminococcaceae (408 taxa), Lachnospiraceae (333 taxa), and Prevotellaceae (195 taxa), which were relatively stable across different treatments. Greater relative abundances of Tenericutes at the phylum level, Pseudomonadales at the order level, Mollicutes at the class level, and Pseudomonas at the genus level were observed in a grazing period than in the other two treatments (NPF and OHF) (P < 0.05). In the OHF group, due to the high nutritional quality of the forage, Tibetan sheep can produce high concentrations of short-chain fatty acids (SCFAs) and NH3-N by increasing the relative abundances of key bacteria in the rumen, such as Lentisphaerae, Negativicutes, Selenomonadales, Veillonellaceae, Ruminococcus 2, Quinella, Bacteroidales RF16 group, and Prevotella 1, to aid in nutrients degradation and energy utilization. The levels of beneficial bacteria were increased by the oat hay diet; these microbiotas are likely to help improve and maintain host health and metabolic ability in Tibetan sheep to adapt to cold environments. The rumen fermentation parameters were significantly influenced by feeding strategy in the cold season (P < 0.05). Overall, the results of this study demonstrate the strong effect of feeding strategies on the rumen microbiota of Tibetan sheep, which provided a new idea for the nutrition regulation of Tibetan sheep grazing in the cold season on the Qinghai-Tibetan Plateau. IMPORTANCE During the cold season, like other high-altitude mammals, Tibetan sheep have to adapt their physiological and nutritional strategies, as well as the structure and function of their rumen microbial community, to the seasonal variation of lower food availability and quality. This study focused on the changes and adaptability in the rumen microbiota of Tibetan sheep when they adapted from grazing to a high-efficiency feeding strategy during the cold season by analyzing the rumen microbiota of Tibetan sheep raised under the different management systems, and it shows the linkages among the rumen core and pan-bacteriomes, nutrient utilization, and rumen short-chain fatty acids. The findings from this study suggest that the feeding strategies potentially contribute to variations in the pan-rumen bacteriome, together with the core bacteriome. Fundamental knowledge on the rumen microbiomes and their roles in nutrient utilization furthers our understanding of how rumen microbial adaptation to harsh environments may function in hosts. The facts obtained from the present trial clarified the possible mechanisms of the positive effects of feeding strategy on nutrient utilization and rumen fermentation in harsh environments.

Short Term Effect of Ivermectin on the Bacterial Microbiota from Fecal Samples in Chinchillas (Chinchilla lanigera)

The gastrointestinal microbiota plays an important role in health of the host animals and the detrimental influence of pharmaceutical treatment on the fecal microbiota receives an increasing concern. The clinical use of ivermectin on chinchillas has not yet been evaluated. The purpose of our study was to assess the influence of ivermectin injection on the fecal bacterial microbiota of chinchillas. A with-in subject, before and after study was performed on 10 clinically healthy chinchillas during a 14-day period, all chinchillas received the same ivermectin treatment, and the microbiota from their fecal samples before and after administration were compared as two experimental groups. Fecal samples were collected on day 0 (before ivermectin administration) and day 14 (post ivermectin administration). Fecal bacterial microbiota was analyzed by bacterial 16S rRNA gene sequencing. No clinical abnormalities were observed post subcutaneous administration of ivermectin. No significant alteration was found in the abundance and diversity of fecal bacterial microbiota after treatment, but the dominant position of some bacterial species changed. In conclusion, ivermectin administration was associated with minimal alternations of the fecal bacterial microbiota in healthy chinchillas, and these changes had no observed negative effect on general health of chinchillas in short term.

