Rumen Microbial Community Research Articles

Effect of Isopropyl Ester of Hydroxy Analogue of Methionine on Rumen Microbiome, Active Enzymes, and Protein Metabolism Pathways of Yak

This study aims to investigate the effect of methionine analogue 2-hydroxy-4-methylthiobutanoic acid isopropyl ester (HMBi) on the rumen microbial community, microbial carbohydrate-active enzymes (CAZy), and protein metabolism pathways in yak. Twenty-four male Maiwa yaks (252.79 ± 15.95 kg) were selected and randomly divided into groups that received the basal diet alone, or a diet supplemented with different amounts of HMBi (5 g, 10 g or 15 g). At the phylum level, the group receiving 5 g of HMBi showed a considerably higher relative abundance of Lentisphaerae than the other treatment groups (p < 0.05). The relative abundance of Actinobacteria decreased linearly with the increase in HMBi supplemental levels (p < 0.05). The relative abundance of Prevotella increased linearly with the increasing level of HMBi supplementation (p < 0.05). The relative abundance of Butyrivibrio linearly decreased (p < 0.05), and the relative abundance of Alistipes tended to linearly decrease (p = 0.084). The addition of HMBi had linear or quadratic effects on the relative abundance of CAZy enzymes and functional proteins in the rumen of yak (p < 0.05). Conclusively, these results indicated that feeding yaks a diet supplemented with HMBi is an excellent strategy to enhance carbohydrate breakdown, and improve rumen microbial structure and function.

Rumen fermentation and microbiota in Shami goats fed on condensed tannins or herbal mixture

BackgroundPhytochemical compounds can modify the rumen microbiome and improve rumen fermentation. This study evaluated the impact of supplementation with tannin and an herbal mixture containing ginger (Zingiber officinale), garlic (Allium sativum), Artemisia (Artemisia vulgaris), and turmeric (Curcuma longa) on the rumen fermentation and microbiota, and histology of rumen tissue of goats. Eighteen Shami male goats were divided into three groups (n = 6): non-supplemented animals fed the basal diet (C, control); animals fed basal diet and supplemented with condensed tannin (T); and animals fed basal diet and supplemented with herbal mixture (HM). Each animal received a basal diet composed of Alfalfa hay and a concentrate feed mixture.ResultsGroup HM revealed higher (P < 0.05) rumen pH, total volatile fatty acids (VFA), acetic, propionic, isobutyric, butyric, isovaleric, and valeric. Principal Co-ordinate analysis (PCoA) showed that rumen microbial communities in the control group and supplemented groups were distinct. The supplementation increased (P < 0.05) the relative abundances of phylum Bacteroidota and Proteobacteria and declined (P < 0.05) Firmicutes and Fibrobacterota. Additionally, the dominant genus Prevotella and Rikenellaceae RC9 gut group were increased (P < 0.05) and the family Ruminococcaceae was declined (P < 0.05) due to the supplementation. The supplementation decreased (P < 0.05) the archaeal genus Methanobrevibacter and increased (P < 0.05) Candidatus Methanomethylophilus. Tannin supplementation in T group shortened the rumen papillae.ConclusionsThe results revealed that the herbal mixture might be used to alter the rumen microbiota to improve rumen fermentation.

From transients to permanent residents: the existence of obligate aerobic microorganisms in the goat rumen.

The rumen serves as a complex ecosystem, harboring diverse microbial communities that play crucial ecological roles. Because previous studies have predominantly focused on anaerobic microorganisms, limited attention has been given to aerobic microorganisms in the goat rumen. This study aims to explore the diversity of aerobic microorganisms in the rumen and understand their niche and ecological roles. Rumen fluid samples were collected from 6 goats at different time points post-morning feeding. pH, NH3-N, and volatile fatty acid (TVFA) concentrations were measured, while In vitro cultivation of aerobic microorganisms was performed using PDA medium. Internal Transcribed Spacer (ITS) and 16S sequencing unveiled microbial diversity within the rumen fluid samples. Evidence of obligate aerobic microorganisms in the goat rumen suggests their potential contribution to ecological functionalities. Significantly, certain aerobic microorganisms exhibited correlations with TVFA levels, implying their involvement in TVFA metabolism. This study provides evidence of the existence and potential ecological roles of obligate aerobic microorganisms in the goat rumen. The findings underscore the significance of comprehensively deciphering goat rumen microbial communities and their interactions, with aerobes regarded as permanent residents rather than transients. These insights form a solid foundation for advancing our understanding of the intricate interplay between goat and their aerobic microorganisms in the rumen.

Effects of Tail Vegetable Fermented Feed on the Growth and Rumen Microbiota of Lambs.

