Advances in Rumen Microbiome Science: Emerging Technologies for Sustainable Livestock Production
A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Veterinary Microbiology".
Deadline for manuscript submissions: 31 March 2026 | Viewed by 816
Special Issue Editors
Interests: microbiota; metagenomics; viral WGS; phylogeny; molecular typing
Special Issues, Collections and Topics in MDPI journals
Interests: ruminant nutrition; microbiology; milk quality; meat quality
Special Issues, Collections and Topics in MDPI journals
Special Issue Information
Dear Colleagues,
The ruminal microbiome—the synergistic consortium of bacteria, archaea, protozoa, fungi, and viruses inhabiting the forestomach of ruminants—drives the bioconversion of recalcitrant plant fiber into nutrients, underpins animal productivity, and represents the largest natural source of anthropogenic methane. Elucidating its composition and function is therefore pivotal for improving feed efficiency, reducing greenhouse gas emissions, safeguarding animal health, and securing sustainable protein production.
Despite the fact that rapid progress has been made, fundamental knowledge gaps persist. We still lack the strain-level resolution of key fibrolytic and methanogenic guilds across breeds, ages, and production systems; temporal dynamics during critical physiological transitions remain under-sampled; cross-kingdom interactions, especially viral predation and protozoal symbioses, are poorly quantified; and integrative models linking microbial activities to host genetics, immune tone, and metabolite fluxes are missing.
Several trends are poised to close these gaps. Long-read metagenomics and single-cell genomics are revealing novel lineages previously masked by assembly fragmentation. Layered multi-omics (metatranscriptomics, metaproteomics, and metabolomics) combined with spatially resolved omics and rumen-organoid platforms are uncovering micro-niche functional heterogeneity. Machine learning pipelines leveraging global rumen databases are beginning to predict community responses to diet and climate stressors, enabling data-driven precision feeding strategies.
This Special Issue welcomes the submission of contributions that (i) integrate multi-omics datasets to map metabolic handoffs; (ii) dissect archaeal–bacterial syntropy underlying methanogenesis and explore alternative hydrogen sinks; (iii) characterize the rumen virome and its potential for phage therapy; (iv) manipulate protozoa and anaerobic fungi for enhanced fiber degradation; (v) elucidate host genetic and epigenetic determinants of microbiome assembly; (vi) evaluate plant secondary metabolites, nanoparticles, or microbiome-modulating enzymes as antibiotic alternatives; (vii) model microbiome shifts under heat stress, water scarcity, and novel forages; and (viii) develop synbiotic or engineered consortia for climate-smart livestock. Collectively, these efforts will contribute towards achieving transformative and sustainable ruminant production globally.
Reviews, original research, and communications are welcome to be submitted to this Special Issue
Dr. Simone Peletto
Guest Editor
Dr. Lorenzo Danilo Granados-Rivera
Guest Editor Assistant
Manuscript Submission Information
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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.
Keywords
- ruminal microbiome
- metagenomics
- methanogenesis
- feed efficiency
- multi-omics
- host–microbe interactions
- microbial ecology
- rumen fermentation
- climate mitigation
- precision livestock
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