Effects of Two Different Straw Pellets on Yak Growth Performance and Ruminal Microbiota during Cold Season

The Tianzhu white yaks (Bos grunniens) live on the Qinghai-Tibet Plateau. During winter, a lack of resources and low nutritional levels seriously affect their growth performance. In this study, we aimed to explore the effect of supplementation straw pellets on the growth performance and ruminal microbiota of yaks. Overall, at 6 (6M, n = 24), 18 (18M, n = 26), 30 (30M, n = 20), 42 (42M, n = 24), and 54 (54M, n = 22) month old Tianzhu white yaks were selected (total n = 116) and divided into the mixed straw + grazing (MSG), corn straw + grazing (CSG), and the grazing control (G) groups according to age and gender. Their growth performance was measured as per different dietary treatments. The rumen microbial community structure and levels of VFAs were analyzed from the 6M, 30M, and 54M male yaks from each group. The supplementary diets led to an increase in the ADG, which was the highest in the MSG group. The MSG group exhibited the highest level of acetate and total VFAs (TVFAs) among the three groups (p < 0.05). In addition, the 16S rRNA sequencing results proved that the microbial composition was dominated by the members of Firmicutes and Bacteroidetes. Christensenellaceae R-7 group was significantly abundant in the CSG and MSG groups compared to the G group (p < 0.05). Principal coordinate analysis (PCoA) revealed that the bacterial community structure of rumen in the MSG and CSG groups was considerably different from that in the G group; 6M samples exhibited different rumen microbial diversity compared with the other samples. Correlation analysis revealed that Christensenellaceae_R-7_group was positively correlated with the levels of acetate, TVFAs, and ADG. These results demonstrated that mixed straw pellets improved the growth performance of yaks, increased the abundance of Christensenellaceae R-7_group involved in cellulose degradation in the rumen, and produced large amounts of VFAs, which were absorbed by yaks, thus increasing their ADG. This study provides new insights into the effects of straw pellet supplementation on the changes in the rumen microbiota and growth performance of yaks.

Mannan Oligosaccharides Promoted Skeletal Muscle Hypertrophy through the Gut Microbiome and Microbial Metabolites in Mice

Mannan oligosaccharides (MOSs) have been implicated in the animal growth rate, health indices, and lipid oxidative stability. MOSs have been indicated to maintain intestinal health and anti-inflammatory effects via modulation of gut microbiota. Furthermore, the role of MOSs in modulating skeletal muscle function is largely unknown. Here, this study aimed to investigate the effects of MOS supplementation on muscle function and muscle mass in mice. Additionally, the possible underlying mechanisms, including the contributions of gut microbiota and microbial metabolites, were explored. In our study, 3-week-old C57BL/6J male mice (body weight of approximately 10.7 ± 1.1 g) were given pure water or pure water with 1% MOS. To study the effect of MOSs on gut-microbiota-derived metabolites, serum metabolic profiles were analyzed through untargeted metabolomic profiling. Moreover, we detected the downstream signals of differential metabolites, and decanoic acid (DA) was selected as our target spot. Then, DA was used to treat C2C12 cells, and we found that DA promotes C2C12 cell differentiation via the GPR84 and PI3K/AKT signaling pathways. In conclusion, these results showed that MOS supplementation improves muscle function and muscle mass. Additionally, gut microbiome and microbial metabolites were regulated by MOSs, and DA may be one of the most important links between the gut microbiome and skeletal muscle function regulation.

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 gastrointestinal microbiome of browsing goats (Capra hircus)

Despite the growing interest in the ruminants' gastrointestinal tract (GIT) microbiomes' ability to degrade plant materials by animal husbandry and industrial sectors, only a few studies addressed browsing ruminants. The present work describes the taxonomic and functional profile of the bacterial and archaeal communities from five different gastrointestinal sections (rumen, omasum-abomasum, jejunum, cecum and colon) of browsing Capra hircus, by metabarcoding using 16S rRNA genes hypervariable regions. The bacterial communities across the GITs are mainly composed of Bacillota and Bacteroidota. Prevotella was the leading bacterial group found in the stomachs, Romboutsia in the jejuna, and Rikenellaceae_RC9_gut_group, Bacteroides, UCG-010_ge, UCG-005, and Alistipes in large intestines. The archaeal communities in the stomachs and jejuna revealed to be mainly composed of Methanobrevibacter, while in the large intestines its dominance is shared with Methanocorpusculum. Across the GITs, the main metabolic functions were related to carbohydrate, amino acid, and energy metabolisms. Significant differences in the composition and potential biological functions of the bacterial communities were observed among stomachs, jejuna and large intestines. In contrast, significant differences were observed among stomachs and jejuna verse large intestines for archaeal communities. Overall different regions of the GIT are occupied by different microbial communities performing distinct biological functions. A high variety of glycoside hydrolases (GHs) indispensable for degrading plant cell wall materials were predicted to be present in all the GIT sections.