This study explored the impact of integrating fermented feed into the starter diet of lambs, focusing on growth, health, serum antioxidants, immune markers, rumen fermentation, and microbial communities. Thirty-six ten-day-old female Tail Han lambs were randomly divided into three experimental groups, which were separately fed with alfalfa hay (LA group), tail vegetable fermented feed (LB group), and tail vegetable fermented feed supplemented with 0.1% microbial inoculants (LC group) during the experimental period. This study assessed the influence of fermented feed on various parameters, including growth performance, fiber degradation, rumen fermentation, enzymatic activities, and ruminal histomorphology. The results indicate that compared to the control group, the addition of fermented feed can increase the daily weight gain of lambs. Simultaneously, the addition of fermented feed can enhance the total antioxidant capacity of serum (p < 0.05). The addition of fermented feed promoted the increased height of villi in the duodenum or jejunum of lambs (p < 0.05), and the ratio of villi height to crypt depth in the LB and LC groups was also improved (p < 0.05). The addition of fermented feed increased the richness and diversity of the rumen microbial community in lambs (p < 0.05), primarily increasing the relative abundance of Ruminococcus_1, Ruminococcaceae_UCG-005, Lachnospiraceae, and Lachnospiraceae_NK4A136_group.

Dietary β-hydroxybutyric acid improves the growth performance of young ruminants based on rumen microbiota and volatile fatty acid biosynthesis.

The ketone body β-hydroxybutyric acid (BHB) plays critical roles in cellular proliferation and metabolic fuel utilization; however, its effects on the rumen microbiota remain unknown. Here, three doses of BHB (low, medium, and high) were supplemented to early-weaned goat kids. Compared with controls, the beneficial effects of BHB on growth and rumen development were observed in goats at 90 days of age (d). The low dose of dietary BHB increased the concentration of rumen acetate, propionate, and butyrate on d90. The sequencing results of the rumen microbiota revealed marked shifts in rumen microbial community structure after early-weaned goat kids consumed BHB for 2 months. The signature bacterial ASVs for each treatment were identified and were the main drivers contributing to microbial interactions in the rumen. The bacteria associated with rumen weight were also correlated with body weight. Some classified bacterial signatures, including Prevotella, Olsenella umbonate, and Roseburia faecis, were related to rumen volatile fatty acids and host development. Overall, dietary BHB altered rumen microbiota and environments in young goats, which contributed to rumen development and growth.

Ensiled diet improved the growth performance of Tibetan sheep by regulating the rumen microbial community and rumen epithelial morphology.

The aim of this study was to investigate the effects of ensiled agricultural byproducts from Qinghai-Tibet plateau on growth performance, rumen microbiota, ruminal epithelium morphology, and nutrient transport-related gene expression in Tibetan sheep. Fourteen male Tibetan sheep were randomly assigned to one of two diets: an untreated diet (without silage inoculum, CON, n = 7) or an ensiled diet (with silage inoculum, ESD, n = 7). The total experimental period lasted for 84 d, including early 14 d as adaption period and remaining 70 d for data collection. The ESD increased average daily gain (P = 0.046), dry matter intake (P < 0.001), ammonia nitrogen (P = 0.045), microbial crude protein (P = 0.034), and total volatile fatty acids concentration (P < 0.001), and decreased ruminal pH value (P = 0.014). The proportion of propionate (P = 0.006) and the copy numbers of bacteria (P = 0.01) and protozoa (P = 0.002) were higher, while the proportion of acetate (P = 0.028) was lower in the sheep fed ESD compared to CON. Pyrosequencing of the 16S ribosomal RNA gene revealed that ESD increased the relative abundance of Firmicutes, Ruminococcus, Lachnospiraceae_AC2044_group, Lachnospiraceae_XPB1014_group, and Christensenellaceae_R-7_group in the rumen (P < 0.05), while decreased the relative abundance of Bacteroidota, Prevotellaceae_UCG-003, and Veillonellaceae_UCG-001 (P < 0.05). Analyses with PICRUSt2 and STAMP indicated that the propionate metabolism pathway was enriched in the sheep fed ESD (P = 0.026). The ESD increased the rumen papillae height (P = 0.012), density (P = 0.036), and surface area (P = 0.001), and improved the thickness of the total epithelia (P = 0.018), stratum corneum (P = 0.040), stratum granulosum (P = 0.042), and stratum spinosum and basale (P = 0.004). The relative mRNA expression of cyclin-dependent Kinase 2, CyclinA2, CyclinD2, zonula occludens-1, Occludin, monocarboxylate transporter isoform 1 (MCT1), MCT4, sodium/potassium pump, and sodium/hydrogen antiporter 3 were higher in the rumen epithelial of sheep fed ESD than CON (P < 0.05). Conversely, the relative mRNA expressions of Caspase 3 and B-cell lymphoma-2 were lower in the sheep fed ESD than CON (P < 0.05). In conclusion, compared with an untreated diet, feeding an ensiled diet altered the rumen microbial community, enhanced nutrient transport through rumen epithelium, and improved the growth performance of Tibetan sheep.

