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Ruminants rely on the rumen for the anaerobic fermentation of fibrous plant materials, facilitated by a complex microbial community of bacteria, archaea, fungi, and ciliates. Among them, ruminal ciliates significantly influence ruminal fermentation, methane production, nitrogen utilization efficiency, and microbial interactions. This study examined the impact of ciliate inoculation on ruminal fermentation, microbial composition, and functional profiles in fauna-free conditions. Six treatments were tested: control (no ciliates), small entodinia, Epidinium spp., isotrichids, Ophryoscolex spp., and a mixed inoculum. Using QIIME2 to analyze 16S rRNA gene sequences, the study revealed group-specific effects on methane production, volatile fatty acids (VFAs), and microbial diversity. Small entodinia inoculation increased Streptococcus abundance, while isotrichids enriched Megasphaera, enhancing butyrate production. Alpha diversity indices indicated reduced richness in the ciliate-inoculated groups, reflecting predation on prokaryotes. Beta diversity showed distinct microbial and functional profiles among the treatments. Functional analysis highlighted elevated glycerolipid metabolism in isotrichid groups, associated with Bacteroides and Megasphaera, suggesting roles in lipid metabolism and oxidative stress resistance. Despite limited ciliate cell counts, the study emphasizes ciliate-specific interactions and the role of lactic acid-associated bacteria in shaping ruminal fermentation. [ABSTRACT FROM AUTHOR]

This study examined the effects of different forage sources on the ruminal bacteriome, growth performance, and carcass characteristics of Hanwoo steers during the fattening stage. In Korea, where high-concentrate feeding is common, selecting suitable forage is crucial for sustainable beef production. Fifteen 23-month-old Hanwoo steers, weighing an average of 679.27 ± 43.60 kg, were fed the following five different forage sources: oat hay (OAT), rye silage (RYE), Italian ryegrass (IRS), barley forage (BAR), and rice straw silage (RSS), alongside 1.5 kg of dry matter concentrate daily for five months. Carcass traits were evaluated post-slaughter, and rumen fluid samples were analyzed using full-length 16S rRNA gene sequencing to determine the bacteriome composition. The forage source significantly affected the alpha-diversity indices and bacteriome biomarkers linked to the feed efficiency and ruminal fermentation. Differences in the backfat thickness and meat yield index were noted, with alpha-diversity indices correlating with carcass traits. The phylum Planctomycetota, especially the family Thermoguttaceae, was linked to nitrogen fixation in high-protein diets like IRS, while the genus Limimorpha emerged as a biomarker for the meat yield. These findings highlight the importance of forage selection during late fattening to optimize beef production, considering diet and bacteriome shifts. [ABSTRACT FROM AUTHOR]

Ruminal ciliates are a fundamental constituent within the rumen microbiome of ruminant animals. The complex interactions between ruminal ciliates and other microbial guilds within the rumen ecosystems are of paramount importance for facilitating the digestion and fermentation processes of ingested feed components. This review underscores the significance of ruminal ciliates by exploring their impact on key factors, such as methane production, nitrogen utilization efficiency, feed efficiency, and other animal performance measurements. Various methods are employed in the study of ruminal ciliates including culture techniques and molecular approaches. This review highlights the pressing need for further investigations to discern the distinct roles of various ciliate species, particularly relating to methane mitigation and the enhancement of nitrogen utilization efficiency. The promotion of establishing robust reference databases tailored specifically to ruminal ciliates is encouraged, alongside the utilization of genomics and transcriptomics that can highlight their functional contributions to the rumen microbiome. Collectively, the progressive advancement in knowledge concerning ruminal ciliates and their inherent biological significance will be helpful in the pursuit of optimizing rumen functionality and refining animal production outcomes. [ABSTRACT FROM AUTHOR]

Methane production in ruminants is primarily due to the conversion of metabolic hydrogen (H 2 ), produced during anaerobic microbial fermentation, into methane by ruminal methanogens. While this process plays a crucial role in efficiently disposes of H 2 , it also contributes to environmental pollution and eliminating methane production in the rumen has proven to be challenging. This study investigates the use of probiotics, specifically propionate-producing bacteria, to redirect accumulated H 2 in a methane-mitigated environment. For this objective, we supplemented experimental groups with Lactiplantibacillus plantarum and Megasphaera elsdenii for the reinforced acrylate pathway (RA) and Selenomonas ruminantium and Acidipropionibacterium thoenii for the reinforced succinate pathway (RS), as well as a consortium of all four strains (CB), with the total microbial concentration at 1.0 × 10 10 cells/mL. To create a methane-mitigated environment, 2-bromoethanesulfonate (BES) was added to all experimental groups at a dose of 15 mg/0.5 g of feed. BES reduced methane production by 85% in vitro , and the addition of propionate-producing bacteria with BES further decreased methane emission by up to 94% compared with the control (CON) group. Although BES did not affect the alpha diversity of the ruminal bacteriome, it reduced total volatile fatty acid production and altered beta diversity of ruminal bacteriota, indicating microbial metabolic adaptations to H 2 accumulation. Despite using different bacterial strains targeting divergent metabolic pathways (RA and RS), a decrease in the dominance of the [ Eubacterium ] ruminantium group suggesting that both approaches may have a similar modulatory effect. An increase in the relative abundance of Succiniclasticum in the CB group suggests that propionate metabolism is enhanced by the addition of a propionate-producing bacterial consortium. These findings recommend using a consortium of propionate-producing bacteria to manage H 2 accumulation by altering the rumen bacteriome, thus mitigating the negative effects of methane reduction strategies., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Jeong, Yu, Kang, Kim and Park.)