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.

Effects of Different Roughages on Growth Performance, Nutrient Digestibility, Ruminal Fermentation, and Microbial Community in Weaned Holstein Calves

This study aimed to assess the effects of feeding with different forage sources and starter concentrations on growth performance, nutrient digestibility, ruminal fermentation, and the microbial community in weaned Holstein calves. A total of 54 Holstein calves (body weight (BW) = 77.50 ± 5.07 kg; age = 70 ± 2.54 days) were assigned to 1 of 3 treatment groups (n = 18/group) that were offered diets with different forages: (1) peanut vine (PV), (2) oat hay (OH), or (3) an alfalfa hay + oat hay combination (alfalfa hay:oat hay =1:1, AO). Starter and forage intakes were recorded daily, while BW and growth parameters were assessed at 15-day intervals. The apparent digestibility of nutrients was determined. Ruminal fluid samples were collected and used to detect relevant indicators. A difference was observed for the forage × age interaction for all feed, nutrient intake, BW, ADG, and body structure parameters (P &lt; 0.05). The final BW, average daily feed intake (ADFI), and average daily gain of the PV calves were higher than those of calves from the other groups (P &lt; 0.05). The ruminal propionate concentration evidently increased in calves of the AO group (P &lt; 0.05). The abundances of Rikenellaceae_RC9_gut_group and Shuttleworthia showed distinct responses to feeding with different forages (P &lt; 0.05) at the genus level. The relative abundance of Shuttleworthia was negatively related to rumen pH and acid detergent fiber digestibility (P &lt; 0.05) and strongly positively related to propionate concentration (P &lt; 0.01). A positive correlation was found between Ruminococcus_1 abundance and butyrate concentration and neutral detergent fiber digestibility (P &lt; 0.05). The relative abundances of Succiniclasticum and Prevotella_7 were negatively related to butyrate concentration (P &lt; 0.05). In conclusion, there was an interaction between the factors (forage × age). The peanut vine used as a forage source promoted a higher starter concentrate intake compared to other diets and increased with the calves' age. The growth performance and rumen bacterial community of the calves were further improved. These results indicate that peanut vine can be used as the main source of forage in the diets of weaned calves.

Effects of lactic acid-producing bacteria as direct-fed microbials on the ruminal microbiome

The objective of this study was to evaluate ruminal microbiome changes associated with feeding Lactobacillus plantarum GB-LP1 as direct-fed microbials (DFM) in high-producing dairy cow diets. A dual-flow continuous culture system was used in a replicated 4 × 4 Latin square design. A basal diet was formulated to meet the requirements of a cow producing 45 kg of milk per day (16% crude protein and 28% starch). There were 4 experimental treatments: the basal diet without any DFM (CTRL); a mixture of Lactobacillus acidophilus, 1 × 10⁹ cfu/g, and Propionibacterium freudenreichii, 2 × 10⁹ cfu/g [MLP = 0.01% of diet dry matter (DM)]; and 2 different levels of L. plantarum, 1.35 × 10⁹ cfu/g (L1 = 0.05% and L2 = 0.10% of diet DM). Bacterial samples were collected from the fluid and particulate effluents before feeding and at 2, 4, 6, and 8 h after feeding; a composite of all time points was made for each fermentor within their respective fractionations. Bacterial community composition was analyzed through sequencing the V4 region of the 16S rRNA gene using the Illumina MiSeq platform. Sequenced data were analyzed on DADA2, and statistical analyses were performed in R (RStudio 3.0.1, https://www.r-project.org/) and SAS 9.4 (SAS Institute Inc.); orthogonal contrasts were used to compare treatments. Different than in other fermentation scenarios (e.g., silage or beef cattle high-grain diets), treatments did not affect pH or lactic acid concentration. Effects were mainly from overall DFM inclusion, and they were mostly observed in the fluid phase. The relative abundance of the phylum Firmicutes, family Lachnospiraceae, and 6 genera decreased with DFM inclusion, with emphasis on Butyrivibrio_2, Saccharofermentans, and Ruminococcus_1 that are fibrolytic and may display peptidase activity during fermentation. Lachnospiraceae_AC2044_group and Lachnospiraceae_XPB1014_group also decreased in the fluid phase, and their relative abundances were positively correlated with NH₃-N daily outflow from the fermentors. Specific effects of MLP and L. plantarum were mostly in specific bacteria associated with proteolytic and fibrolytic functions in the rumen. These findings help to explain why, in the previous results from this study, DFM inclusion decreased NH₃-N concentration without altering pH and lactic acid concentration.