Can meta-omics revolutionize our understanding of rumen methane emissions?

Abstract The global challenge of methane emissions from enteric fermentation is critical, as it contributes significantly to atmospheric greenhouse gases and represents a loss of energy that could otherwise be utilized by ruminants. With the increasing demand for dairy and meat products, finding effective methods to reduce methane production is essential. This review explores the use of advanced meta-omics techniques – including metagenomics, metatranscriptomics, metaproteomics, and metabolomics – to deepen our understanding of ruminal methane production and identify potential strategies for its mitigation. These high-throughput technologies provide comprehensive insights into the rumen microbial communities and their metabolic functions by analyzing DNA, RNA, proteins, and metabolites directly from environmental samples. Metagenomics and metatranscriptomics offer a detailed view of microbial diversity and gene expression, while metaproteomics can identify specific enzymes and proteins directly involved in methane production pathways, revealing potential targets for mitigation strategies. Integrating these meta-omics approaches allows for a holistic understanding of the microbial processes that drive methane emissions, enabling the development of more precise interventions, such as tailored dietary modifications and the use of specific inhibitors. This review underscores the importance of a multi-omics strategy in characterizing microbial roles and interactions within the rumen, which is crucial for devising effective and sustainable methods to reduce methane emissions without compromising livestock productivity.

Using a multi-omics approach to explore potential associations with rumen content and serum of cows with different milk production levels based on genomic predicted transmitting ability for milk and phenotypic milk production.

This study aims to compare rumen microbiome and metabolites between second lactation dairy cows in the 75th percentile (n = 12; 57.2 ± 5.08 kg/d) of production according to genomic predicted transmitting ability for milk (GPTAM) and their counterparts in the 25th percentile (n = 12; 47.2 ± 8.61 kg/d). It was hypothesized that the metagenome and metabolome would differ between production levels. Cows were matched by days in milk (DIM), sire, occurrence of disease, and days open in previous lactation. For an additional comparison, the cows were also divided by phenotype into high (n = 6; 61.3 ± 2.8 kg/d), medium (n = 10; 55 ± 1.2 kg/d), and low (n = 8; 41.9 ± 5.6 kg/d) based on their milk production. Samples were collected 65 ± 14 DIM. Rumen content was collected using an oro-gastric tube and serum samples were collected from the coccygeal vessels. High-resolution liquid chromatography-mass spectrometry (LC-MS) was used for rumen and serum metabolite profiling. Shotgun metagenomics was used for rumen microbiome profiling. Microbiome sample richness and diversity were used to determine alpha and Bray-Curtis dissimilarity index was used to estimate beta diversity. Differences in metabolites were determined using t-tests or ANOVA. Pearson correlations were used to consider associations between serum metabolites and milk production. There was no evidence of a difference in rumen metabolites or microbial communities by GPTAM or phenotype. Cows in the phenotypic low group had greater serum acetate to propionate ratio and acetate proportion compared to the cows in the phenotypic medium group. Likewise, serum propionate proportion was greater in the medium compared to the low phenotypic group. Serum acetate, butyrate, and propionate concentrations had a weak positive correlation with milk production. When investigating associations between rumen environment and milk production, future studies must consider the impact of the ruminal epithelium absorption and post-absorption processes in relation to milk production.

- Invited Review - Understanding the functionality of the rumen microbiota: searching for better opportunities for rumen microbial manipulation.

Rumen microbiota play a central role in the digestive process of ruminants. Their remarkable ability to break down complex plant fibers and proteins, converting them into essential organic compounds that provide animals with energy and nutrition. Research on rumen microbiota not only contributes to improving animal production performance and enhancing feed utilization efficiency but also holds the potential to reduce methane emissions and environmental impact. Nevertheless, studies on rumen microbiota face numerous challenges, including complexity, difficulties in cultivation, and obstacles in functional analysis. This review provides an overview of microbial species involved in the degradation of macromolecules, the fermentation processes, and methane production in the rumen, all based on cultivation methods. Additionally, the review introduces the applications, advantages, and limitations of emerging omics technologies such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics, in investigating the functionality of rumen microbiota. Finally, the article offers a forward-looking perspective on the new horizons and technologies in the field of rumen microbiota functional research. These emerging technologies, with continuous refinement and mutual complementation, have deepened our understanding of rumen microbiota functionality, thereby enabling effective manipulation of the rumen microbial community.

