Editorial: Unravelling the Unknown of the Rumen Microbiome: Implications for Animal Health, Productivity, and Beyond

Alejandro Belanche^1*Grzegorz Bełżecki²Emma Hernandez-Sanabria³Gonzalo Martinez Fernandez⁴Eva Ramos-Morales⁵Gabriel De La Fuente Oliver⁶

• ¹Faculty of Veterinary Medicine, University of Zaragoza, Zaragoza, Spain
• ²Department of Animal Nutrition, The Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences,, Jabłonna, Poland
• ³Katholieke Universiteit Leuven Departement Microbiologie Immunologie en Transplantatie, Leuven, Belgium
• ⁴CSIRO Queensland Biosciences Precinct, Saint Lucia, Australia
• ⁵Estacion Experimental del Zaidin, Granada, Spain
• ⁶Universitat de Lleida Departament de Ciencia Animal, Lleida, Spain

consolidate cutting-edge contributions that bridge existing knowledge gaps, providing a deeper understanding of ruminal microbial ecology and its implications for host physiology, productivity, and environmental outcomes.The contributions compiled in this Research Topic demonstrated the value of a multidisciplinary approach, combining omics-driven exploration of microbial communities with applied nutritional sciences and systems biology. The articles tested novel hypotheses and offered practical solutions, moreover they provided a comprehensive and updated overview of the rumen microbiome and its complex interplay with ruminant physiology, nutrition, and health. A total of 45 manuscripts were submitted, of which 29 (including one corrigendum) were accepted, encompassing a wide range of ruminant species (cattle, sheep, goats, yak and red deer) as well as in vitro studies. The published articles can be classified in the following categories. Eight published articles explored the use of agro-industrial by-products and novel feeds in ruminant nutrition, including a review on the degradation mechanisms of lignocellulose by ruminants. Li et al. (2025) studied the impact of chili straw supplementation in sheep and found improvements in growth performance and beneficial changes in fungal populations at 10% inclusion. A companion publication demonstrated that rumen fermentation was also enhanced when this by-product was included at different proportions in the diet (Li et al., 2024). Hou et al. (2025) evaluated black goji berry (Lycium ruthenicum) as forage at 20-30% inclusion, reporting improved growth performance and overall health in sheep, with increased apparent NDF digestibility and immune system indicators, without compromising liver function. The use of saline pasture in Qinghai Tibetan sheep was investigated by Jia et al. (2025). A mixture of saltalkali-tolerant grasses was compared with common non-saline grass pastures in sixty Tibetan rams (2-3 months old). Results showed significant changes in meat quality traits, such as colour, as well as increased amino acid content. Gene expression related to protein metabolism was upregulated, and higher concentrations of antioxidants such as flavonoids were detected.Three studies investigated the use of by-products in Hu sheep. Ren et al. (2025) reported that oats grain supplementation induced significant shifts in microbial composition, increasing the abundance of Acidobacteriota, Proteobacteria, Chloroflexi, and Actinobacteriota, as well as overall alpha diversity. Metabolically, oats grain supplementation reduced isobutyric acid and citraconic acid while increasing azelaic acid. Jiao et al. (2025) tested three corn varieties in whole-plant silage and found that two of them improved lamb production by increasing dry matter intake, growth performance, and gastrointestinal fermentation. These findings highlight the importance of selecting appropriate corn silage varieties to optimize both production performance and animal health, offering novel insights into the interplay between dietary composition and the rumen microbiota. Lu et al. (2024) Three articles addressed strategies to optimize rumen microbial fermentation. Viquez-Umana et al. ( 2025) studied the effects of protein levels and feeding patterns, showing that the rumen microbiome and fermentation pattern (i.e. pH and VFA proportions) remained stable despite variations in dietary CP supply, suggesting compensatory mechanisms. In yaks, Gou et al. (2025) demonstrated that optimizing concentrate-to-forage ratios is critical to balancing production goals, rumen pH and feed costs. Bai et al. (2024) highlighted microbial shifts that support adaptation to cold-season environments, including enhanced fibre degradation, total VFA, acetate proportion and reduced nitrogen excretion. Six research articles investigated the effects of bioactive compounds and feed additives on rumen microbiota, productivity and health. Klein et al. (2025) Four articles addressed the mitigation of rumen methanogenesis. Martinez-Fernandez et al. (2024) demonstrated that supplementation with commercial wood biochar or custom-made wheat straw biochar with nitrates reduced methane emissions in cattle by up to 12.9% under controlled feeding conditions, though no effect was observed in grazing systems. The authors concluded that effective methane mitigation in grazing animals requires additives with greater efficacy and persistence in the rumen to overcome the variability of grazing environments. Pu et al. (2025) reported that replacing corn silage with fermented bakery by-products reduced methane production in beef calves by shifting rumen fermentation from acetate to propionate.Two reviews provided broader perspectives in methane mitigation strategies. Frazier et al. (2024) examined links between the rumen microbiome and climate change, discussing functional redundancy, microbial succession, and methane mitigation within ecological theory frameworks (e.g., Black Queen Dynamics, Island Biogeography Theory, Neutral Theory). Pressman and Kebreab (2024) critically evaluated mechanistic models of rumen fermentation, focusing on their ability to predict methane emissions based on feed fractions, microbial groups, fermentative products, rumen pH, redox balance, and passage rates. Together, these works provide a comprehensive overview of methane modelling and its application to rumen function. Four publications, plus one corrigendum (Skarlupka et al., 2024a), described proposed the use of gut microbial correlations as a prediction tool. Yang et al. (2025) reported correlations between rumen and rectal bacterial composition and dairy cow performance, linking specific microbial communities with increased propionate production, enhanced gluconeogenesis, and reduced inflammation. In addition, Skarlupka et al. (2024) developed a novel non-invasive colorimetric method using oral swabs, finding that swab coloration correlated with microbial composition. Hou et al. (2024)