Effect of Oregano Oil and Cobalt Lactate on Sheep In Vitro Digestibility, Fermentation Characteristics and Rumen Microbial Community

Simple Summary

In the context of a shortage of feed resources and a complete ban on veterinary antibiotics, searching for green additives that can improve the production performance of ruminants has become a popular research topic. Oregano essential oil (EO) inhibits rumen gas production (GP) and regulates animal digestive metabolism, and cobalt lactate (Co) can improve feed digestibility. However, previous studies on EO of oregano and Co showed different results. Therefore, the present study aimed to investigate the effects of different EOC addition levels on rumen in vitro fermentation and rumen bacterial community composition, and the experimental data obtained showed that all five EOC (0.1425% cobalt lactate + 1.13% oregano essential oil + 98.7275% carrier) addition levels in this experiment had no significant effect on nutrient digestibility. However, the addition of 1500 mg·L⁻¹ EOC significantly improved rumen fermentation parameters and altered the microbiota composition. All presented data provide a theoretical basis for the application of oregano essential oil and cobalt in ruminant nutrition.

Abstract

The objective of this experiment was to evaluate the effect of different EOC (0.1425% cobalt lactate + 1.13% oregano essential oil + 98.7275% carrier) levels on in vitro rumen fermentation and microbial changes. Six EOC levels (treatments: 0 mg·L⁻¹, CON; 50 mg·L⁻¹, EOC1; 100 mg·L⁻¹, EOC2; 400 mg·L⁻¹, EOC3; 800 mg·L⁻¹, EOC4 and 1500 mg·L⁻¹, EOC5) were selected to be used to in vitro incubation. The in vitro dry matter digestibility (IVDMD), in vitro neutral detergent fiber digestibility (IVNDFD), in vitro acid detergent fiber digestibility (IVNDFD), pH, ammonia-nitrogen (NH₃-N) concentration, total volatile fatty acid (TVFA) concentration and microbial protein (MCP) concentration were measured after 48 h incubation, after which the groups with significant nutrient digestibility and fermentation parameters were subjected to 16S rRNA sequencing. The results showed that the total gas production (GP) of the EOC5 group was higher than that of the other groups after 12 h of in vitro incubation. TVFA, NH₃-N and MCP concentrations were also shown to be higher in group EOC5 than those in other groups (p < 0.05), while NH₃-N and MCP concentrations in the EOC2 group were lower than those in other groups significantly (p < 0.05). The molar ratio of acetic acid decreased while the molar ratio of propionic acid increased after the addition of EOC. 16S rRNA sequencing revealed that the rumen microbiota was altered in response to adding EOC, especially for the EOC5 treatment, with firmicutes shown to be the most abundant (43.1%). The relative abundance of Rikenellaceae_RC9_gut_group was significantly lower, while the relative abundance of uncultured_bacterium_f_Muribaculaceae and Succiniclasticum was significantly higher in the EOC5 group than those in other groups (p < 0.05). Comprehensive analysis showed that EOC (1500 mg·L⁻¹) could significantly increase gas production, alter sheep rumen fermentation parameters and microbiota composition.