Comparative Rumen Metagenome and CAZyme Profiles in Cattle and Buffaloes: Implications for Methane Yield and Rumen Fermentation on a Common Diet.

A study was undertaken to compare the rumen microbial community composition, methane yield, rumen fermentation, and CAZyme profiles between cattle and buffaloes. The primary aim of this study was to ascertain the impact of the host species on the above when diet and environmental factors are fixed. A total of 43 phyla, 200 orders, 458 families, and 1722 microbial genera were identified in the study. Bacteroidetes was the most prominent bacterial phylum and constituted >1/3rd of the ruminal microbiota; however, their abundances were comparable between cattle and buffaloes. Firmicutes were the second most abundant bacteria, found to be negatively correlated with the Bacteroidetes. The abundances of Firmicutes as well as the F/B ratio were not different between the two host species. In this study, archaea affiliated with the nine phyla were identified, with Euryarchaeota being the most prominent. Like bacterial phyla, the abundances of Euryarchaeota methanogens were also similar between the cattle and buffaloes. At the order level, Methanobacteriales dominated the archaea. Methanogens from the Methanosarcinales, Methanococcales, Methanomicrobiales, and Methanomassiliicoccales groups were also identified, but at a lower frequency. Methanobrevibacter was the most prevalent genus of methanogens, accounting for approximately three percent of the rumen metagenome. However, their distribution was not different between the two host species. CAZymes affiliated with five classes, namely CBM, CE, GH, GT, and PL, were identified in the metagenome, where the GH class was the most abundant and constituted ~70% of the total CAZymes. The protozoal numbers, including Entodiniomorphs and Holotrichs, were also comparable between the cattle and buffaloes. Results from the study did not reveal any significant difference in feed intake, nutrient digestibility, and rumen fermentation between cattle and buffaloes fed on the same diet. As methane yield due to the similar diet composition, feed ingredients, rumen fermentation, and microbiota composition did not vary, these results indicate that the microbiota community structure and methane emissions are under the direct influence of the diet and environment, and the host species may play only a minor role until the productivity does not vary. More studies are warranted to investigate the effect of different diets and environments on microbiota composition and methane yield. Further, the impact of variable productivity on both the cattle and buffaloes when the diet and environmental factors are fixed needs to be ascertained.

Response of rumen microorganisms to pH during anaerobic hydrolysis and acidogenesis of lignocellulose biomass

Rumen microorganisms can efficiently degrade lignocellulosic wastes to produce volatile fatty acids (VFAs). pH is a key factor in controlling the type and yield of VFAs by affecting the microorganisms involved in rumen fermentation. However, the effects of different pH on rumen microbial diversity, communities, and mechanisms are unclear. In this study, the hydrolysis and acidogenesis of corn straw and diversity, communities, and mechanisms of rumen microorganisms were explored at different initial pHs. Results showed that the highest hemicellulose, cellulose, and lignin degradation efficiency of corn straw was 55.2 %, 38.3 %, and 7.01 %, respectively, and VFA concentration was 10.2 g/L at pH 7.0. Low pH decreased the bacterial diversity and increased the fungal diversity. Rumen bacteria and fungi had different responses to initial pHs, and the community structure of bacteria and fungi had obviously differences at the genus level. The core genera Succiniclasticum, Treponema, and Neocallimastix relative abundance at initial pH 7.0 samples were significantly higher than that at lower initial pHs, reaching 6.01 %, 1.61 %, and 5.35 %, respectively. The bacterial network was more complex than that of fungi. pH, acetic acid, and propionic acid were the main factors influencing the bacterial and fungal community structure. Low pH inhibited the expression of functional genes related to hydrolysis and acidogenesis, explaining the lower hydrolysis and acidogenesis efficiency. These findings will provide a better understanding for rumen fermentation to produce VFAs.

Effect of Garlic Straw with Silage Corn Stalks on Hu Sheep Rumen Fermentation and Microbial Community In Vitro.

