Case study: Microbiome insights that improve poultry performance

In brief:

• The poultry microbiome is a critical but largely invisible driver of digestion, immunity, nutrient utilization, and overall flock performance, knowledge of which can provide targeted intervention for production optimization.
• Advances in sequencing, multi-omics, and AI interpretation now allow microbiome data to be translated into actionable strategies.
• Real-world case studies show that microbiome diversity and SCFA-producing bacteria directly correlate with performance outcomes and economic returns.

Why the microbiome matters

The microbiome is a whole ecosystem; a community of bacteria, fungi, viruses, and their genes that inhabit the bird, and function as a dynamic ecosystem influencing digestion, immunity, metabolism, and overall health.

Key microbiome functions include the breakdown of complex carbohydrates (including fiber) and the synthesis of beneficial metabolites such as short-chain fatty acids (SCFAs) and vitamins.

Microbiome diversity is key to optimizing its function. In particular, shifts in litter microbiome composition and changes in specific microbial groups correlated with indicators of gut imbalance and altered nutrient utilization.

Figure 1. Why the microbiome matters

In poultry production, we cannot directly observe internal physiological changes as they occur. Instead, blood biomarkers combined with microbiome profiles provide an indirect yet powerful window into the bird’s internal status, helping us detect early disruptions in health or metabolism that may not be visible externally. Birds cannot talk to tell us where it hurts or if they feel atypical pigmentation, so using tools such as blood testing through platforms such as Verax™, can help deduce what is wrong. 

Microbiome analysis is an ever-evolving tool to close this visibility gap from traditional performance metrics and provide a deeper biological understanding of bird performance, such as organ function, bacterial overgrowth, feed conversion efficiency, and inconsistent feed responses.

From data to insights: technology evolution

dsm-firmenich Animal Nutrition & Health is a pioneer in the microbiome space. While early culturing methods were limited due to the inability to culture many microbial species, the introduction of 16S rRNA gene sequencing expanded visibility, allowing broader profiling of microbial diversity. As time went on, more advanced approaches, such as metagenomics, delivered a comprehensive overview of microbial communities, while metatranscriptomics and metaproteomics provide insight into active microbial functions and metabolic activity. With these microbiome-based diagnostics, microbial signatures can be used to diagnose and predict disease risk. AI-based interpretation translates complex omics datasets into practical recommendations for nutrition, biosecurity, and antibiotic reduction strategies.

Real-world value add: microbiome diversity drives performance

Microbiome insights help improve poultry performance by optimizing gut function and microbial metabolism in the bird. By supporting beneficial microbial pathways and improving nutrient utilization, microbiome-targeted solutions can enhance growth performance, feed efficiency, and resilience to enteric stress in poultry flocks.

While microbiome management may also influence the presence of certain bacteria associated with food safety (e.g., Salmonella), the primary goal in this context is improving bird health and performance, rather than directly addressing food-borne pathogen risks. Food safety outcomes represent a related but distinct objective that typically requires additional interventions across the production chain.

Case study: why one complex thrived, and another struggled

A large producer provides a clear link between microbiome structure and performance outcomes. Two poultry complexes with identical genetics, feed, and production systems showed divergent results: Complex X delivered strong year-round performance, while Complex Y experienced decreased weight gain and increased mortality after day 16, particularly during fall and winter.

Cecum sampling revealed that alpha diversity increased as the microbiome developed in Complex X, while Complex Y failed to diversify beyond an early stage.

Cecum samples - Alpha diversity

Functional analysis showed a higher abundance of genes related to butyrate metabolism in Complex X at 12 days of age. 

The charts show that SCFAs support gut health by nourishing beneficial microbes, strengthening the gut barrier, reducing inflammation, and enhancing nutrient absorption, aligning directly with the superior performance observed. Furthermore, our data indicate that two species differentiate the two complexes and are associated with butyrate production, namely Anaerobutyricum and Blautia, both well-established SCFA producers.

A less complex microbial community weakened colonization resistance, reducing competition and immune stimulation, and creating space for pathogens. In contrast, stronger microbiome complexity supported a protective gut barrier and improved nutrient absorption.

Microbiome biomarkers identified early dysbiosis linked to poor winter performance. High associations between blood carotenoid levels and Lactobacillus species led to recommendations for probiotic inclusion and maintenance of butyrate levels throughout the growth cycle.

Results

The economic impact was quantified: a three-point improvement in feed conversion translated to US$108,000 per year, based on US$1,800 per week over a five-month period.

What’s Next?

Microbiome data becomes most powerful when combined with production history, management practices, blood biomarkers, and veterinary observations, allowing producers to base interpretations in an on-farm context.

In practice, this enables targeted interventions based on how birds are actually responding under specific site management conditions.

By integrating microbiome insights with day-to-day management decisions, producers can move from reactive problem-solving to proactive performance optimization, delivering more from less.