Nitrogenous emissions from ruminant livestock production are of increasing public concern and, together with methane, contribute to environmental pollution. The main cause of nitrogen-(N)-containing emissions is the inadequate provision of N to ruminants, leading to an excess of ammonia in the rumen, which is subsequently excreted. Depending on the size and molecular structure, various bacterial, protozoal and fungal species are involved in the ruminal breakdown of nitrogenous compounds (NC). Decelerating ruminal NC degradation by controlling the abundance and activity of proteolytic and deaminating microorganisms, but without reducing cellulolytic processes, is a promising strategy to decrease N emissions along with increasing N utilization by ruminants. Different dietary options, including among others the treatment of feedstuffs with heat or the application of diverse feed additives, as well as vaccination against rumen microorganisms or their enzymes have been evaluated. Thereby, reduced productions of microbial metabolites, e.g. ammonia, and increased microbial N flows give evidence for an improved N retention. However, linkage between these findings and alterations in the rumen microbiota composition, particularly NC-degrading microbes, remains sparse and contradictory findings confound the exact evaluation of these manipulating strategies, thus emphasizing the need for comprehensive research. The demand for increased sustainability in ruminant livestock production requests to apply attention to microbial N utilization efficiency and this will require a better understanding of underlying metabolic processes as well as composition and interactions of ruminal NC-degrading microorganisms.

Bacillus spp. seem to be an alternative to antimicrobial growth promoters for improving animals’ health and performance. However, there is little information on the effect of Bacillus spp. in combination with different dietary crude protein (CP) levels on the ileal digestibility and microbiota composition. Therefore, the objective of this study was to determine the effect of Bacillus spp. supplementation to low- (LP) and high-protein diets (HP) on ileal CP and amino acid (AA) digestibility and intestinal microbiota composition. Eight ileally cannulated pigs with an initial body weight of 28.5 kg were randomly allocated to a row-column design with 8 pigs and 3 periods of 16 d each. The assay diets were based on wheat-barley-soybean meal with two protein levels: LP (14% CP, as-fed) and HP diet (18% CP, as-fed). The LP and HP diets were supplemented with or without Bacillus spp. at a level of 0.04% (as-fed). The apparent ileal digestibility (AID) and standardized ileal digestibility (SID) of CP and AA was determined. Bacterial community composition from ileal digesta was analyzed by Illumina amplicon sequencing and quantitative real-time PCR. Data were analyzed as a 2 × 2 factorial design using the GLIMMIX procedures of SAS. The supplementation with Bacillus spp. did not affect both AID and SID of CP and AA in growing pigs. Moreover, there was no difference in AID of CP and AA between HP and LP diets, but SID of cystine, glutamic acid, glycine, and proline was lower (P < 0.05) in pigs fed the HP diets. The HP diets increased abundance of Bifidobacterium spp. and Lactobacillus spp., (P < 0.05) and by amplicon sequencing the latter was identified as predominant genus in microbiota from HP with Bacillus spp., whereas dietary supplementation of Bacillus spp. increased (P < 0.05) abundance of Roseburia spp.. The HP diet increased abundance of Lactobacillus spp. and Bifidobacterium spp.. The supplementation of Bacillus spp. resulted in a higher abundance of healthy gut associated bacteria without affecting ileal CP and AA digestibility, whereas LP diet may reduce the flow of undigested protein to the large intestine of pigs.

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

Zearalenone (ZEN) and fumonisins (FUM) jeopardize fertility and health in cattle; yet, their toxigenic effects on rumen health and microbiota, both being crucial for animal health, are not clarified. This study determined the effects of a short-term exposure to ZEN or FUM on the rumen ecosystem, and further evaluated acute implications on health parameters. Six cows were fed a basal diet with 40% grain (dry matter basis) and exposed to either 5 mg of ZEN or 20 mg of FUM daily for two consecutive days each, separated by a 7-days washout period. The exposure to ZEN or FUM led to a reduction of Lachnospiraceae and Prevotellaceae in the rumen. Similarly, ZEN lowered the ruminal pH and total short-chain fatty acid concentration, despite increased rumination activity of the cows. Fumonisins increased the number of observed features and significantly impacted β-diversity structure and metagenome predicted function. At the systemic level, FUM exposure suggested an immediate hepatotoxic effect, as evidenced by increased liver enzyme concentrations, which were accompanied by altered heart and respiratory rates. Similarly, ZEN increased the body temperature up to a mild fever. Concluding, short-term exposure to ZEN and FUM can harm the rumen ecosystem and acutely impair systemic health.

The transition from milk to solid diets drastically impacts the gut microbiome of calves. We explored the microbial communities of ruminal fluid and feces of Holstein calves when fed milk on d 7 of life, and when fed solid feeds based on either medium- or high-quality hay with or without concentrate inclusion (70% in fresh matter) on d 91. Ruminal fluid and feces had distinct microbial compositions already on d 7, showing that niche specialization in early-life gut is rather diet-independent. Changes between d 7 and d 91 were accompanied by a general increase in microbial diversity. Solid diets differed largely in their carbohydrate composition, being reflected in major changes on d 91, whereby concentrate inclusion was the main driver for differences among groups and strongly decreased microbial diversity in both matrices. Fecal enterotyping revealed two clusters: concentrate-supplemented animals had an enterotype prevalent in Prevotella, Succinivibrio and Anaerovibrio, whereas the enterotype of animals without concentrate was dominated by fibrolytic Ruminococcaceae. Hay quality also affected microbial composition and, compared to medium-quality, high-quality hay reduced alpha-diversity metrics. Concluding, our study revealed that concentrate inclusion, more than hay quality, dictates the establishment of niche-specific, microbial communities in the rumen and feces of calves.

Pre-ensiling treatments can significantly influence the composition of lucerne (Medicago sativa L.) silages (LS). Besides dry matter (DM) content and availability of water-soluble carbohydrates (WSC), wilting intensity may exert a strong impact on the crude protein (CP; nitrogen [N] × 6.25) fractions. The present study aimed to evaluate the effects of DM level, wilting intensity, and sucrose addition on N compounds and fermentation products in LS. Pure lucerne stand (cultivar Plato) was wilted with either high or low intensity to DM contents of 250 and 350 g kg⁻¹, respectively, and ensiled with or without the addition of sucrose. Non-protein-N (NPN) concentration in LS was affected by all pre-ensiling treatments and with 699 g kg⁻¹ CP, NPN was lowest in high-intensity wilted high-DM LS with sucrose addition. No effects were observed on in vitro-estimated concentrations of utilizable CP at the duodenum, a precursor to metabolizable protein. Sucrose addition and higher DM level decreased acetic acid and ammonia-N concentration in the silages. Therefore, the present study demonstrated the beneficial manipulation of CP fractions in LS by high-intensity wilting to higher DM contents and that the provision of WSC may be necessary for sufficient silage fermentation and protein preservation.