Garlic, an important economic crop, provides nutrient-rich straw. When appropriately balanced with silage corn stalks, it is a high-quality forage resource. However, studies on the impact of garlic straw with silage corn stalks on Hu sheep's digestive metabolism and rumen microbiota are scarce. In this study, different addition ratios of garlic straw and silage corn stalks were utilized for in vitro experiments. We designed six experimental groups (CON, G0, G20, G40, G60, G80, and G100) based on varying ratios of garlic straw to silage corn stalks. Rumen microbiota was analyzed through 16S rRNA sequencing. Nutrient composition analysis indicated that garlic straw's relative feeding value (RFV) closely resembled that of silage corn stalks. After 24 h of fermentation, dry matter digestibility and in vitro gas production significantly increased, reaching peak values at a 60% addition ratio. Furthermore, volatile fatty acids (VFAs) such as acetic, propionic, and butyric acid exhibited elevated contents, with the highest yields observed at 60% inclusion. At the genus level, Prevotella, Rikenellaceae RC9 gut group, and Succiniclasticum were identified as the dominant bacterial groups. The gas production test showed a significant decrease in the G80 group compared to others. Microbial analysis revealed a higher abundance of Prevotella in G80 compared to G20, offering valuable insights for reducing greenhouse gas emissions from ruminant animals. Finally, this study predicted the impact of garlic straw with silage corn stalks' addition on Hu sheep's metabolic pathways and biological functions of the rumen microbiota. This research highlights the potential for effectively utilizing garlic straw as a feed resource for Hu sheep and proposes a rational proportion for combining garlic straw with silage corn stalks.

Exploring the microbial diversity and characterization of cellulase and hemicellulase genes in goat rumen: a metagenomic approach

BackgroundGoat rumen microbial communities are perceived as one of the most potential biochemical reservoirs of multi-functional enzymes, which are applicable to enhance wide array of bioprocesses such as the hydrolysis of cellulose and hemi-cellulose into fermentable sugar for biofuel and other value-added biochemical production. Even though, the limited understanding of rumen microbial genetic diversity and the absence of effective screening culture methods have impeded the full utilization of these potential enzymes. In this study, we applied culture independent metagenomics sequencing approach to isolate, and identify microbial communities in goat rumen, meanwhile, clone and functionally characterize novel cellulase and xylanase genes in goat rumen bacterial communities.ResultsBacterial DNA samples were extracted from goat rumen fluid. Three genomic libraries were sequenced using Illumina HiSeq 2000 for paired-end 100-bp (PE100) and Illumina HiSeq 2500 for paired-end 125-bp (PE125). A total of 435gb raw reads were generated. Taxonomic analysis using Graphlan revealed that Fibrobacter, Prevotella, and Ruminococcus are the most abundant genera of bacteria in goat rumen. SPAdes assembly and prodigal annotation were performed. The contigs were also annotated using the DOE-JGI pipeline. In total, 117,502 CAZymes, comprising endoglucanases, exoglucanases, beta-glucosidases, xylosidases, and xylanases, were detected in all three samples. Two genes with predicted cellulolytic/xylanolytic activities were cloned and expressed in E. coli BL21(DE3). The endoglucanases and xylanase enzymatic activities of the recombinant proteins were confirmed using substrate plate assay and dinitrosalicylic acid (DNS) analysis. The 3D structures of endoglucanase A and endo-1,4-beta xylanase was predicted using the Swiss Model. Based on the 3D structure analysis, the two enzymes isolated from goat’s rumen metagenome are unique with only 56–59% similarities to those homologous proteins in protein data bank (PDB) meanwhile, the structures of the enzymes also displayed greater stability, and higher catalytic activity.ConclusionsIn summary, this study provided the database resources of bacterial metagenomes from goat’s rumen fluid, including gene sequences with annotated functions and methods for gene isolation and over-expression of cellulolytic enzymes; and a wealth of genes in the metabolic pathways affecting food and nutrition of ruminant animals.

Response of rumen fermentation and microbiota to dietary supplementation of sodium selenite and bio-nanostructured selenium in lactating Barki sheep

Dietary selenium (Se) sources affects the structure of the rumen microbial community and rumen fermentation. This study evaluated the effects of sodium selenite (SS) and bio-nanostructured selenium (SeNSM) on rumen fermentation and structure of rumen microbial community of lactating Barki ewes. Twenty one lactating Barki ewes were assigned into three groups based on their body weight and milk yield. The experiment lasted for 50 days, whenever, the control group was fed basal diet; group SS received basal diets plus sodium selenite as inorganic source of Se; and group SeNSM received basal diet plus organic selenium bio-nanostructured. Ruminal pH and volatile Fatty Acids (VFA) was lower (P < 0.05) in SeNSM group compared to control. Principle Coordinate Analysis separated the microbial communities into three clusters based on feeding treatment. The bacterial community was dominated by phylum Bacteroidetes and Firmicutes that were affected (P < 0.05) by Se sources. Specifically Bacteriodetes was higher (P < 0.05) in SS and SeNSM groups; and Firmicutes was higher (P < 0.05) in the control group. Moreover, the predominant bacterial genera were Prevotella, Rikenellaceae RC9 gut group, Unclassified_Bacteroidales, which were higher (P < 0.05) in SeNSM group. The methanogenic community belonged to phylum Euryarchaeota and was significantly decreased (P < 0.05) by Se supplementation. Principal component analysis based on rumen fermentation parameters, and relative abundances of bacteria and methanogens revealed three distinct clusters. These findings suggest that Se supplementation affected the relative abundances of dominant bacterial groups, declined rumen methanogens and SeNSM supplementation showed some positive impacts on some fibrolytic bacteria.

