The Fermentation of Carbohydrates and Proteins in the Gut of Monogastric Animals

Gut microbial fermentation is a rapidly advancing field in monogastric animal nutrition, offering transformative insights into nutrient utilization, intestinal integrity, and overall metabolic regulation. Historically, research emphasized the contribution of dietary fibre and carbohydrates in fostering beneficial microbiota and generating short-chain fatty acids that support anti-inflammatory and energy-related functions. However, recent studies have revealed that an excess of undigested protein may skew fermentation toward proteolytic processes, producing metabolites such as ammonia, branched-chain fatty acids, phenols, and biogenic amines—compounds that can compromise health and efficiency. While nutritional science has substantially enhanced our understanding of carbohydrate fermentability, protein digestibility, and microbial interactions, knowledge gaps persist in elucidating how fibre and protein characteristics interact within the gut ecosystem to influence fermentation balance, nutrient absorption, and production performance. This underscores the need to refine feed formulation strategies, integrate novel functional ingredients, and align nutritional interventions with microbial and host physiology to achieve optimal health and sustainability outcomes.

This Research Topic aims to address the nutritional challenge of managing fibre and protein fermentation dynamics in the gastrointestinal tract of monogastric animals. The overarching goal is to define how dietary composition and feed formulation strategies can be optimized to promote beneficial carbohydrate fermentation and suppress detrimental proteolytic activities. Key questions include how the physicochemical properties of fibre and protein influence microbial metabolism, how nutrient-microbe interactions shape energy and nitrogen efficiency, and how innovative techniques—such as advanced fibre characterization, metabolomics, and microbiome profiling—can elucidate the mechanistic links between diet, microbial fermentation, and host performance. By consolidating interdisciplinary approaches, this Research Topic seeks to generate actionable knowledge that enhances nutrient utilization efficiency, supports gut health, and informs the development of sustainable, precision-tailored feeding systems.

This Research Topic encompasses nutritional, microbiological, physiological, and technological perspectives on modulating gut fermentation in monogastric species, with a special emphasis on feed formulation and the optimization of nutrient utilization. It welcomes studies addressing, but not limited to, the following themes:

• Connections between dietary fibre sources, fermentability, and their roles in microbial functional activity and nutrient recovery
• Impacts of protein fermentation on nitrogen metabolism, hindgut physiology, and metabolic efficiency
• Relationships between fermentation metabolites, gut health, and animal welfare
• Characterization of gut microbial ecology underpinning carbohydrate and protein fermentation processes
• Integration of feed formulation, microbiome analytics, metabolomics, and digestive physiology to link nutrient design with metabolic outcomes
• Evaluation of innovative feeding strategies, functional ingredients, and processing technologies to steer fermentation toward beneficial pathways
• Exploration of nitrogen efficiency, environmental sustainability, and practical implications across pigs, poultry, rabbits, horses, and companion animals

By fostering a multidisciplinary exchange across nutrition, microbiology, and animal physiology, this Research Topic aims to advance evidence-based feeding practices that strengthen productivity, health, and sustainability in monogastric production systems.

Original research articles, reviews, short communications, and perspectives integrating nutrition, fermentation microbiology, animal physiology, and environmental impacts are particularly welcome.

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Case Report
• Clinical Trial
• Editorial
• FAIR² Data
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• ... View all formats

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Case Report
• Clinical Trial
• Editorial
• FAIR² Data
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Review
• Systematic Review
• Technology and Code

Keywords: Poultry, Swine, Nutrition, Microbiota, Intestinal fermentation, dietary fibre, protein fermentation, gut microbiota, intestinal health, monogastric animals, microbial metabolism

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.