Hanwoo and Jeju Black cattle (Jeju Black) are native breeds of Korean cattle. Jeju Black cattle are recognized as natural monuments and are known to exhibit slower growth rates compared to Hanwoo. While several studies have analyzed the genetic characteristics of these cattle, there has been limited research on the differences in their microbiome. In this study, rumen fluid was obtained from three Hanwoo steers and three Jeju Black steers, and three different diets (total mixed rations [TMRs] for growing, early fattening, and late fattening periods) were used as substrates for in vitro fermentation. The in vitro incubation was conducted for 3 h and 24 h following a 2 × 3 factorial arrangement. After both incubation periods, fermentation characteristics were analyzed, and ruminal microbiome analysis was performed using 16S rRNA gene sequencing, employing both QIIME2 and PICRUSt2. The results revealed significant differences in the ruminal microbiota due to the inoculum effect. At the phylum level, Patescibacteria and Synergistota were found to be enriched in the Jeju Black inoculum-treated group. Additionally, using different inocula also affected the relative abundance of major taxa, including Ruminococcus, Pseudoramibacter, Ruminococcaceae CAG-352, and the [ Eubacterium ] ruminantium group. These microbial differences induced by the inoculum may have originated from varying levels of domestication between the two subspecies of donor animals, which mainly influenced the fermentation and microbiome features in the early incubation stages, although this was only partially offset afterward. Furthermore, predicted commission numbers of microbial enzymes, some of which are involved in the biosynthesis of secondary metabolites, fatty acids, and alpha amylase, differed based on the inoculum effect. However, these differences may account for only a small proportion of the overall metabolic pathway. Conversely, diets were found to affect protein biosynthesis and its related metabolism, which showed differential abundance in the growing diet and were potentially linked to the growth-promoting effects in beef cattle during the growing period. In conclusion, this study demonstrated that using different inocula significantly affected in vitro fermentation characteristics and microbiome features, mainly in the early stages of incubation, with some effects persisting up to 24 h of incubation., Competing Interests: No potential conflict of interest relevant to this article was reported., (© Copyright 2024 Korean Society of Animal Science and Technology.)

Ruminal protozoa, especially entodiniomorphs, engulf other members of the rumen microbiome in large numbers; and they release oligopeptides and amino acids, which can be fermented to ammonia and volatile fatty acids (VFAs) by amino acid-fermenting bacteria (AAFB). Studies using defaunated (protozoa-free) sheep have demonstrated that ruminal protozoa considerably increase intraruminal nitrogen recycling but decrease nitrogen utilization efficiency in ruminants. However, direct interactions between ruminal protozoa and AAFB have not been demonstrated because of their inability to establish axenic cultures of any ruminal protozoan. Thus, this study was performed to evaluate the interaction between Entodinium caudatum , which is the most predominant rumen ciliate species, and an AAFB consortium in terms of feed degradation and ammonia production along with the microbial population shift of select bacterial species ( Prevotella ruminicola , Clostridium aminophilum , and Peptostreptococcus anaerobius ). From an Ent. caudatum culture that had been maintained by daily feeding and transfers every 3 or 4 days, the bacteria and methanogens loosely associated with Ent. caudatum cells were removed by filtration and washing. An AAFB consortium was established by repeated transfers and enrichment with casamino acids as the sole substrate. The cultures of Ent. caudatum alone (Ec) and AAFB alone (AAFB) and the co-culture of Ent. caudatum and AAFB (Ec + AAFB) were set up in three replicates and incubated at 39°C for 72 h. The digestibility of dry matter (DM) and fiber (NDF), VFA profiles, ammonia concentrations, pH, and microscopic counts of Ent. caudatum were compared among the three cultures. The co-culture of AAFB and Ent. caudatum enhanced DM degradation, VFA production, and Ent. caudatum cell counts; conversely, it decreased acetate: propionate ratio although the total bacterial abundance was similar between Ec and the Ec + AAFB co-culture after 24 h incubation. The ammonia production and relative abundance of C. aminophilum and P. anaerobius did not differ between AAFB alone and the Ec + AAFB co-culture. Our results indicate that Ent. caudatum and AAFB could have a mutualistic interaction that benefited each other, but their interactions were complex and might not increase ammoniagenesis. Further research should examine how such interactions affect the population dynamics of AAFB., Competing Interests: No potential conflict of interest relevant to this article was reported., (© Copyright 2023 Korean Society of Animal Science and Technology.)

The gastrointestinal (GI) tract, including the rumen and the other intestinal segments of cattle, harbors a diverse, complex, and dynamic microbiome that drives feed digestion and fermentation in cattle, determining feed efficiency and output of pollutants. This microbiome also plays an important role in affecting host health. Research has been conducted for more than a century to understand the microbiome and its relationship to feed efficiency and host health. The traditional cultivation-based research elucidated some of the major metabolism, but studies using molecular biology techniques conducted from late 1980's to the late early 2000's greatly expanded our view of the diversity of the rumen and intestinal microbiome of cattle. Recently, metagenomics has been the primary technology to characterize the GI microbiome and its relationship with host nutrition and health. This review addresses the main methods/techniques in current use, the knowledge gained, and some of the challenges that remain. Most of the primers used in quantitative real-time polymerase chain reaction quantification and diversity analysis using metagenomics of ruminal bacteria, archaea, fungi, and protozoa were also compiled.