Comparative analysis of rumen metagenome, metatranscriptome, fermentation and methane yield in cattle and buffaloes fed on the same diet.

A study to compare the rumen microbial community composition, functional potential of the microbiota, methane (CH4) yield, and rumen fermentation was conducted in adult male cattle and buffaloes fed on the same diet. A total of 41 phyla, 169 orders, 374 families, and 1,376 microbial genera were identified in the study. Bacteroidetes and Firmicutes were the two most dominant bacterial phyla in both cattle and buffaloes. However, there was no difference in the abundance of Bacteroidetes and Firmicutes in the rumen metagenome of cattle and buffaloes. Based on the abundance, the Proteobacteria was the 3rd largest phylum in the metagenome, constituting 18-20% in both host species. Euryarchaeota was the most abundant phylum of the methanogens, whereas Methanobacteriales and Methanobrevibacter were the most abundant orders and genera in both species. The methanogen abundances were not different between the two host species. Like the metagenome, the difference between the compositional and functional abundances (metagenome vs. metatranscriptome) of the Bacteroidetes and Firmicutes was not significant, whereas the proteobacteria were functionally less active than their metagenomic composition. Contrary to the metagenome, the Euryarchaeota was the 3rd most functional phylum in the rumen and constituted ~15% of the metatranscriptome. Methanobacteriales were the most functional methanogens, accounting for more than 2/3rd of the total archaeal functionality. These results indicated that the methanogens from Euryarchaeota were functionally more active as compared to their compositional abundance. The CH4 yield (g/kg DMI), CH4 emission (g/kg DDM), dry matter (DM) intake, and rumen fermentation did not vary between the two host species. Overall, the study established a substantial difference between the compositional abundances and metabolic functionality of the rumen microbiota; however, feeding cattle and buffaloes on the same diet resulted in similar microbiota composition, metabolic functionality, and CH4 yield. Further studies are warranted to investigate the effect of different diets and environments on the composition and metabolic functionality of the rumen microbiota.

Replacing dietary alfalfa hay with nettle benefits rumen ph balance and microbiota in rumen and feces with minimal effects on performance and digestibility in dairy cows

This study investigated the effects of replacing alfalfa hay (AH) with nettle hay (NH) in total mixed rations (TMR) of lactating cows, focusing on lactation performance, nutrient digestibility, and rumen and fecal microbial community structure. Twenty multiparous Holstein cows with similar days in milk (DIM = 91 ± 8), milk production (43 ± 3 kg/d), milk fat (3.81 ± 0.39%), and milk protein (3.05 ± 0.19%) were randomly assigned to two groups (n = 10) in a single-factor test design. Groups fed AH or NH had free access to water for 80 days, including a 20-day pre-feeding period. The results revealed no significant differences in nutrient intake, apparent digestibility, milk yield and composition, and feed efficiency between groups. However, the NH group displayed a decrease in the percentage of milk fats (NH = 3.82%, AH = 4.16%) and proteins (NH = 3.16%, AH = 3.31%). Additionally, the NH group exhibited higher rumen pH (NH = 6.34, AH = 6.10) and isovalerate concentration (NH = 2.46, AH = 1.92 mmol/L). Amplicon sequencing revealed differences in rumen fluid and feces microbiota between AH and NH groups. In rumen, the relative abundance of opportunistic pathogens such as Burkholderiaceae was 68.18% lower in NH than AH. At the genus level, the NH group had lower relative abundance of Ruminococcaceae V9D2013 species, which positively correlated with milk fat content. In feces, the relative abundances of Bacteroidetes and Verrucomicrobia were significantly lower in the NH group. At the family level, the relative abundances of Lachnospiraceae and Veillonellaceae were 10.45% and 193% higher, respectively, in the NH group. These differences were also observed at the genus level. Collectively, the findings suggest that the NH diet positively affected gastrointestinal function and increased the abundance of beneficial microbiota. In conclusion, replacing AH with NH positively affects rumen pH and gastrointestinal microbiota in dairy cows with negligible effects on milk yield and nutrient digestibility, but these effects need to be further investigated.