Effect of Dietary Protein Levels on Dynamic Changes and Interactions of Ruminal Microbiota and Metabolites in Yaks on the Qinghai-Tibetan Plateau

To improve performance and optimize rumen function in yaks (Bos grunniens), further knowledge on the appropriate dietary protein levels for ruminal microbiota and the metabolite profiles of yaks in feedlot feeding is necessary. Current understanding of dietary protein requirements, ruminal microbiota, and metabolites is limited. In this study, yaks were fed a low-protein diet (L; 9.64%), middle low-protein diet (ML; 11.25%), middle high-protein diet (MH; 12.48%), or a high-protein diet (H; 13.87%), and the effects of those diets on changes and interactions in ruminal microbiota and metabolites were investigated. Twenty-four female yaks were selected, and the effects on ruminal microbiota and metabolites were investigated using 16s rRNA gene sequencing and gas chromatography time-of-flight/mass spectrometry (GC-TOF/MS). Diets containing different protein levels changed the composition of the rumen bacterial community, the H group significantly reduced the diversity of ruminal microbiota (p < 0.05), and the number of shared amplicon sequence variants (ASVs) between the H group and the other three groups was lower, suggesting that the ruminal microbiota community fluctuated more with a high-protein diet. In rumen, Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant bacteria at the phylum level, and Bacteroidetes was significantly less abundant in the MH group than in the L and ML groups (p < 0.05). Prevotella_1, Rikenellaceae_RC9_gut_group, and Christensenellaceae_R-7_group had the highest abundance at the genus level. Prevotellaceae was enriched in the low-protein groups, whereas Bacteroidales_BS11_gut_group was enriched in the high-protein groups. Rumen metabolite concentrations and metabolic patterns were altered by dietary protein levels: organic acid metabolites, antioxidant-related metabolites, and some plant-derived metabolites showed variation between the groups. Enrichment analysis revealed that significant changes were concentrated in six pathways, including the citrate cycle (TCA cycle), glyoxylate and dicarboxylate metabolism, and butanoate metabolism. Network analysis showed promotion or restraint relationships between different rumen microbiota and metabolites. Overall, the rumen function was higher in the MH group. This study provides a reference for appropriate dietary protein levels and improves understanding of rumen microbes and metabolites.

Dynamics of rumen bacterial composition of yak (Bos grunniens) in response to dietary supplements during the cold season

This study aimed to explore the rumen bacterial community of yak in response to dietary supplements during the cold season. In addition, the rumen fermentation products were also analyzed. Twenty-one female domestic yaks were randomly divided into three groups i.e., pure grazing (GG) group, grazing plus oats hay supplement (OG) group, and grazing plus concentrate supplement group (CG). Rumen contents were collected after 90 days to assess rumen fermentation parameters and bacterial community. The GC group presented higher concentrations of ammonia nitrogen (P < 0.001), and total volatile fatty acids (TVFA) (P < 0.001), and lower rumen pH (P < 0.001) compared to other experimental groups. The CG group displayed higher proportions of propionate, butyrate, isobutyrate, and isovalerate while lower A/P ratio compared to other experimental groups. Shannon, Chao1, and ACE values were significantly lower in the OG group compared to GG and CG groups. Anosim test showed significant differences in bacterial community structure between groups but the PCA plot was not very informative to see these differences. Bacteroidetes, Proteobacteria, and Firmicutes were the three dominant phyla in all groups. The genera Oscillospira was more abundant in GG and OG groups. Higher relative abundance of Ruminococcus and Clostridium was observed in the GG group, while Ruminobacter, Corynebacterium, and Selenomonas were more abundant in the CG group. These findings will help in improving our understanding of rumen bacteria in yaks in response to changes in diet.