Metagenomics-Based Analysis of the Effect of Rice Straw Substitution for a Proportion of Whole-Plant Corn Silage on the Rumen Flora Structure and Carbohydrate-Active Enzymes (CAZymes)

The purpose of this study was to investigate the effects of replacing a portion of whole-plant corn silage with straw on the rumen microbial community structure and carbohydrate-active enzyme activity. The experiment employed a single-factor randomized trial design, with eight late-lactation Chinese Holstein dairy cows being randomly divided into two groups of four replicates each. The control group (CS group) was fed a diet consisting of alfalfa silage and a mixture of alfalfa and whole-plant corn silage, while the experimental group (RS group) received a diet in which one-third of the corn silage was replaced with straw while keeping the other components unchanged. The experiment lasted for a total of 21 days, with a pre-feeding period of 14 days and a formal period of 7 days. The rumen fluid collected on day 21 was used for the rumen fermentation parameters and metagenomic analysis. The concentrations of acetic acid, propionic acid, butyric acid, and total volatile fatty acids (TVFA) in the rumen of RS group cows were significantly lower than those in the CS group (p &lt; 0.01). The ratio of acetic acid to propionic acid was significantly higher in the RS group compared to the CS group (p &lt; 0.01). Metagenomic sequencing revealed that at the genus level, compared to the CS group, the abundance of unclassified bacteria, Bacteroides, Alistipes, Butyrivibrio, Chlamydia, Fibrobacter, unclassified Ruminococcaceae, and unclassified Bacteroidetes in the rumen of RS group cows increased, while the abundance of Eubacterium decreased ([LDA &gt; 3.6], p &lt; 0.05). Compared to the CS group, the enzymatic activities of α-L-arabinofuranosidase (EC3.2.1.55), β-xylosidase (EC3.2.1.37), β-glucosidase (EC3.2.1.21), β-glucosylceramidase (EC3.2.1.45), xylanase (EC3.2.1.8), and arabinanase (EC3.2.1.99) in the rumen of RS group cows increased (p &lt; 0.05). According to the correlation analysis, Alistipes, Bacteroides, and Butyrivibrio showed a significant negative correlation with propionic acid (p &lt; 0.05) and a significant positive correlation with the acetic acid-to-propionic acid ratio (p &lt; 0.05). They also showed a significant positive correlation with GH2, GH3, GH20, GH29, GH43, GH78, GH92, CE1, GT4, β-glucosidase (EC3.2.1.21), α-L-arabinofuranosidase (EC 3.2.1.55), β-xylosidase (EC 3.2.1.37), β-glucosylceramidase (EC 3.2.1.45), xylanase (EC 3.2.1.8), and arabinanase (EC 3.2.1.99) (p &lt; 0.05). In summary, straw can not only alter the composition and structure of the rumen microbiota in cows but also affect the relative abundance of CAZymes at different levels within the rumen. Cows may, thus, potentially improve the degradation efficiency of straw diets by increasing the abundance of certain rumen microbiota and enzymes.

PSIX-19 Association of the Rumen Microbiota with Carcass Merit and Beef Quality

Abstract The microbial community in the rumen has an important role in the health and production of beef cattle providing up to 70% of the daily energy requirements from the metabolism of otherwise non-digestible dietary carbohydrates. Diet is often the largest determinant of rumen microbiome composition, but it is also affected by host age, genetics, and sex. Performance attributes such as average daily gain and feed efficiency have all been linked to the rumen microbiome and recent studies with relatively small numbers of cattle have also suggested there may be an association with certain beef quality traits such as marbling, which largely determines the carcass value. Thus, the objective of this study was to evaluate the association of the rumen microbiota with carcass merit and beef quality traits. Two hundred steers were slaughtered, and rumen samples were collected immediately post-slaughter. Subsequently, carcass merit and meat quality attributes were evaluated. The rumen microbiota of these animals was then characterized using 16S rRNA gene sequencing. Although we did not identify a significant association between marbling score and the structure of the rumen microbiota (PERMANOVA; P &amp;gt; 0.05), there were significant associations between rumen microbial community structure and commercial weight, dressed weight percentage, drip loss, and intramuscular fat content (P &amp;lt; 0.05). There were also individual bacterial taxa that were correlated with various carcass merit and beef quality traits. Members of the Acidaminococcus genus were negatively associated with both intramuscular fat content and marbling score (P &amp;lt; 0.10) while Coprococcus, Christensenellaceae R-7 group, Lachnospiraceae NK3A20 group, Moryella, and Prevotella were among those genera positively correlated with intramuscular fat content (P &amp;lt; 0.10). Christensenellaceae R-7 group, Lachnospiraceae NK3A20 group, Moryella, and Prevotella were also significantly associated with dressed weight percentage. Commercial weight was positively correlated with the genera Catonella, Prevotellaceae NK3B31 group, Pseudoramibacter, Selenomonas, and Sutterella and negatively associated with Oribacterium and Ruminococcaceae UCG-001 (P &amp;lt; 0.10). Therefore, bacteria within these genera may be ideal targets for future microbiome-based strategies to improve carcass merit and beef quality.

331 Investigating the Ruminal Metagenome of Grass and Forage-Fed Bison to Uncover Metabolic Activities That Impact the Efficiency of Plant Fiber Utilization

Abstract The ability of bison to thrive on grass and forage-based diets is of great interest for the bison industry. However, raising bison on pasture presents challenges, including longer finishing times. While some producers overcome this by feeding grain or concentrate to bison, this practice conflicts with the concept of natural production. Considering that bison maintain better on feed of poor quality compared with domesticated grazers, it can be inferred that there is great potential for improving their productivity on pastures. Because ruminants rely on symbiotic microorganisms to break down and ferment plant polysaccharides into nutrients they can absorb and assimilate, the metabolic capabilities of rumen microbial communities in bison would likely have an important role in contributing to the efficiency of their host. To gain further insight, we investigated the ruminal metagenome of six grass-fed bison. Raw sequence reads generated using an Illumina Miseq (2x250) platform from ruminal microbial genomic DNA were assembled into genomic contigs using custom written Perl scripts. A total of 6,297 contigs, representing a combined total length of 23,822,104 nucleotides, were obtained for all samples. Coding sequences were identified and annotated using RAST (Rapid Annotation using Subsystem Technology), which was followed by assignment to metabolic pathways using references from KEGG (Kyoto Encyclopedia of Genes and Genomes), with a particular focus on carbohydrate metabolism and amino acid synthesis. This analysis resulted in the identification of nine of the ten enzymes necessary for glycolysis, indicating the capacity to metabolize glucose into pyruvate. Two outcomes were predicted for pyruvate: conversion to lactate through lactate dehydrogenases (EC 1.1.1.27, EC 1.1.1.28), as well as the production of acetate through the sequential activity of pyruvate-flavodoxin oxidoreductase (EC 1.2.7.1), phosphate acetyltransferase (EC 2.3.1.8), and acetate kinase (EC 2.7.2.1). Propionate and butyrate were also predicted as end-products being produced in bison rumen, as well as synthesis of precursors for aromatic amino synthesis through the Chorismate-Shikimate pathway. In addition, enzymes involved in the fermentation of five-carbon sugars, such as arabinose (EC 5.1.3.4, EC 2.7.1.16, and EC 5.3.1.4) and xylose (EC 2.7.1.17 and EC 5.3.1.5), were also identified. Characterization of the metabolic potential of ruminal bacteria from pasture-fed bison, such as the utilization of glucose and pentose sugars that form the backbone of structural polysaccharides to produce short chain fatty acids and essential amino acids, will provide further insight on the use of forage and grass-based diets by these animals.

403 Awardee Talk: Characterization of Rumen Microbiome and Immune Genes Expression of Crossbred Beef Steers with Divergent Residual Feed Intake Phenotypes

Abstract We investigated whole blood and hepatic mRNA expressions of immune genes and rumen microbiome of crossbred beef steers with divergent residual feed intake (RFI) phenotype to identify relevant biological processes underpinning feed efficiency in beef cattle. Low-RFI beef steers (n = 20; RFI = - 1.83 kg/d) and high-RFI beef steers (n = 20; RFI = + 2.12 kg/d) were selected from a group of 108 growing crossbred beef steers (average BW = 282 ± 30.4 kg) fed a high-forage total mixed ration after a 70-d performance testing period. At the end of the 70-d testing period, liver biopsies and blood samples were collected for total RNA extraction and cDNA synthesis. Rumen fluid samples were also collected for analysis of the rumen microbial community. The mRNA expression of 84 genes related to innate and adaptive immunity was analyzed using pathway-focused PCR-based arrays. Differentially expressed genes were determined using P-value ≤ 0.05 and fold change (FC) ≥ 1.5 (in whole blood) or ≥ 2.0 (in liver). Gene ontology analysis of the differentially expressed genes revealed that pathways related to pattern recognition receptor activity, positive regulation of phagocytosis, positive regulation of vitamin metabolic process, vascular endothelial growth factor production, positive regulation of epithelial tube formation and T-helper cell differentiation were significantly enriched (FDR &amp;lt; 0.05) in low-RFI steers. In the rumen, the relative abundance of PeH15, Arthrobacter, Moryella, Weissella and Muribaculaceae was enriched in low-RFI steers, while Methanobrevibacter, Bacteroidales_BS11_gut_group, Bacteroides and Clostridium_sensu_stricto_1 were reduced. Our study found that low-RFI beef steers exhibit increased mRNA expression of genes related to immune cell functions in whole blood and liver tissues, specifically those involved in pathogen recognition and phagocytosis regulation. Additionally, these low-RFI steers showed differences in relative abundance of some microbial taxa which may partially account for their improved feed efficiency compared with high-RFI steers.